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https://openalex.org/W2981064212
https://psyarxiv.com/2d7um/download
English
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Scholarly Communication and Open Access in Psychology: Current Considerations for Researchers
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Laura Bowering Mullen Rutgers, The State University of New Jersey 1 1 Author Note g , g y , y Correspondence concerning this article should be addressed to Laura Bowering Mullen, Behavioral Sciences Librarian; Open Access Specialist, Rutgers University-New Brunswick Libraries, Library of Science and Medicine, Piscataway, NJ 08854. 2 Contents Scholarly Communication and Open Access in Psychology: Current Considerations for Researchers Contents However, most published works that focus on scholarly communication issues do not target the specific discipline, and instead take a more “one size fits all” approach. When it comes to scholarly communication, practices and traditions vary greatly across the disciplines. It is important to look at issues such as open access (of all types), reproducibility, research data management, citation metrics, the emergence of preprint options, the evolution of new peer review models, coauthorship conventions, and use of scholarly networking sites such as ResearchGate and Academia.edu from a disciplinary perspective. Important issues in scholarly publishing for psychology include uptake of authors’ use of open access megajournals, how open science is represented in psychology journals, challenges of interdisciplinarity, and how authors avail themselves of green and gold open access strategies. This overview presents a discipline- focused treatment of selected scholarly communication topics that will allow psychology researchers and others to get up to speed on this expansive topic. Further study into researcher behavior in terms of scholarly communication in psychology would create more understanding of existing culture as well as provide early career researchers with a more effective roadmap to the current landscape. As no other single work provides a study of scholarly communication and open access in psychology, this work aims to partially fill that niche. Scholarly communication and open access practices in psychological science are rapidly evolving. However, most published works that focus on scholarly communication issues do not target the specific discipline, and instead take a more “one size fits all” approach. When it comes to scholarly communication, practices and traditions vary greatly across the disciplines. It is important to look at issues such as open access (of all types), reproducibility, research data management, citation metrics, the emergence of preprint options, the evolution of new peer review models, coauthorship conventions, and use of scholarly networking sites such as ResearchGate and Academia.edu from a disciplinary perspective. Important issues in scholarly publishing for psychology include uptake of authors’ use of open access megajournals, how open science is represented in psychology journals, challenges of interdisciplinarity, and how authors avail themselves of green and gold open access strategies. This overview presents a discipline- focused treatment of selected scholarly communication topics that will allow psychology researchers and others to get up to speed on this expansive topic. Contents Abstract…………………………………………………………………………………….. 4 Recent History of Scholarly/Scientific Communication Specific to Psychology………… 8 Interdisciplinary Research and Collaboration in Psychology …………………….……… 9 Coauthorship and Assignment of Credit in Psychology Scholarship……………….…… 11 Information Overload and Inertia for Changing the Existing System…………....……… 14 Digital Object Identifiers (DOIs) for every Article and other Research Output….………. 16 An ORCID iD for every Researcher………………………………………………………. 17 The Growth of Open Access: A Boon for Authors, Readers, Researchers, and Institutions.18 Institutional Open Access Policies and the Institutional Repositories used for their Implementation…….…………….……………………………………………....……. ….. 20 Green Open Access: Strategies for Author Self-archiving of Works in Digital Repositories and other Services…………………………………………………………………………. 22 The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals…... 27 Subject or Disciplinary Repositories Available for Psychology Authors and Researchers... 33 Innovations in Peer Review and Open Peer Review: Examples from Psychology………... 40 The “Gold Road:” Open Access Journals and Psychology…………………….….………. 43 Subscription or Traditional Journal Publishing in Psychology……………………………. 45 Predatory Journals, Publishers and Conferences: A Growing Phenomenon, and the “Whitelists” that Assist Researchers with Vetting Journals……………………………………………... 51 Major Online Indexes for Open Access Journals and Articles in Psychology……………. 54 Open Access “Mega-Journals” (OAMJs) and their Significance to Scientific Communication in Psychology…………………………………………………………………………….…… 59 An Evolving Funder Environment Requiring More Open Access Compliance…………… 62 Open Access and Research/Citation Impact in Psychology……………………………...... 66 Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology.68 3 Open Research Practices for Psychological Science: Guidelines, Standards and Incentives for more Open Publication Practices in Psychology…………………………………………... 74 Publication Bias, Excess Success, Retractions and Preregistration of Studies in Psychology…………………………………………………………………………………. 77 Preregistration of Research Studies in Psychology…………………………………………79 Traditional Citation Metrics and the Journal Impact Factor in Psychology………………. 80 Another Popular Metric for Evaluation of Individual Researchers and even Journal Publications: the h-index…………………………………………………………………………………. 88 Scholarly Collaboration Networks: Featuring ResearchGate and Academia.edu…………. 90 Sharing Works Outside the “Formal” Scholarly Communication System, including the Sci-Hub Phenomenon………………………………………………………………………………... 94 More Public and Social Media Engagement for the Results of Research in Psychology…. 96 Author Submission of Work to Psychology Journals and the “In Person” Conference…… 100 Sustainability of the Societies: Will Open Access Harm the Societies that Serve Psychology? ……………………………………………………………………………………………... 102 The Role of Academic Libraries Today in Advancing Research and Scholarly Communication ………………………………………………………………………………………………103 Conclusion…………………………………………………………………………………. 106 References………………………………………………………………………………….. 109 4 Abstract Scholarly communication and open access practices in psychological science are rapidly evolving. Scholarly Communication and Open Access in Psychology: Current Considerations for Researchers Across the disciplines, scholarly communication is in a time of disruption and transition. It is important to understand the current landscape through a disciplinary lens, and from a stakeholder perspective. Whether researcher, author, librarian, or publisher, this is a fast moving time of rapid change, largely due to technological advances and the power and reach of the internet. In terms of psychology, some traditional aspects of scholarly publishing remain the same, while many others continue to evolve. Authors find themselves writing for the more global audience that the internet continues to enable. Sharing articles online with colleagues near and far has become part of research culture, and collaboration is now possible across and between institutions and countries. Publishers are adapting to a changing culture of scholarly sharing and networking that authors have come to expect from the internet culture. Universities want to take advantage of services that showcase the work of their authors, using new metrics and research information systems that demonstrate impact in an age of assessment. One major aspect of this new scholarly landscape is the phenomenon of open access. Open access has grown and become mainstream and many versions of a single article can exist in multiple institutional or subject repositories online. Readers find these early articles more easily discoverable via searching the popular Google Scholar, and by using new tools such as Unpaywall (http://unpaywall.org/), a free service that provides enhanced discoverability and access to available repository versions of subscription articles. (Chawla, 2017a) Alternately, the Open Access Button (https://openaccessbutton.org/) can assist readers unaffiliated with subscribing institutions in accessing the scholarly literature. The future of scholarly publishing is in some ways unclear, but it does include more open access of all types, enhanced collaboration, more online sharing of research results, and increasing accessibility to the data that underlies and supplements scholarly publications. Funders are increasingly mandating that authors and universities provide open access to the results of taxpayer funded research, even as there are fewer research dollars available than in the past. Research libraries are also undergoing seismic changes, and librarians are increasingly taking on consulting roles in scholarly communication and open access areas. Contents Further study into researcher behavior in terms of scholarly communication in psychology would create more understanding of existing culture as well as provide early career researchers with a more effective roadmap to the current landscape. As no other single work provides a study of scholarly communication and open access in psychology, this work aims to partially fill that niche. 5 Scholarly Communication and Open Access in Psychology: Current Considerations for Researchers In this complex environment, faculty, students and researchers may be seeking information on products, systems, new modes of publishing, and other strategies so that they may be able to take advantage of the myriad opportunities that the internet is providing to share the results of research. Communication of research findings to the public via the internet has become an expectation of funders, universities and readers, and psychological science has many opportunities to reach larger audiences of interested readers than in the days when print materials could be accessed on site in public research libraries or via interlibrary loan by request of the reader from their public libraries. The transformational move from print to electronic dissemination of research information was messy and chaotic at times, but at this point it can be said that most of the research level 6 journal literature in psychology has been moved to the online environment, accessed either free or via library or personal subscriptions on the internet. Many traditional aspects remain, such as the specific field differences in scholarly communication practices that continue on. The standards for scholarly communication in psychology will continue based on field traditions and transitions through evolutions in technology as well as various factors such as a continued emphasis on assessment of scholars and universities. The wheels of change turn slowly in the promotion and tenure systems and cultures of most universities, many of whom have adopted an “audit culture” that has added increasing pressure to a system that requires faculty to demonstrate impact. The traditions of scientific communication within disciplinary culture, particularly in the case of some new behaviors such as sharing preprints (which existed in the paper world in some disciplines and made the transition easily to the online situation), predate the internet. Over time, it is assumed that some scientific communication in the electronic realm might promote the development of more similarities in the way disciplines behave online. Studies about the way that various disciplines approach the newer aspects of scholarly communication and open access have shown that there is no “one size fits all” and that there is still great variety in the way disciplinary scholarship is funded and disseminated to readers and researchers. Scholarly Communication and Open Access in Psychology: Current Considerations for Researchers (Kling & McKim, 2000) Psycholoquy was 7 started by Harnad in 1990 with support from the American Psychological Association and Princeton University, and was an early electronic journal that was associated with the successful Cambridge University Press-published journal “Behavioral Brain Sciences (BBS).” Harnad reported in 1996 that it was much more difficult to get authors to submit to the electronic Psycholoquy than it was to the print counterpart BBS, and that Psycholoquy was a “slow starter.” (Taubes, 1996) However, in those early days of electronic scholarly publishing, Harnad (also affiliated with the CogPrints eprints archive he launched in 1997) and some others had started a revolution in publishing psychological science that still continues in today’s publishing space. It has taken many more years to realize open access than Harnad and his colleagues could have imagined when they began innovating in the 1990s. started by Harnad in 1990 with support from the American Psychological Association and Princeton University, and was an early electronic journal that was associated with the successful Cambridge University Press-published journal “Behavioral Brain Sciences (BBS).” Harnad reported in 1996 that it was much more difficult to get authors to submit to the electronic Psycholoquy than it was to the print counterpart BBS, and that Psycholoquy was a “slow starter.” (Taubes, 1996) However, in those early days of electronic scholarly publishing, Harnad (also affiliated with the CogPrints eprints archive he launched in 1997) and some others had started a revolution in publishing psychological science that still continues in today’s publishing space. It has taken many more years to realize open access than Harnad and his colleagues could have imagined when they began innovating in the 1990s. Harnad was also the author of the famous “subversive proposal,” posted to a mailing list in 1994, that asked all researchers to make their papers freely available on the internet. At that time, Harnad had also been editing the aforementioned journal Behavioral and Brain Sciences, which included “open peer commentary,” all of these were early efforts toward “open online access and interaction." (Poynder, 2014) At the time that the first issues of BBS were published, only one other scholarly journal, Current Anthropology (CA) was using open peer commentary, successfully at that, and that was the inspiration for BBS’s own open, post publication review concept. Scholarly Communication and Open Access in Psychology: Current Considerations for Researchers Severin, Egger, Eve, & Hurlimann concluded in 2018 in a study that analyzed all of the existing discipline- specific studies on “open access publishing practices and barriers to change” that: Over the last three decades, scholarly publishing has experienced a shift from “closed” access to OA as the proportion of scholarly literature that is openly accessible has increased continuously. The shift towards OA is however even across disciplines in two respects: first, the growth of OA has been uneven across disciplines, which manifests itself in varying OA prevalence levels. Second, disciplines use different OA publishing channels to make research outputs OA. (p.1) While psychology appears in some large scale bibliometric (and other) studies of amount and type of open access, for example, there seem no large surveys of current psychology faculty and other researchers that would assist in painting a picture of how authors make their work OA, and why. More research into the scholarly communication behavior of psychological scientists would help to facilitate change in the system by allowing a true understanding of the pressures as well as the opportunities at play in the current scholarly communication and open access ecosystem in the discipline. It is not clear how psychology is positioning itself to move forward intentionally to take advantage of all of the ways to most effectively disseminate and utilize research results in this internet-enabled scholarly publishing environment. Psychology does not jump out as a leader among disciplines in opening up its literature to a wider swath of readers and researchers. The wheels of change have turned slowly. Psychology’s current focus on aspects of open science and reproducibility are positive and visible reminders of some aspects of a move toward openness. Some early pioneers in the electronic communication space for psychology (and one of a “core group of enthusiasts” that are the key players in the early days of the open access movement) include cognitive scientist Stevan Harnad, the editor of Psycholoquy, a very early electronic peer reviewed journal introduced in 1990. Scholarly Communication and Open Access in Psychology: Current Considerations for Researchers ("Editorial," 1978) To this day, Behavioral and Brain Sciences enjoys one of the highest impact factors in behavioral sciences (20.415, #1 in Behavioral Sciences and Psychology, Biological and #2 in Neurosciences (2015 Thomson Reuters, now Clarivate Analytics Journal Citation Reports). Harnad’s subversive proposal was more fully presented in the 1995 book “Scholarly Journals at the Crossroads: A Subversive Proposal for Electronic Publishing.” (Okerson & O'Donnell, 1995). This “subversive proposal” is often referenced today in conversations around open access. Besides the move of many publishers to embracing digital publication processes, for the most part, journal publishing has not really changed for hundreds of years as the vehicle for certification of scientific research results. Many articles in the literature describe the process of scholarly publishing, providing valuable historical background information. (Nosek & Bar-Anan, 2012) There is a long history to consider when discussing potential changes to the scholarly communication system of psychological science. The traditional systems of scholarly journal publishing have been with us for more than 350 years. (Guedon, 2001). Since 1665, when the Journal des Sçavans (France) and the Philosophical Transactions of the Royal Society of London (England) began publishing “with the intent to advance scientific knowledge by building on colleagues’ results and (to) avoid duplication of results, and established both the principles of scientific priority and peer review.” (Larivière, Haustein, & Mongeon, 2015, p. 1) In this long history, authors have never been paid for writing and contributing scholarly articles to the literature, and publishers have taken care of the publishing process, often managing the peer review process. Since the advent of the internet, some of the publishing and sharing practices of scientists have been disrupted and transformed, but scholarly communication in psychology still has its focus on the publication of research results using traditional vehicles such as peer reviewed journals and scholarly book chapters. Some aspects of the publishing process may be considered anachronistic, and many experiments are ongoing, with and without publisher 8 cooperation. Innovation is constantly pushing boundaries of the system that is ingrained and familiar to all faculty and researchers. Some are wary of the changes that the internet has brought to scholarly communication in psychology, some welcome innovations, and some see a role in pushing the envelope toward looking beyond traditional journal publication altogether. Scholarly Communication and Open Access in Psychology: Current Considerations for Researchers Those seeking new methods seek to ensure the rapid and wide dissemination of research results on the internet, with many also pushing for not only public reader access to psychology scholarship but to define open access to include optimal reuse and remixing of content. This definition of open access, sometimes called “libre open access” and carrying a Creative Commons Attribution (CC- BY) license allows the most reuse, sharing and innovation and facilitates the ability of researchers to build on previous research results. Recent History of Scholarly/Scientific Communication Specific to Psychology 9 (Yang & Chiu, 2009) Further work on clinical psychology and its subdisciplines studied the organization of the literature and citations in clinical psychology (another “hub”), and it was further demonstrated that the scholarly communication practices of the subdisciplines of clinical psychology do not readily cross boundaries and publication behavior is more insular than might be expected. As for the subdisciplines of clinical psychology, researchers tended to publish in the literature of their own subdisciplines, rarely venturing across boundaries into the other subdisciplines or even to outside literature. The subdiscipline of cognitive-behavioral psychology’s articles’ citations are most likely to cross boundaries out into the journal literature of more general psychology and other related fields. (Kiselica & Ruscio, 2014) Studies that continue to analyze the structure of scientific communication within psychology and outside of its boundaries would be helpful for understanding exactly how and where collaboration is occurring, or where possibilities for interdisciplinary, cross disciplinary or transdisciplinary work exist today. Recent History of Scholarly/Scientific Communication Specific to Psychology By studying journal citation data in a variety of ways, it becomes easier to understand the structure and organization of psychology as a scientific discipline. Scientific and bibliometric analysis of the literature of psychological science within the larger ecosystem continues to demonstrate that “psychology is a hub science” and by 2000, seven hub disciplines could be identified and mapped based on a “similarity measure based on co-citations.” Not surprisingly, given scientific specialization over the past century, contemporary sciences no longer originate from a single source. Instead, seven hub sciences can be identified: mathematics, physics, chemistry, earth sciences, medicine, psychology, and the social sciences. Yes, psychology emerged as one of the hub disciplines of science! (Cacioppo, 2007) Creating these maps allows visualization of the importance of psychology to other fields. For instance, “public health, neuroscience, neurology, radiology, cardiology, and genetics are sciences that fall between psychology and medicine” on the map. A major study by Boyack, Klavans & Borner in 2005 used citation data from one million articles published in 7,121 journals (both citing and cited journals, and more than 23 million references) that were published in the year 2000 and sourced from the former Thomson Reuters (now Clarivate Analytics) Science Citation Index and Social Sciences Citation Index. The result was a “mapping of science,” based on the journals’ “citation interlinkages,” and demonstrated location of each scientific discipline relative to others around it. The impact of disciplines on other disciplines, and degrees of interdisciplinarity (high for psychology) is visible. (Cacioppo, 2007); (Boyack, Klavans, & Borner, 2005) As a follow up (in 2009) to Boyack et al.’s work, Yang and Chiu delved deeper into the “hub” of psychology, studying networks using citation records taken from the PsycINFO database over a 40-year span (1979-2009). Within psychology, it has been shown using journal citation studies that clinical psychology has been identified as an important “knowledge broker,” for other related areas of psychology. A knowledge broker is defined thus: “a journal becomes a knowledge broker when it absorbs knowledge from one set of journals, integrates and transforms the knowledge, and disseminates the end products to another set of journals” (p.349). It is interesting to note how the roles of new journals (in this case, APA journals), impact the other established journals. This work provides an update after a lengthy absence of other similar studies (since 1985) that specifically focus on psychological science. Interdisciplinary Research and Collaboration in Psychology Bergmann, Dale, Sattari, Heit & Bhat (2016), also focusing on the journal Cognitive Science, discussed another new metric for interdisciplinarity, based on co-author publication history. A published article that has co-authors with quite different publication histories can be deemed relatively “interdisciplinary,” in that the article reflects a convergence of previous research in distinct sets of publication outlets. In recent work, we have shown that this interdisciplinarity metric can predict citations. Here, we show that the journal Cognitive Science tends to contain collaborations that are relatively high on this interdisciplinarity metric, at about the 80th percentile of all journals across both social and natural sciences. (p.1) This study focused not on citation patterns but instead on whether scientists previously publishing papers in other domains were coauthoring papers together in Cognitive Science and looking at “coauthor publication history.” Scores on interdisciplinarity are then compared to other scientific fields and journals, especially within a group of cognitive science and neuroscience journals. (Bergmann et al., 2016) Porter and Rafols (2009) looked at Neurosciences and five other research domains (all subject categories in Web of Science) to see whether science was becoming more interdisciplinary over the thirty-year span from 1975-2005. Using a “combination of interdisciplinary metrics with science mapping enables us to characterize research interdisciplinarity with a detail not previously available” (p. 740) and it was concluded that “science is indeed becoming more interdisciplinary, but in small steps. Research knowledge transfer, as evidenced by citation, draws mainly on neighboring fields. Only slowly do we see increase in the small proportion of sources from more disparate disciplines” (p.741) and “particularly striking is the extent to which research is now a team effort” (p. 740) In Neurosciences, it was also shown that there was a 90% increase over the time span in the number of authors per paper. The emergence of a greater emphasis on “team science” is an important trend that follows (or creates an enhanced environment for) interdisciplinary research. Many recent studies of interdisciplinarity are important for psychology, and do seem to suggest that one of the personal costs of interdisciplinary research could be a lessening of a scientists’ productivity in terms of quantity of papers published, or even getting credit where credit is due for various parts of the research and publication process. Interdisciplinary Research and Collaboration in Psychology Interdisciplinary research is a target interest of funding agencies, and is a general trend in research. Funders are quite specific on this point: “In recognition of the promise that interdisciplinary research holds for addressing complex scientific problems with societal implications, the National Science Foundation (NSF) directs grant reviewers to consider a proposal’s plan to disseminate findings across disciplinary bounds in order to have a broader impact.” (Solomon, Carley, & Porter, 2016, p. 2) The 2015 book Rethinking Interdisciplinarity Across the Social Sciences and Neurosciences discusses many of the pragmatic issues of actually doing research and publishing in the integrated space where disciplines come together. Aspects of the cultures of disciplines and fields in terms of issues such as co-authorship patterns must evolve with interdisciplinarity. (Callard & Fitzgerald, 2015) The field of Cognitive Science, considered highly interdisciplinary, has been the focus of recent studies that have focused on citation patterns in journals. One study focused on two of the highest impact factor journals, Science and Nature, which include content in areas of psychology. These high profile journals cover all fields of science, are multidisciplinary and cited at a very high rate. A recent study of cited references by Solomon et al. (2016) focused on how interdisciplinary Science and Nature’s content is in comparison to the level of interdisciplinary research found in a representative disciplinary title, Cognitive Science. Science and Nature have such a wide reach that anything published therein is likely result in a higher “diffusion of knowledge.” However, in comparison to other fields studied (Cell Biology and Physical Chemistry), the field of Cognitive Science, showed a high integration score (the relative degree to which one subject area’s journals -as defined by Web of Science- cite those of other subject areas, indicating a diversity of cited references). Using metrics such as Integration and Diffusion scores, developed by the National Academies Keck Futures Initiative can help to measure interdisciplinarity by assessing the diversity of a paper’s cited references. It must be noted that it is difficult to study interdisciplinarity and there are other available measures as well. The Solomon et al. study also demonstrated that, as measured by their cited references, the articles in Science and Nature studied within each of the fields “are not significantly more 10 interdisciplinary than are those sampled in the disciplinary journals” (for instance, the journal Cognitive Science). Interdisciplinary Research and Collaboration in Psychology Using a selection committee to make a final call on proposals after a vetting period, each submission to the PSA is considered based on “factors such as how important the research quesiton is, what impact it might have on the field, and how feasible data collection would be.” (Chawla, 2017b) Suggestions for ways to enhance the reproducibility of published research include calls for more collaboration and team science, and also for using team science with student training. This would ensure early experience with wide collaboration for students engaged in research. A working example of this concept, demonstrated by conducting replications with students in research methods courses in psychology is “The Collaborative Replications and Education Project (CREP)” (https://osf.io/wfc6u/) An example of team science and wide collaboration from the behavioral sciences is the “Many Labs” replication project, where “dozens of laboratories implementing the same research protocol to obtain highly precise estimates of effect sizes, and evaluate variability across samples and settings.” (Munafò et al., 2017) Many Labs projects demonstrate results in replicability by “crowdsourcing dozens of laboratories running an identical procedure.” (Klein et al., 2014, p.151) The massive Many Labs 2 project involved participants from 36 countries and territories conducting “preregistered replications of 28 classic and contemporary published findings.” (Klein et al., 2018, p.447) The results of this study were published as a Registered Replication Report (as a single article) in the Research Practices section of Methods and Practices in Psychological Science, which is the home (after 2017) for APS Registered Replication Reports. (https://www.psychologicalscience.org/publications/ampps) Another initiative, the “Psychological Science Accelerator (PSA), led by Christopher Cartier (Ashland University, Ohio), is bringing together 170 labs on six continents that will allow researchers to collect data on a massive scale. Using a selection committee to make a final call on proposals after a vetting period, each submission to the PSA is considered based on “factors such as how important the research quesiton is, what impact it might have on the field, and how feasible data collection would be.” (Chawla, 2017b) Interdisciplinary Research and Collaboration in Psychology While collaboration is a laudable goal for the advancement of science, in at least one study in biomedicine, there may need to be more conversation around incentives for researchers. The UK Academy of Medical Sciences studied this issue and found that “academic reward and recognition systems have failed to match the needs of team and large scale collaborations"(p.7) and another team at MIT has called for a new “science of collaboration” to look at all aspects of this complex phenomenon in practice. (Allen, 2017) There are many issues with the effective design, incentivizing, management and assessment of the elaborate environment of collaboration, whether global, national or even local. Making sure that scholarly communication practices keep up with the needs of researchers working in 11 collaborative research environments will need to continue as an important focus of universities, consortia, and funders. Suggestions for ways to enhance the reproducibility of published research include calls for more collaboration and team science, and also for using team science with student training. This would ensure early experience with wide collaboration for students engaged in research. A working example of this concept, demonstrated by conducting replications with students in research methods courses in psychology is “The Collaborative Replications and Education Project (CREP)” (https://osf.io/wfc6u/) An example of team science and wide collaboration from the behavioral sciences is the “Many Labs” replication project, where “dozens of laboratories implementing the same research protocol to obtain highly precise estimates of effect sizes, and evaluate variability across samples and settings.” (Munafò et al., 2017) Many Labs projects demonstrate results in replicability by “crowdsourcing dozens of laboratories running an identical procedure.” (Klein et al., 2014, p.151) The massive Many Labs 2 project involved participants from 36 countries and territories conducting “preregistered replications of 28 classic and contemporary published findings.” (Klein et al., 2018, p.447) The results of this study were published as a Registered Replication Report (as a single article) in the Research Practices section of Methods and Practices in Psychological Science, which is the home (after 2017) for APS Registered Replication Reports. (https://www.psychologicalscience.org/publications/ampps) Another initiative, the “Psychological Science Accelerator (PSA), led by Christopher Cartier (Ashland University, Ohio), is bringing together 170 labs on six continents that will allow researchers to collect data on a massive scale. Coauthorship and Assignment of Credit in Psychology Scholarship Increasingly, teams have been dominating over solo efforts in research production in the sciences and social sciences. In a 2007 study of millions of articles by Wuchty, Jones & Uzzi showed that psychology, economics and political science showed the largest shift, and that, over a 45-year period “with regard to average team size, psychology, the closest of the social sciences to a lab science, has the highest growth (75.1 %)…” (p. 1037). The study also showed that writing papers in teams produced the highest impact research. Similar to the situation in many other fields, co-authorship rose in all areas of psychology during the years 1980-2013. In a study of 4.5 million articles from the social sciences that included psychology (taken from the Social Sciences Citation Index) Henriksen analyzed fields of psychology and determined that co-authorship is up in all areas of psychology. For 10 categories of psychology (not including Psychoanalysis Psychology where co-authorship is found less often), the percentage of co-authored articles rose from 1980 figures of 47.4%-65.5% to 2013 figures of 82.2-92.1%. Throughout the 30-year time period, mean numbers of co- authored articles in the 10 total categories of Psychology went from 1980 numbers of 1.4-2.3 12 authors per article to 2013 numbers of 2-5.3. Psychoanalysis was once again an outlier with median number of authors per article most likely to be one. (Henriksen, 2016) In recent years, there has been more emphasis on the issues around co-authorship and assigning credit for an article as well as the difficulty that trends in multiple authorship in psychology and other sciences are causing. Conventions exist for placement of coauthors on articles in most fields. “In psychology, for example, the first author is usually (but not always) the researcher who has done the most work.” (Chawla, 2015b). Describing authorship conventions in psychology, Chambers (2017) describes the published order of authors (with numerous caveats and exceptions) thus: The first-named author is usually the researcher who made the greatest intellectual contribution to the study and, again usually (but not always), the person who took responsibility for data analysis and much of the interpretation. Typically, the first author is also expected to take the lead in writing the paper and coordinating the drafting process with the other coauthors. After the first author, the next most important position is the last author. Coauthorship and Assignment of Credit in Psychology Scholarship The TACS page lists publishers and journals that adopt the CRediT taxonomy as well as whether they commit to requiring ORCID iDs for corresponding and other authors. Publishers listed at this stage include the PLOS, Nature Research, and Science families of journals. Because all authorship conventions vary so much across and between disciplines, understanding how credit is conferred (and understood when it comes to markers such as author order on articles) is essential, especially in today’s “audit culture” of university research, including reporting personal impact for promotion and tenure in psychology. Today’s move toward cross- and interdisciplinary work compounds the issues with defining credit for individual work via the list of authors on an article because “order of authorship can vary by discipline, which poses problems in adjusting for shared authorship when scientists work in different disciplines or publish interdisciplinary work.” (Ruscio et al., 2012, p. 141) Some issues in scholarly communication in psychology continue to resurface. Looking back at scientific communication in psychology from 50 years ago, it is found that psychological science has not been immune to various crises in its publishing practices. Garvey & Griffith (1972) analyzed the situation occurring with the psychological literature in the early 60s, and it is almost amazing how an analysis of the issues with the print tradition (with articles held in bricks and mortar libraries) so evocatively describes a situation similar to today’s, albeit missing the total disruption of the internet. (Garvey & Griffith, 1972) Garvey and Griffith detail the existence of somewhat of a crisis in the early sixties, where only about 2000 scientists seemed responsible for the entire literature of psychology. The system of scholarly communication in psychology at this time has not appreciably changed-as a system-even if the tools have radically changed. Common aspects remain some fifty years later, now having moved online. These core behaviors that remain are the formal and informal ways scholars share ideas, the importance of scholarly societies, then need for robust peer review systems, the existence of preprints (or technical reports) for informal pre-publication sharing, a lag time from submission to publication in major journals, the long delay before articles would be abstracted in Psychological Abstracts, and the role of the major conference in the discipline for establishing reputation and networks. Coauthorship and Assignment of Credit in Psychology Scholarship The last author, or senior author, is usually the principal investigator-the top dog who made the study possible either by holding the grant that funded it or by supervising the student that conducted it. (p.164) There have been calls over the years for the development of some kind of formula that would assign credit for various aspects of the authoring of a journal article, but there are no hard and fast rules for psychology. Many studies have discussed the need to determine how best to assign credit for authorship. (Wagner, Dodds, & Bundy, 1994) One example, now dated, comes from Winston (1985) who developed a weighted point system that would assign a number of points for the various tasks required to produce a scholarly article. For instance, points would be assigned for “conceptualizing and refining research ideas, literature search, creating research design…” (p. 516) The collaborators on an article would agree as a group that the contributor with the highest number of points would be senior author. Studies in the 1970s and 80s showed differing opinions on how to assign authorship credit, but “psychologists overwhelmingly believed that power and status should never enter into the determination of authorship credits.” (Winston, 1985, p. 515) APA also makes resources available to assist with the issues of authorship, such as how to determine and negotiate authorship. (American Psychological Association, 2018) Today, the discussion around assigning credit for the different roles of authors in collaborative writing of papers continues. Rather than leave author order to chance or one author’s understanding of prevailing conventions, systems and standards are being proposed to enhance transparency and consistency around actual practices. Standards could be adopted by societies, funders and publishers. McNutt et al. (2018), reporting in a recent article in PNAS, recommend that journals adopt common and transparent standards for authorship, outline responsibilities for corresponding authors, adopt the Contributor Roles Taxonomy (CRediT) (docs.casrai.org/CRediT) methodology for attributing contributions, include 13 this information in article metadata, and require authors to use the ORCID persistent digital identifier (https://orcid.org). (p.2557) McNutt et al. (2018) also report on the recently created National Academy of Sciences bpage entitled Transparency in Author Contributions in Science (TACS) McNutt et al. (2018) also report on the recently created National Academy of Sciences webpage entitled Transparency in Author Contributions in Science (TACS) (http://www.nasonline.org/about-nas/Transparency_Author_Contributions.html). Information Overload and Inertia for Changing the Existing System The availability of this deluge of journal articles creates challenges for scientists, whether for keeping up, or for more requests for reviews, or for discovery in an internet article level discovery environment. More than 50 million scholarly articles have been published, but half of all of those articles have been published in only the last 25 years. (Jinha, 2010) For many of us, our roles as authors, librarians, faculty members or publishers have included a close relationship to the print journal, and its associated systems of abstracting and indexing, access, reading and preservation. Today, electronic access to scholarly journals from laptop, iPad or cell phone from outside the library or office is the norm. However, focus on peer review and journal impact factor remain. Studies have shown that peer review, for instance, is an element of the traditional scholarly communication system that faculty and researchers find essential for certification of scholarship. (Michael, 2016a) Surveys of faculty and ongoing research by Harley, Acord, Earl- Novell, Lawrence & King (2010) have provided a lot of data and analysis of the current situation with the scholarly communication system that most academic faculty work within and many endeavor to maintain. These studies show a conservative posture about many existing systems, especially as they surround assessment of faculty scholarship. There is no mistaking the fact that more research on this whole system of peer review and especially academic promotion and tenure is necessary in order to create a sustainable system for the future of scholarly communication in the various disciplines. (Harley, 2013) Incentives also drive the system, and faculty may be loath to make the large scale changes to scientific communication to a more open system that is certainly possible. Incentives may need to originate from senior scholars in a field as there are career concerns for early career researchers hoping to see change in the system to more “open.” There are many new aspects to the ecosystem as of late. There has been a move to article- level discovery, new methods of measuring personal impact have emerged, and millions of authors are signing up for scholarly collaboration networks like ResearchGate or Academia.edu. Open access journals utilize a variety of business models in comparison to the subscription model, while still maintaining rigorous peer review. Coauthorship and Assignment of Credit in Psychology Scholarship (Garvey & Griffith, 1972) Journals were important for final certification of scholarship, brands mattered, and there was a desire for research to “speed up.” Of interest in Garvey and Griffith’s works of decades ago (written before the advent of the internet) is the description of the informal system of preprints in psychology, providing current information exchange but only to a niche readership. The situation was described in 1967 by Garvey and Griffith as “the chain of events in a fast-moving research area, may begin with publication lag being so great that current information needs are unsatisfied. As a result, the exchange of preprints among scientists working in this area will increase” (Garvey & Griffith, 1967, p. 1012). Over time, this situation would eventually become formalized and possibly give rise to new scholarly journals. Today, we see preprint servers (such as PsyArXiv) emerging in psychology, adding the promise of sharing 14 current research with any potential reader, researcher or practitioner via the internet around the world. How will this sharing affect psychology? Adding impetus at this point in time is a sometimes overwhelming deluge of publications to discover and read in one’s field, formal and informal, with university rankings and quantification of individual and institutional impact taking center stage. Information Overload and Inertia for Changing the Existing System (John Bohannon, 2014) The familiar online library catalog is beginning to be replaced on library websites by a web-scale discovery service’s “one stop shop” single search box that leads to journals, books, articles and all kinds of electronic subscriptions (and some open access content). Library collections may be more difficult to browse, with researchers finding the web providing a different kind of serendipitous article-level discovery of relevant research papers (with all of their various versions, some possibly open access). Paper journal volumes, in the past browsed within a single volume taken off the library shelf, have often been moved off to remote storage or recycled. The package of the bound paper journal has been replaced by vast online library discovery systems of tagged articles. It becomes more important than ever to understand how systems of scholarly communication work in each discipline or subfield. There is no “one size fits all” to this system. One constant has been the need for each discipline to organize its scholarship within a current, constantly developing and easily understood set of parameters, enabled by useful systems and tools that can maximize the visibility of an individual’s scholarship as well as to showcase the collective work of a field. Individual scholars as well as the important publications of each field will need to find ways to continue to demonstrate impact and remain highly relevant to an increasingly cross-disciplinary culture. For those readers needing to access the literature, which is now comprised of a global readership searching the internet for peer-reviewed scholarship, there has been an exponential growth in available journal articles and other digital content. In 2015, there were more than 28,000 scholarly journals worldwide, containing more than 2 million articles every year, with continuing growth of 3-3.5 percent each year. (Research Information Network CIC, 2015) By mid-2018, The STM Report: An Overview of Scientific and Scholarly Publishing stated that “there were about 33,100 active scholarly peer-reviewed English-language journals… (plus a further 9,400 non-English-language journals), collectively publishing over 3 million articles a year.” (Johnson, Watkinson, & Mabe, 2018, p.5) Time spent discovering and reading relevant literature may continue to present a challenge as far as “keeping up” for busy scientists. Information Overload and Inertia for Changing the Existing System That said, where there is money to be made from eager authors, the phenomenon sometimes known as “predatory publishing” has grown exponentially in this “gold” open access space. Unscrupulous operators work the internet, creating bogus journals that attract authors with low article processing charges and opportunity for quick publication. Some authors know that journals are bogus, but just need to get an article published no matter what the outlet (and knowingly choose to submit to a low quality journal title). Writing and researching for publication has become more complex, with the need to sift through a deluge of academic papers online in order to discover an exhaustive list of potential papers to read and add to popular citation management tools like EndNote (Clarivate), RefWorks There are many new aspects to the ecosystem as of late. There has been a move to article- level discovery, new methods of measuring personal impact have emerged, and millions of authors are signing up for scholarly collaboration networks like ResearchGate or Academia.edu. Open access journals utilize a variety of business models in comparison to the subscription model, while still maintaining rigorous peer review. That said, where there is money to be made from eager authors, the phenomenon sometimes known as “predatory publishing” has grown exponentially in this “gold” open access space. Unscrupulous operators work the internet, 15 (ProQuest) or Zotero (an open source option). Mendeley (now owned by Elsevier) is a popular product that adds collaboration, data options and even career networking to citation management. Strategies for discovering relevant scholarly literature have changed, as library search has added other new “web scale discovery” tools to the familiar abstracting and indexing services. Google Scholar (with its unpublished coverage criteria, covering everything it deems “scholarly” since its beta release in 2004) seems the most ubiquitous search tool. Its use is only growing. (John Bohannon, 2014) (ProQuest) or Zotero (an open source option). Mendeley (now owned by Elsevier) is a popular product that adds collaboration, data options and even career networking to citation management. Strategies for discovering relevant scholarly literature have changed, as library search has added other new “web scale discovery” tools to the familiar abstracting and indexing services. Google Scholar (with its unpublished coverage criteria, covering everything it deems “scholarly” since its beta release in 2004) seems the most ubiquitous search tool. Its use is only growing. Digital Object Identifiers (DOIs) for every Article and other Research Output In fact, lengthy or not, reference lists accessed online now include actionable persistent links such as DOIs (Digital Object Identifiers), that create an enhanced environment for the reader that allows direct linking through to available background reference papers. Rather than returning to online indexing and abstracting sources, library databases, Wikipedia references, or Google Scholar, readers now click through from one article to another seamlessly. This is especially true for the growing corpus of open access articles easily accessed by anyone wanting to read or use them. Papers that have been made open access, and the widespread adoption of DOI links on most articles make this system more effective for all researchers and readers. One large seamless system of interlinking content, with as much content as possible available to be clicked through by the largest numbers of potential readers and researchers is coming to fruition, albeit slowly and not including all literature, obviously. There are currently 10 registration agencies that can assign DOIs, but the most popular are CrossRef (mainly used by publishers) and DataCite (often used by repositories and for data). Most of the links seen in Wikipedia, for instance, use CrossRef DOIs. It is estimated that “CrossRef has registered 67% of all DOIs in existence.” (Himmelstein et al., 2018, p. 15) One anecdotal issue with DOIs is that some researchers feel that any article with a DOI is then “certified” as an authentic piece of scholarship, somehow has an imprimatur placed on it, or that it confers some sort of peer review. This is not the case, of course. The DOI (assigned by a registration agency) simply provides a unique and persistent identifier for articles (of all types), is clickable in online versions (resolving directly to the article) and is now required if available for citations using APA Style. This requirement for use of citations formulated with DOIs in APA Style has likely made DOIs more well known to readers and researchers of the psychology literature. All publishers now need to use DOIs and so this persistent identifier on citations is becoming ubiquitous in the scholarly publishing landscape. The availability of DOIs (from CrossRef or DataCite, for instance) has enhanced the discovery process for researchers, particularly because these persistent identifiers are now being included on all research products, whether articles, chapters, data, or even preprints. Using DOIs in citations ensures fewer broken links and lost access to cited content. Information Overload and Inertia for Changing the Existing System In one study of trends in publication patterns in the neuroscience and psychology categories and from 2006-2015 using Web of Science and Journal Citation Reports (JCR), the steadily rising number of papers can be seen as well as a shift toward “the more psychological and behavioural side of brain science” and also of note is the rise in number of citations authored by Chinese neuroscientists. (Neuroskeptic, 2017; Yeung, Goto, & Leung, 2017) For psychology, the “information explosion” has produced some distinctive challenges for authors and researchers, such as the enormous growth in the number of cited references in articles, a practice that has pros and cons, and is tolerated by editors and reviewers. Rather than 16 just keeping up, the exponential growth of the research literature in psychology has altered author behavior and publisher expectations around issues of increasing rate of citations, for instance. Some have called for an end to the practice of excessive or gratuitous citation lists, citing a tradeoff between writing and pages of citations in articles with strict page limits. (Adair & Vohra, 2003) Once again, electronic publication would seem to allow for less strict limits on pages or other aspects of a print environment. However, boundaries are needed. The number of self-citations has also been of interest to psychology, especially as it relates to possible effects on the important journal impact factor. (Anseel, Duyck, De Baene, & Brysbaert, 2004) In a study of referencing practices in psychology journal articles and how authors view the articles they cite, it was seen that authors tended to view self-citations as very important to the paper (outside of other reasons). (Safer & Tang, 2009) Studying self-citation practices is an interesting aspect of the impact calculations of the journal literature. Digital Object Identifiers (DOIs) for every Article and other Research Output The seamless online environment facilitates search and discovery (and thereby 17 research) via this web of DOIs, thereby enhancing easy access for all who surf the web looking for scholarly information in psychology or other fields. A related development in making citations in articles more visible, more searchable and likely more citable by other researchers is a recent initiative whereby publishers have worked together to agree to make all references of articles, including their DOIs openly available. If the article is subscription-based and behind a paywall, all references will still be “separable” (able to be accessed and analyzed without having to access the article), open and visible (and machine readable) for use by researchers. This initiative, entitled “The Initiative for Open Citations I4OC (https://i4oc.org/) is a collaboration between scholarly publishers, researchers, and other interested parties to promote the unrestricted availability of scholarly citation data.” Publishers enable the realization of this work via their assignment of DOIs through the CrossRef service. Clearly, the scholarly communication landscape is enhanced by all publishers in all disciplines linking articles, making all research products (including this amazing wealth of citations) discoverable and usable. An ORCID iD for every Researcher In addition to persistent identifiers (DOIs) for publications and other products of research such as data sets, it is now a fact that authors also need to be correctly identified and linked to their outputs in this new research environment. The use of unique, persistent digital identifiers now extends to the researcher, many of whom are expected to register for the ORCID iD (https://orcid.org/). The use of researcher identification systems (especially ORCID) to disambiguate one researcher from another with similar name makes discovery and attribution more accurate. An important development for scholarship has been the development of one major open and portable author identification system that authors across disciplines and countries can use. A single persistent ID and profiling system that is used by researchers, universities, publishers, grant funding agencies and others creates a worldwide network of researchers and papers, all with accurate author details. Many researchers, institutions, funders and publishers (all members) are now working with ORCID, a not-for profit organization that serves the research community in an open and transparent manner. (ORCID, 2017) An added bonus is the ease of use of ORCID’s systems, and even early career researchers can become part of the research environment by registering for an ORCID iD at orcid.org, which takes only about 30 seconds. Automated features that can automatically add papers discovered by Scopus, CrossRef, and DataCite (for data and contents of some institutional repositories), for instance, make updating one’s ORCID profile very easy and may someday be able to spin off a current CV for a researcher at the point of need. Some libraries and librarians are also involved in institutional implementations of the ORCID iD, adding librarian expertise to these new scholarly communication initiatives at the institutional level. Many institutional members work with ORCID to integrate their various university systems in an ORCID implementation, allowing seamless transfer of author profile, funder and publication information (and more) into various processes. This saves faculty time by automating linkages and scholarly communication processes and adds an important new piece to the researcher ecosystem bring built by universities today. In time, all systems in use by psychology researchers will likely be requiring 18 the ORCID iD, whether for grant or publication submission, or for adding to university profiling or current research information systems. An ORCID iD for every Researcher The ORCID iD has become an integral part of every researcher’s individual profile and more and more universities expect that faculty and even graduate students will have an ORCID iD. As the global information landscape evolves, author lists become longer, and the sheer number of researchers writing for publication grows exponentially, there has been a need to ensure correct attribution of authors. This can be accomplished via use of the ORCID iD, which is available to all scientists. In fact, it has been stated that China’s Ministry of Public Security estimates that “1.1 billion people, that is, roughly 85 percent of China’s population, share just 129 surnames.” (Tran & Lyon, 2017, p.172) This is an illustration of the difficulties that funders, publishers and other researchers may have with ensuring correct attribution of scholarly work. The ORCID iD is currently in use (as of August 2018), by more than 5 million researchers worldwide. Other researcher identification systems, such as Scopus Author Identifier (Elsevier) or ResearcherID (Clarivate) now work with ORCID. The Growth of Open Access: A Boon for Authors, Readers, Researchers, and Institutions Opening up access to the peer reviewed results of research articles and data has been an unprecedented public good, thanks in part to the powers of the internet (and some changes to traditional publisher permissions) to disseminate information to all corners of the globe. Research funders have made a significant impact by mandating open access to the products of funded research. Whether a researcher unaffiliated with the subscription riches of a well- endowed university, a reader needing access to research articles and data, a practitioner not associated with a research institution and its collections of books and journals, or a young person interested in learning more about psychological science in order to pursue a career, increasing the options for free and open access to research results in a benefit to research and to society. Most citizens can’t or won’t pay the high prices that commercial publishers charge to access single articles and many publicly accessible research libraries now limit the time that the public can access electronic subscriptions on site. For many cash-strapped researchers, and even those who object to paywalls on principle, accessing needed scholarly articles can be an incredible burden. For whole areas of the globe, subscription-based, traditional scholarly research publications are out of reach. One of the only questions left is not when, but how to continue to evolve an open access environment that reaches the goals of wide dissemination of research to all that need to access or discover it. It is impossible to calculate the impact of the lack of access to the scholarly literature that faces many readers around the world. There is one major initiative that provides an alternative for the research literature needs of developing nations. The multifaceted program, Research4Life, made up of 5 programs including Hinari (Research for Health) which is managed by the World Health Organization (in partnership with publishers and other organizations) and delivers free or low cost access to the scholarly peer reviewed literature to researchers in 8700 institutions in low-and middle-income nations. Major psychology-related publishers are partners in Hinari, including American Psychological Association, Springer Nature, SAGE Publishing, National Institute of Mental Health, Taylor & Francis, Society for 19 Neuroscience, and others. At present (2018), there are 70 countries where Hinari delivers free content from a long list of scholarly publishers. The Growth of Open Access: A Boon for Authors, Readers, Researchers, and Institutions (https://www.research4life.org/) Open access has arrived, and is now considered to be here to stay, or even “inevitable” and shows growth in all areas. (Lewis, 2012) As of 2013, with numbers now obsolete, a study of availability of scholarly publications estimated the numbers of openly available English- language papers at about 27 million, or about a quarter of all online scholarly publications including articles, conference papers, and dissertations. (Khabsa & Giles, 2014) Taking into account all versions of papers that are freely available to read on the internet (including papers that authors have self-archived or paid traditional subscription journals to publish as open access), the figure may rise much higher. In studies carried out by the Science-Metrix consultancy for the European Commission claims that researchers can “search the internet for any research article published in 2011, and you have a 50-50 chance of downloading it for free.” (Van Noorden, 2013, p. 386) There is an upward trajectory of open access materials easily found with an internet search. Morrison, whose blog, Dramatic Growth of Open Access, announced in a December, 2018 post that 2018 was the “best year yet for net growth of open access” as measured by numbers of open access documents that can be discovered in online repositories and aggregators. Clearly, the experience of hitting a paywall (with prices that can reach about 41 U.S dollars per article) when searching for and discovering scholarly publications may be evolving in a positive direction. A global audience is now able to discover the literature of psychology, often from the convenience of home, or on a mobile device at the point of need. This vastly extends the reach and usefulness of the psychological science literature. Obviously, it is in the interest of all authors (and their publishers) looking to reach more readers to work for the open access and public accessibility of the discipline’s literature. Open access has arrived, and is now considered to be here to stay, or even “inevitable” and shows growth in all areas. (Lewis, 2012) As of 2013, with numbers now obsolete, a study of availability of scholarly publications estimated the numbers of openly available English- language papers at about 27 million, or about a quarter of all online scholarly publications including articles, conference papers, and dissertations. The Growth of Open Access: A Boon for Authors, Readers, Researchers, and Institutions (Khabsa & Giles, 2014) Taking into account all versions of papers that are freely available to read on the internet (including papers that authors have self-archived or paid traditional subscription journals to publish as open access), the figure may rise much higher. In studies carried out by the Science-Metrix The open access landscape is complex. The growth of open access repositories, numbers of articles flowing into repositories, open access journals (and the articles in them) shows no signs of slowing. As an example, the two most popular open access “mega-journal” outlets, PLOS ONE and Nature’s Scientific Reports published a total of 38,088 articles in 2015 alone; 27,488 articles for PLOS ONE (down 9.3% from 2014) and 10,600 articles for Nature’s Scientific Reports (up 169.4% from 2014). (Wakeling et al., 2016) These are by far the most prolific of the types of titles that psychological scientists are considering in the mix of journal publication options. Psychology is heavily represented in these megajournals (and other open access journals) and in repositories of all types. Authors need to understand their publication options, as well as their rights as authors in terms of sharing their work widely, and publishers and libraries need to find their places in a new landscape and adjust accordingly. In fields of psychology, all types of open access have been introduced and are working effectively to disseminate scholarship to a global audience. Open access journals, hybrid subscription journals that contain a few OA articles in each issue, fully open access monographs, and author self-archiving of legal, post peer-reviewed versions of postprints (authors’ accepted manuscripts) in both institutional and subject/disciplinary repositories as well as the existence of many more “author’s original” preprints on the web have all become commonplace. A discussion of all of these methods of making articles and conference papers open access will often illustrate 20 the difficulty that authors face in decision-making about their choice of publication outlets as well as online dissemination strategies. Often, in the academy, the college or university library has taken up various open access roles related to development of institutional repositories, services related to author self-archiving of articles (green open access), and assistance with making supplementary data widely available from the institutional repository. Institutional Open Access Policies and the Institutional Repositories used for their Implementation Many universities have passed open access policies, usually by the vote of faculty governance bodies such as university senates or faculty councils. Institutional open access policies, particularly the popular “Harvard style” policies seek to ensure the ability of scholars to share their work via the retention of some rights to share and post accepted versions of their work out of the institutional repository. The development and passage of institutional open access policies such as the popular “Harvard model open access policy” Many universities have passed open access policies, usually by the vote of faculty governance bodies such as university senates or faculty councils. Institutional open access policies, particularly the popular “Harvard style” policies seek to ensure the ability of scholars to share their work via the retention of some rights to share and post accepted versions of their work out of the institutional repository. The development and passage of institutional open access policies such as the popular “Harvard model open access policy” (https://osc.hul.harvard.edu/modelpolicy/) can be seen as a popular statement by faculty at universities that open access is necessary and expected for wide impact. Open access policies help to preserve author rights to self-archive accepted manuscripts of research articles on the internet without fear of reprisal while increasing the amount of a university’s scholarly available to a global readership. (https://osc.hul.harvard.edu/modelpolicy/) can be seen as a popular statement by faculty at universities that open access is necessary and expected for wide impact. Open access policies help to preserve author rights to self-archive accepted manuscripts of research articles on the internet without fear of reprisal while increasing the amount of a university’s scholarly available to a global readership. Having a university open access policy lets publishers and others know that the university retains the rights for its authors to self-archive “accepted manuscript versions” of their work in the institutional repository (even before or after having signed a copyright transfer agreement) with the institution retaining only the nonexclusive right to make the works widely available on the internet via the institutional repository. Many universities in North America have passed OA policies, including Harvard, MIT, Rutgers, University of California, and more than 100 others as of this writing (August, 2018) that make up the membership of COAPI (Coalition of Open Access Policy Institutions) (https://sparcopen.org/coapi/). The Growth of Open Access: A Boon for Authors, Readers, Researchers, and Institutions Librarians provide consulting for psychology faculty and researchers around strategies for making their works open access, both from the institutional repository and also from other available services such as disciplinary repositories or preprint servers. Some psychology faculty members and others have stepped into roles as open access advocates, or as developers of new tools or policies that increase open access to the discipline’s scholarly literature. Institutional Open Access Policies and the Institutional Repositories used for their Implementation COAPI, an organization of North American institutions passing and implementing open access policies ensures the availability of a welcoming community focused on developing and maintaining best practices in this area. The number of universities passing policies, developing institutional repositories, and the number of articles in these repositories continues to increase each year. This type of repository-based open access, often called “green open access” carries no cost to authors and often results in final author versions (usually accepted manuscripts) of published articles being widely available on the internet to a global readership. The handy book entitled Open Access, authored by Peter Suber, one of the world’s most recognizable experts on this topic, provides an excellent introduction to this topic, and is freely available on the internet. (Suber, 2012) Not only found in North America, open access policymaking is an area of growth around the world. There are more 21 open access policies being passed all the time by universities, other research institutions, and funders. Internationally, at the time of this writing (August, 2018) there are more than 900 open access policies and mandates listed in ROARMAP (Registry of Open Access Repository Mandates and Policies) (http://roarmap.eprints.org/). For the creators of works of scholarship, the articles, conference proceedings and other works contributed without expectation of payment, open access policies stipulate that the author self-archive each article in the institutional repository, ensuring the works’ discoverability by readers on the open web. Some repositories also employ automated processes that crawl the web (or target other aggregated sources of open access content) in search of articles authored by the university’s faculty that can be added to the institutional repository. Often, implementation of the policy is carried out using the expertise of the university library and its librarians. Librarians, especially subject specialists holding positions in research libraries are able to share information effectively with departmental faculty on how OA works within the disciplinary context. These conversations allay faculty concerns that may arise when OA comes up. Even without a policy in place, many university libraries provide consulting on author strategies for making the results of research open access. For open access strategies for psychology faculty, a good source of information on strategies and practices for increasing the reach of scholarship via open access would be the library’s subject specialist in psychology, or the scholarly communication librarian or repository manager. Institutional Open Access Policies and the Institutional Repositories used for their Implementation Even retrospective works may be able to be self-archived in the institutional or disciplinary repository, and librarians can consult with faculty and others on those possibilities. Many faculty authors are interested in marketing of their scholarly works to more communities and to new readers outside of those in the usual niche areas served by subscription publishers. For the reader of the works of psychological science, whether researcher, practitioner or the public, passage of university open access policies have resulted in more access to this material. This is especially true where faculty and researchers take it upon themselves to commit to making sure each of their works of scholarship is available online via the self-archiving of a legal version of it (such as an accepted manuscript) in the institutional repository at the time of acceptance for publication, or by publishing in a fully OA journal (or book). For those affiliated with universities that have top tier electronic subscriptions, there is often a great dismay upon leaving the university and its subscription access to the research literature. Once a researcher becomes unaffiliated with a university and its research library or becomes a practitioner, access to the subscription research literature that was formerly taken for granted becomes an issue and is often turned off, even for alumni. We do not know who the readers of the scholarly literature are, and public access ensures that anyone will be able to read (and build upon) the articles, conference papers and other scholarship that enhances the reach of psychology. An important goal of university open access policies would be to gather the scholarship of a university together to showcase it and make it available on the internet. Departments and schools (or other academic units) of a university can make their collective works available online in an aggregated manner so that any reader or researcher in the world can access this corpus. The aim of these institutional policies is to ensure expanded access to the research outputs of universities, creating visibility and impact for the institution and its faculty and students. 22 Public as well as private funders have also instituted open access policies, and university policies complement these nicely. Institutional Open Access Policies and the Institutional Repositories used for their Implementation Universities will also likely want to maintain stewardship over the research data generated along with the publication, and funders have, in many cases, moved toward mandating that the data underlying the scholarly work also be made open access. One helpful resource where a researcher can see the requirements for open access by funders is the SHERPA Juliet database (http://v2.sherpa.ac.uk/juliet/). Failure to comply with open access policies now comes with consequences for future funding from the agency for any university and/or the principal investigator (PI). Many funding agencies in the past only encouraged open access and are now have moved to mandating it. Researchers will now find future funding in jeopardy if there is a lack of compliance with certain funder mandates. All researchers will need to understand open access strategies and potential costs (and sources of funding for those costs) as well as noting various compliance rules before beginning funded research. This will ensure that open access will be possible if it is stipulated, even if grant funding has run out or other issues surface. Not all psychology scholarship is funded, of course, and this does not impact the need to comply with the university open access policies in many cases as well. Open access policies passed by universities may also create an environment more focused on “open” in terms of university scholarly communication practices around publications and research data. Focusing on “open” in all aspects of psychology research and publication, including data, will create a new environment based around transparency that will produce positive change in the discipline’s scholarly output. Green Open Access: Strategies for Author Self-archiving of Works in Digital Repositories and other Services According to SHERPA/RoMEO and the APA’s website, the default policy for sharing articles in APA journals classifies them as “RoMEO green,” and no embargo or delay is listed for posting of the final author version (often the Word document after completion of peer review). APA Journals states: “Authors of articles published in APA journals — the authoritative document, i.e., peer reviewed publication of record — may post a prepublication copy of the final manuscript, as accepted for publication as a word processing file, on their personal website, their employer's server, in their institution's repository, reference managers (e.g., Mendeley) and author social networks (e.g., Academia.edu and ResearchGate) after it is accepted for publication.” There are conditions set by APA that do prevail when authors are posting their own Word document version of an article (after peer review) at the time of acceptance for publication. These caveats include: placing a specific statement on the cover sheet or front of the posted article stating that the author’s copy may not be an exact replica of the published version of record, the deposited version must link to the final version on the publisher website, and carry an APA copyright notice. (American Psychological Association, 2015). This type of publisher permission for authors to be able to self-archive their final accepted manuscript, making it open access on the web to readers and researchers worldwide, is a common scenario. Most publishers allow this posting with or without embargo, and with or without special conditions, but some are much more restrictive, issuing rules that make it more difficult for authors who wish to share their work online, and for readers who discover scholarly content and cannot read it without encountering roadblocks. While many universities make subscription content available to their affiliates (faculty, staff or students of the institution only), sometimes scholars forget about the legions of practitioners, budding scientists, unaffiliated researchers, students that have graduated, alumni of most universities, and readers around the globe who need to read the scholarly literature of psychology, and cannot access it online due to paywalls or issues of non-affiliation. For those ensconced comfortably in academia, a familiar refrain might be the “everyone who needs access to the material has it somehow.” This is not the case, and one can imagine how the reach of psychological science is impacted. Green Open Access: Strategies for Author Self-archiving of Works in Digital Repositories and other Services Authors publishing in traditional subscription journals need to share their work, and many want to or have to (due to funder or university mandates) deposit a version of their article in their institutional or disciplinary repository. These repositories are crawled by Google and other search engines, making the content available on the web. The majority of traffic to article versions in digital repositories comes in from search engines, particularly Google Scholar, and not as frequently by readers and researchers visiting the repositories directly. This wide online availability on the internet (via a Google search of author or targeted keywords) ensures easy discovery by anyone doing simple web keyword searches. Publishers vary greatly on how and whether they accommodate this “green open access” (repository route) for their articles. A look at the database, “SHERPA/RoMEO: Publisher copyright policies & author self-archiving” (www.sherpa.ac.uk/romeo/), which is searchable by journal title or publisher name turns up examples of self-archiving policies for publishers of psychology journals. These policies on self-archiving would range, for example, from more OA- amenable publishers like American Psychological Association (APA) and Association for Psychological Science (APS), whose rules (according to SHERPA/RoMEO) allow authors to self-archive and share accepted manuscript versions (as well as unrefereed preprints) -to the journals from some commercial publishers, an example being Taylor & Francis with Psychological Inquiry that requires a 12 month embargo (delay) before the author’s accepted manuscript can be made available online. Psychological Inquiry is also an example of a hybrid 23 journal that has an open access option for the publisher’s version of record (VoR), and charges 2950 USD to publish the final version as a fully open access article. Hybrid journals, a popular option for commercial publishers, offer a mix of some traditional subscription content and some articles that have been made open access in the same issue. The articles have been made open access, alongside other traditionally published articles because the author, funder or university has paid an APC (article processing charge). APCs are highest for commercial publishers at this juncture. This is a pain point for libraries already paying subscription prices for these commercial journals, and terms such as “double-dipping” have come to identify the practice of charging for both subscriptions and author-side payments (APCs) as well. Currently, individual institutions as well as whole countries have pushed back, requiring “offsetting” agreements or other accommodations for managing the costs inherent in the system. Green Open Access: Strategies for Author Self-archiving of Works in Digital Repositories and other Services The issue of “paywalls” has become the major roadblock (although there are others), and has led to much consternation, and even was the 24 subject of a recent documentary film entitled, Paywall: The Business of Scholarship. (https://paywallthemovie.com/) In terms of commercial publishers, Perspectives in Psychological Science is an APS (Association for Psychological Science) journal, but is published by the commercial publisher, SAGE. Unlike some of the others, SAGE has a liberal self-archiving policy and other open access practices that allow authors to share their work widely, possibly driving some traffic back to the journal and the publisher. Libraries would find SAGE to be the kind of publisher that facilitates the wide dissemination that authors and universities seek. (Mullen & Ross, 2016) Although many worry about harm to publishers, in terms of subscription cancellations or other negative consequences, at this point, that has not been the case. (Suber, 2016) In fact, various analyses, including one report from BernsteinResearch (Aspesi & Luong, 2014) are able to state that “11 years after the Berlin Declaration on Open Access, however, the rise of Open Access appears to inflict little or no damage on the leading subscription publishers” (p. 1) and that “OA funding may in fact be adding to the profits of STM.” (p. 1) All major publishers now have open access options for authors and funders. Publishers are all also cognizant of the wide sharing of the research literature that currently exists (outside of established legal channels) that only continues to grow, and will deal with that somehow as time goes on. There may be confusion over multiple versions of the same paper on the internet but there are clear methods of identifying versions in a repository, superseding an older version with a more current one, and finally linking to the version of record. It is true today that iterations of a single paper may have different DOIs, possibly causing concern or confusion. However, this is the expected scenario going forward. Each version of a paper needs its own DOI to identify that particular version for purposes of citation. Green Open Access: Strategies for Author Self-archiving of Works in Digital Repositories and other Services For traditional publishing, posting of the version of record online is disallowed. A small proportion of journal publishers allow the version of record to be placed in an institutional repository in compliance with mandates (funder or institutional), or even shared legally and openly on the web. A 2009 study reported that at that time, 5-19% of publishers allowed self-archiving of publisher versions. (Morris, 2009) The SHERPA/RoMEO website includes a listing (2015) of “Publishers allowing use of their PDFs in Repositories” (http://www.sherpa.ac.uk/romeo/PDFandIR.php?la=en). One example of a publisher allowing publisher branded copies to be self-archived is PsychOpen (http://www.psychopen.eu/). Even with all of the rules about self-archiving of peer reviewed articles easy to find (in author instructions or in services like SHERPA/RoMEO), there is evidence that plenty of authors post versions of record to their own websites, or to other web services. (Björk, Laakso, Welling, & Paetau, 2014) In fact, many publishers that do not allow publisher versions to be posted to institutional repositories do allow posting to personal websites. This often strikes scholars as somewhat confusing. While institutional repositories are widely available to those affiliated with universities, and the subject/disciplinary repositories (and scholarly networking services such as ResearchGate) also provide valuable visibility for authors that self-archive their work, studies show that many authors prefer to place their works on personal websites. (Björk et al., 2014) While a popular option, using the personal (or departmental) website does not provide the preservation or migration of digital formats that digital repositories do. Repositories also employ a high level of search engine optimization (SEO), aiding discoverability of works more effectively than many personal or institutional websites. In a smaller 2009 study from Carnegie Mellon University that looked at faculty practices of placing electronic copies of their articles on faculty webpages, it was found that “publisher policy appears to neither influence the decision to self-archive nor the article version that is self-archived. Disciplinary norms are influential but not necessarily the driving factor” (p.225) and in this case, the university’s psychology department showed one of the highest rates of providing access to full-text open access versions of articles on faculty webpages. (Covey, 2009) Online curricula vitae (CVs) have been studied to ascertain whether researchers are adding hyperlinks to openly available versions of articles, possibly furthering the reach of these articles. Green Open Access: Strategies for Author Self-archiving of Works in Digital Repositories and other Services Green OA, the “repository route” to open access makes papers available on the internet, often using an author version just before publication, the post-peer reviewed “Accepted Manuscript (AM).” This version may also be known as the “postprint.” Postprint versions, (accepted articles, post peer review), usually have the same intellectual content as the published version of record. Some authors whose articles have undergone revisions are reticent about depositing versions that may not be identical, word for word, to the publisher version due to copyediting, or other changes made in the final publication process. However, some authors prefer to self-archive their accepted manuscript version as the “best available version,” finalized as they prefer, with minor possible differences from the publisher-copyedited version of record. When self-archiving a work of scholarship, authors have control over the final iteration of their accepted manuscript, and they may add changes that have been made by copyediting to the deposited version as they wish. Each version of the article has its own DOI and is citable as an individual research output. Repositories practice “version control” and are able to direct readers from a superseded version to the most current version of the article. This information can now be prominently displayed on the article’s cover sheet in the repository, directing readers via seamless linking to the publisher version of record. This final publisher version may be imprinted with the CrossMark logo, indicating the most current authoritative publisher version. For those wishing to self-archive older papers, a perennial problem is lack of author access to their accepted manuscript versions at any later point in time. Those working with authors on self-archiving their papers know that it is easiest for authors to 25 deposit their articles in the institutional repository “at the point of acceptance for publication,” because this is the moment in time when the author is most likely to have the article’s accepted manuscript right at hand for the simple deposit. It is possible now for repository managers or authors to retrieve the author’s accepted manuscript from some publisher manuscript submission systems. (https://openaccessbutton.org/direct2aam) The final published version of record (often in PDF) is often proprietary to the publisher, and authors are restricted from archiving this version in repositories or elsewhere on the web (unless they have paid an APC to the publisher to allow this posting in the case of a hybrid or fully OA journal). Green Open Access: Strategies for Author Self-archiving of Works in Digital Repositories and other Services In a survey of European authors, in comparison to what publishers allow, there was not a significant use of the practice of linking to OA versions on online CVs. (Kousha & Thelwall, 2014) 26 Whereas publishers, libraries, the public and other stakeholders are motivated to move to a more open access environment for scholarly journals, there is evidence that the scientists that actually write the articles and often sign them away to the publisher (only retaining some rights to share their own works on the internet) are a group that may prefer the status quo. Within the current system of scholarly communication, with established incentives and rewards in place, getting published in as high an impact journal title as possible is the key to career advancement, and is still the real or perceived route to promotion and tenure in many cases. Many authors don’t necessarily want change in the system, especially if there is any career risk. They routinely sign publication agreement forms, often signing their rights away, and possibly only later want to make greater use of the works than what the publisher allows. Other times, they sign an exclusive license. Most publishers (but certainly not all) contribute “rules” for sharing various versions on the internet on the aforementioned SHERPA/RoMEO service. Of course, some authors either do not understand what rights they are signing away, or simply don’t pay attention to this final step in what may be a long publication process. Some authors simply post articles wherever they want, such as on personal websites or scholarly networking services, not even considering doing otherwise. Since they wrote the articles, they consider the work shareable. There is misunderstanding by authors over which versions of articles are allowable, and even questions about how to find information on how to share research publications on the web. Today’s culture of sharing is so pervasive in practice that authors are sometimes shocked to find that publishers do not allow the wide sharing of articles on the internet. Sharing of the publisher proprietary branded version is, in most cases, illegal. The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals Unrefereed early versions, known as preprints or “author’s originals (AO)” are a topic of significant current interest to authors, funders, and publishers. Interestingly, the choice of using preprints to disseminate scholarship has had a long history in psychology. Garvey & Griffith (1972) described how informal scholarly communication in the early 1960s included the practice of dissemination of preprints as a way to seek comments and feedback on research. Before the internet made sharing early versions of articles (allowable by most publishers) easy, Unrefereed early versions, known as preprints or “author’s originals (AO)” are a topic of significant current interest to authors, funders, and publishers. Interestingly, the choice of using preprints to disseminate scholarship has had a long history in psychology. Garvey & Griffith (1972) described how informal scholarly communication in the early 1960s included the practice of dissemination of preprints as a way to seek comments and feedback on research. Before the internet made sharing early versions of articles (allowable by most publishers) easy, psychological scientists used other means to distribute these early versions. “In 1963, for example, about half of the authors of articles published in major psychology journals distributed an average of 10 preprints.” (p.131) Further, psychological scientists used other means to distribute these early versions. “In 1963, for example, about half of the authors of articles published in major psychology journals distributed an average of 10 preprints.” (p.131) Further, preprint distribution appears to serve both the recipient and the author. Over 60 per cent of those authors who distributed preprints received feedback that prompted them to modify their manuscripts. These modifications were not simply a matter of improvement in the grammar and style of the manuscript but, instead, involved significant modifications such as reanalysis of data, redefinition of concepts, etc. Consequently, preprint distribution is, for many authors, an effective means of obtaining independent evaluation of the scientific worth of their work. (p.131) preprint distribution appears to serve both the recipient and the author. Over 60 per cent of those authors who distributed preprints received feedback that prompted them to modify their manuscripts. These modifications were not simply a matter of improvement in the grammar and style of the manuscript but, instead, involved significant modifications such as reanalysis of data, redefinition of concepts, etc. Consequently, preprint distribution is, for many authors, an effective means of obtaining independent evaluation of the scientific worth of their work. Green Open Access: Strategies for Author Self-archiving of Works in Digital Repositories and other Services Publishers at one time were liberal with regards to author self-archiving, but in recent years, even though more publishers are known to be “green” according to SHERPA/RoMEO, a more restrictive environment may be seen, with longer publisher embargoes emerging and more rules attached to use of any version of an article, particularly in an institutional repository. (Gadd & Troll Covey, 2016) This will necessitate the use of proactive strategies and workarounds for universities that want to showcase their scholarship or comply with funder mandates. In psychology, time from article acceptance to publication could be two years, although some publishers now place “in press” articles online (Nosek & Bar-Anan, 2012). For authors of accepted articles, many will want to self-archive the author’s accepted manuscript even before the publisher’s earliest posting. By placing an accepted manuscript online, early impact may be demonstrated. Many open repositories and other services disseminating “green” article versions can provide usage statistics, usually in the form of downloads from specific geographic areas. This type of alternative metrics service allows an author to create a narrative about a specific work, being able to suggest that impact may be demonstrated by charts and visualizations showing tens or hundreds of downloads from many countries (in a specific time period, for instance). It can be very compelling for an author to open up access to scholarship through making works (in early versions such as preprints or accepted manuscripts) freely available on the internet, and then to watch the reader traffic that ensues. Some universities deploy large real- time mapping visualizations that show downloads of institutional scholarship as it is happening. Depositing green copies of papers online as soon as they are accepted for publication accomplishes many goals for the scholar, namely getting the work out as soon as it is accepted, 27 getting novel ideas date stamped, often before the final publisher version of record is made available. This allows early sharing of the DOI from the repository, and early download statistics can start to accrue. Self-archiving is also an effective way of marketing one’s work online, as Google Scholar crawls repositories and makes papers available on the internet within a short time frame. When the published article becomes available, repository versions can link to that publisher-supplied DOI. The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals Instead, the scientist relies heavily on informal networks of information exchange to keep abreast of current activities and the current views of the community on the value and relevance of specific research problems. (p.128) Where some publishers lament the extent of the sharing that goes on in scholarly networking platforms, such as ResearchGate or Academia.edu, it is important to remember that wide sharing was always the goal of productive psychological scientists. At this point, the most well-known preprint server is unquestionably arXiv, an integral part of the established disciplinary culture of physics, mathematics, computer science and related fields. An early innovation of the scientific communication systems in disciplines that use it, arXiv, developed in 1991 by Paul Ginsparg at Los Alamos National Laboratory and taken over by Cornell University in 2001, is now supported by more than 50 universities. Recently, Cornell announced arXiv’s transition from its Library to Cornell Computing & Information Science (CIS). (https://cis.cornell.edu/arxiv-looks-future-move-cornell-cis) At one time, arXiv asked for support from universities that had many uploading authors. (Bjӧrk, 2014) Still, even with nearly 1,500,000 papers in arXiv as of this writing (August, 2018), there are always questions raised about sustainability for all of these services, or the possibility of buyout by some commercial firm with interests of a different kind. It is noted that Elsevier recently acquired both Mendeley and SSRN (Social Sciences Research Network). Still, the preprint culture solidified in the scholarly landscape by arXiv and now being established in multiple new disciplinary areas during 2016 alone is notable. Where some publishers lament the extent of the sharing that goes on in scholarly networking platforms, such as ResearchGate or Academia.edu, it is important to remember that wide sharing was always the goal of productive psychological scientists. At this point, the most well-known preprint server is unquestionably arXiv, an integral part of the established disciplinary culture of physics, mathematics, computer science and related fields. An early innovation of the scientific communication systems in disciplines that use it, arXiv, developed in 1991 by Paul Ginsparg at Los Alamos National Laboratory and taken over by Cornell University in 2001, is now supported by more than 50 universities. Recently, Cornell announced arXiv’s transition from its Library to Cornell Computing & Information Science (CIS). The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals (p.131) This focus on getting completed articles (before peer review) out to colleagues in order to solicit feedback is now facilitated through disciplinary preprint servers and institutional repositories that serve to put “author’s originals (AO)” on the internet so the sharing can be maximized. In this current practice. we see echoes of the scientific communication practices of 50 years ago. The Author’s Original (AO) is just one version of a work that can exist along continuum, with clarity regarding versions provided for readers by the use of consistent NISO (National Information Standards Organization) versioning language terms. (NISO/ALPSP Journal Article Versions (JAV) Technical Working Group, 2008) Use of standardized terms assists with the issue of the identification of versions of a particular work, where each article may have many iterations on the internet. Institutional repositories often use the addition of “cover sheets” on each article to identify version of the article as well as to provide a link to any final publisher version that may be available to the reader. Many preprints exist only in this early version, and are never formally published. They exist, identified by their DOIs (or “handles”) online as a unique contribution to the research literature of a discipline or university. Preprints may be considered as “author’s originals” or “works in progress” on a scientist’s publication record. 28 The establishment of informal networks of scientists has been paramount throughout recent history in psychology, leading Garvey & Griffith (1972) to discuss the results of their study that found that: In other words, research ideas and problem development cannot be primarily influenced by the published channels of scientific information exchange. In a study of over 200 research efforts in psychology, we found that ideas for less than one out of seven originated from sources such as journal articles, presentations at national meetings, etc. Instead, the scientist relies heavily on informal networks of information exchange to keep abreast of current activities and the current views of the community on the value and relevance of specific research problems. (p.128) In other words, research ideas and problem development cannot be primarily influenced by the published channels of scientific information exchange. In a study of over 200 research efforts in psychology, we found that ideas for less than one out of seven originated from sources such as journal articles, presentations at national meetings, etc. The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals (https://cis.cornell.edu/arxiv-looks-future-move-cornell-cis) At one time, arXiv asked for support As for preprints, there are many who question why the successful model that arXiv represents has not translated to other disciplines. Even though the culture of social sciences supports fairly traditional scholarly communication systems, recently, SocArXiv (Peet, 2016) was developed after the model of arXiv. SocArXiv is a new preprint server for the social sciences that is overseen by a distinguished steering committee and is partnering with the University of Maryland, the Center for Open Science and SHARE (a higher education initiative, http://www.share-research.org/). (P. Cohen, 2016) These are early days for these efforts, and the future of these innovations in scholarly communication (for those disciplines not accustomed to such sharing of early unrefereed versions) is still unclear. The impetus may be growing for change, and some publishers will innovate and provide options for authors. Other publishers may not evolve and continue with the status quo, not offering authors the choice to share their work more widely and prior to publication. There may be other pressures on authors to use preprints. In 2017, the National Institutes of Health (NIH) followed the lead of the UK’s Medical Research Council (MRC) and as of March 27, 2017, began to allow preprints to be submitted as part of the 29 grant proposal process. There was some contentious discussion during the decision-making process about the use of these “interim research products” and issues with use of non-peer reviewed papers in proposals. However, response from scientists has been positive. (Vence, 2017b) As online preprints continue to proliferate, there is an important new option in psychology due to the establishment and development of the new dedicated preprint service, PsyArXiv. (Center for Open Science, 2017a) This new preprint option for psychology, PsyArXiv was launched in December, 2016. PsyArXiv is one of the open source disciplinary preprint services made available by the Center for Open Science and run by its Open Science Framework (OSF) Preprints service. Center for Open Science (COS) is an established innovator in the open science landscape. COS grew, in its first four years from a staff of two to an organization of 60 staff with an 8 million USD operating budget, and its OSF software was used (as of 2017) by 50,000 scientists that are sharing their research methods and data. (Winerman, 2017). Historically, this issue of “prior publication” was addressed in psychology in 1996: The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals It will be interesting to watch the progress of this psychology preprints initiative: how many authors participate, how papers evolve to more final publication, and how the existence of preprints will interface with formal journal publication. PsyArXiv follows the recent launches of bioRxiv (operated by Cold Spring Harbor Laboratory), and ChemRxiv (established by the American Chemical Society). Two other new preprint services opening alongside PsyArXiv are the aforementioned SocArXiv and also engrXiv for engineering. This is a rapidly developing phenomenon for many disciplines. As these services become more popular and proliferate, a proposal to connect and centralize preprint services in an initiative called “The Commons” could resonate in an increasingly cross-disciplinary scholarly landscape. The proposal for The Commons states: “The Commons will connect preprint services in a community-based model. For the typical user discovery interface, The Commons will facilitate discovery of preprints on various hosted preprint services and guide users to engage with the preprint on that hosting service.” (Nosek, 2017) Along with this new emphasis on preprints in many disciplines (including psychology), occasional discussions sometimes persist about a once debated topic, the “Ingelfinger rule.” (Altman, 1996) The Ingelfinger rule developed traction as it forbade duplicate or prior publication of any research that would be submitted to a peer reviewed journal. How does this idea translate in an age of internet posting of research results, especially preprints? The number of publishers expressly allowing posting of preprints online has seemed to put this issue to rest. There may be added incentives and advantages for authors of having early versions of articles available for all to read on the internet. Preprints may catch the eye of journal editors seeking promising content for their publications. There is evidence that “preprint editors” in some fields are examining preprint servers to discover promising articles for possible publication in their journals, for example, as is the case with PLOS Genetics and BioMed Central’s Genome Biology. (Vence, 2017a) Uploading articles to disciplinary preprint servers may be an effective way of marketing to editors seeking relevant articles for their publications. Historically, this issue of “prior publication” was addressed in psychology in 1996: 30 One of the most widely publicized Internet publication policies came from the American Psychological Association (1996) whose interim policy asserted: Authors are instructed not to put their manuscripts on the Internet at any stage (draft, submitted for publication, in press, or published). The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals Authors should be aware that they run a risk of having (a) their papers stolen, altered, or distributed without their permission and, very importantly, (b) an editor regard such papers as previously “published” and not eligible as a submission— a position taken by most APA journal editors. In addition, after acceptance for publication, the publisher is the copyright holder. APA does not permit authors to post the full text of their APA-published papers on the Internet at this time, as developments in the on-line world cannot be predicted. The APA will, however, closely follow such Internet developments. The P&C Board will establish a task force in June 1997 to investigate developments and recommend a longer term APA policy. (Kling & McKim, 2000, p. 1312) This policy certainly evolved. Many (if not most) journal and publisher policies today allow posting of preprints in repositories and other web services, and in some disciplines, there is an established culture around archiving preprints. Major psychology publishers do allow the posting of preprints. Some have some minor rules around the practice. APA is an example of a publisher that does allow preprints to be self-archived. As for permissions to post preprints on the open web, the SHERPA/RoMEO service lists APA’s permission to post preprints, and the APA website (http://www.apa.org/pubs/authors/posting.aspx) lists this information: APA Journals Internet Posting Guidelines Update effective November 25, 2015 If a paper is unpublished, the author may distribute it on the Internet or post it on a website but should label the paper with the date and with a statement that the paper has not (yet) been published and is not therefore the authoritative document of record. (Example: "Draft version 1.3, 1/5/16. This paper has not been peer reviewed. Please do not copy or cite without author's permission.") These early, original articles, once deposited in an institutional or subject repository (or on a preprint server like PsyArXiv), do pick up downloads and citations and can serve to establish early authority, as well as provide a mechanism for authors to receive constructive feedback on early drafts. This serves the purpose of crowdsourcing informal review, and feedback can improve later drafts. The announcement that the third party platform service, Hypothesis, would partner with some of the preprint services of Center for Open Science (including PsyArXiv) to provide the ability for readers to annotate and discuss preprints was welcome. The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals This valuable enhancement allows the community to provide constructive feedback on a preprint within the text (rather than in comments at the end), aiding efforts at transparency and collaboration in scholarly communication in psychology. (https://web.hypothes.is/blog/hypothesis-live-on-cos- osf/) Posting a preprint online also date stamps the article, aiding efforts at getting current work out quickly, as well as preventing “scooping.” Being scooped would be one of the 31 considerations researchers would consider when disclosing results before a paper is submitted for publication. Thursby, Haeussler, Thursby, & Jiang (2018) found a lack of research about how the disciplines view “prepublication open disclosure,” and studied reasons and motivations as to why scientists do or do not share results before publication via posting of preprints (but also by using web postings or conference presentations to disclose). While psychology was not one of the nine specific fields analyzed by Thursby et al., for “scientific disclosure before publication,” results showed that “across all fields, obtaining feedback is the most important,” (p.2) and that the motivations to disclose (and the timing of disclosure) varied across fields. In the disciplines, levels of competition and commercialization matter a lot to decisions to disclose, with lowest levels of both competition and commercialization found in social sciences and mathematics. Further, “not coincidentally, social sciences and mathematics have a greater degree of disclosure to general audiences than medical basic science” (p. 10) and “social scientists are the most likely to disclose at the conceptual stage.” (p.2) Seeking a greater understanding about how and when psychology researchers disclose research results before formal publication would assist publishers, developers of preprint services, and conference organizers in making services available that would attract those seeking to get their work out as early as possible to the widest potential readership in order to spur innovation and further research. This practice of posting preprints has been the culture of some fields such as high-energy physics and computer science, with their preprint server, arXiv, since the early 1990s. As of this writing, it remains to be seen whether the practice of sharing preprints online via repositories or services like PsyArXiv, for instance, will become standard practice in psychological science. It also depends on how much commentary and open peer review are desirable and acceptable as articles develop from preprint stage to more final versions. The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals In psychology, with PsyArXiv still relatively new, it remains to be seen whether there will be an appetite for sharing non peer- reviewed versions of articles online. The emergence of PsyArXiv will also serve to demonstrate whether in psychology a preprint environment will behave like the established culture of arXiv’s, or whether the discipline’s researchers will instead stick to the publishing status quo. Authors posting papers on PsyArXiv are able to choose to license their work using the two Creative Commons licenses that the service supports, whether to put the work in the public domain, or to use the popular CC-BY license. CC-BY, which allows for liberal reuse of the work while requiring attribution, is the most popular on PsyArXiv so far. As of April, 2018, 57% of authors have chosen CC-BY, 29% have chosen CC0 (public domain) and 13% have not placed a license on their uploaded work. (Moshontz, 2018) Adding an option for a more restrictive CC license may encourage authors to post longer form preprints that may develop into monographs later. These authors of longer form works can put no license on their works in repositories or preprint servers, but this approach is less than ideal even if it does signal that the author wants to retain copyright while receiving feedback from the community on the content contained in a longer than customary preprint (in the case of the possibility of a resulting book contract). This allows early posting of book-length manuscripts, sharing the content with a community, or multiple disciplinary communities. While most book publishers would not consider an already posted manuscript, some open access publishers (such as SAGE Open), do allow posting of a draft or early version of a possible publication before it is submitted for review. 32 Preprints in many disciplinary areas can often be posted by authors directly on the web (via preprint servers or various repositories) as they are not yet peer reviewed or in a “submitted” or “accepted” category, and therefore are not yet under the control of a traditional publisher. The term “preprints” can be problematic as the word has been used in different ways by some journals and publishers as a way to describe any version of an article as it exists online before formal publication. The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals A reader might see use of this term to describe accepted versions that have not yet been assigned pagination or an issue number, or for papers that are submitted manuscripts under review (but posted online by the author). More recently, use of the term may be more universally identified and understood as the “author’s original (AO)” (to use the NISO term) article which has not undergone peer review by a publisher. Some articles will never end up undergoing peer review, but instead will remain online in preprint form, circulating and being read widely by interested readers and researchers. These preprints are cited with their DOIs in the literature of many disciplines, and that would be the expectation for psychology as well. Preprints that never go on to more formal publication can still demonstrate informal impact through the counting of institutional and subject repository downloads and via the use of other alternative metrics. In terms of the publisher’s proprietary versions (including article versions such as “Proof” or “Version of Record),” recent takedown notices levied against university websites and scholarly communication networks by publishers (including APA) may make authors increasingly wary about posting the publisher’s version of an article online. On the other hand, it may embolden those that want to share their work and don’t want to be dissuaded or even threatened by the same publisher that was chosen for submitting the work. Distribution of takedown notices often gets attention quickly, and to avoid this scenario, authors may turn to depositing preprints in services and institutional repositories, taking advantage of the more liberal publisher permissions that currently exist for preprints. For now, many authors continue to deposit versions other than the allowable preprint in digital repositories and on websites. It remains to be seen whether recent actions by publishers to send out takedown notices when “illegally posted” articles on websites are discovered will make a difference and cause authors to abandon posting final publisher versions on the internet (and possibly switch to depositing earlier prepublication versions online). In a recent high profile example from 2017, the American Psychological Association (APA), began a pilot program that initially started by analyzing where final versions of five APA journals could be found posted illegally. APA then began sending Digital Millenium Copyright Act (DMCA) notices of infringement (takedown notices) to those sites that had posted these publisher final versions online. The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals The program eventually expanded to all 29 APA-published journals. Universities informed their authors that they must remove APA articles that were posted illegally from university websites. The negative reaction from authors was swift. APA responded by refocusing their efforts away from sending notices to individual authors. Takedown notices instead went to pirate sites and popular scholarly collaboration networks such as ResearchGate and Academia.edu as well as to 80 universities. (Mills, 2017) On June 16, 2017, McCook (2018) reported that: 33 the publisher had sent takedown letters-citing the Digital Millennium Copyright Act (DMCA), which enables internet users to protect their own content — to nearly 350 academic institutions (and 12,460 letters to piracy sites). The spokesperson told us the APA doesn’t plan to send any more letters to academic websites ‘at this time’. But the publisher is still discussing whether to rescind the takedown notices that academic sites have already received. Up to now, there has been no successful way to manage the dissemination of scholarly articles in final publisher version of record that occurs around the web. Takedown notices or lawsuits that target authors (or their universities) would seem to be a counterproductive strategy that could drive authors away from submission to certain publishers’ offerings and would refocus attention on a publisher’s posting guidelines. This kind of program is just not good for authors, libraries or readers’ relationships with publishers. This leaves publishers in a position where they may have no real recourse but to acknowledge the sharing of published scholarship that is going on. It leaves authors in a position where they may acknowledge that they know the rules (once they sign the copyright transfer agreement) but don’t necessarily agree with those rules and they want to ensure that there is open access and wide sharing of the article’s version of record. The practice of posting articles on the web may just become so commonplace as to become unstoppable by any publisher or other entity. In any case, publishers will not want to resort to suing their own authors, and may also understand that some sharing may be driving traffic (and possibly some resulting impact) to their articles and websites. After all, added visibility of an article is always good for publishers and citing conventions will drive researchers to seek out the publisher version of record if it is accessible to them. The Continuing Emergence of Preprints: Online Dissemination of Authors’ Originals If there is no subscription access, other versions will suffice. It is unclear, at this juncture, how article sharing (or in what form) will or will not create the kind of harm that would cause an end or an irreversible disruption to traditional scholarly publishing as it currently exists. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers Many psychology researchers have searched for scholarly publications or uploaded their own works to one of the few online disciplinary or subject repositories that are available for psychology. Unlike some other disciplines, psychology does not necessarily have an ingrained culture of participation in subject or disciplinary repositories, but works can be found across a few of the major repositories. Participation in subject or disciplinary repositories is another green OA strategy useful in the goal of wide dissemination of psychology papers. Certain of the subject repositories have risen above the entire landscape of digital repositories not only in sheer size and volume of content, but in their centrality to certain fields as the gathering place for scholarship and collaboration. Studies have placed four major subject repositories in this position. SSRN (Social Science Research Network) is multidisciplinary but has prominence especially for law and economics scholars, PubMed Central (PMC) is the largest subject repository and the target of biomedical scholarship, arXiv has, since the early 1990s been central to physics, mathematics, computer science and other related fields, and RePEC is well known and used by economists. (Li, Thelwall, & Kousha, 2015) None of these four largest subject repositories has a particular focus on psychological science, and some studies have 34 shown that a higher percentage of archived open access papers overall can be found in fields that have a dedicated subject repository. Such is the case with biomedical sciences, and also is reflective of the effects of the NIH mandate. PMC has arrangements with many publishers for deposit of papers associated with NIH funding, and as of August, 2018 lists five million publicly accessible articles. Without a strong preprint culture feeding it, most papers in PMC are accepted manuscript versions of published articles or final publisher versions. One available online repository of interest to some areas of psychology is SSRN. SSRN is often viewed as a collaborative, sharing site for researchers and their early abstracts and papers in social sciences disciplines, and currently (as of August, 2018) it holds more than 800,000 research papers. SSRN is described on its website thus: “SSRN is devoted to the rapid worldwide dissemination of research and is composed of a number of specialized research networks” (https://www.ssrn.com/en/). One specialized research channel of interest to psychology is the Cognitive Science Network, which contains more than 22,000 papers as of August, 2018. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers 35 Subject repositories and/or “eprint archives” for psychology (and using the example of cognitive science), may not have evolved to attain the level of visibility of arXiv, for instance, but the two archives do share a long and common history. An early eprint repository that focused on cognitive science, neuroscience and a few other related disciplines, CogPrints, was founded (and is still moderated today) by cognitive scientist Stevan Harnad. CogPrints was launched in 1997 following the success of the eprints model that had been in place since the founding of arXiv for the use of the physics community by physicist Paul Ginsparg in 1991. Harnad wanted to extend the eprints model, which relied on author self-archiving of preprints and other papers to an electronic archive for cognitive science and related fields, even as he acknowledged the field differences that existed between physics/computer science and cognitive sciences in the sharing of unrefereed preprints. CogPrints was developed by Harnad based on software developed by Ginsparg at Los Alamos. (Taubes, 1996) The CogPrints archive now contains more than 4000 papers (as of August, 2018), with more than 1700 psychology articles included, and since the 1990s has demonstrated that cognitive science has had an eprint culture for almost as long as arXiv has served the physics and computer science community. Subject/disciplinary repositories can be considered complementary to institutional repositories, which serve a different mission of making a university’s publications and research output discoverable-across all disciplines- and available to a global readership. Institutional open access policies require and facilitate deposit in an institutional repository in order to showcase all of the institution’s scholarship. Crawled by search engines such as Google, both institutional and disciplinary repository contents will be discovered by all searchers, while a much smaller group of searchers visit the repository itself to search for content. It has been reported that institutional repositories’ contents are more discoverable than those of SSRN, for instance. One study demonstrates that SSRN content appears to searchers more slowly than papers in the institutional repository do, and represents different groups of searchers. Google keyword searches will pick up content in the institutional repository more quickly than searches of SSRN. The takeaway from this study is that using more than one repository strategy for uploading publications (such as depositing papers in SSRN and an IR) will achieve a greater readership than one or the other repository alone. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers SSRN was started in 1992 (SSRN was never strictly an open access repository per se) and as of May, 2016 is owned by Elsevier. This raises some questions about its continuing with “business as usual.” SSRN was started in 1994 by a small group of scholars whose backgrounds were mainly in economics and legal scholarship and it evolved as a business that offers various subscription services alongside its use as a repository of articles, working papers, conference papers and other scholarship. Over time, SSRN became one of the largest subject/disciplinary digital repositories, and is used by some researchers in psychology to upload papers. Eventually, SSRN was a corporation with a budget of more than one million dollars and more than a thousand volunteers were performing much of the labor (along with a small paid staff). (Bjӧrk, 2014). Still run by Gregg Gordon, (formerly President & CEO of SSRN before the Elsevier acquisition), SSRN is at this point still a heavily used networking, collaboration and research paper sharing site, especially for working papers and preprints in the social sciences and humanities (including content from the cognitive sciences). One of the compelling aspects of SSRN is its use of rankings (of authors, papers, and institutions). (N. Cohen, 2008) In certain fields, like law, faculty may even worry about use of their institutional repository (IR) for a secondary deposit of articles, fearing a “dilution” of their SSRN downloads, which could create a resulting drop in the rankings. It has been demonstrated that deposit in the IR allows access of important scholarship (especially early versions containing current research results) to readers that are outside the primary group served by the SSRN channel. Deposit in more than one repository service, such as in the institutional repository as well as in SSRN broadens readership and exposes the work to new readers and researchers. (Donovan & Watson, 2012) It would seem advantageous for SSRN depositors to attract new reader traffic by moving outside of SSRN, especially since this practice does not damage SSRN rankings. There is no “rule” on where a given early version article can be deposited online and various channels have their own readership so multiple channels of dissemination of a researcher’s work is possible. Preprints or accepted manuscripts can be deposited in multiple repository services online. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers (Donovan & Watson, 2012) While this study focuses on Law scholarship, it would make sense that depositing a single article in more than one repository will only increase its visibility and reach potentially different groups of readers. These reader groups may be mutually exclusive and thus extend the outward reach of the work. It is not always a straightforward business for authors or others to ascertain whether publisher permissions allow or accommodate the deposit of papers into a subject or disciplinary repository. While many publishers make information about author self-archiving of preprints and other versions of article available on their websites or by adding information to the popular SHERPA/RoMEO service, it is often more difficult to find this information for subject/disciplinary repositories. Studies have shown that while many publishers expressly allow self-archiving on personal websites or institutional repositories, the permissions for archiving in subject repositories is more problematic and the number of publishers allowing deposit is lower. For example, in a study by Laakso et al. of 1.1 million subscription articles published in 2010 (in accepted manuscript or publisher version), it was found that 80.4% could be uploaded (allowed It is not always a straightforward business for authors or others to ascertain whether publisher permissions allow or accommodate the deposit of papers into a subject or disciplinary repository. While many publishers make information about author self-archiving of preprints and other versions of article available on their websites or by adding information to the popular SHERPA/RoMEO service, it is often more difficult to find this information for subject/disciplinary repositories. Studies have shown that while many publishers expressly allow self-archiving on personal websites or institutional repositories, the permissions for archiving in subject repositories is more problematic and the number of publishers allowing deposit is lower. For example, in a study by Laakso et al. of 1.1 million subscription articles published in 2010 (in accepted manuscript or publisher version), it was found that 80.4% could be uploaded (allowed 36 by the publisher) to an institutional or subject repository (or personal website) within the first year of publication. Further analysis of this number showed that publishers were much more permissive about allowing the accepted manuscript to be uploaded to institutional repositories (79.9% of articles) or personal websites (78.1%) than they were to subject repositories (only 32.8%). Subject or Disciplinary Repositories Available for Psychology Authors and Researchers At the time of this analysis, only about 12% of articles available for self-archiving in repositories actually were being made available open access via a repository. (Laakso, 2013) The practice of author self-archiving of non-proprietary earlier versions of articles or “green” open access has had a slow start but is the stated focus of most institutional repositories and open access policies. The continuing forward movement of green open access is still in the hands of authors and the research community and would grow much faster if they would take the simple action of uploading their papers with a few simple steps, thereby allowing Google and other search engines to disseminate these works to worldwide readers. Many authors do not self- archive and Stevan Harnad advocated early and often for them to simply perform “a few keystrokes,” taking very little time out of busy schedules to deposit each scholarly work in a repository (enabling open access at no cost to them). Psychology also appears as a percentage of open access papers in repository collections in biomedicine, while not showing large percentages of open access papers archived in any particular subject repository. There is clearly not a culture of using one subject repository in psychology. In fact, in a large scale study completed for the European Commission in 2014 that reported the availability of OA content by discipline, the category of “Psychology and Cognitive Science” did not show up in the top disciplines making papers available by either green (self- archiving in repositories) or gold (journals route) open access. However, in this large scale study that used the Scopus database, Psychology and Cognitive Science was the second highest grouping in the “other OA category,” showing a proportion of 43% of open access papers to total papers published. The authors defined “other OA” in this study as papers freely available to readers due to their availability on the internet in services such as aggregator sites, “hybrid” articles (open access articles in subscriptions journals where the author has paid an article processing charge), or even articles found posted outside of publisher permissions. (Archambault et al., 2014) Overall, in all disciplines studied, this analysis reports that: as of April 2014, more than 50% of the scientific papers published in 2007, 2008, 2009, 2010, 2011, and 2012 can be downloaded for free on the Internet. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers This is an important finding as only one year ago, in April 2013, the proportion of papers that was freely available was just a hair below 50% (49.54%) in 2011 and did not reach that mark for any other year. (Archambault et al., 2014, p. 2) as of April 2014, more than 50% of the scientific papers published in 2007, 2008, 2009, 2010, 2011, and 2012 can be downloaded for free on the Internet. This is an important finding as only one year ago, in April 2013, the proportion of papers that was freely available was just a hair below 50% (49.54%) in 2011 and did not reach that mark for any other year. (Archambault et al., 2014, p. 2) Open access availability is increasing. It would seem clear that psychology is a disciplinary area that could really benefit from placing more focus on open access and setting a goal of ensuring at least public reader access to much more of its scholarship. Green OA is attainable for most papers (sometimes with embargo), and may be seen as an author responsibility if more of the disciplinary literature is to reach every possible reader. It is not clear whether having available a disciplinary or subject repository (like the major ones found in other disciplines (such as with 37 arXiv for physics, for instance) would create more momentum. Recently, the aforementioned preprint server PsyArXiv has become a target for preprints in psychology. PsyArXiv will provide another vehicle for changing the open access culture in psychology. Even as psychology establishes a reputation for its leadership in areas of reproducibility and other areas of open science, will the discipline increase its uptake of open access practices or will it fall behind other disciplinary areas? Some would rather see a focus on a move to more open access by focusing not so much on many versions of articles freely available online in subject, disciplinary, or institutional repositories, but instead to focus on more open access journal publication. Gold open access (the “journals route”) is felt by some (for instance, by some funders in the UK) as the gold standard of OA because rather than earlier versions such as author’s originals or accepted manuscripts, it is the version of record (proprietary publisher branded version) that is made available on the internet. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers Of course, publishers place the most restrictions on the “version of record,” and that is the version most scholars would want to cite if at all possible. APA style, according to the 6th edition of the Publication Manual of the American Psychological Association (section 6.24 and 6.32) states that “As with references to material in print or other fixed media, it is preferable to cite the final version (i.e., archival copy or version of record; see section 6.24)” and further, it is stated that “if the most current version available was an advance release version at the time you originally cited it, recheck the sources and update its publication status as close as possible to the publication date of your work (see section 6.32).” (American Psychological Association, 2010) When authors do cite subject repository versions, at least one study has focused on how these major subject repositories end up providing citations to the cross-disciplinary scholarly journal literature. It was found that there is indeed a lot of citation activity outside the primary disciplines served by the major subject repositories. This shows that subject repositories can be valuable vehicles for disseminating articles outside of the primary disciplinary groups. (Li, Thelwall, & Kousha, 2015) There are many options for the scholar who wants to (or must) archive every article in one or more digital repositories using green open access, maybe too many. Many institutions have set out an expectation that all scholarly works must be self-archived (or harvested by automated methods) into the institution’s digital repository due to existing open access policies of the institution or funders. Authors will also want to participate in the repositories that represent their fields. The fact that scholars are in tune with the disciplinary communication norms of their fields may make the concept of deposit in institutional repositories seem redundant. It can be difficult to explain the purported value of self-archiving work in an institutional repository once researchers have aligned themselves with one or more of the disciplinary repositories or peer scholarly networking services. Many scholars may want to stick with, and affiliate with disciplinary (and not institutional) self-archiving solutions. Every scholar likely has chosen a preferred open access service (or sharing platform) that works and many are not eager to change behavior. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers Institutions with open access policies in place do realize higher institutional repository self-archiving rates, and so this is considered one strategy that an institution can have in place in order to place an importance on the need to make institutional scholarship freely available on the internet (to the extent possible). With pressure on institutions to take steps to rise in all of the various rankings, ensuring that all of a university’s research output is freely available online may become a priority. be part of a larger network. Many institutions are involved in efforts now to aggregate all of the institutional repositories into a large scholarly network, creating a critical mass of freely available scholarly literature for the world’s readers. Various aspects of the value of scholars’ self-archiving in the institutional repository include the gathering of the works of all faculty together in one place (allowing discoverability and reporting of aggregated university scholarship), making university works visible for enhanced collaboration across the institution (and across disciplines), making sure every work has an associated DOI so every article or book chapter can be listed in profiles such as ORCID’s, making sure all the works of every scholar are curated, preserved over time (formats migrated) and ensuring full text online access to the papers of every scholar from the institutional repository. One very important factor that authors may not always know is that publishers often allow self-archiving of the accepted manuscript of the paper (usually not the publishers’ version of record) in more than one repository. Therefore, while an author may want to share papers in many ways, there is no limit on the ability of the author to participate in a variety of repositories or other collaborative solutions for any given paper in its preprint or postprint (accepted manuscript) version. In fact, making any paper available legally online may drive traffic to the publisher version, creating a “win-win” for readers, authors and journals/publishers. There are many strategies that authors can take advantage of and a currently emerging role of academic librarians is to consult with faculty on the various “green” open access options available to authors today. Authors are especially interested in open access solutions that don’t carry the costs of the gold open access options, seeking instead these many green open access options for marketing their work and helping their scholarship reach new readers. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers The extra work (even spending the small amount of time required) of self-archiving with the institution often does not resonate in the same way as participation in the subject-based repository or other discipline-based solution. Busy researchers do not often see as much personal value to building a collection of work in an institutional solution that may not 38 be part of a larger network. Many institutions are involved in efforts now to aggregate all of the institutional repositories into a large scholarly network, creating a critical mass of freely available scholarly literature for the world’s readers. Various aspects of the value of scholars’ self-archiving in the institutional repository include the gathering of the works of all faculty together in one place (allowing discoverability and reporting of aggregated university scholarship), making university works visible for enhanced collaboration across the institution (and across disciplines), making sure every work has an associated DOI so every article or book chapter can be listed in profiles such as ORCID’s, making sure all the works of every scholar are curated, preserved over time (formats migrated) and ensuring full text online access to the papers of every scholar from the institutional repository. One very important factor that authors may not always know is that publishers often allow self-archiving of the accepted manuscript of the paper (usually not the publishers’ version of record) in more than one repository. Therefore, while an author may want to share papers in many ways, there is no limit on the ability of the author to participate in a variety of repositories or other collaborative solutions for any given paper in its preprint or postprint (accepted manuscript) version. In fact, making any paper available legally online may drive traffic to the publisher version, creating a “win-win” for readers, authors and journals/publishers. There are many strategies that authors can take advantage of and a currently emerging role of academic librarians is to consult with faculty on the various “green” open access options available to authors today. Authors are especially interested in open access solutions that don’t carry the costs of the gold open access options, seeking instead these many green open access options for marketing their work and helping their scholarship reach new readers. For psychology, more readers can only confer benefits to authors and to society. Practitioners would all have access to the latest literature. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers (2018) analyzed a different data set (from oaDOI, a free service that “determines OA status for 67 million articles”) that comprised three different sets of 100,000 articles each. This study estimated an overall OA proportion of the scholarly literature of 28%, and growing. In terms of looking specifically at psychology (in terms of its inclusion as a category in the NSF Specialties), this study showed that of 2,257 papers in the psychology sample, 1586 articles are not open access (70.3%), 122 (5.4%) were “bronze OA” (the delayed publisher OA), 2.0% were hybrid, 4.7% were gold OA, and 397 of the articles were green open access (17.6 %). Once again, comparing the Psychology sample in the Piwowar et al. (2018) study to the NSF category, Health, with a similar sample size of papers (2,121), a full 13% were bronze open access, once again showing a distinct disciplinary difference in how the Health publishers make papers open access on their platforms over time. This one small example of bronze OA uptake by percentage demonstrates why discussions of open access cannot be a “one size fits all” treatment. Those presenting information to mixed disciplinary audiences about OA or other aspects of scholarly communication cannot make broad pronouncements about current or future directions that will resonate with all groups. For the reader or librarian accessing the medical literature, making one’s work green OA may not seem as essential as much of the current literature (except for the most recent 6 months) may already be available on the publisher platform, or in PubMed Central. If the bronze OA category grows in biomedicine, it still does not jeopardize the sale by publishers of the most valuable content in current journal articles. Only recently have these breakdowns in types of open access allowed researchers to see the differences in access by discipline. Each discipline and subfield can be said to have a certain “culture of open access behavior” which could be studied further. Understanding these specific cultures would be valuable to open access policy efforts, customization of approaches by funders, education of scholarly communication librarians, and to all efforts at understanding scientific culture in the disciplines. The open access conversation in the disciplines must be more nuanced in order to resonate with more authors and stakeholders. the sample. However, the types of open access show quite a different result. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers In Clinical Medicine, the Gold OA percentage was 7.5%, 22.3 % were Bronze OA (a huge difference), and Green OA was 9.7%. Therefore, more biomedical researchers (than psychological scientists) are accustomed to publishers making articles freely available on their own platforms after a short time period. Another study by Piwowar, et al. (2018) analyzed a different data set (from oaDOI, a free service that “determines OA status for 67 million articles”) that comprised three different sets of 100,000 articles each. This study estimated an overall OA proportion of the scholarly literature of 28%, and growing. In terms of looking specifically at psychology (in terms of its inclusion as a category in the NSF Specialties), this study showed that of 2,257 papers in the psychology sample, 1586 articles are not open access (70.3%), 122 (5.4%) were “bronze OA” (the delayed publisher OA), 2.0% were hybrid, 4.7% were gold OA, and 397 of the articles were green open access (17.6 %). Once again, comparing the Psychology sample in the Piwowar et al. (2018) study to the NSF category, Health, with a similar sample size of papers (2,121), a full 13% were bronze open access, once again showing a distinct disciplinary difference in how the Health publishers make papers open access on their platforms over time. This one small example of bronze OA uptake by percentage demonstrates why discussions of open access cannot be a “one size fits all” treatment. Those presenting information to mixed disciplinary audiences about OA or other aspects of scholarly communication cannot make broad pronouncements about current or future directions that will resonate with all groups. For the reader or librarian accessing the medical literature, making one’s work green OA may not seem as essential as much of the current literature (except for the most recent 6 months) may already be available on the publisher platform, or in PubMed Central. If the bronze OA category grows in biomedicine, it still does not jeopardize the sale by publishers of the most valuable content in current journal articles. Only recently have these breakdowns in types of open access allowed researchers to see the differences in access by discipline. Each discipline and subfield can be said to have a certain “culture of open access behavior” which could be studied further. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers For psychology, more readers can only confer benefits to authors and to society. Practitioners would all have access to the latest literature. Institutions with open access policies in place do realize higher institutional repository self-archiving rates, and so this is considered one strategy that an institution can have in place in order to place an importance on the need to make institutional scholarship freely available on the internet (to the extent possible). With pressure on institutions to take steps to rise in all of the various rankings, ensuring that all of a university’s research output is freely available online may become a priority. Looking at the average of all self-archived papers in psychology for the time period 2005-2010, Gargouri, Lariviѐre, Gingras, Carr, and Harnad (2012) reported that 28% of all psychology journal articles published each year could be accessed free on the web. The percentage of green OA for psychology has continued to grow in recent years. Martín-Martín, Costas, van Leeuwen and López-Cózar (2018) also reported percentages of types (colors) of open access found across Web of Science disciplinary categories, including Psychology. For a large sample of openly available articles found to have full text links in Google Scholar, for Psychology, 57.8% of the sample were open access. By type (color) of OA, 2.8% of the sample was gold OA (published in open access journals), 4.2% were “Bronze OA,” a category where all content is made freely available to the public online after a certain time period by the publisher, and 18.9% of articles were “green OA,” found only in institutional or subject repositories. To compare these numbers to the Clinical Medicine category, for instance, demonstrates the large variability of results from one discipline to the next. It should also be noted that even subfields have great variations within a larger category. In comparison, the category Clinical Medicine had very similar total percentage of freely available articles (to Psychology), recorded at 56.9% of 39 the sample. However, the types of open access show quite a different result. In Clinical Medicine, the Gold OA percentage was 7.5%, 22.3 % were Bronze OA (a huge difference), and Green OA was 9.7%. Therefore, more biomedical researchers (than psychological scientists) are accustomed to publishers making articles freely available on their own platforms after a short time period. Another study by Piwowar, et al. Innovations in Peer Review and Open Peer Review: Examples from Psychology Innovations in peer review were summarized in a report commissioned by the Wellcome Trust in 2015, with major trends identified. This analysis was an attempt to inform the research community about the issues with peer review in a current scholarly communication landscape that focuses more and more on evaluation of researchers and institutions as evidenced by publications in high impact journals. This study reiterated the importance that the research community places on the “principle of peer review” and that the issue of the “practice of peer review” is instead at issue. (Research Information Network CIC, 2015) With the number of articles submitted to journals in the range of 3 million per year (and with a reviewer spending approximately 6 hours per review), it may be obvious that the system may be overburdened. (Jubb, 2016) Peer reviewers are not paid, and this part of the publication process must be managed, and can be a challenging part of the editor’s role. Difficulty in finding reviewers with appropriate expertise for a deluge of article submissions, dissatisfaction with non-publication that can sometimes be due to the appearance of one negative online review can all lead to publication delays. This, in turn, can lead to issues with the currency of the psychological science literature. Even with robust peer review systems in place, and an emphasis on high impact journals for career advancement and reputation, there is evidence that “the fraction of highly-cited articles published in non-elite journals increased steadily from 1995-2013. While the elite journals still publish a substantial fraction of high-impact articles, many more authors of well-regarded papers in a diverse array of research fields are choosing other venues.” (Acharya et al., 2014, p.1) This study, using Google Scholar Metrics (https://scholar.google.com/scholar/metrics.html) also found that, due to accessibility of the research literature, more researchers are citing “work published everywhere,” and over time a larger percentage of citations are going to articles in non-elite journals where “elite” was defined as the 10 most cited journals in each of 261 subject categories reported by Scholar Metrics. Many studies have shown how peer review is valued by scientists. However, there is room for improvement, according to studies of researcher attitudes. Subject or Disciplinary Repositories Available for Psychology Authors and Researchers Understanding these specific cultures would be valuable to open access policy efforts, customization of approaches by funders, education of scholarly communication librarians, and to all efforts at understanding scientific culture in the disciplines. The open access conversation in the disciplines must be more nuanced in order to resonate with more authors and stakeholders. Still, only the largest subject repositories are great contributors to the volume of “green” open access articles on the web. Bjӧrk’s 2010 research on subject repositories does not show a huge emphasis on subject repositories in psychological sciences. He reported in 2010 that although 43% of all self-archived manuscript copies can be found in subject repositories, a full 94% of all of these can be found in arXiv or PubMedCentral. Bjӧrk compares subject repositories and institutional repositories and notes that the subject repositories lack some of the advantages that institutional repositories enjoy such as sustainable support from universities, an environment where more publishers allow self-archiving, and a trend toward open access policies promoting more self-archiving in the institutional repositories. Subject/disciplinary repositories (outside of the largest ones) may not be a growth area. For the largest repositories, other factors such as the role they have played for many years as part of disciplinary publishing culture may promote their continued success. Those fields (which don’t include psychology) that rely on their subject repositories already had a working paper or preprint tradition prior to 40 the advent of the internet, and of course, NIH created an upward trajectory for PubMed Central with their public access mandate. Funder mandates could make a difference for psychology archiving in repositories. SSRN, arXiv and RePEC were subject repositories that were natural extension of earlier disciplinary preprint culture of certain disciplines. (Bjӧrk, 2014) However, scholarly communication in psychology did not develop in ways that promoted the natural growth of subject repositories and at this point, it would not seem that this would be an expected development in the future. PsyArXiv, with its set of open science services, may be the option that psychology has been waiting for, and may one of the game changers for scholarly communication in the discipline. Innovations in Peer Review and Open Peer Review: Examples from Psychology (Mulligan, Hall, & Raphael, 2013) There are also issues with time lag and other negative consequences of a sometimes lengthy review process (for authors and journals) when the result is often “revise and resubmit.” (Cochran, 2016) Journals, editors and researchers alike need to be able to speed up the publication process in these high stakes times, and all delays are more difficult to manage. While 41 much is changing, there is always an emphasis on the need to maintain robust peer review systems. Peer review systems and practices are currently undergoing many innovations and experiments. For instance, European Journal of Neuroscience is beginning to publish full, bylined reviews attached to articles. According to the journal, “Open reviews, the argument goes, are more thorough and constructive-and the rich scientific debates they reveal can be a valuable educational tool.” (Vlasits, 2017) The editors-in chief state in an editorial that “we believe this is the future.” (Foxe & Bolam, 2017; Vlasits, 2017) The first experiments in open peer review, such the one Nature trialed in 2006, were not pursued due to low uptake. Things have evolved, as we even see the announcement that Elsevier will add an open peer review option to all of their journals by 2020. This option will be phased in, and follows the successful 2014 pilot (with five journals) of their “Publishing Peer Review” reports trial which demonstrated that many reviewers (from many different fields) were happy to have their reports published and have their names revealed. Elsevier also reports that the results of surveys show that open peer review does increase the quality of review reports. Elsevier gives published reviews their own DOIs, allowing those reviews to be “counted” as a type of publication output and included on CVs, for instance. (Pool, 2017) Many psychological scientists looking to publish in newer open access journal titles such as the funder supported title eLife will find a different type of openness around peer review, and also a practice of reviewers discussing the paper with each other, synthesizing the reviews, and then publishing the review alongside the paper. Many of the working scientists that review for eLife sign their reviews. (Vlasits, 2017) As another incentive, the Publons service (https://publons.com/home/), which is partnering now with many publishers, is creating a profiling service where reviewers can receive credit for completing reviews. Innovations in Peer Review and Open Peer Review: Examples from Psychology (Publons, 2017) Another newer initiative will pay reviewers a small fee (a part of the APC) for their work, whether the article is accepted or rejected. Collabra, a title initiated in 2105 by University of California Press, aimed to include articles from many disciplines, including behavioral sciences. (Chawla, 2015a) Recently, Collabra has “become a brand for our Open Access program of journals at UC Press, over time.” Collabra: Psychology is now accepting papers and is the official journal of the Society for the Improvement of Psychological Science (SIPS). With an esteemed editorial board, “Collabra: Psychology and SIPS are excited to unite in a shared mission to improve psychological science, and scholarly communications broadly, through policies that support transparency, openness, diversity, and rigorous, ethical scientific research practices.” (University of California Press, 2017) Researchers in psychology will find many types of peer review processes going on in traditional subscription journals, the established open access journals, and the innovators that are moving toward new systems of publishing and journal certification systems. In 2016, one of the most interesting peer review trials of an innovation in the discipline involved publisher BioMed Central’s open access journal, BMC Psychology. The goal of this trial was focused on the need to reduce publication bias using a “results-free” peer review process where reviewers do not see outcomes (as they do not have access to the results or discussion), but instead focus on approach 42 and methods. At the end of the review process (when results and discussion are made available), the same reviewers would expect that the “accepted” articles’ results and discussion would not “deviate unjustifiably from the stated aims and methods. We believe that this could help reduce publication bias by basing the decision to publish purely on the scientific rigor of the study design.” (Grant, 2016) PLOS ONE, “the first multidisciplinary open access journal,” includes many articles in psychological science. PLOS ONE is also a pioneer among new models of peer review, and now many of the open access “megajournals” follow its practices. The PLOS ONE model features the type of peer review where each article is reviewed by editors and reviewers for technical soundness, not for the potential impact of the publication to the field. Each article’s assigned Academic Editor is responsible for the peer review process. The expert readership weighs in with post-publication feedback, adding to the impact of the article to its field. Innovations in Peer Review and Open Peer Review: Examples from Psychology (PLOS ONE, 2017b) Taking open peer review a step further, the title F1000Research uses immediate publication “with no editorial bias” and a transparent peer review process that includes post publication commentary and availability of open underlying data. (F1000Research, 2017) F1000Research, was launched in 2013 by Vitek Tracz (creator of BioMed Central). Tracz felt that “peer review is sick and collapsing under its own weight” and that issues such as anonymous review leading to delayed publication were just some of the issues with the traditional practices. (Rabesandratana, 2013, p.67) Another innovation in peer review, the use of “cascading (or portable) peer review,” where an article’s reviews are passed, upon rejection at a first choice journal to another title in the same publisher’s stable is in use by some major publishers. This option is somewhat controversial in terms of how well it serves a particular publication that may be “downstream” from the journal of first submission. Convenience is one positive for authors, saving them time and trouble in investigating a new publisher and publication outlet. Management of the review process within a publisher’s stable of journals is also attractive for publishers. In one example of cascading peer review in neuroscience, it is stated: The Neuroscience Peer Review Consortium (http://nprc.incf.org) is a cross-publisher transfer alliance covering some 40 journals that forward reviews upon authors’ request, but take-up is small. Some publishers think that cross-publisher transfers reflect credit on them as good citizens; but as another said, ‘why would I want to transfer an author, and the work we have put into a paper, to another publisher?’ Even when they are willing to make reviews portable, the manual intervention in editorial management systems may be a disincentive.” (Jubb, 2016, p. 17) Where some major publishers already have cascading peer review systems in place (while others have decided not to do so), Elsevier has recently been awarded a U.S. Patent for their version, Where some major publishers already have cascading peer review systems in place (while others have decided not to do so), Elsevier has recently been awarded a U.S. Patent for their version, labeled “Online peer review system and method” (described as the “proprietary waterfall system”). Much debate ensued online over the necessity and potential negative consequences of patenting a peer review system. (Aspire Scientific, 2016) 43 Peer reviewers have been challenged by the evolution of the article itself. Innovations in Peer Review and Open Peer Review: Examples from Psychology An article may no longer be a familiar text document. In many cases, the article “package” contains both text and published supplementary data. Over time, in some publications, the article text became less significant if the reader lacked access to all of the linked supplementary material. With the increasing prevalence of outbound links to sources of data sets, journals still had to vouch for the credibility and quality of the supplementary material, and that caused delays and issues for already overburdened reviewers. For example, in 2010, the Journal of Neuroscience announced that it would no longer include, host or review supplementary data alongside articles, citing time lag as busy reviewers were encountering a larger amount of data to review. Supplementary data could be hosted on an external site, with a pointer from the article. (Maunsell, 2010) Peer review currently continues under intense discussion and remains as an essential (but fraught) piece of the scientific communication system for psychology and all disciplines. As practices and tools continue to change, the underlying importance of peer review remains. There are issues with how to best peer review research data. With the trend in growth of openly available research data (both underlying data deposited in repositories and supplementary materials to formally published journal articles), peer review of data has become a larger issue for researchers, publishers, and especially for reviewers that may need guidance on how to complete an effective review. With practices still developing, peer reviewers of research data will need very specific guidelines on the various aspects of this process. (Carpenter, 2017) The “Gold Road:” Open Access Journals and Psychology There are many fully open access journals (where all content in each issue is OA) available to psychology researchers for submission of their articles. Many carry article processing charges (APCs), but the majority do not. A very complex environment exists at present when it comes to scholarly publishing and access to the peer reviewed literature. Library subscriptions still pay for the cost of institutional subscriptions, and authors don’t pay to publish papers in the traditionally published journals (but often sign away their copyright in their articles to the publishers). Certain articles may be made open access for a fee in an otherwise subscription supported journal (hybrid), or institutional memberships may be available from open access publishers to subsidize the APCs of affiliated authors (such as the case with BioMed Central, for example), and in many cases there are no fees to libraries or authors because publishing is subsidized by societies, libraries or others. An example from the author’s institution of a quality open access psychology journal that carries no fees for readers, authors or libraries is Pragmatic Case Studies in Psychotherapy (PCSP) an open access, “peer-reviewed e-journal of systematic case studies & case study method articles” which has published 52 issues to date, and is indexed in PsycINFO. (https://pcsp.libraries.rutgers.edu/index.php/pcsp/index) PCSP is published by the Rutgers Graduate School of Applied and Professional Psychology (GSAPP) and the Rutgers University Libraries using Open Journal Systems (OJS) software, a popular open source journal publication system that is associated with more than 10000 journals. To date (since it began publishing in 2004), articles in PCSP have been downloaded more than 500,000 times by a global readership. Peer reviewed journals that do not charge authors or libraries do not differ from other scholarly publications in the field and are subject to the same scrutiny as 44 subscription publishers would be. Libraries are free to add them to collections, readers find them on the internet, and authors are able to publish without securing funding or paying fees. Open access journals are included in all major abstracting and indexing services as long as they reach the benchmarks for quality set out by coverage teams responsible for content at the database producers. Library collections also strive to include openly accessible scholarly content. The “Gold Road:” Open Access Journals and Psychology A quick look at the WorldCat database (https://www.worldcat.org/) shows that more than 500 libraries have added PCSP to their collections, demonstrating a significant global reach for this openly accessible peer-reviewed psychology journal. For psychology researchers, granting agencies may now have new rules that about the expectation of open access for the articles and data that emanate from funded research. Researchers need to understand the various fees and licensing rules that their eventual publications must take into account in order to comply with funder policies. Many funders pay for the cost of publishing either directly through a line item in grants (as does Wellcome Trust) or in some cases, the funders actually publish the journal, as is the case with the journal eLife. In an interesting development, funders are now also publishers. eLife, an open access biomedical and life science journal is actually published by the funders Howard Hughes Medical Institute, Max Planck Society, and Wellcome Trust. eLife, from its founding in 2012 to 2017 did not charge authors fees to publish, but has picked up traction and in February, 2017, began instituting an APC of 2500 USD. This approach was always part of eLife’s plan for sustainability in the open access market. (Butler, 2016) Wellcome Trust has an open access policy for the research that they fund, and they provide funds to cover article processing charges. All Wellcome-funded articles must be made available in open repositories. (Nosek & Bar-Anan, 2012) Wellcome also requires the use of liberal licenses on the paid up articles, using the CC-BY license, which even allows downstream commercial reuse. (Wellcome, 2017a) Going forward, after April, 2017, Wellcome-funded papers must be published in journals that comply with the new requirements (for licensing and deposit in repositories). The list of those publishers that are compliant with Wellcome rules include major psychology publishers such as the American Psychological Association (APA). (Wellcome, 2017b) An example of a private funder with an open access policy that will pay APCs is the Bill & Melinda Gates Foundation, which also requires final publisher versions of articles supported by their funds to be made openly available at the time of publication. Interestingly, while an embargo period of 12 months on any paper was allowed between 2015 and 2017, after 2017, papers (and data) must be made available immediately. The “Gold Road:” Open Access Journals and Psychology The Gates Open Access Policy also requires the use of the CC-BY license on the article and stipulates that all data that underlies the article also be made open access. (Bill & Melinda Gates Foundation, 2016) Some publishers have had issues with this kind of policy, especially those from funders that do not allow embargoes (delays) on articles that report research that they’ve funded. Some publishers, like the American Association for the Advancement of Science (AAAS) and its flagship journal Science announced special accommodations for working with Gates as some of the funder’s stipulations present challenges for this publisher and a few others. Gates signed on to pay AAAS a fixed sum 45 of money (100,000 USD) for the first year (2017) of the pilot in order to pay for open access publication of Gates-funded articles. (Van Noorden, 2017) The Gates/AAAS pilot ended in June, 2018 after 26 papers (more may appear) had been published in 18 months (16 in the first pilot year). (Van Noorden, 2018) Obviously, the per article APC paid to AAAS was significant. Many authors that choose an open access journal (or want to use a hybrid option in a subscription journal that is already monetized by subscription revenue) are faced with the need to pay an APC in order to publish. APCs range from very small amounts to 5,000 USD or more per article. The cost of APCs is all over the map and there seems no standard fee. For instance, the OA publisher Frontiers raised its APC for its title, Frontiers in Psychology from 2490 USD to 2950 USD in one year (2017-2018), an increase of 18%. (Morrison, 2018) In order to pay APCs, authors may be able to use existing grant money, apply to departments or research offices, or request a waiver from the publisher. Waivers are no longer as available as they once were for most authors, with the exception of some authors from low-and middle-income countries. (Lawson, 2015) Universities have, in many cases, instituted special funds (often referred to as OA Funds) to which authors can apply to receive funds to pay APCs for article publication. The “Gold Road:” Open Access Journals and Psychology Whether an individual institution is a signatory of the principles of a solution like COPE (Compact for Open Access Publishing Equity), or has developed another type of fund to assist authors in paying APCs, this is another avenue for institutions can support faculty authors that don’t have grant funding to facilitate the funding of individual open access articles. Some publishers will also point authors to lists of available university-based funds. Many of these funds set up to assist authors with paying APCs do not fund articles published in hybrid journals, instead they are more apt to pay for the APCs of fully open access journals where, without assistance, the university’s authors would not be able to publish at all in the journal of their choice. Most hybrid journals offer authors of accepted articles a choice of traditional publishing or the use of the open access option via the payment of the APC. A comprehensive list of university-based OA funds is available from SPARC (Scholarly Publishing and Academic Resources Coalition). (SPARC, 2017) Many authors that choose an open access journal (or want to use a hybrid option in a subscription journal that is already monetized by subscription revenue) are faced with the need to pay an APC in order to publish. APCs range from very small amounts to 5,000 USD or more per article. The cost of APCs is all over the map and there seems no standard fee. For instance, the OA publisher Frontiers raised its APC for its title, Frontiers in Psychology from 2490 USD to 2950 USD in one year (2017-2018), an increase of 18%. (Morrison, 2018) In order to pay APCs, authors may be able to use existing grant money, apply to departments or research offices, or request a waiver from the publisher. Waivers are no longer as available as they once were for most authors, with the exception of some authors from low-and middle-income countries. Subscription or Traditional Journal Publishing in Psychology Universities passing open access policies and asking their libraries to implement them are considered to be signalling support for the added resources required to support the development and staffing of repository efforts and associated outreach. Open access outreach requires targeted and sustainable outreach over time by both user services librarians, and the technical services colleagues with whom they collaborate on open access initiatives. Because psychology research spans many fields and traditions, open access and open data efforts require discipline-based open access expertise in implementation efforts. Alongside this work, libraries must make available the journal, book and video collections required for researchers (or effective, seamless delivery mechanisms to ensure access to needed scholarly content). Adding financial support in some cases for open access funds that assist authors with paying article processing charges for open access (or sometimes hybrid) articles, and supporting efforts at building a community controlled (or community aligned) infrastructure to support green open access initiatives further adds costs to sometimes underresourced academic library systems. Libraries are paying for open access in support of a transition in the way scholarly communication happens in the future. Librarians are a natural fit for this work with their knowledge and expertise in scholarly publishing, collection development, deep engagement with disciplinary faculty and students, and experience in both collection development and user services in research libraries. Some library leaders have proposed plans for supporting this “transition to open” that would ask academic libraries to set aside a certain percentage of their budgets for support of an open community infrastructure that would be built and aid in the transformation of scholarly communication. Lewis (2017) proposed the “2.5% Commitment,” where libraries would agree to the commitment that “every academic library should commit to contribute 2.5% of its total budget to support the common infrastructure needed to create the open scholarly commons.” While this support could cause some stress for already burdened libraries, intense discussion has ensued around the necessity of libraries taking on responsibility for support for development of new scholarly communication paradigms by contributing financial backing for this commons. The cost to library budgets via their institutions to at least one of the major commercial publishers, Elsevier, has been the focus of many protests. such as the Cost of Knowledge campaign and its “won’t publish” (with Elsevier) petition. Subscription or Traditional Journal Publishing in Psychology Even though open access publishing is growing, there are of course, many other ways that scholarly content is disseminated, including the traditional subscription route where costs are borne by libraries and their institutions. Today, articles are also sold by publishers in a pay per view environment where readers can “pay by the drink.” Familiar to researchers is the “paywall” that is encountered when the reader is asked to pay a fee to read or download the article, sometimes for a specified period of hours. In many ways, the paywall issue has fueled the open access movement because many readers cannot pay to read an article, especially because the buyer does not really know whether the article will even be useful at the point of discovery. If an article is not needed, there is no return policy. Some journals are also monetized by advertising revenue, but that model is not widespread in psychology. Libraries have always spent a great deal of staff time, besides the funding via subscription revenue, on making journal articles easily accessible to institutional affiliates, whether in the days of print volumes, or now online in PDF format. Large FTE (full time 46 equivalent number of faculty and students) institutions pay more, even as people wonder why the transition to electronic distribution did not mitigate some of the traditional costs that were inherent in the print-based system of production and distribution. Costs to libraries and institutions of the content from some commercial publishers are often deemed unsustainable. Libraries supporting open access initiatives via their institutional repositories end up carrying costs on both sides. They are usually the responsible party in their institutions for the infrastructure costs as well as the staffing needs that open access initiatives require. Some libraries also carry responsibility for administering and sometimes paying for the open access funds that assist authors with paying APCs. Universities passing open access policies and asking their libraries to implement them are considered to be signalling support for the added resources required to support the development and staffing of repository efforts and associated outreach. Open access outreach requires targeted and sustainable outreach over time by both user services librarians, and the technical services colleagues with whom they collaborate on open access initiatives. Because psychology research spans many fields and traditions, open access and open data efforts require discipline-based open access expertise in implementation efforts. Subscription or Traditional Journal Publishing in Psychology Alongside this work, libraries must make available the journal, book and video collections required for researchers (or effective, seamless delivery mechanisms to ensure access to needed scholarly content). Adding financial support in some cases for open access funds that assist authors with paying article processing charges for open access (or sometimes hybrid) articles, and supporting efforts at building a community controlled (or community aligned) infrastructure to support green open access initiatives further adds costs to sometimes underresourced academic library systems. Libraries are paying for open access in support of a transition in the way scholarly communication happens in the future. Librarians are a natural fit for this work with their knowledge and expertise in scholarly publishing, collection development, deep engagement with disciplinary faculty and students, and experience in both collection development and user services in research libraries. Some library leaders have proposed plans for supporting this “transition to open” that would ask academic libraries to set aside a certain percentage of their budgets for support of an open community infrastructure that would be built and aid in the transformation of scholarly communication. Lewis (2017) proposed the “2.5% Commitment,” where libraries would agree to the commitment that “every academic library should commit to contribute 2.5% of its total budget to support the common infrastructure needed to create the open scholarly commons.” While this support could cause some stress for already burdened libraries, intense discussion has ensued around the necessity of libraries taking on responsibility for support for development of new scholarly communication paradigms by contributing financial backing for this commons. equivalent number of faculty and students) institutions pay more, even as people wonder why the transition to electronic distribution did not mitigate some of the traditional costs that were inherent in the print-based system of production and distribution. Costs to libraries and institutions of the content from some commercial publishers are often deemed unsustainable. Libraries supporting open access initiatives via their institutional repositories end up carrying costs on both sides. They are usually the responsible party in their institutions for the infrastructure costs as well as the staffing needs that open access initiatives require. Some libraries also carry responsibility for administering and sometimes paying for the open access funds that assist authors with paying APCs. Subscription or Traditional Journal Publishing in Psychology The Cost of Knowledge boycott was started by Cambridge mathematician Timothy Gowers in 2012 against Elsevier (http://thecostofknowledge.com/) and at the time of this writing (December, 2018) lists more than 17000 signatories who have agreed not to publish, do editorial work, or referee for Elsevier. The Cost of Knowledge was a protest against Elsevier’s business practices, specifically high 47 subscription prices, the “big deal” business model, and the publisher’s support for various legislative initiatives. (Gowers, 2012) In an evaluation by Heyman et al. (2016) of the effect of that petition on the future publishing habits of the 16,000 that had signed the petition agreeing not to publish, a study of the signatories from Chemistry and Psychology (500 signatories each) demonstrated that 17% of the psychology authors that signed the petition then went on to publish with Elsevier in the four years following the initiation of the campaign. The study took into account factors that affect authors’ decisions on where to publish, such as issues of author order. In psychology, first and last author may be “typically reserved for the lead investigator and the supervisor or department head.” (p.2) The signatories in psychology may have been coauthors, and not in the position to choose the publication outlet. However, for Psychology, even of the 46% that had coauthors, 26% of signatories were first author and 26% were in the last author position. (Heyman, Moors, & Storms, 2016) It will be interesting to continue to watch how various actions by academics affect publishers (or whether they don’t). It may seem that publishers are immune from this sort of action at this point, and they continue on without repercussions (except a temporary spate of negative publicity). These boycotts may not have had much of a real effect, particularly on the publisher’s bottom line or rate of submissions from authors eager to publish in known high impact titles with name value. A prominent example for psychological science is the petition and action aimed at the journal Cognition, an Elsevier journal ranked 11/85 in the Experimental Psychology category in the Journal Citation Reports (JCR) in terms of impact factor in 2015. With an article processing charge (APC) considered excessive by some levied at authors who want or need to make the publisher version of an article open access, those in the Cognition community started a petition to get that fee reduced by Elsevier. Subscription or Traditional Journal Publishing in Psychology In addition, also at Cognition, there is a movement to require authors to make versions of articles (preprints and postprints) available “green” open access via author self-archiving in preprint servers such as PsyArXiv or presumably in open access institutional repositories that are available at most universities. Authors using a strategy for self- archiving also satisfy the requirements of institutional or funder OA policies. At Cognition, the journal is calling this new requirement, “Instant Open Archiving” and the practice is focusing on depositing and updating versions of preprints. (Barner, Levy, & Snedeker, 2016) This practice requires very little extra work on the part of the author and is a common part of self-archiving behavior of many authors of traditionally-published scholarly articles. As the practices of some commercial publishers continue to raise the ire of researchers, along with boycotts of titles and other protest actions, some entire editorial boards have walked away from a publisher’s title. One example is when the Elsevier journal Lingua saw its board leave, and ultimately form a new journal, Glossa: A Journal of General Linguistics, an open access journal published by OA publisher Ubiquity Press. Sometimes, what has occurred is that when the board leaves, the publisher just goes ahead and forms a new editorial board, keeping the journal it owns in publication and leaving the field with two journals where the older title still retains some name value. Both journals may continue successful publication in the field, with likely many readers unaware of the situation that transpired. 48 Recently, members of the European Society for Cognitive Psychology (ESCoP) learned that, rather than continue with the publication of their journal, Journal of Cognitive Psychology (JCP) (formerly European Journal of Cognitive Psychology (EJCP)), the society would start a new rigorously peer reviewed open access journal. JCP has been published by Taylor & Francis and the society wished to move toward more open access availability. It was not possible for the society to reach its open access goals by remaining with the current publisher. The journal will have reasonable publication charges and follows open science principles. (Mathot, 2016) Taylor & Francis was amenable to the journal’s new open science policy, including that the society had proposed adoption of the Transparency and Openness Promotion (TOP) Guidelines and other measures, and offered the option of an annual open access supplement. Subscription or Traditional Journal Publishing in Psychology After discussion, the executive committee of the ESCoP came to the conclusion that the compromises being offered did not jibe with the open access aspirations of the society for its journal, and the relationship with the publisher was severed. The new Journal of Cognition (JoC) took the place of the Journal of Cognitive Psychology as the official journal of the ESCoP. After April 1, 2017, the society owns the title (instead of a commercial publisher) and the full board of associate editors remains with the new title, which has a global focus, not a European one. (Hartsuiker & Morey, 2017) However, this is not the first time that an editorial board has walked away from a publisher and started a new open access journal, only to have the publisher, in this case, Taylor & Francis continue to own the former title. In these cases, the publisher develops a new editorial board and the former title continues to receive submissions and retain its place in the memories of many authors and readers. Those starting the new journal often wish a clean break and success for the new journal, but the old title still retains followers and reputation that may hinder evolution of the new title for some time. Academic libraries, historically the places that have made scholarly journal content available to faculty, students and sometimes the public have struggled for some time with sustainability of the status quo. Accessing (and licensing) rather than owning and archiving material has often reached somewhat of a breaking point. Prices to universities for commercial publisher content, reported to reach millions (even as libraries fall under non-disclosure clauses about pricing) have resulted in strain and sometimes have necessitated major journal cancellation projects. Cancellation projects have become more difficult in recent years due to “big deal” bundling of content in packages. According to Nosek & Bar-Anan (2012): For example, subscriptions to Elsevier journals alone cost MIT $2 million per year (MIT Libraries, n.d.), Purdue $2.3 million per year (Westberg, 2012) and Washington University’s School of Medicine $1 million per year ("The Elsevier Boycott," 2012). Cutting access to journals is a major cost savings. Subscription or Traditional Journal Publishing in Psychology In 2010, institutions such as Georgia Tech, University of Washington, University of California San Francisco, and Oregon State have each dropped hundreds of subscriptions in order to save hundreds of thousands of dollars per year (Peine, 2011), at the cost of reducing their researchers’ access to the literature. (p.228) Major stressors in the system have included the unsustainable outlay of institutional funds for commercial journals, and “publish or perish” pressures that focus on journal impact factor for 49 authors choosing outlets for their best scholarship. Faculty need access to all major journals as well as the more niche titles that represent their subfields. Psychology faculty and researchers may not even realize that their sought-after high impact journals of choice for their publications are tied to commercial publishers with their associated higher prices for subscriptions, pay per view options, and author fees. For their part, libraries have made subscription content available remotely from the faculty laptop or other mobile device, and readers may have lost the connection between the library and the journal content. Some may ask, “why do we need a library anymore?” The library is the middleman but may struggle with relevance in terms of being the go to place for journal collections. That association of the reader of journal articles with the library may have been severed for most faculty and students at this point. The provision of seamless electronic access to the research literature, delivered on any device, at the point of need is a goal of academic libraries. Some libraries that subscribe to commercial publishers’ offerings have become more invested in making sure that their university’s authors do not sign away copyright to those same publishers, preventing them in many cases from making versions of their articles immediately available from the institutional repository. Many libraries are using the Liblicense Model License in their negotiations with publishers in order to assert the right of university authors to have more rights to the content that they have produced and provided to the commercial publisher that is selling the same content back to the university at sometimes unsustainable prices. (Liblicense CRL, 2014) The license can set out expectations that the publisher will take a broader view that provides benefits to the author and institution (and possibly funder as well) that provided the content in the first place. Subscription or Traditional Journal Publishing in Psychology This would include rights such as liberal self-archiving rights to deposit content in the institutional repository, for instance. Major publishers of “must-have” journals bundle titles into packages, making cancellation of individual titles a challenge (or even impossible). Large science packages, the “big deals” may consume the library budget, causing concern and dismay among humanists and others about availability of monographs and single journal titles that often show lower use in today’s usage numbers-driven assessment reports. In fact, by 2013, a study by Lariviѐre et al. (2015) of 45 million papers indexed in in Web of Science from 1973-2013 demonstrated that five large commercial firms published 50% of scholarly papers, with the most consolidation seen in social sciences (70% of all papers from five publishers). In fact, in natural and medical sciences, Reed-Elsevier, Springer, and Wiley-Blackwell were named, and “three publishers account for more than 47% of all papers in 2013…” (p.3) The trend in the concentration of publishing in social sciences and humanities among a handful of publishers is even more pronounced. This increase in the proportion of scientific output from a few publishers has been driven by the creation of new journals and due to publisher acquisitions of established journals. For psychology, the study results were dramatic, “with the top five publishers increasing from 17% (of papers) in 1995 to 71% in 2013.” (Larivière et al., 2015, p.7) Commercial publishers do not have the same mission or motivations as the society publishers, and psychology’s learned societies still have a very prominent place in the scientific communication system for the discipline. APA’s mission and vision statement (from the current 50 strategic plan at http://www.apa.org/about/apa/strategic-plan/) includes the following, reiterating the organization’s major importance for psychological scientists: strategic plan at http://www.apa.org/about/apa/strategic-plan/) includes the following, reiterating the organization’s major importance for psychological scientists: The American Psychological Association aspires to excel as a valuable, effective and influential organization advancing psychology as a science, serving as: A uniting force for the discipline, the major catalyst for the stimulation, growth and dissemination of psychological science and practice, The primary resource for all psychologists…. m the plan), in one of the goals of the organization, (Goal 3) the APA seeks to: increase recognition of psychology as a science. The APA’s central role in positioning psychology as the science of behavior leads to increased public awareness of the benefits psychology brings to daily living. Subscription or Traditional Journal Publishing in Psychology Enhance psychology’s prominence as a core STEM (Science, Technology, Engineering and Mathematics) discipline… (American Psychological Association, 2016b) The scientific publishing system has been dysfunctional for a long time, with university and funder budgets unable to keep up, while commercial publisher revenues continue to rise. As an example, the evolution of profits of Reed-Elsevier (looking at the 1991-2013 period) shows profit margins continuing to increase. For Elsevier’s Scientific, Technical & Medical division in particular, the profit margin has remained strong over time, for instance increasing from 30.6% in 2006 to 38.9% in 2013. (Larivière et al., 2015) Other commercial publishers also enjoy healthy profit margins. In fact, the unsustainability of the system which librarians knew well, may have been the impetus for some librarians, lamenting the “serials crisis” to look for a future where open access would provide a potential solution for the inability of library budgets to keep up with annual subscription price increases. Along the way, the serials crisis became an early motivator, but not the only reason that many libraries, librarians and academic faculty became driven to embrace open access (particularly of the “green(repository)” model). As time has evolved, institutional repositories disseminate many open access versions of articles published by commercial publishers. The connection of open access with a solution to the “serials crisis” has evolved and the two are not conflated as often at this point in time. For their part, some commercial publishers have diversified more by moving into development of other scholarly communication-related services like “research information systems” (known as RIS or CRIS) that provide a variety of research and reporting solutions for institutions (for example, Elsevier’s Pure), or altmetrics tools (such as Elsevier’s Plum Analytics), or citation management/collaboration products for researchers (such as Elsevier’s Mendeley). There have been many proposed solutions, some radical, to fix the situation with journal publishing. For now, a growing chorus of stakeholders has been discussing the potential “flip” of the system from the traditional, subscription, closed access model to a worldwide adoption of an author or funder-pays model. This worldwide flip, a disruption without precedent, is under intense discussion at present. The current landscape supports many types of publishing business models, from traditional to the most innovative, and the eventual end point remains to be seen. Subscription or Traditional Journal Publishing in Psychology The possibility of a “flip” of the traditional system to a gold open access future has been 51 discussed in many sectors in recent years. The very future of scholarship seems at stake, but in this new situation, it seems likely that publishers will still retain a revenue stream that will sustain them. (Solomon, Laakso, & Bjӧrk, 2016) Summaries from industry market forecasting reports allude to the future trends expected of gold open access, paid by APCs. (Simba Information, 2016) In 2018, a press release from Simba Information that announced their report, Open Access Journal Publishing 2018-2022, stated that “once viewed as a threat by traditional journal publishers, the global push for open access (OA) to research papers has delivered a fast- growing revenue stream that will continue to scale upwards” and that since their first report on this topic in 2014, “we were decidedly less optimistic about open access publishing than we are today.” The success of the gold open access model, especially for the author pays model, will be contingent upon author attitudes toward this type of open access, how much authors are really willing to pay, and to what publishers. (Tenopir et al., 2016). The availability of funder support for APCs in all disciplines that have such support will also need to further evolve in order to assure funding for submitting authors. How quickly this largescale change in scholarly communication, from a mostly electronic traditional subscription model where libraries pay subscriptions to a new model where most scholarship is funded by authors via their granting agencies or their institutions (at least for the sciences) is in large part dependent on the choices authors make and the needs that they have to share their work with the public, with taxpayers, or much more widely with colleagues. A corollary question is whether authors will choose the most liberal reuse licenses (from Creative Commons) for their work or whether they will want to go with more restrictive permissions if allowed by funders and universities. As the “big deals” evolve, discussions of what are referred to as “Read and Publish” models have been introduced. Some universities, consortia and even whole countries are exploring these models where “the ‘Big Deal’ license that bundles together access to a publisher’s subscription content with the ability to publish openly through its journals without paying individual APCs” is a focus (initially due to Europe’s funder mandates). Subscription or Traditional Journal Publishing in Psychology (Schonfeld, 2018). In the U.S. in 2018, The University of California System (made up of 10 campuses and 100 libraries) entered into negotiations where UC stipulated that the 10 million USD annual fee paid to Elsevier for journal subscriptions would need to be renegotiated to also include open access to the works of the UC system’s authors. This action was extremely high visibility due to the UC system’s large (almost 10 percent of the U.S.) level of research output. (McKenzie, 2018) These read and publish agreements are examples of the transformation of the scholarly communication system as it continues to evolve into something decidedly different and hopefully less chaotic and complex. Studies of how this new publishing landscape will affect psychology researchers and their universities and funders will be advantageous in understanding how the discipline’s literature (and other research outputs) will be affected. communication system as it continues to evolve into something decidedly different and hopefully less chaotic and complex. Studies of how this new publishing landscape will affect psychology researchers and their universities and funders will be advantageous in understanding how the discipline’s literature (and other research outputs) will be affected. Predatory Journals, Publishers and Conferences: A Growing Phenomenon, and the “Whitelists” that Assist Researchers with Vetting Journals Predatory Journals, Publishers and Conferences: A Growing Phenomenon, and the “Whitelists” that Assist Researchers with Vetting Journals As open access articles proliferate, there are some that conflate open access publishing with the phenomenon of unscrupulous publishers. As more “predatory” (bogus, fake or 52 fraudulent) publishers and journals seeking submissions flood the inboxes of many academics, some attribute some of this growth to the rise of open access. Of course, there are many high status journals that are open access, some having the highest impact factors in their respective disciplines. It is not the business model of a journal but the quality of its articles, judged by the scientific community, that separates the wheat from the chaff. However, a recent concern has arisen that due to various factors inherent in the global scholarly communication system, some authors do, in fact, intentionally choose to publish in journals that have been labeled “predatory,” even paying the usually lower APCs themselves, in order to get published. These articles are showing up in the search results of PubMed and other places online (and are cited in other studies), possibly affecting the quality and credibility of the scientific record. (Manca et al., 2017) It is not only the inexperienced author that may get caught up in fraudulent journals, but there have been reports of well-known researchers publishing their work in bogus or fake journals. There are various explanations for this, but it is unclear why experienced scholars would fall prey to predatory publishers. (Retraction Watch, 2016) As it does appear that some researchers are choosing to publish in these fraudulent outlets, maybe universities and research departments would be interested in this phenomenon. One recent study analyzes possible rewards for publishing in predatory journals. (Pyne, 2017) The so-called predatory publishers often display distinguished editorial boards on their websites, when in fact board members may have no knowledge of their position at the journal. As of January, 2017 (when it ceased publication), there were more than 1000 of these publishers recorded on Beall’s List, a service that tracked these journals and publishers. Some publishers may just be new, or from geographically underrepresented regions and may be trying to break into OA publishing, but the vast majority are scam publishers. There have been many attempts to demonstrate how these journals will publish just about anything. Predatory Journals, Publishers and Conferences: A Growing Phenomenon, and the “Whitelists” that Assist Researchers with Vetting Journals (OMICS International, 2017) However, OMICS now garners the distinction of being the first publisher to be sued by the U.S. Federal Trade Commission for fraudulent practices. (Federal Trade Commission, 2016) Early career researchers or those from certain geographical locations may especially vulnerable to these schemes that offer to quickly publish an article in a scholarly-sounding journal, or to present a paper at a familiar-sounding disciplinary conference. There have been many online guides prepared around this topic to help researchers identify quality publication outlets for their work. One high profile initiative, the product of publisher’s groups and other interested organizations is a useful checklist entitled “Think. Check. Submit” (https://thinkchecksubmit.org/) which provides helpful information that can be used by authors to avoid the so-called “predatory” publishers. This tool gives all authors some guidelines to follow as they seek to ensure that open access journals under consideration are credible. (https://thinkchecksubmit.org/) which provides helpful information that can be used by authors to avoid the so-called “predatory” publishers. This tool gives all authors some guidelines to follow as they seek to ensure that open access journals under consideration are credible. Once there was money to be made from authors eager to publish or present their work at conferences, unscrupulous parties set up shop to collect that money as well. The phenomenon of fake/bogus conferences is also growing and many psychology researchers at all stages of their careers have likely been invited to present at meetings that may even have names very similar to well-regarded conferences. Researchers eager to present their work may fall prey to conferences that either do not really happen, or are not credible. (Asadi, Rahbar, Rezvani, & Asadi, 2017) It has been stated that “open access” is the reason for the exponential growth of predatory publishers, journal, and conferences. While open access is now a popular business model, used in various ways by all types of credible publishers, it should not be conflated with the use of the internet for publication schemes that are fraudulent. In every discipline and field, researchers need to be aware of the situation. Conflating open access with predatory publishing muddies the waters as scientific publishing is moving forward using open access methods of different types. Open access is a business model here to stay, so a more constructive strategy may be to make sure all available vetting tools are available in the OA landscape. Predatory Journals, Publishers and Conferences: A Growing Phenomenon, and the “Whitelists” that Assist Researchers with Vetting Journals To demonstrate the lack of rigor of peer review in a wide cross-section of OA journals, Bohannon (2013) sent bogus papers, papers that should be easily identified as such to large numbers of open access journals, and had them accepted. (Bohannon, 2013) This sting operation, while somewhat controversial in its tactics, did point out a variety of nefarious business practices of many new bogus journals. This sting was followed by many others that showed similar results. In order to get a handle on this situation, some fields have analyzed the predatory publishing landscape from a specific disciplinary perspective. Publishing lists of problem publishers for each field may serve as a means of warning for those scholars that may not be able to readily identify some of these publishers. As an example, in a study of predatory publishing in neuroscience and neurology, 87 so-called predatory journals were identified as currently active (in 2016) in neurosciences, and those journals published 2404 articles between 2012 and 2016. (Manca et al., 2017) One can assume that these articles are now finding their way into the scholarly record of neuroscience. It would be interesting to track the trajectory of these articles to see their eventual citation impact. A recent example from psychology illustrates just how clever the spammers have become. In a discussion of the offerings of the bogus publisher, American Research Institute for 53 Policy Development and their title listed as Journal of Psychology & Behavioral Science, that title’s location and description revealed the following: “…that address is also listed as the office for the Journal of Psychology & Behavioral Science, but it is the bogus version, also run by the ARIPD, and should not be confused with the real Journal of Psychology & Behavioral Research.” Both fake journal URLs use the same format—an acronym for the journal immediately followed by “net.com” so be on the lookout for that elsewhere.” (Weinberg, 2016) Many faculty and other researchers in psychological science have likely received solicitations in recent years from the publisher, OMICS Group (or OMICS International). OMICS boasts a sizeable list of more than 700 open access journals, such as the title, Journal of Psychology and Psychotherapy. The OMICS website even includes a definition of the term “psychology” alongside its long list of psychology journal offerings. Major Online Indexes for Open Access Journals and Articles in Psychology The Directory of Open Access Journals (DOAJ) is a major index for fully open access journals and articles. This index, a major arbiter of quality for open access journals from around the world does exclude journals and articles that use embargoes (delays on publication) and those that employ the hybrid model (where only some articles in a journal have been paid up to be open access). This index has become a major source of open access content (journals as well as articles) and is included in many library catalogs and discovery systems. DOAJ also functions as somewhat of a whitelist for open access journals, especially since it required all journals to resubmit extensive information about a lengthy list of publishing practices in order to make sure each title reached the more stringent benchmarks for coverage in the index. As of March 2015, the index had winnowed down its list of included titles due to this quality assurance process, and from then on, all newly submitted journals to DOAJ had to attain certain specific characteristics in order to qualify for inclusion. The quality vetting process includes analyzing each open access journal for peer review process, copyright, plans for access by users, revenue sources, archiving plan, and more. DOAJ completed its reapplication process in December, 2017, with all included journals having reapplied to be included in the index. DOAJ can now be considered as a whitelist of fully open access journals. DOAJ carefully analyzed 6359 reapplications and 2058 were rejected, along with removing 2860 journals during this process because they did not reapply for inclusion. This entire process removed 40% of all journals in the database. (Directory of Open Access Journals (DOAJ), 2017b) The major index, one probably found in all academic libraries (with all of its journal coverage vetted) for search and discovery of the scholarly literature in psychology is PsycINFO (produced by the American Psychological Association). Any journal seeking coverage by PsycINFO must meet strict criteria for inclusion. PsycINFO is likely one of the most recognized and popular resources in any academic library. It was produced in print (as Psychological Abstracts) for 80 years (from 1927-2006) and so has a long history as a resource for those looking for trusted scholarly articles in psychology. Predatory Journals, Publishers and Conferences: A Growing Phenomenon, and the “Whitelists” that Assist Researchers with Vetting Journals Instead of using “blacklists,” researchers will need to avail themselves of whitelists which contain credible lists of vetted open access journals in every field. One example is the Directory of Open Access Journals (DOAJ), which in September 2018 listed 240 journals in the category of Psychology (and more than 54 55,500 psychology articles). (Directory of Open Access Journals (DOAJ), 2017a) Another entrant into this space is The Journal Blacklist from Cabell’s International. This database is likely not widely known as it is a subscription database only available in some libraries. (https://www2.cabells.com/about-blacklist) Major Online Indexes for Open Access Journals and Articles in Psychology PsycINFO may now be utilized as well as a whitelist for psychology journals, and adds value by indexing all quality journal titles that meet its coverage criteria regardless of business model employed by the journal publisher. Open access journals listed in PsycINFO are searchable alongside subscription journal content and all are chosen after a rigorous application process (using published criteria) for relevance to the disciplines covered, scope, peer review, quality of publication practices and more. (American Psychological Association (APA), 2017) Since many subscription journals include some author- pays articles in various issues (hybrid), those articles are also included in PsycINFO, and the index now includes an indicator that identifies this open access content, and articles are searchable by this filter. There are many open access journals that meet and even exceed these 55 coverage guidelines. As of June, 2017, PsycINFO included 190 fully open access journals in its coverage list, bringing added credibility and visibility to each of those titles. More than ever in this time of information overload, there is value in having a vetted discipline-based abstracting and indexing service that uses human indexing and is responsive to the needs of researchers, searchers and authors. Looking at a very large scale international survey of discovery that looked at the trend from 2005-2015 demonstrates that the use of abstracting and indexing tools are still valued in psychology. (T. Gardner & Inger, 2016) Searchers find that some aspects of PsycINFO searching cannot be replicated easily by using other tools and methods. For example, searching for articles by type of methodology adds value for the searcher and offers a contrast to the scattershot discovery process that a Google or Google Scholar search provides. There are many options for those doing serious research in psychological science. Academic librarians and their libraries serve up the collections, tools and services that facilitate research, and many libraries do include Google Scholar and other free tools as part of their suite of offerings. Besides PsycINFO, there are many library subscription databases (as well as freely available indexes (such as PubMed) that index psychology content. Academic and research libraries usually pull these resources together in subject lists of databases that are accessed on site or remotely by university affiliates and sometimes also on site by the general public. All of these indexes would include access to a subject-based corpus of open access journal article content. Major Online Indexes for Open Access Journals and Articles in Psychology There are other sources that psychology researchers can use to vet journals for quality. Examples would be the publishers that are listed as members on the websites of the Open Access Scholarly Publishers Association (OASPA), the Committee on Publication Ethics (COPE), and the World Association of Medical Editors (WAME). According to the OASPA website, these three organizations “have collaborated in an effort to identify principles of transparency and best practice for scholarly publications and to clarify that these principles form part of the criteria on which membership applications will be evaluated.” (Redhead, 2013) Interestingly, at present, there have been so many recent requests for membership that COPE has had to issue a statement that they need to suspend membership applications for a brief time because of volume. (Committee on Publication Ethics (COPE), 2017) Journals that have been added to research library collections or library discovery services have usually been vetted for appropriate quality before being added to collections. Coverage by Ulrichsweb: Global Serials Directory (www.ulrichsweb.com/), another library database that indicates peer review status of a journal title, and coverage in all major citation and subject indexes such as Web of Science, Scopus, and many others accessed via research libraries indicates a diligent vetting process. A major search engine for open access content, one used widely by faculty, students, practitioners and public would be Google, or especially the heavily used Google Scholar. Google Scholar has become prominent in the landscape of search (including search that starts in a library), and even looking at a comparison with Google, “people working in psychology have a strong preference for Google Scholar.” (T. Gardner & Inger, 2016) Google Scholar provides a cross-disciplinary search of open access content, offering a selection of available versions of articles. Much psychology content may be discovered via a search of Google Scholar. With all 56 available versions of an article displaying, searchers will be able to freely access the author’s manuscript, or if they are affiliated with a subscribing institution, they will be able to click through to access the otherwise paywalled content. Thus, Google Scholar is an excellent search engine for searching for open access content, and for checking to see if a free version of a subscription article has been made available by its author. The size of Google Scholar is still unknown, frustrating attempts to compare it with other citation databases. Major Online Indexes for Open Access Journals and Articles in Psychology Unlike PsycINFO, Google Scholar is not transparent about its coverage; for instance, about its criteria of what it deems “scholarly” is not available. In fact, a Google Scholar search will also turn up articles from all publishers, and those deemed bogus or fraudulent would be included in results as well. One negative aspect is that Google Scholar searches do return results including articles in so- called “predatory” journals, so the coverage is fairly comprehensive as far as all journals are concerned (without quality checks of any kind). It would seem a positive development for new search services to provide good alternatives to the comprehensive and popular Google Scholar. It is estimated that Google Scholar indexes 87 percent of all of the scholarly papers on the web, and a rough estimate published in 2014 showed about 114 million English language papers published (with approximately 100 million indexed in Google Scholar). The same study estimated that one in four scholarly papers overall are freely and publicly available on the web. (Khabsa & Giles, 2014) It would seem to be important to include Google Scholar in any search for psychology content, particularly open access content. Use of Google Scholar has certainly become a quick shortcut and alternative to subscription databases for many searchers seeking scholarly articles from many sources, or free versions of peer reviewed articles that are otherwise not owned by libraries (or are behind publisher paywalls). Many libraries partner with, and include Google Scholar alongside all of the other indexes and databases available to users directly from the library website. Libraries partnering with Google Scholar facilitate seamless access to subscription full text content. The value of Google Scholar as a freely available and easy to use discovery mechanism as well as a portal to a vast open access content is an amazing value add to the scholarly communication system for psychology and all other disciplines. For those seeking only openly available articles, there is no comprehensive solution for an article-based delivery system that would include all OA content. One category that is problematic for discovery in libraries and on the open web are the open access articles in “hybrid journals” that have been made open access individually as part of traditional subscription journals. These articles, having been made open access through payments by authors (or funders) appear alongside paywalled articles in subscription journals. Major Online Indexes for Open Access Journals and Articles in Psychology It has been difficult to study these random open access articles in the usual discovery systems or search results due to a lack of consistency around clear identification of the open status of these articles. (Chumbe, MacLeod, & Kelly, 2015) There is also a decided lack of analysis as well as a lack of transparency that prevents researchers at this time from understanding the effect of hybrid publishing on the open access landscape overall, and especially its effect on scholarly communication in psychology. In one study of hybrid open access articles published from the year 2007 to 2013, there was a “strong sustained growth in the volume of articles published as hybrid OA…” (Laakso & Björk, 2016, p. 919) In this same study (of the hybrid OA journal article output for the major 57 commercial publishers) for the Scopus journal category, Psychology, Laakso & Bjӧrk reported numbers of articles made OA in hybrid journals as 19 in 2007 with a steady rise until 2013, when the category included 471 articles. Overall, Bjӧrk (2017) reports steady growth of numbers in this hybrid category, stating that “The number of journals offering the hybrid option has increased from around 2,000 in 2009 to almost 10,000 in 2016. The number of individual articles has in the same period grown from an estimated 8,000 in 2009 to 45,000 in 2016.” (p.1) Uptake of hybrid has not been high, but the majority of traditional journals, especially those published by commercial publishers now include some open access articles alongside closed access articles within the same issue. For instance, in psychology, open access articles funded by author (or funder, such as Gates) payments can be found among the articles listed in tables of contents from commercial subscription-based journals published by Elsevier, Wiley, SAGE, Taylor & Francis and others. These hybrid journal titles, funded mainly by subscription revenues, also have some author or funder-paid articles that are published open access within an issue. Many traditionally-published subscription journals now have a hybrid OA option. For example, the American Psychological Association has a hybrid option available for all of its subscription journals, and charges an APC of 3000 dollars per article to publish the final publisher branded version of the article OA within a regular issue. Authors choose the traditional publishing route, or the open access option, for each article. Major Online Indexes for Open Access Journals and Articles in Psychology (http://www.apa.org/pubs/authors/open-access.aspx) Concerns around double-dipping or the possibility that any single open access article may be paid for twice (by the subscriber and by the author) have been part of open access conversations. This has led to the advent of offsetting deals from commercial publishers anxious to allay any of these concerns about the monetization of any given article in a subscription issue. There is concern over the total cost of publication of a system that includes hybrid journal publication, and where universities and/or funders are paying for subscriptions as well as APCs. APCs for articles in hybrid journals also tend to be higher than fees for article publication in fully open access journals. Due to the concern over the double-dipping issue, many university funds do not pay APCs for articles published in hybrid journals. In the U.K., where there has been a concern over the “total cost of publication” issue which takes into account the hybrid journal publishing taking place by commercial publishers, there has been a move to establish principles for publishers and academic institutions for negotiations around these offset agreements with an aim to reduce the additional cost of publication that is occurring. (Guy & Holl, 2016) Many institutional open access policies are misunderstood to require that every article be made open access, thereby requiring either publication in a fully open access journal that charges APCs or, in the case of an article being published in a traditional journal, the requirement to pay for this hybrid publication. Many U.S. institutional OA policies are focused instead around green open access, and as subscribers to the traditional journal literature, many institutions do not expect or desire that any author will pay that commercial publisher to make an article OA at the publisher site. This “green OA approach” also preserves academic freedom, allowing for authors to publish in the journal of their choice, whether closed or open access. 58 Academic freedom has arisen in discussions of new funder initiatives requiring open access to funded research. Looking at the open access landscape going forward in all disciplines that rely on grant funding, there will be more change and disruption as mandates increase in strength. It is becoming clear that funders’ patience with paywalls, embargoes and other impediments to open access is running out. Major Online Indexes for Open Access Journals and Articles in Psychology On September 4, 2018, Science Europe’s open access consortium, COAlition S, made up of 13 research funders from 13 countries (supported by the European Commission and the European Research Council) launched the “Plan S” initiative. The Plan consists of one target and 10 principles with the stated goal of “full and immediate OA to research publications.” (https://www.scienceeurope.org/coalition-s/) The Bill & Melinda Gates Foundation and Wellcome Trust signed on shortly after the initial announcement, and the conversation also quickly made its way from Europe to the U.S. This particular mandate, unlike others, does not offer accommodations for some of the usual requirements of subscription publishers. Plan S’s key principle requires that “After 1 January 2020, scientific publications (based) on the research funded by public grants provided by national and European research councils and funding bodies, must be published in compliant Open Access journals or on compliant Open Access platforms.” (https://www.scienceeurope.org/wp-content/uploads/2018/09/Plan_S.pdf) The announcement goes on to describe the rest of the requirements, stating that funders and universities (not individual researchers) would pick up the cost of open access publication, that the principles would apply to monographs as well (although it is understood that this part would take more time), and that the hybrid model would be disallowed. There is also language that supports the development of repositories and open archives. There was immediate reaction from stakeholder communities, especially in regard to the strong open access position of Plan S, and its emphasis on author rights and fully compliant open licensing. When Plan S moves forward, certain impediments currently existing in the system, such as embargoes, double dipping via hybrid and the “one off” rules of certain publishers that are considered roadblocks to self-archiving of accepted manuscripts will no longer be allowed. While those that view open access to the results of research as a goal for the dissemination of scholarly works on a global scale were emboldened and excited by the unveiling of Plan S, there were also faculty members and other stakeholders that considered Plan S as an affront to academic freedom. Funders would stipulate that authors could not publish research results in some of the most impactful journal titles (and highly regarded society titles), thereby potentially disadvantaging those authors from career advancement, awards or other aspects of the prestige economy. Major Online Indexes for Open Access Journals and Articles in Psychology In a November 5, 2018 published letter entitled “Reaction of Researchers to Plan S; Too far, too risky: An Open Letter from Researchers to European Funding Agencies, Academies, Universities, Research Institutions, and Decision Makers” (https://zenodo.org/record/1477914#.W-9SWeJRdPY), about 800 scientists (as of November, 2018) laid out their concerns, such as the negative effect on learned societies that would occur if hybrid journals were banned as publication outlets, support of fully OA journals likely increasing the costs of the system, issues of the use of the liberal CC- BY license for every article, the too narrow mechanism required by the funders to achieve OA (“journals route only”), issues of preprints, and disciplinary differences in OA culture. (Rabesandratana, 2018) Another letter with hundreds of signatures from supportive academics and other open access advocates followed the earlier letter that opposed Plan S. (Rabesandratana, 2018) Another letter with hundreds of signatures from supportive academics and other open access advocates followed the earlier letter that opposed Plan S. (Rabesandratana, 2018) Another letter with hundreds of signatures from supportive academics and other open access advocates followed the earlier letter that opposed Plan S. 59 (http://michaeleisen.org/petition/signatures.php) A strong statement of support and an implementation plan was the response to Plan S from the Fair Open Access Alliance (FOAA). https://www.fairopenaccess.org/wp-content/uploads/2018/10/Fair-Open-Access-Alliance- recommendations-Plan-S.pdf/. FOAA, which includes member, Psychology in Open Access (PsyOA), is described as “facilitating conversion to fair open access of journals in psychology.” (http://psyoa.org/) The development and implementation of Plan S may signal somewhat of a tipping point for the change to a different kind of future for scholarly communication, with open access to publications and to other research outputs now an expectation for research funding. The funders may increasingly make the open access rules, and publishers will need to adapt or risk losing funded authors. This potentially large disruption to the status quo will indeed include the major and minor publishers of psychological science research. Open Access “Mega-Journals” (OAMJs) and their Significance to Scientific Communication in Psychology PLOS ONE’s output is by far the highest in the category, while Scientific Reports is second in production. These were the only two OAMJs publishing more than 10,000 articles in 2015 alone. Certain of the OAMJs are more popular in one geographic region or another, for instance, demonstrating that there are distinctive characteristics to each of these publication outlets. (Wakeling et al., 2016) A search of Google Scholar (for those unaffiliated with a university’s databases), or a search of any subscription subject (or citation) database will include results from OAMJs. The formal citation impact of OAMJs (as compared with traditional journals) will need continuing study over the coming years; some early analyses are available now. In terms of citation studies, outside of the elite journals, it appears that the OAMJs may be performing similarly to traditional journals in the same impact factor range, less vigorous peer review notwithstanding. This could demonstrate that it is possible for OAMJs to achieve similar citation patterns using a very different system of peer review (reviewing only for scientific soundness and not eventual contribution to science). (Björk & Catani, 2016) With the major difference likely to be how promotion and tenure committees or national research assessment systems view the peer review status of the OAMJs, this phenomenon is here to stay. While some may have used the term “peer review lite” to initially describe how the OAMJs’ systems differ, it may not be well known that the peer review performed, for instance by PLOS ONE (after a paper passes a quality control check and the paper is assigned to an Academic Editor with relevant expertise), that “The majority of PLOS ONE submissions are evaluated by 2 external reviewers, but it is up to the Academic Editor to determine the number of reviews required.” (PLOS ONE, 2017a) The newer type of peer review employed by the OAMJs where papers are reviewed for technical soundness (but not beyond that threshold) has caused some added focus on the aforementioned issue of cascading peer review, especially as used by larger publishing firms that may be rejecting many otherwise good quality papers from elite titles with low acceptance rates. Studies have shown that many rejected papers find a home in the same publisher’s OAMJ (but this practice is not exclusive to OAMJs), and that option to move the paper to the OAMJ is presented at the time of the rejection. Open Access “Mega-Journals” (OAMJs) and their Significance to Scientific Communication in Psychology The future of the traditional journal is not clear, and there are many concerns relating to the sustainability of societies and other factors closely tied to scholarly publishing. The very future of journals has been a question as “‘nobody reads journals,’ says science publisher Vitek Tracz, who has made a fortune from journals. ‘People read papers.’” (Rabesandratana, 2013, p.66) Clearly, article-level discovery is here to stay, evidenced by popularity of the open access mega-journals (OAMJs) like PLOS ONE and Springer Nature’s Scientific Reports which publish thousands of articles in a single issue each year, all discoverable via Google Scholar and other search engines, and all open access. In fact, contrary to many disciplines where commercial publishers are publishing much of the literature, the proportion of the biomedical literature has actually declined in recent years due to author traffic moving to some of the mega-journals, particularly in the case of PLOS ONE, which published more than 30,000 articles in one issue per year. (Larivière et al., 2015). There is likely no denial that the open access mega-journals, beginning with the introduction of PLOS ONE in 2006 have disrupted scholarly journal publishing’s “business as usual.” With thousands of articles per issue, a business model funded solely by article processing charges (APCs) that may be considered “reasonable” (at least in comparison to commercial publisher APCs), and most importantly, a peer review model that only reviews for technical and scientific soundness rather than the more traditional peer review system that is utilized by high impact disciplinary journals. OAMJs also cover a wide span of subject areas in each annual issue rather than a focusing on any specific disciplinary or subfield niche. Popular examples well known to psychological scientists are PLOS ONE, SAGE Open, Nature’s Scientific Reports, F1000 Research (known for post-publication reviewing) and others. Collectively, the OAMJs flood the internet with many thousands of research articles, all open access, each year. This leads to rapid dissemination of current scientific research on the internet, all optimized for article-level delivery. One study reporting sheer volume and growth of numbers of articles published each year showed that in a sample of 11 OAMJs, 44,820 articles were published in 2015, an increase of 15% over the 2014 figure (33,995)-a figure representing 2.5% of all 2015 articles indexed in 60 Elsevier’s Scopus database. Open Access “Mega-Journals” (OAMJs) and their Significance to Scientific Communication in Psychology (Spezi et al., 2017) Average acceptance rates for OAMJs are often reported to be significantly higher than for traditional subscription publications. (Sugimoto, Larivière, Ni, & Cronin, 2013) Journal Impact Factor (JIF) and acceptance rate are still values that may matter when conferring prestige on all scholarly journal titles. The OAMJs are no different, with widely differing impact factors and other characteristics that distinguish one from another. There are not many sources that compare acceptance rates among journals (or publishers) in psychology. A directory available at some academic libraries in print some years ago, Cabell’s Directory of Publishing Opportunities in Psychology and Psychiatry contained analytical information on psychology journals. That print product is now subsumed into a database that covers 18 disciplines (including Psychology) that is able to compare and contrast hundreds of psychology journals by various factors, including acceptance rate. Acceptance rates are used, (along with Journal Impact Factor) by many in academia as proxy for quality and elite status. Using Cabell’s data, it has been reported that open access journals in the psychology category 61 (not only the OAMJs) have significantly higher acceptance rates than non-open access journals listed in Cabell’s. PLOS ONE, for instance, reported an acceptance rate of about 69% in 2012 (Sugimoto et al., 2013) and in 2017, reports an acceptance rate of about 50%. (McCook, 2017) By comparison with the traditionally “elite” journals that are thought to rise above the rest in the general/multidisciplinary category, AAAS’s Science reports a rejection rate around 93%. (Larivière, Lozano, & Gingras, 2014) Before the phenomenon of OAMJs entered the landscape, it was once reported that rejection rates were very high for psychology authors, approaching 70- 80%. (Adair & Vohra, 2003) In comparison, rates are lower for biology (50%) or physical sciences (20%), and rejection rates were also predictive of citation rates. Historically, articles in the Experimental category enjoyed lower rejection rates and had a higher impact according to Social Sciences Citation Index. (Rotton, Levitt, & Foos, 1993) It has been difficult for various reasons to ascertain how the OAMJs such as PLOS ONE or Scientific Reports represent research literature in the various fields of psychology. Open Access “Mega-Journals” (OAMJs) and their Significance to Scientific Communication in Psychology Thus, it is not possible at this time to provide granular information on how these publications may or may not be affecting the dissemination of research results in psychology, especially how psychology would be represented in subject classifications focused on “science and medicine” or “biology and life sciences.” Each of the OAMJs seems to have a different disciplinary focus (even though they are all multi-field publications. One journal, SAGE Open, was an important entrant in the field of OAMJs, as it focused on covering more of the social sciences and the humanities with an accessible publishing model and very reasonable APC (even for those without funding). Authors without funding could often afford a low APC (if that were an option) and would also be able to choose an open access journal option from a familiar publisher. SAGE Open (in 2015) had published 15.1% of its articles under the category of “psychology.” However, PLOS ONE, in the same year published almost 5000 articles in the “social sciences” category. For PLOS ONE, in 2015, 94.6% of articles were assigned the PLOS subject category of “Biology and Life Sciences.” In a comparison of PLOS ONE and Springer Nature’s Scientific Reports using “proportion of journals citing the two largest OAMJs,” PLOS ONE had a higher percentage of articles in the Scopus “Psychology” category than did Scientific Reports (which focuses much more on physical sciences). (Wakeling et al., 2016) SAGE Open (launched by SAGE Publishing in 2010) publishes all articles open access with reasonable fees, but also follows a model that works well for green open access institutional repository efforts. Sage Open’s options allow for the needs of authors and universities. Currently, SAGE Open is moving into publishing open access monographs on its platform as part of the program “SAGE Open Long Form.” SAGE will charge a reasonable book publishing charge (BPC) and the monographs will be published with the liberal CC-BY license. Further comparisons between PLOS ONE and Scientific Reports demonstrate that both charge what would likely be considered “reasonable” article processing charges with PLOS ONE’s APC at 1595 USD and Scientific Reports’ (APC) at 1790 USD as of January, 2019. However, there are some subtle (or not so subtle) differences. In 2015, the Journal Impact Factor for Scientific Reports was reported as 5.228 while PLOS ONE’s was listed at 3.057. Open Access “Mega-Journals” (OAMJs) and their Significance to Scientific Communication in Psychology Similar data in Journal Citation Reports for 2017 reports Journal Impact Factor for Scientific Reports at 4.122 and PLOS ONE at 2.766. PLOS ONE’s strict open data policy may be an issue, and Scientific 62 Reports’ policy might be seen by some as less onerous because it only asks that authors share data upon request, rather than having data availability as a requirement (except in rare exceptions). There also appears to be a slightly faster time to publication for Scientific Reports. These two journals appear destined for comparison and are obviously both important to psychological science. Whereas Springer Nature has a large stable of other subscription and gold open access journals surrounding its Scientific Reports, the PLOS journals are monetized strictly by APCs, with 91% of all PLOS papers published in 2015 found in PLOS ONE. Only 9% of articles were split among six other PLOS titles. (Davis, 2016) In 2017, PLOS published 7% fewer papers, and in 2018, publication output was down another 11%. Also, in 2017, Scientific Reports “overtook PLOS ONE as the largest scientific journal.” (Davis, 2018) Do the OAMJ’s have any dilution effect on the available disciplinary journals? Clearly, the open access mega- journals are a phenomenon to watch when it comes to scholarly communication in psychology. http://datasharing.sparcopen.org/ An Evolving Funder Environment Requiring More Open Access Compliance In recent years, funders in the United States and abroad began to mandate that the products of scholarship resulting from taxpayer funded research be made publicly available. Beginning with the NIH in (2005) and culminating in 2013 in the U.S. with the White House Directive (also known as the Obama Directive), the federal funder situation has evolved to encompass any U.S. federal agency that distributes more than 100 million dollars in research and development funding each year. (Stebbins, 2013) The list of these U.S. funders is lengthy and includes funders that have not previously dealt much with open access, including the various issues surrounding green open access and repositories. There was some scrambling for agencies to get up to speed by deadline. Publishers moved quickly to develop the CHORUS service which focuses on solutions for funder compliance. CHORUS has more than 100 members and signatories including the American Psychological Association and the Association for Psychological Science. (CHOR, 2017) At almost the same time, a university solution (SHARE) focused more on institutional repository self-archiving (green OA) was being developed to include a notifications service when a research output was made available. (http://www.arl.org/focus-areas/shared-access-research-ecosystem-share#.Wx2anyAh1PZ) Many of the large U.S. federal funders currently under the directive are supporting psychology research. The monthly newsletter of the APA Science Directorate has listings of current funding opportunities available in psychology. (Directorate, 2017) Also, the database Grants.gov is a searchable resource useful for discovery of psychology grant opportunities. On these lists, common funders include National Science Foundation (NSF), National Institutes of Health (NIH), Department of Health & Human Services (DHHS), and Department of Defense (DOD). These agencies are all examples of the lengthy new list of funders that have new rules with regard to open access availability for publications and data with which authors of the scholarly literature must comply. A comprehensive list of these new federal funders’ open access requirements with links to their implementation plans may be found at http://datasharing.sparcopen.org/ 63 Not only U.S. federal funders, but also private funders are developing more robust open access requirements as a condition of funding. Where data policies and open access mandates used a strategy of positive encouragement in the past that was not focused on compliance, more funders are moving to penalize researchers or institutions that do not comply. This has resulted in increased compliance and more open data, but there is still room for improvement. An Evolving Funder Environment Requiring More Open Access Compliance NIH and Wellcome Trust have both withheld funding from those that have not complied with the open access policies of the funders for previous work. (Van Noorden, 2014a) Compliance is not a given, even with policies having more “teeth.” With more and more funders, both in the U.S. and abroad mandating that the publications and data emanating from funded research be open access, there is at least one study of more than 1.3 million articles whose open access status has been analyzed to determine whether these publications have actually been made OA as required by their funders. Lariviѐre and Sugimoto (2018) were able to demonstrate that rates of compliance with OA rules (for 12 selected funding agencies), even within psychology (p.484), for instance, "vary greatly by funder." (p. 483) While some disciplines reach nearly full compliance (as seen in biomedicine, clinical medicine and health research), other discipline's rates of compliance are much lower. As for lower rates of compliance, "although researchers cite norms and needs within disciplines as a reason not to comply with open-access mandates, we believe that the funding agency is a stronger driver of open access than is the culture of any particular discipline." (p. 483) More study is needed to understand how (and how often) funded research is being made OA (as mandated) in psychology. Researchers seeking funds from certain U.S. federal funders will need to make plans up front for complying with the new open access rules. The Obama directive was followed up in 2015 by a letter sent to all research offices of the Association of American Universities (AAU) and Association of Public and Land-grant Institutions (APLU) which stipulated that research data must be made publicly available (to the extent possible) and offered advice to universities on compliance with new rules. (Vaughn, 2015) Adding open access to research data to the previous focus on text publications was a game-changer for authors, publishers and universities. Member universities had to grapple with the research data management issue more seriously and monitor compliance at the local level. A focus on the research data that underpins published scholarship is a foundation of open science. This new directive (and other follow on initiatives) promises to continue to open up the psychology literature to researchers as well as the public (and more of the practitioner community) that needs access to it. An Evolving Funder Environment Requiring More Open Access Compliance For psychology, there is a need to ensure that research data is openly available online for reuse and replication of studies (within certain parameters of course). One issue with which psychology grapples involves problems with replication and reproducibility of research results (both publications and data). Opening up research data for innovation and reuse will add needed transparency to future research. This is an area of scholarly communication that needs to evolve in order to add clarity around privacy issues, data citation practices, and licensing of data. Another aspect of open access and open licensing involves use of the research literature itself as the object of study. Sarma (2017) goes on to: 64 use the phrase scientific literature text mining to refer to data analysis of the scientific corpus, rather than the data sets that are produced by research studies. One can think of scientific literature text mining as representing a full-fledged generalization of review articles, systematic reviews, and meta-analyses whereby sophisticated tools from the modern data science toolkit are utilized to extract novel insights from the scientific corpus itself. (p.2) Each discipline will have different practices in aspects of public and open access to research data, and the psychological science community will develop and share best practices in this dynamic new area. Universities and researchers are partnering with commercial and nonprofit data management services (such as figshare, https://figshare.com/), as well as a variety of domain and institutional repositories (such as Inter-university Consortium for Political and Social Research (ICPSR)) and local university repositories) to develop solutions for archiving of data as required by funders, some putting a focus the entire lifecycle of the data. (Inter-university Consortium for Political and Social Research (ICPSR), 2017) The need for information and assistance in preparing research data management plans is going to become more necessary as more funders require them. Writing data management plans may be new to many researchers and many university libraries and research offices provide guidance and services in this area. This is skill set that will need to be added to scholarly communication education for researchers. A useful addition to the literature would be discipline-specific information on writing data management plans for psychological science, but there are some general guides available in the literature that provide tips for novices to the process. An Evolving Funder Environment Requiring More Open Access Compliance (Michener, 2015) One useful book with practical information for psychology is Managing your Research Data and Documentation by Berenson (2018). Many universities (usually via their libraries) are utilizing their institutional repositories to share, store and preserve research data. These digital institutional repositories have a mission of gathering, preserving and disseminating institutional scholarship and are able to ensure the availability of research data over time. Institutional repositories can link text publications and other research products to any supplemental and/or underlying data. Universities may one day decide that rather than just focusing on institutional open access policies that mandate public access to publications such as peer-reviewed article scholarship, that the research data produced at the institution must be publicly accessible on the internet for proof of funder compliance as well as for increased visibility and for demonstrating institutional impact. It is question open for discussion as to why universities have moved to develop open access policies that target publications, but they have not yet developed similar policies around curating and preserving the research data that emanates from funded research. Developing such policies would allow more focus on the development of university solutions for managing and preserving faculty and student research data, while ensuring university compliance with funder policies stipulating open data. The university is responsible for ensuring compliance (rather than the PI in most cases) and faculty and other researchers are in need of services and solutions for managing research data. University policies around research data would raise visibility of the need for discipline-based university-provided in house or outsourced solutions (such as development of appropriate platforms and repository services) for the complex area of research data management. 65 There is a large volume of studies that show that the research impact of scholarly publications is increased via open access. (SPARC Europe, 2015) Recent studies also show a citation advantage for sharing data as well. (Piwowar & Vision, 2013). Other universities do not necessarily focus on their institutional repository solutions, but instead have developed a suite of services (often as part of the library) that includes assistance with use of research data management tools and services such as the popular free, open source DMPTool (https://dmptool.org/) that has been used by many thousands of researchers to create data management plans. Data policies have also been developed by publishers. An Evolving Funder Environment Requiring More Open Access Compliance An early adopter that is home to many psychology-related articles, PLOS developed an open data policy in 2014. (Bloom, Ganley, & Winker, 2014). By 2016, 60,000 articles in the PLOS journals were sharing open data sets, and PLOS has made available some useful examples in an Open Data Collection. (Lowenberg, Ross, & Ganley, 2016) Where there are no data policies per se, some editors do not want to review papers where the data are not freely accessible. One high profile case for psychology involved a consulting editor for APA’s Journal of Experimental Psychology: Learning, Memory, and Cognition (where there is no formal open data policy), making the decision to reject papers where data are not open, or there is no reason stated for the lack of transparency. (Naik, 2017) This reviewer, Gert Storms, is one of hundreds of signatories to the Peer Reviewers’ Openness Initiative, which is a coalition of reviewers that agree that papers must have open underlying data (or provide specific information about why data can’t be open) in order to proceed through peer review. (Morey et al., 2016) Ubiquity Press’s Journal of Open Psychology Data (https://openpsychologydata.metajnl.com/) publishes “data papers,” and describes those articles as “a publication that is designed to make other researchers aware of data that is of potential use to them for scientific and educational purposes.” Each paper describes methods used to create the dataset, discusses reuse potential and provides a link to the data set in an online data repository. Research articles might refer readers to the complementary data paper. As this focus on open data evolves, publishers will need to provide clarity around issues of open and transparent data for studies where there are no privacy or other such concerns to prevent this. Open data is a major tenet of the emerging open science movement, and psychology, with its current focus on reproducibility, is on the forefront in the development of disciplinary policies, tools and practices. In fact, in a major new publication, Open Science by Design: Realizing a Vision for 21st Century Research (2018) from The National Academies Press mentions psychology as a major force for open science, stating “New standards for data and code sharing in fields such as biomedical research and psychology are making it easier for researchers to reproduce and replicate reported work, strengthening scientific rigor and reliability.” (p. An Evolving Funder Environment Requiring More Open Access Compliance 1) A relatively new concern for those producing and creating organization around research data, as well as for those researchers wanting to use the data of others is the climate of legal uncertainty and the many questions researchers may have about intellectual property rights as they relate to research data. Particularly, issues of copyright, trade secrets, patents and Creative Commons licensing all come into play. It is useful for all who deal with rights surrounding research data to have an understanding of the issues. Carroll’s article analyzing the intellectual 66 property law that comes into play with sharing research data covers the issues well. (Carroll, 2015) law that comes into play with sharing research data covers the issues well. (Carroll It may be difficult to find information on research data management that is specific to the discipline, and there cannot be a “one size fits all” approach to this topic. More information and published examples are needed about how research data is managed and curated in specific subfields. Specific strategies and practices would be welcomed, such as the Borghi and Van Gulick (2018) analysis of research data management practices and perceptions in the field of neuroimaging. Although best practices are developing, psychology is still a long way from realizing a high level of access to open data. Even though the funder environment and the culture of the discipline may be moving more toward “open” when it comes to data, managing, curating and preserving that data may be still a work in progress for the profession. A 2015 survey of faculty in all disciplines showed that 90 percent still manage their data on their own computer. (Wolff, Rod, & Schonfeld, 2016) Research data management is complex in psychological science, but there are excellent examples of guidelines and specifications available for review by researchers and others interested in the development of appropriate programs. For example, the recent publication of recommendations from initiatives of the German Psychological Society (Deutsche Gesellschaft fur Psychologie, DGPs) sets out clear guidelines for managing research data that is specific to psychological science. Issues such as storage of primary data, clarifying what constitutes a “trustworthy data repository,” the use of DOIs for identification of data, the need to request support from third party funders, data privacy and copyright, rights of data sharers (to use embargoes, for instance), and duties of the secondary users of data are covered. An Evolving Funder Environment Requiring More Open Access Compliance In terms of trusted repositories, solutions such as PsychData or a “developed university repository” are mentioned. (Schonbrodt, Gollwitzer, & Abele-Brehm, 2017) Those repositories that are able to fulfill 16 requirements may be assessed by experts and receive the “Data Seal of Approval” (https://www.datasealofapproval.org/en/) after a peer review process. Open Access and Research/Citation Impact in Psychology One issue that has persisted in terms of open access is the question of whether publishing openly increases the impact of scholarship. Many studies demonstrate that open access increases research impact, with only a very few studies refuting this assertion. (McKiernan et al., 2016) These studies are aggregated on a website produced by SPARC Europe entitled The Open Access Citation Advantage (OACA). (SPARC Europe, 2015) In another large study completed in 2016 of 3.3 million papers published from 2007-2009 (and indexed in the Web of Science), it was demonstrated that not only is there a citation advantage due to open access, it is “green” open access (OA due to repository deposited versions of papers) that produced the maximum research impact. When broken down by discipline, “Psychology & Cognitive Sciences (with more than 70,000 papers studied) also showed this open access impact, with the most impact for green OA articles. Hybrid articles were not included in this study. In terms of traditionally published articles, “publishing in paywalled journals is the least impactful strategy overall.” (Archambault, Cote, Struck, & Voorons, 2016) 67 In an earlier cross-disciplinary study (2005) of ten disciplines including psychology (replicating earlier studies of single disciplines), it was also found that making papers OA confers a citation advantage. All disciplines in this 2005 study showed an OA citation advantage, with psychology showing a 108% higher citation advantage for papers that are OA (in comparison to 36% for biology, for instance). (Hajjem, Harnad, & Gingras, 2005) Researchers must take note of open access strategies that can produce the most citation advantage for their papers. Institutions may promote the deposit of all university-authored scholarship in the institutional repository via the passage of open access policies in order to, in part, maximize the impact of the collective scholarship of all of its researchers. Both individual faculty members as well as institutions benefit from passing open access policies and developing institutional repositories and associated services that promote maximal green open access. For studies analyzing the open access citation or research advantage for monographs, no such aggregation of positive studies results as is available for articles. However, there have been some analyses and suggestions of how the book literature might be studied for impact, and even if online usage is positively affected and enhanced by open access, a citation advantage is more difficult to ascertain. Open Access and Research/Citation Impact in Psychology (Snijder, 2016) Snijder also remarks on an issue that is starting to infiltrate academia, and that is the existence of a newer “audit culture” that attempts to assess productivity or research impact of university faculty: Lastly, if the importance of bibliometric analysis as a proxy for research quality is growing, it is vital to understand if there are significant dissimilarities between articles and monographs. Identifying specific differences between journal articles and books and the factors that underlie these differences will enable a comparison of scholarly impact of monographs and articles based on sound principles. (p.1873) The Clarivate Analytics-produced index, Book Citation Index (a part of the Web of Science Core Collection) includes citation information (including “cited reference searching” for books that were produced from 2005 to the present). As this corpus of material continues to develop, studies will likely analyze the citation patterns of books. As more fully open access books (that use book processing charges-BPCs) to fund publication are made available, it will be possible to consider metrics for books in the same way as for articles and conference proceedings. As far as OA citation advantage for books, in time there will be ways to quantitatively describe the impact of books because some commercial and other scholarly publishers (including university presses such as the Luminos platform from University of California Press, (https://www.luminosoa.org/)) are now moving to offering an open access “author pays” model that levies BPCs in order to publish. While BPC amounts vary tremendously, using the example of Luminos, “the baseline $15,000 publishing cost is broken down into manageable amounts for the researcher, the university, the library, and us.” (https://www.luminosoa.org/site/for_authors/) Fees are certainly lower for nonprofit publishers than they are for commercial presses. Commercial publishers also charge BPCs in open access programs for books. It is early yet to see what kind of uptake and subsequent citation impact can be expected for the author pays book programs, especially at the high fees that some charge. Established university subvention and open access funds will find the high BPCs of the 68 commercial publishers challenging and it remains to be seen whether (and from where) other funding will be available to authors interested in providing wide OA to their books. A useful addition to guides for authors of books in psychology would be the creation of a list of potential funding sources where open access funding assistance could be sought. Open Access and Research/Citation Impact in Psychology The situation with open access monographs is fast evolving, and the recent report from the British Academy for the Humanities and Social Sciences announcing that the UK Reference Exercise Framework (REF) in its 2027 iteration had included an intention to extend an open access requirement for articles to include those research outputs published in books or other long form scholarly works. (British Academy, 2018). Many psychology researchers decide to submit chapters to edited books. Book chapters in edited works have often been problematic in terms of citation impact and discoverability and many are behind a paywall. Bishop (2012) described the situation in a blog post entitled “How to bury your academic writing.” She describes the lack of citedness and visibility of book chapters and suggests that “researchers who write book chapters might as well bury the paper in a hole in their garden.” (Bishop, 2012) Open access has been mentioned as one method that can be used to mitigate the visibility problem of chapters, particularly green open access. There are many considerations and strategies that might be used for ensuring more visibility for book chapters. (Dunleavy, 2017) As book chapters are still an important and valued vehicle in psychology, both authors and publishers may need to expend more effort on the discoverability of these works. Even though not included in easily found sources of “rules” around self-archiving by authors in repositories (such as those found in SHERPA/RoMEO), publishers have taken note of the marketing effect of allowing single chapters to be self-archived in institutional repositories or scholarly networking services such as ResearchGate. Adding book chapters alongside other works in collections of articles in repositories allows these works to receive individual DOIs (assigned by the repository), and these persistent identifiers allow the chapters (especially if they don’t already have an assigned DOI) to participate more fully in the article-level economy that is promoted by seamless linking on the internet. Chapters with associated DOIs also facilitate inclusion in services that take advantage of the DOI environment such as Google Scholar. Book chapters now appear in publicly available Google Scholar Metrics profiles alongside books. Open Access and Research/Citation Impact in Psychology In one study of UK academics (using the LSE PPG dataset), it was shown that, in psychology, the proportion of total cites (from various sources) to UK book chapters published from 2010 to 2013 was 5.5% This same dataset showed that “book chapters are almost completely uncited in psychology and economics.” (Bastow, 2014) The ability of book chapters to have a chance to perform in the same open access and citation impact environment as journal articles will be a game changer for publishers and authors seeking to bolster the situation for book chapters and the citations to them. Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology The evolving scientific discipline of “meta-research” is important and pertinent to the future of research in psychological science, and has as its purpose the improving and evaluation of research practices and scientific publication. Meta-research can be categorized into five major areas: Methods, Reporting, Reproducibility, Evaluation and Incentives, and those areas cover 69 “how to perform, communicate, verify, evaluate, and reward research.” (Ioannidis, Fanelli, Dunne, & Goodman, 2015, p.2) Surely some issues for scholarly communication in psychology surround the replication of research results. A novel and innovative study is often of more interest to an editor than a redo of previous research that sets out to provide evidence of reproducibility. The rise of open data practices in psychology holds promise for increasing the ability of scholars to replicate the scientific studies published by others. The availability of the data behind the research creates the transparency needed to ensure the validity and usefulness of research results. (McKiernan et al., 2016) Replication studies have not been common in psychology. Today, those scientists wishing to undertake and discuss replication studies have more options than in the past, and can use blogs, preprint servers, and may decide to use a publication outlet that welcomes (and even solicits) replications, such as F1000 Research (with its Preclinical Reproducibility and Robustness channel) or Nature’s Scientific Data. Psychology has an interesting example of collaboration and replication found in APS’s Perspectives on Psychological Science. The publication seeks nominations for replication of influential articles and the original author is engaged with the scientists doing the replication, and offers perspective on the result. The final results are published as a type of article called a “Registered Replication Report” (RRR)” described at https://www.psychologicalscience.org/publications/replication. ("Go forth and replicate!," 2016) In psychology, even fabrication of research results has been a topic in the news media. In recent years, as researchers pursue the question of replication and of reproducibility, there is not always an easy answer to getting at the “truth” of the findings. Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology When popular outlets such as the New York Times and Scientific American picked up on the study known as the Reproducibility Project: Psychology (Center for Open Science, 2016), of which the results and analysis was subsequently published in Science in 2015, many took notice and an article in Scientific American even labelled the issue “Psychology’s Credibility Crisis.” (Horgan, 2016) The original 2015 article in Science by the Open Science Collaboration (OSC) stated that “we report a large-scale, collaborative effort to obtain an initial estimate of the reproducibility of psychological science.” (Open Science Collaboration, 2015, p. aac4716-1) This study involved conducting replications of 100 studies in three psychology journals (Psychological Science, Journal of Personality and Social Psychology, and Journal of Experimental Psychology: Learning, Memory and Cognition.) and mainly covered the subdisciplines of cognitive and social-personality psychology. The researchers examined five indicators and OSC concluded in a 2015 research article summary that “a large portion of replications produced weaker evidence for the original findings despite using materials provided by the original authors, review in advance for methodological fidelity, and high statistical power to detect the original effect sizes.” (p.943) Some studies paint a more positive picture. In a study of 100 top psychology journals (using 5-year impact factor), Makel et al. provided an analysis of replications that showed a 70 replication rate of 1.07%. with an increasing number of replications being published over time. Results demonstrated that: replication rate of 1.07%. with an increasing number of replications being published over time. Results demonstrated that: contrary to previous findings in other fields, this study found that the majority of replications in psychology journals reported similar findings to their original studies (i.e., they were successful replications). However, replications were significantly less likely to be successful when there was no overlap in authorship between the original and replicating articles. (Makel, Plucker, & Hegarty, 2012, p.537) Following the OSC study of reproducibility, in some areas of psychology, response was swift. Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology Bakker & Wicherts (2011) present the results of a study and offer some ideas and recommendations that would help to remedy this situation: In order to study the prevalence, nature (direction), and causes of reporting errors in psychology, we checked the consistency of reported test statistics, degrees of freedom, and p values in a random sample of high- and low-impact psychology journals. In a second study, we established the generality of reporting errors in a random sample of recent psychological articles. Our results, on the basis of 281 articles, indicate that around 18% of statistical results in the psychological literature are incorrectly reported. (p. 666) Recommendations for establishing best practices to reduce “misreporting of statistical errors” that followed the study include: the need to follow closely the rules for reporting as set out in the Publication Manual of the American Psychological Association, reiterating that “statistical results should be accompanied by effect sizes and CIs when possible,” making sure the results are checked by both coauthors and reviewers, using “sound statistical reviewing,” and not using the error prone copy/paste feature, and ensuring that all raw data is available. (Bakker & Wicherts, 2011, p.666) Even with the publication of corrective guidelines about the use and misuse of p-values, for instance, by the American Statistical Association in 2016 (and many other such guidelines published over the years), the problems of “misuse of statistical procedures and poor methods has persisted and possibly grown. In fields such as psychology, neuroscience and medicine, practices that increase false discoveries remain not only common, but normative” (p.2) and that “many prominent researchers believe that as much as half of the scientific literature—not only in medicine, by also in psychology and other fields—may be wrong.” (p.2) In fact, for many years (since early exhortations about increasing power published in 1962), studies in psychology have suffered consistently from low statistical power. (Smaldino & McElreath, 2016) The prevalence of statistical reporting errors in articles in psychology journals has been studied by other researchers and shown to be high. (Nuijten, Hartgerink, van Assen, Epskamp, & Wicherts, 2015). The availability of helpful new automated tools that have been created in order to efficiently carry out the work of checking statistics comes with some notes of caution about effects on researcher and journal reputation. One of those tools is the free, open-source R package and web app, “statcheck” (http://statcheck.io.). Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology In Science, a published comment that followed (Gilbert, King, Pettigrew, & Wilson, 2016, p.1037-b) insisted that “the data are consistent with the opposite conclusion, namely, that the reproducibility of psychological science is quite high” and that “OSC’s data clearly provide no evidence for a ‘replication crisis’ in psychological science.” Science went on to publish the original authors’ response to that comment, concluding that “OSC2015 provides initial, not definitive, evidence-just like the original studies it replicated” (Anderson et al., 2016, p. 1037-c). One study revisiting the results of the aforementioned Open Science Collaboration initiative, (Reproducibility Project: Psychology) listed “publication bias in the psychological literature” as one factor in the Project’s “failure to replicate many target effects.” Etz & Vandekerckhove (2016) explain that: We conclude that the apparent failure of the Reproducibility Project to replicate many target effects can be adequately explained by overestimation of effect sizes (or overestimation of evidence against the null hypothesis) due to small sample sizes and publication bias in the psychological literature. We further conclude that traditional sample sizes are insufficient and that a more widespread adoption of Bayesian methods is desirable. (p.1) There are other factors affecting reproducibility, for instance small sample size and low power. Button et al., analyzing the situation for neuroscience, “show that the average statistical power of studies in the neurosciences is very low. The consequences of this include overestimates of effect size and low reproducibility of results.” (Button et al., 2013, p. 365) Others concur that in the Reproducibility Project: Psychology’s findings, various explanations, for instance, small sample size may account for some of the low level of replication found in this large-scale project, and that the headlines that result from such a study informing the scientific community about a “crisis in psychological science” may be unnecessarily alarmist. (Patil, Peng, & Leek, 2016) In fact, some feel that rather than a crisis, the last seven (or so) years of improvements that have followed the decades when experimental psychologists were largely unaware of the problems that existed with data collection and analysis can be looked at very positively. A series of important events that began in 2010-2012 created a level of large-scale awareness and a series of changes that can be said to have led to “psychology’s renaissance.” (Nelson, Simmons & Simonsohn, p. 512) 71 Errors in statistical calculations and reporting are also found in the psychology literature. Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology Statcheck “automatically extracts reported statistical results from papers and recalculates p-values” and works very well for psychology because APA reporting style requires reporting statistics in a consistent manner (and accuracy of the tool is decreased for those statistics that do not conform to APA statistical reporting conventions). (Nuijten, 2018) In a study using statcheck that included psychology articles from four major publishers (two others would not allow the text mining necessary to do the research) constituting more than 50,000 articles and approximately 700,000 statistical test results, Hartgerink (2016) explains that “this dataset of statistical results and accompanying metadata can be used to inspect if specific papers include potential statistical errors or for trends in statistical results over time.” (p.2) 72 Following this extensive study of a large subset of the psychology literature, the results will be posted to PubPeer, “an online platform for post-publication peer review.” (https://pubpeer.com/) This initiative to put all of the studies in PubPeer will open up all of the articles to scrutiny and possible correction if needed. So far, reaction from researchers has been mixed. Hartgerink suggests that publishers might want to run the statcheck algorithm on all papers before publishing. (Chawla, 2016a) There has been pushback against this use of PubPeer without having contacted authors, and also questions about the use of the statcheck algorithm. One German research society, the Deutsche Gesellschaft fur Psychologie (DGPs) has called for an end to this use of PubPeer (based on statcheck), citing concern for researcher reputation. (Chawla, 2016b) In another study of statcheck accuracy, Nuijten found “statcheck to be very effective at flagging inconsistencies and gross inconsistencies, with an overall accuracy of 96.2% to 99.9%.” (Nuijten, 2018) Following the aforementioned analysis on the reproducibility of the scientific literature in psychology (OSC), Baker (2016) reported on a Nature survey that returned 1576 responses on a questionnaire focused on whether scientists feel there is a crisis in reproducibility in research: The data reveal sometimes-contradictory attitudes towards reproducibility. Although 52% of those surveyed agree that there is a significant ‘crisis’ of reproducibility, less than 31% think that failure to reproduce published results means that the result is probably wrong, and most say that they still trust the published literature. Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology (p.452) The same survey also revealed that “more than 70% of researchers have tried and failed to reproduce another scientist’s experiments, and more than half have failed to reproduce their own experiments.” The survey also was focused on asking respondents to rate different approaches to improving reproducibility in science. (p.452) In 2011, a proposal labeled “Simple Solution to the Problem of False-Positive Publications” that listed six possible requirements for researchers, and four guidelines for reviewers that could possibly be remedies for some of the issues facing psychological science research and publication was put forth. These six requirements encompassed rules around data collection and reporting of experimental conditions, for instance, while not imposing a burden. The guidelines for reviewers, among other recommendations, would ensure that the rules for accepted practice would be followed. (Simmons, Nelson, & Simonsohn, 2011) A follow up survey of 1292 psychologists was undertaken to determine if they would support these requirements and guidelines, and in general, whether they were open to change. While psychologists were found to be open to change, a majority of respondents did not support having hard and fast rules based on some of the requirements as a condition of publication. Respondents did consider the requirements to be standards of good practice even if they did not support all of them as conditions of publication. One requirement, that “authors must report all experimental conditions, including failed manipulations” did receive majority support as a condition of publication. A reminder was also issued that any sort of standards affecting the publication process must take into account the wide variety and diversity of psychological science research. (Fuchs, Jenny, & Fiedler, 2012) 73 Outside of current studies and controversy surrounding them, scholarly communication in psychology depends on a discussion of what gets published (and where) and what has impact. The research community will decide its direction in order to continue to build on credible research results. Achieving a degree of transparency and openness is integral to the research process if reproducibility of results is a goal. Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology The American Psychological Association has also come out with the news that they have created a new position for an “Open Science and Methodology Chair” to work with its authors, reviewers, editors and publications board to understand and develop best practices for the evolving landscape of open science in psychological research.” (Mills, 2018) Clearly, there is momentum to the move to openness for the publication and sharing of research results (including data) in psychology. Incentivising open research and publication behavior is one way to ensure that researchers prioritize openness in practice. Nosek et al. (2015) mention that universities, funders and publishers provide different incentives for researchers focused on impact, and there is little coordination of effort toward openness. Some early career researchers have been willing to speak out about the benefits of practicing open science even while needing to succeed in the current academic environment with its existing system of incentives and evaluation practices. Incentivising open research and publication behavior is one way to ensure that researchers prioritize openness in practice. Nosek et al. (2015) mention that universities, funders and publishers provide different incentives for researchers focused on impact, and there is little coordination of effort toward openness. Some early career researchers have been willing to speak out about the benefits of practicing open science even while needing to succeed in the current academic environment with its existing system of incentives and evaluation practices. (McKiernan et al., 2016) At least one university has written an explicit statement in an advertisement for an available position that seeks to attract candidates who practice and will practice open science behaviors. The statement from the department of psychology at Ludwig- Maximilians-Universität (LMU) München reads (translated from German), “Our department embraces the values of open science and strives for replicable and reproducible research. For this goal we support transparent research with open data, open material, and pre-registrations. Candidates are asked to describe in what way they already pursued and plan to pursue these goals.” (F. Schonbrodt, 2016) In a May, 2018 update, LMU’s psychology department now uses an explicit hiring policy statement in all of its professorship job advertisements. Currently, “if you want to join the LMU psychology department as a professor, you should better have some open science track record.” (F. Schonbrodt, 2018). In the U.S. Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology on March 21, 2018, Southern Methodist University (SMU)’s Department of Psychology adopted an “open sciences practices policy for conducting research in the department.” Candidates are asked to describe in what way they already pursued and plan to pursue these goals.” (F. Schonbrodt, 2016) In a May, 2018 update, LMU’s psychology department now uses an explicit hiring policy statement in all of its professorship job advertisements. Currently, “if you want to join the LMU psychology department as a professor, you should better have some open science track record.” (F. Schonbrodt, 2018). In the U.S. on March 21, 2018, Southern Methodist University (SMU)’s Department of Psychology adopted an “open sciences practices policy for conducting research in the department.” (https://www.smu.edu/Dedman/Academics/Departments/psychology) The policy recommends preregistration, data sharing and uploading preprints and states that “adopting the policy will be viewed very favorably by the chair and faculty members’ efforts to adhere to the policy will be recognized in their annual reviews.” (https://www.smu.edu/- g ( p /media/Site/Dedman/Academics/Departments/Psychology/2018/Policy-on-Open-Science- 032218.pdf?la=en) There are other coming pressures that will affect all researchers. The U.S. National Institutes of Health (NIH) is increasing its focus on the need for all grant submissions to demonstrate scientific rigor and reproducibility. This follows on earlier initiatives that promoted discussions about reproducibility in psychological science, for example in 2011 when the National Institute on Aging partnered with the Association for Psychological Science and the NIH Office of Behavioral and Social Science Research. (Desoto, 2016) Importantly, the NIH 2016-2020 strategic plan states: “NIH will take the lead in promoting new approaches toward 74 enhancing the rigor of experimental design, analysis, and reporting” and also will focus on “ensuring compliance with policies for open access to the published literature and data sharing.” (National Institutes of Health, 2016, p.35). NIH’s Grants & Funding webpage (https://grants.nih.gov/reproducibility/index.htm) describes scientific rigor as “the strict application of the scientific method to ensure robust and unbiased experimental design, methodology, analysis, interpretation, and reporting of results. This includes full transparency in reporting experimental details so that others may reproduce and extend the findings” and that “the NIH plans to require formal instruction in rigorous experimental design and transparency to enhance reproducibility for institutional training, institutional career development, and individual fellowship applications no sooner than 2017.” Much of the new focus on open science will affect the research practices of early career researchers going forward. Replication and Reproducibility: Recent “Meta-research” Issues Important to Psychology All researchers, but in particular, the early career researchers will need to keep up with all new scholarly communication paradigms. That group can learn strategies for marketing early works, can follow the impact of their work in new metrics services and collaborate globally via new communication modes. For those early career researchers interested in open access and related areas, there are ways to engage. One global conference that focuses specifically on engaging early career researchers with “open” is OpenCon, a three-day annual conference that alternates between the U.S. and Europe, and provides an opportunity for intense learning and collaboration about open access, open data and open education. ("OpenCon 2017," 2017) Open Research Practices for Psychological Science: Guidelines, Standards and Incentives for more Open Publication Practices in Psychology There are many examples of the move to more open research practices now evident in the scholarly communication landscape for psychology. In terms of coalescing around shared standards, the example of the eight standards (and three levels) that make up the Transparency and Openness Promotion (TOP) Guidelines (http://cos.io/top/) demonstrates evidence of action by the scientific community to tackling issues such as reproducibility and data sharing. The TOP Guidelines are described on their webpage as “transparency, open sharing, and reproducibility are core values of science, but not always part of daily practice. Journals, funders, and scholarly societies can increase reproducibility of research by adopting the Transparency and Openness Promotion (TOP) Guidelines…” The eight standards are citation standards, data transparency, analytic methods (code) transparency, research materials transparency, design and analysis transparency, preregistration of studies, preregistration of analysis plans, and replication. (Nosek et al., 2015) The list of signatories to the TOP Guidelines (over 5000 journals and organizations at the time of this writing in September, 2018) demonstrates participation and support by psychology publishers and journals for the ideals proffered in the Guidelines. Acknowledging disciplinary differences is paramount in this area and journals reporting the research results of psychological science will need time to reach a level of data sharing that, for instance, economics has achieved thus far (Nosek et al., 2015). Collaboration between publishers, authors, and other stakeholders will be necessary in developing the trust that will make sure everyone in the system understands 75 what needs to be made open and when, and how articles, data, code and other results of research will be produced and shared. The Association for Psychological Science (APS) and the Society for Personality and Social Psychology (SPSP), along with many individual psychology journals, are some of the signatories on the TOP Guidelines, and are utilizing some of the standards in their publications. Some journals proudly display badges to signify compliance with open practices. An early example of a journal using open scientific practices and extending incentives such as badges to authors for using them was Psychological Science (Association for Psychological Science) (Eich, 2014). Instructions for authors for manuscripts accepted after Jan. 1, 2014 indicate that three badges are available: Open Data, Open Materials, and Preregistration. The APS webpage also publishes lists of recipients of badges, and full information for earning them. Open Research Practices for Psychological Science: Guidelines, Standards and Incentives for more Open Publication Practices in Psychology (Association for Psychological Science, 2016) As for results, when Psychological Science started the badges program in January, 2014, about 3% of articles included open data, and by the first half of 2015, that rate had risen to nearly 40% of articles. This was not the case for other psychology journals in the comparison group of publications without badges where incidence of open data was still low. Also, before badges, and in the comparison group, the study found that there was little actual sharing of data that was complete or usable. (Kidwell et al., 2016) As of the July 2018 issue of Psychological Science, “13 of the 15 ‘regular’ articles received the data badge (nine also received the materials badge and we had three of the once-rare triple-badgers). We’re not done yet.” (Lindsay, 2018) Interestingly, it has also been suggested that authors may want to display badges on their curricula vitae as a way of signalling their use of open practices (in addition to the presentation of badges on the published paper alone). (Aarts, 2017) Another study that sought to determine whether data sharing practices are becoming more open and transparent looked at articles in all issues for 2012 of 4 APA journals (Emotion, Experimental and Clinical Psychopharmacology, Journal of Abnormal Psychology and Psychology and Aging). Authors of the total of 394 papers were all contacted and asked to share their data, and only 38% of authors were willing and/or able to share their data. In fact, that APA’s Ethical Principles of Psychologists and Code of Conduct stipulate how data is to be shared in psychology journals. (Vanpaemel, Vermorgen, Deriemaecker, & Storms, 2015) Some reviewers have also begun to take a strong stand on open data, stating that after January, 2017, they will reject papers if underlying data is not available for the process, or an adequate explanation has been given if it can’t be. Scientists are adding their names as signatories on the Peer Reviewers’ Openness Initiative, which hopes to increase transparence in psychology. (Naik, 2017) In another response to a new scholarly communication landscape in psychology, the APA introduced a new and innovative open access journal in 2013, Archives of Scientific Psychology. Open Research Practices for Psychological Science: Guidelines, Standards and Incentives for more Open Publication Practices in Psychology This innovative publication covers all areas of psychology, and uses a unique approach that is summarized by seven attributes: all articles are open access via the internet for all readers worldwide, the description of methods used in each study is freely available on the internet, and the authors have made the data available (after agreement by the journal’s review committee regarding usage) for verification of results. Two versions (one for scientists and one for the 76 public) of each article’s Abstract and Method section are made available for readers. Two abstracts are prepared, one for retrieval of the scientific article and one that is written in nontechnical language for the public, and the Method section also includes a brief nontechnical summary. Comments by scholars and the authors’ responses to them may also be published alongside the article. (Cooper & VandenBos, 2013). While the approach includes time spent on presenting the material in the article for a lay audience (and this is a laudable contribution), it will be interesting to see whether this extra step is meaningful for researchers and faculty authors that generally write and publish for promotion and tenure, not for communicating with the public. At least one study of promotion and tenure criteria shows that engaging with the public effectively around one’s scholarly work does not necessarily help to advance an academic career. (June, 2018) The APA’s Archives of Scientific Psychology became the first adopter of the JARS (Journal Article Reporting Standards), published in 2011. (Cooper, 2011) Authors submitting articles to this publication complete a questionnaire version of the JARS, including detailed information on rationale, method, results and interpretation, and the Method section of the article links to it. Updated JARS (for qualitative and quantitative research) were published by APA in 2018. JARS information is made freely available from multiple APA-related sites. (Kazak, 2018) Archives of Scientific Psychology is the first APA journal to require sharing of research data by all authors. (Cooper, 2011). APA Journals now utilizes a specific data repository to make data associated with this publication available (https://osf.io/view/apa/). Clearly, the publication of Archives of Scientific Psychology uses a groundbreaking new approach to open access, open data and other open practices, and does serve as a model and an experiment to see how authors will respond and how soon other journals will follow suit. Open Research Practices for Psychological Science: Guidelines, Standards and Incentives for more Open Publication Practices in Psychology Availability of open data is necessary to combat fraud and to allow replication and reuse of research results. In a 2011 case of scientific fraud, it is felt that the lack of openness and availability of research data can be listed as a factor that contributed to the large scale misconduct carried out over a period of years by the Dutch social psychologist Diederik Stapel. (Verfaellie & McGwin, 2011) In a review article, Gross (2016) examined the many issues with scientific misconduct (described as encompassing fabrication, falsification and plagiarism) that involve all disciplines, including psychology. The prevalence of questionable research practices (QRPs) by research psychologists has been the focus of a recent study and was found to be “surprisingly high.” Interestingly, “relatively high rates of QRPs were self-reported among the cognitive, neuroscience, and social disciplines, and among researchers using behavioral, experimental, and laboratory methodologies (for details, see Data Analysis in the Supplemental Material). Clinical psychologists reported relatively low rates of QRPs.” (John, Loewenstein, & Prelec, 2012, p.529) The issues of transparency and reproducibility are not unique to psychology but will need to be addressed going forward. Open source tools, such as the open lab notebooks in daily use by scientists create a culture of openness, and many are in use or development today. (Buck, 2015) PLOS has created the Open Source Toolkit to stimulate discussion and curation around the use 77 of open source hardware and software in research. ("Open Source Toolkit: a global forum for open source hardware and software research and applications," 2017). There is increasing use of GitHub in many science disciplines, for example in neuroscience. “GitHub.com, a hugely popular website for collaborative work on software code” allows scientists to post data and others to add to that data. (Perkel, 2016) Of course, the 2018 acquisition of GitHub by Microsoft (https://news.microsoft.com/2018/06/04/microsoft-to- acquire-github-for-7-5-billion/) may cause some open source advocates to move in a different direction. Tools are now available to both facilitate the peer review of code and enhance the reproducibility of reported scientific findings right from the article. Code now can be cited with its DOI, and the platform Code Ocean is in use by researchers in psychology to share results in an open manner. This useful value add to scholarly publishing has been trialed at some Nature Research journals: Code Ocean is a computational reproducibility platform that aims to make code more readily executable and discoverable. Open Research Practices for Psychological Science: Guidelines, Standards and Incentives for more Open Publication Practices in Psychology The platform, which is based on Docker, hosts the code and data in the necessary computational environment and allows users to re-run the analysis in the cloud and reproduce the results, bypassing the need to install the software. (Pastrana & Swaminathan, 2018) At present, Code Ocean is also being used by other publishers of psychology content, such as Taylor & Francis, where the Code Ocean widget is being integrated into the article, allowing readers to run the code right from the article. (https://codeocean.com/press-release/taking-the- journal-article-to-the-next-level-taylor-francis-partner-with-code-ocean) The first two psychology journals from Taylor & Francis that will integrate Code Ocean into articles are Comprehensive Results in Social Psychology and Journal of Social Psychology. Code Ocean has built a solution to the need for computational reproducibility in psychology and delivered a practical and useful tool to the researcher and reader. At present, there may be a lack of use of the type of “container” technology (such as Docker) in psychology and scientists at Code Ocean have begun to detail step by step instructions for the use of the technology that underlies the platform. (Clyburne-Sherin & Green, 2018) The psychology article of the future will likely be a much enhanced package that ensures a heightened ability for readers and researchers to replicate and assess the results of research in real time. Publication Bias, Excess Success, Retractions and Preregistration of Studies in Psychology In diverse fields of cognitive science, evidence exists for the prevalence of publication and selective reporting biases. (Ioannidis, Munafò, Fusar-Poli, Nosek, & David, 2014). Ioannidis et al. provide analysis of the many studies of reported bias and offer some possible solutions to these problems. One example of an important issue is the existence of the persistent trend in the United States where most published studies report positive results. The worsening trend of the increase in the publication of positive outcomes, when studied across disciplines and countries, points out the psychology/psychiatry has one of the higher rates of increase. (Fanelli, 2012). With replication an issue, there is an issue with the “canonization of false facts” and calls for more publication of negative findings. Interestingly, new journals have cropped up that just focus 78 on negative findings, for instance PLOS ONE’s Positively Negative collection. Negative findings might also at least be published online as preprints just to get them into circulation. (Nissen, Magidson, Gross, & Bergstrom, 2016) However, formal publication of negative findings, the aspiration of these new journals, have not necessarily found success. One such publication, Elsevier’s New Negatives in Plant Sciences has been discontinued after the publication of only 12 articles. ("Publisher's Note," 2016); ("Editorial," 2015) Bias against the publication of negative results has many possible explanations, and needs continuing analysis. Increasingly, the article submitted to the journal must reach perfection, even aesthetically, while competing in an ever crowded field of submitted papers in an ever increasing “publish or perish” environment. (Giner-Sorolla, 2012) As to the question of why it is so difficult to publish negative results, there are many issues such as the attraction of proving theories correct, more excitement by journals in publishing positive findings, putting a positive spin on less than positive findings, and the prevalence of the common “file drawer effect.” These issues are all under scrutiny. (Couzin-Frankel, 2013). Once again, a return to open practices and more sharing of all research results, including negative results, is possible now via the internet and only needs cultural and disciplinary practices to evolve (alongside the electronic). Preregistration of Research Studies in Psychology There are many initiatives developing at present that are working to combat problems such as publication bias by using new methods of peer review or modifications to the commonly existing steps in the formal publication process. More open processes help to create new opportunities for enhanced scrutiny of the research process. Preregistration of research studies is one strategy currently being used in psychology. In an example of a journal incorporating preregistration is Cortex (Elsevier), where a new format for empirical articles, “Registered Reports,” will include review of initial manuscripts before data collection commences. Following an “in principle acceptance,” the study will commence exactly as registered, and then a re-review process precedes formal publication. (C. D. Chambers, 2013). As of January, 2019, 156 journals (many in the behavioral sciences) have adopted the use of Registered Reports (sometimes referred to a RRs). A list of these journals is available from There are many initiatives developing at present that are working to combat problems such as publication bias by using new methods of peer review or modifications to the commonly existing steps in the formal publication process. More open processes help to create new opportunities for enhanced scrutiny of the research process. Preregistration of research studies is one strategy currently being used in psychology. In an example of a journal incorporating preregistration is Cortex (Elsevier), where a new format for empirical articles, “Registered Reports,” will include review of initial manuscripts before data collection commences. Following an “in principle acceptance,” the study will commence exactly as registered, and then a re-review process precedes formal publication. (C. D. Chambers, 2013). As of January, 2019, 156 journals (many in the behavioral sciences) have adopted the use of Registered Reports (sometimes referred to a RRs). A list of these journals is available from https://cos.io/rr/#journals. Funders may be able to use RRs as well, especially those funders that want to promote transparency and reproducibility in research. Publication Bias, Excess Success, Retractions and Preregistration of Studies in Psychology Beyond negative results, it is important to study carefully all issues that result in “unpublishable research results” and the important disciplinary differences that render important research unfit for publication and relegated to the “file drawer.” (Tsou, Schickore, & Sugimoto, 2014) In one study that analyzed experimental psychology papers published in the journal Science from 2005-2012, an example of “excess success” was found, showing that 83% of published articles with four or more experiments had positive study results. (Francis, Tanzman, & Matthews, 2014) This was similar to the study in Psychological Science of a four year grouping of articles containing at least four experiments that showed 82% positive results. (Francis, 2014) In a follow up article (to Francis’ study on “excess success”), van Boxtel and Koch (2016) focused on one particular article (their own), which had been flagged by Francis. In an example of the value of this type of analysis, van Boxtel and Koch (2016) stand behind their original study, which had been the focus of earlier independent replication. Wide availability of the literature and of these studies in a more open scholarly publishing landscape (and making sure to ensure more open data availability) can continue to keep these issues on the front burner and allow other scientists to respond both formally and informally. The incidence and analysis of retractions in the literature seems to have become a more common topic of interest. In the past, it was difficult to keep up to date on retractions in one’s field. It is now possible to follow retractions very closely online. The popular Retraction Watch blog is replete with announcements and analysis of recent retractions in psychology as well as other issues that may affect scholarly publishing in psychology. In recent years, notwithstanding some high profile cases of retractions in psychology, particularly of social psychologist Diederik Stapel, with a reported a spectacular 58 retractions as of 2015, (49 of them between 2013 and 2014), psychology has experienced a large increase in the rate of retractions in recent years. (Oransky, 2015) A new database for retractions, the Retraction Watch Database (including more 79 than 18,000 retractions on its launch date), for the first time makes it possible to discover all of psychology’s retractions at once. (Retraction Watch, 2018) Preregistration of Research Studies in Psychology (Munafò et al., 2017) The new journal, Nature Human Behavior makes the registered report format available to authors and “a prerequisite for publication is that authors agree to share publicly their raw data, as well as their materials and any code (through deposition in a suitable repository or inclusion as supplementary material” and “by offering the registered report format, it is the journal’s intention to support the research community’s efforts for transparency, reproducibility, and open sharing.”("Promoting reproducibility with registered reports," 2017, p.1) The adoption of more open practices coupled with open access to all results of research in the eventual publication process creates an optimal result for the scholarly record. Importantly, APA’s Journal of Personality and Social Psychology includes information on preregistration as part of its extensive Open Science guidelines. (https://www.apa.org/pubs/journals/psp/?tab=4) https://cos.io/rr/#journals. Funders may be able to use RRs as well, especially those funders that want to promote transparency and reproducibility in research. (Munafò et al., 2017) The new journal, Nature Human Behavior makes the registered report format available to authors and “a prerequisite for publication is that authors agree to share publicly their raw data, as well as their materials and any code (through deposition in a suitable repository or inclusion as supplementary material” and “by offering the registered report format, it is the journal’s intention to support the research community’s efforts for transparency, reproducibility, and open sharing.”("Promoting reproducibility with registered reports," 2017, p.1) The adoption of more open practices coupled with open access to all results of research in the eventual publication process creates an optimal result for the scholarly record. Importantly, APA’s Journal of Personality and Social Psychology includes information on preregistration as part of its extensive Open Science guidelines. (https://www.apa.org/pubs/journals/psp/?tab=4) While an increase in preregistration strategies helps, this does not necessarily mitigate the issue of underreporting findings of results in published psychology research. In a study by Franco et al. Traditional Citation Metrics and the Journal Impact Factor in Psychology Traditional metrics, such as Journal Impact Factor (JIF) are heavily ensconced in academia. The JIF, a proprietary metric established years ago, has relevance to psychology and all other science and most social sciences disciplines. Debate rages over the JIF, but it maintains its followers in academia, and every year publishers, universities, editors and authors await the new annual JIF numbers to be reported in the Journal Citation Reports (JCR), a subscription index produced by Clarivate Analytics (formerly Thomson Reuters). There are a few whole countries as well that focus on this metric as a proxy for journal quality. Outside of research assessment exercises that use JIF to rank journals (beginning with the U.K.’s Research Assessment Exercise (RAE) in 1986, for instance), some countries even pay cash incentives to authors that are fortunate enough to author an article that is published in a high impact journal. One author in China has reportedly been paid various sums up to the equivalent of 165,000 USD for an article published in a high impact journal. One study reports that the average price of 43,000 USD is paid to a first author from China that is able to get an article published in Science or Nature. These two titles receive the largest cash rewards in China. Outside of those two high impact titles, payments are made for each eligible article based on its journal’s JIF. Smaller sums are paid in some instances even in the U.S by certain institutions. This type of incentivizing the publication of research results is not widespread and can be problematic. (Abritis, McCook, & Retraction Watch, 2017) In today’s article-level publishing landscape, the JIF has little meaning for evaluating the impact of an individual article or author. One major criticism of the continuing use of the impact factor is that all articles in a high impact journal are obviously not of equal quality, and many stakeholders are eager to move instead to article-level metrics along with metrics that evaluate the work of individual scholars such as h-index. There are also issues with the coverage list that Clarivate Analytics uses and there are constant calls for new journals to be added to citation indexes and the Journal Citation Reports (JCR). Another issue with the JIF is that some fields have much higher impact factors across the titles within the discipline and so impact factor cannot be compared across different fields without normalization. Preregistration of Research Studies in Psychology (2016) in psychology, “the first to provide direct evidence of selective underreporting in psychology experiments”(p.8) which compared the final reported results of research published in corresponding journal articles using preregistrations and publicly available data available from the Time-sharing Experiments for the Social Sciences initiative (http:www.tessexperiments.org), where it was found that “published papers diverge substantially from research protocols, with extensive underreporting of outcome variables and experimental manipulations.” (p.11) The findings of this particular study report that the authors: find that about 40% of studies fail to fully report all experimental conditions and about 70% of studies do not report all outcome variables included in the questionnaire. Reported effect sizes are about twice as large as unreported effect sizes and are about 3 times more likely to be statistically significant. (p. 8) that about 40% of studies fail to fully report all experimental conditions and about % of studies do not report all outcome variables included in the questionnaire. 70% of studies do not report all outcome variables included in the questionnaire. Reported effect sizes are about twice as large as unreported effect sizes and are about 3 times more likely to be statistically significant. (p. 8) 80 Continued discussions around publication bias as well as reliance on authors to take advantage of the many strategies (such as preregistration of studies) to make as many of the products of the research process available in a publicly open and accessible manner will be advantageous in creating a more transparent and credible scholarly communication environment for psychology. Chambers’ 2017 book, Seven Deadly Sins of Psychology: A Manifesto for Reforming the Culture of Scientific Practice details the many issues affecting the research and scholarly publishing situation in psychology, including the issues of registered reports as the author suggests potential reforms. This particular book may be considered a “wake up call” for those thinking that there is little need for change in scholarly communication practices in psychology. Traditional Citation Metrics and the Journal Impact Factor in Psychology Particularly for psychology, increasingly crossing into other disciplines and subfields, impact factors may be misunderstood as reported, with much lower numbers for some areas that cross more into social sciences areas, and highest for multidisciplinary journals like Science and Nature that reach a wide cross section 81 of scientists. Comparisons by number can only really be understood by those in the same niche area of scholarship. An added issue for psychology had been the split in the index between the sciences and social sciences, the two major groupings previously used in the JCR. In the newer iteration of the database, all of psychology is searched in one file. JIF can be accessed for each year, or as a five-year metric. Because it is not business model (whether a title is open access or traditional subscription, for instance) of a particular journal, but instead citation traction that determines impact factor, open access journals can certainly attain top impact factors in many disciplines. In the JCR category, Biology, three fully open access (and fairly new) journals, PLOS Biology, eLife and BMC Biology have been in the top five for overall impact every year since 2013. (Clarivate Analytics, 2016) The situation is different for psychology and its fully open access titles. For psychology (all categories in the 2016 JCR), fully open access journals do not show up until title number 93 (of the top 100), sorted by JIF but there are many open access titles listed in journal coverage for the discipline. Two of the Frontiers journals, Frontiers in Human Neuroscience (JIF 3.209) and Frontiers in Psychology (JIF 2.323) are also the top two open access journals by total numbers of cites (12,836 and 14,320, respectively). Clearly, open access titles are important in the list of impactful psychology journal titles. Of course, many psychological scientists are publishing in the multidisciplinary titles such as those published by PLOS. The coverage criteria for Journal Citation Reports is strict, and inclusion in this selective index is the result of a somewhat lengthy application and vetting process. For good or bad, some say that JCR only includes the “elite” journals of every discipline; many feel that inclusion in JCR has real meaning for a journal title. Others feel that the database should be much more inclusive, including journals from outside the U.S and UK/Europe, for instance. Traditional Citation Metrics and the Journal Impact Factor in Psychology A prominent statement, the 2012 San Francisco Declaration on Research Assessment (DORA) states that “there is a pressing need to improve the ways in which the output of scientific research is evaluated by funding agencies, academic institutions, and other parties.” (American Society for Cell Biology) DORA states the deficiencies in the JIF and the use of journal-level metrics in promotion and tenure decisions and makes recommendations for stakeholder groups in moving away from the JIF as a proxy for research quality. At least one journal has even included DORA on their information for authors. Perspectives in Psychological Science, in the information on its website states that “The Association for Psychological Science is a signatory of DORA, which recommends that journal-based metrics not be used to assess individual scientist contributions, including for hiring, promotion, or funding decisions.” (https://us.sagepub.com/en- Due to frustration over unchanging patterns of evaluation for promotion and tenure that rely heavily on impact measured by the JIF, a variety of statements worldwide have been issued asking for reform of systems of evaluation that are entrenched in academia. A prominent statement, the 2012 San Francisco Declaration on Research Assessment (DORA) states that “there is a pressing need to improve the ways in which the output of scientific research is evaluated by funding agencies, academic institutions, and other parties.” (American Society for Cell Biology) DORA states the deficiencies in the JIF and the use of journal-level metrics in promotion and tenure decisions and makes recommendations for stakeholder groups in moving away from the JIF as a proxy for research quality. At least one journal has even included DORA on their information for authors. Perspectives in Psychological Science, in the information on its website states that “The Association for Psychological Science is a signatory of DORA, which recommends that journal-based metrics not be used to assess individual scientist contributions, including for hiring, promotion, or funding decisions.” (https://us.sagepub.com/en- us/nam/perspectives-on-psychological-science/journal201964) Similarly, the Leiden Manifesto offers a list of 10 principles to guide research evaluation and to combat what its framers see as “impact-factor obsession.” (Hicks & Wouters, 2015) In a major exercise that reviewed the uses of various metrics and indicators for assessing the UK research system produced a report entitled The Metric Tide. One purpose of undertaking this large study was to compare the use of metrics and peer review and to make recommendations for going forward. Traditional Citation Metrics and the Journal Impact Factor in Psychology For strictly open access journals in all categories of Psychology in the JCR 2016 (reported in 2017), out of 747 total journals, 36 are listed as fully open access. Total numbers of psychology journals as well as numbers of open access titles have grown since the last annual JCR. The publisher Frontiers, in analyzing the 2015 JCR listings for its psychology titles states “the results are more significant if one considers (that) Frontiers does not engineer the IF by setting a rejection rate, and instead operates an impact neutral peer-review process. Frontiers in Psychology is only 6 years old and the results represented here are based on articles published between 2013-2014 (its 3rd and 4th year in existence).” (Frontiers Communications, 2015) Frustration with the singular use of JIF for evaluating the evolution of a journal title has incentivized some journals to take a broader view of their status, using other tools available from Google, or from resources like Scopus and Web of Science. In order to understand the impact of the first 10 years of the International Journal of Psychology & Psychological Therapy (IJP&PT), the title was studied in the three resources. This case study of a single psychology journal, published in Spain, using the three major citation databases showed once again that “This analysis has highlighted the disparity of the results that each database offers on the same goal: to know by who, when, and how many times a particular article published in a given journal was cited.” (Roales-Nieto & O'Neill, 2012, p.474) Comparing and contrasting results in 82 these three databases creates some level of confusion with those using the various metrics sourced from these resources to evaluate journals, articles and individual scholars. Due to frustration over unchanging patterns of evaluation for promotion and tenure that rely heavily on impact measured by the JIF, a variety of statements worldwide have been issued asking for reform of systems of evaluation that are entrenched in academia. Traditional Citation Metrics and the Journal Impact Factor in Psychology On top of that, for many authors, open access has been associated with the media reports of the many bogus, fake (or predatory) scholarly journals. JIF is another imprimatur that authors and universities use to measure quality of outputs, even when it is not always the most appropriate metric. Keeping up with a deluge of journal titles (and an exponential growth of articles) as well as a variety of complex business models may be a challenge for busy academics. In terms of open access mandates of various kinds, the issue of academic freedom pops up occasionally, setting out the foundation that a basic tenet of academic work is the ability for a faculty member to choose the journal publication outlet unimpeded by outside factors, such as those imposed by funders around open access status of particular journals. For institutional open access policies that focus on green OA, the availability of the “opt out” for any specific article allays any such concerns. As JIF has been the only journal level metric available for many years, in 2016, Elsevier debuted the new journal metric, CiteScore, available as part of the Scopus “basket of metrics.” Because metrics are available for the more than 22,000 journals available in Scopus, CiteScore will necessarily cover a longer list of journals than what is found in JCR, but time will tell whether CiteScore will pick up traction as a true competitor to the JIF. This metric has become visible on journal homepages and provides an alternative measure of journal-based citation metrics. The metrics for journals listed in Scopus in the psychology category can be searched from the freely available CiteScore metrics page. (Elsevier, 2017) Both Web of Science (Clarivate Analytics) and Scopus (Elsevier) provide an increasing variety of article-level metrics which scientists use to demonstrate citation impact for each of their works. These subscription indexes are likely consulted most often at the time of promotion and tenure actions in order to demonstrate research impact of the works of a particular author. While Google Scholar metrics are also widely used, there may be mixed reviews on the formal reporting of Scholar metrics in promotion and tenure actions due to the lack of transparency of the coverage criteria. Adding a next level (beyond only Web of Science and Scopus) of the various alternative metrics available would complete the information available on the impact of a work. Traditional Citation Metrics and the Journal Impact Factor in Psychology Peer review retains an enviable position in the research system and the report states that “peer review, despite its flaws and limitations, continues to command widespread support across disciplines” and “metrics should support, not supplant, expert judgement.” This report provides clear guidelines for the use of “responsible metrics” in evaluation and assessment, and the need to develop a “basket of metrics” that is appropriate to the discipline and subfield. (Wilsdon, 2015) In addition to large differences in impact factor numbers between disciplines (with the need to normalize across disciplines for comparison purposes), there are also vast difference in what each discipline considers its research outputs. Some disciplines are heavily book-based, others publish research primarily as conference proceedings, still other as working papers. For the Unit of Assessment (UoA) 4, Psychology in the REF2014 (comprising the areas of Psychology, Psychiatry and Neuroscience), the total of 9126 submitted research outputs includes: 10 authored books, 1 edited book, 16 chapters in books, 9086 journal articles, 4 conference contributions, 4 website content items, 1 research report, 1 “other” and 3 working papers. This list of output types demonstrates the similarity of the Psychology grouping to Biological Sciences, for instance, in terms of types of outputs, and how differently certain other disciplines represent their scholarly output. (Wilsdon, 2015) Seeing a chart of the four top disciplinary outputs submitted by each individual researcher who is required to do so by the REF allows a snapshot into what type of research outputs are valued by UK researchers in the various disciplines for submission to the highly important research exercises (REF). Some early career researchers have signed onto DORA and other initiatives. However, the JIF does not show signs of going away, and this is one reason that those that work in areas of 83 OA (such as university OA policymaking) must continue to assure faculty authors that an institutional open access policy in no way changes the fact that authors must publish in the journal of their choice. Choice of journal publication is based on many factors, and certainly one of them would be JIF, reflecting the continued “publish or perish” situation that exists in academia today. When working on passage of open access policies and speaking with faculty across the institution, researchers often conflate an open access requirement for self-archiving of article-type scholarship with a mandate to publish in open access journals. Traditional Citation Metrics and the Journal Impact Factor in Psychology All research metrics have different uses and audiences. Librarians in research institutions may be consulted for information around this complex area. Universities may want to make sure that certain librarians and those in research offices are available to consult with faculty and other researchers who are eager to understand the complex basket of metrics available. With increasing accountability expected for university faculty and reporting systems becoming more popular, appropriate use of article and journal-level metrics make a difference in the success of individuals and universities in this increasingly competitive research environment. 84 The open access status of publications has come into play of late in promotion and tenure actions in some institutions. Certain universities are moving toward requiring open access for all faculty (and in some cases, graduate student) publications, via availability in the institutional repository for all materials being submitted in promotion and tenure actions, or for reasons of compliance with funder mandates. In listing examples of universities that are moving toward openness in this way, Shieber and Suber (2017) explain: When the institution considers faculty for promotion, tenure, awards, funding, or raises, and when it reviews their publications as part of this process, then it should limit its review of their research articles to those on deposit in the institutional repository. Or it should use the institutional repository as the mechanism for submitting articles for use or review by internal committees. An example of this trend may be found at Indiana University-Purdue University Indianapolis (IUPUI) in the U.S., where open practices are finding their way into promotion and tenure guidelines. This factor puts a focus on the importance of providing wide availability of the institution’s scholarship as part of researchers’ priorities. (Odell, Coates, & Palmer, 2016) However, recent research into the content of 850 review, promotion, and tenure (RPT) protocols has shown little mention (5%) of open access in guidelines published by institutions. ("Preliminary Findings from the Review, Promotion, and Tenure Study," 2018) There appears little real incentive for today’s scholars to put a priority on making their work OA, at least in terms of formal university promotion and tenure guidelines. In terms of research impact, there are new tools and services emerging all the time. Concern continues to exist about which metrics to use for measuring research, and also about the issue of “gaming” of citation metrics. Traditional Citation Metrics and the Journal Impact Factor in Psychology “Cited reference searching,” a key part of the demonstration of value of a particular article is still a main strategy for seeing all of today’s current articles today that are citing an article from the past. Many publisher websites now also include “citing articles” information conveniently alongside research articles themselves. Some universities may not choose (or be able to) provide subscription access to both Web of Science and Scopus due to cost and also significant overlap between the two. Certainly, others feel that, at this point, both are necessary for current citation analysis and metrics purposes as well as for their usefulness in comprehensive cross-disciplinary search of the scholarly literature. Keeping an eye on the horizon shows new products emerging as competitors to the Elsevier and Clarivate products, for example Dimensions (from Digital Science, https://www.digital-science.com/products/dimensions/) with its freemium model and expanded coverage. group of subject specialists to vet titles for coverage. At its outset, Scopus promised increased behavioral sciences content, more robust reporting of h-index, and a coverage list that included all of the titles included in Web of Science, as well as many more. As Scopus has developed, it group of subject specialists to vet titles for coverage. At its outset, Scopus promised increased behavioral sciences content, more robust reporting of h-index, and a coverage list that included all of the titles included in Web of Science, as well as many more. As Scopus has developed, it A free and heavily used alternative (for those without subscription products or for those that simply prefer its profiling and ease of use) exists in Google Scholar and its own available citation metrics found in the “Google Scholar Citations” service. In terms of what it covers, Google Scholar pushes the limit for coverage of everything that Google considers “scholarly” and does not publish its coverage index, creating a lack of transparency in some ways for the metrics it reports. For psychology, the products of scholarship included can be more wide- ranging than simply journal articles from high impact titles. Searchers using Google Scholar will find a much broader array of coverage, including high quality traditional and open access journal publications as well as items such as blog entries or magazine articles. Traditional Citation Metrics and the Journal Impact Factor in Psychology (Patton, Stahl, & Wells, 2016) Challenges continue to exist with the use of the widening array of citation tools to quantify impact of research. In terms of citation analysis and metrics, the phenomenon of citation analysis and Journal Impact Factor JIF) calculation began with the print citation indexes produced by the Institute of Scientific Information (ISI) and was the brainchild of the late Eugene Garfield. In the print-based past, where the indexes for citation analysis and Journal Impact Factor were found in massive runs of volumes on shelves, psychology could be a challenge for librarians and researchers. Psychology always straddled the two print citation indexes, (Science Citation Index (SCI) and Social Sciences Citation Index (SSCI)) along with the print Journal Citation Reports (for the Journal Impact Factor). The print JCR (and earlier digital iterations of that resource) always presented a challenge for psychology due to the split between sciences and social sciences, with content likely in both sections. Elsevier’s Scopus debuted in 2004, adding new tools and options for citation analysis to the mix. Web of Science (part of Clarivate’s Web of Knowledge) also brought the discipline’s content together and now includes the psychology content all in one completely integrated electronic index, making searching much easier than in the print days where the split between the disciplinary areas sometimes put different sections of the indexes in different physical libraries on the same or different campus. Web of Science was challenged by the development of Scopus where Elsevier endeavored to create an index that was more inclusive in terms of content, hence to be considered less “elite” in its coverage while still employing a 85 group of subject specialists to vet titles for coverage. At its outset, Scopus promised increased behavioral sciences content, more robust reporting of h-index, and a coverage list that included all of the titles included in Web of Science, as well as many more. As Scopus has developed, it has closed the gap in terms of years covered and metrics provided. Both Scopus and Web of Science offer different metrics and ways of presenting them, and both have criteria for coverage that presents a hurdle for some and an imprimatur of quality for others. Traditional Citation Metrics and the Journal Impact Factor in Psychology Many users appreciate the many features it presents, such as pulling together all versions of a single article in one place (preprints, postprints, versions of record, for example) and the possibility of searching across many subjects at once (rather than searching a single subject’s major index). Also, there is no fee for using Google Scholar on the web, which makes it the major discovery tool for connecting the world’s researchers to available works, even works found in repositories or other open access vehicles on the web. Google Scholar is truly a gateway to finding scholarly open access content. According to Google Scholar, the popular Google Scholar Citations resource: provide(s) a simple way for authors to keep track of citations to their articles. You can check who is citing your publications, graph citations over time, and compute several citation metrics. You can also make your profile public, so that it may appear in Google Scholar results when people search for your name…and your citation metrics are computed and updated automatically as Google Scholar finds new citations to your work on the web. (https://scholar.google.com/intl/en/scholar/citations.html) The competition that exists with the citation indexes has ramped up both the number of metrics with which researchers need to grapple and as well as the number of various uses of 86 these analytics. In recent years, and with continuing development of the three major citation analysis databases, Web of Science (Clarivate), Scopus (Elsevier) and Google Scholar, researchers are presented with a variety of data and associated tools with which to analyze scholarly impact. With Web of Science once the only game in town, Scopus has continued to enhance retrospective literature (pre-1996) and other issues of coverage and at this point, can be used in direct comparisons with data in Web of Science. These databases, often accessed by academics through their university libraries (although many do not subscribe to one or both) are able to provide metrics for individual scholars such as h-index, as well as make available cited reference searching. Both provide search capabilities for users built on a quality-controlled corpus of scholarly publications. Comparisons cannot be made between disciplines using any of these tools in terms of metrics, without normalizing data. Certainly, an h-index of a biomedical researcher would differ greatly from that of a humanist. Traditional Citation Metrics and the Journal Impact Factor in Psychology H-index is most often used for evaluation of particular individuals but sometimes is used in the aggregate (departmental h- index, for instance). H-index values differ greatly depending on the source of the data, a reason that many academics may have a preference for Google Scholar as its h-index values will be higher for any given scholar. There have been calls for more cross-disciplinary comparisons of Web of Science, Scopus and Google Scholar. With an emphasis on metrics growing for individuals, universities and even entire countries, it is imperative that those performing evaluations as well as those being evaluated for promotion and tenure understand the strengths and weaknesses of each of these citation databases. Recent studies are making inroads in using the three major citation analysis databases for comparisons of research performance across a variety of disciplines. (Harzing & Alakangas, 2016) Also, each of these resources has a different value to the various disciplines. The literature of psychology is well covered by these citation databases. While there have been many analyses comparing citations found in Web of Science, Scopus and Google Scholar, Martín-Martín, Orunda-Malea, Thelwall, and Delgado López-Cózar (2018) have provided a detailed systematic investigation of nearly two and a half million citations to a set of highly cited documents from 252 GS subject categories, including psychology. Across the subject categories, Google Scholar "consistently found the largest percentage of citations across all areas," far exceeding that found in Scopus and Web of Science. (p.1160). However, the added citations found by Google Scholar were mainly from non-journal sources, such as dissertations, preprints, conference papers and more. Further, "the results suggest that as far as comprehensiveness in discovery of academic output, in all areas Google Scholar citation data is essentially a superset of Web of Science and Scopus, with substantial extra coverage" (p. 1160) and that "the scientific impact of these unique citations themselves is, on average, much lower than that of citations also found by Web of Science or Scopus, suggesting that the GS coverage advantage is mostly for low impact documents. Taken together, these results suggest caution if using Google Scholar instead of Web of Science or Scopus for citation evaluations." (p.1175) The specific findings from this study for psychology may be accessed at https://osf.10/t3sxh Expertise in citation analysis and comparison of tools is often found in the library community, especially with scholarly communication librarians and library subject specialists. Traditional Citation Metrics and the Journal Impact Factor in Psychology A psychology or behavioral sciences librarian could provide discipline-based expertise to users of 87 these products. While librarians, especially in the sciences and social sciences areas have always had expertise in research metrics, this role may indeed become more primary, presenting a strategic asset to the university and its faculty. The importance of the journal, the traditional vehicle of discovery is still represented by the Journal Impact Factor or Elsevier’s CiteScore, but today, the emphasis of discovery is often on the articles, each with a DOI, standing on their own. The move to an article-level economy where some journals (such as PLOS ONE) publish tens of thousands of articles in each single issue has caused disruption. Particularly, in a situation where journals have become unbound in an article level economy, searchers discover articles across a range of journal titles and peripheral subject areas, often using a search engine such as Google Scholar and “the most important literature is increasingly coming from a greater range of journals, not only the journals with the highest IF.” (Lozano, Larivière, & Gingras, 2012, p.2144) Freely available discovery tools such as those from “1science” promise an “inclusive discovery platform aiming to index articles in all peer-reviewed journals, in all fields of research, in all languages and from all over the world.” (https://www.1science.com/1findr/) The internet availability of research articles has created a type of “democracy” for individual articles, where articles are found, used and cited outside of their traditional container, the journal. Lariviѐre et al. (2014) stated that, even for “elite journals,” the situation exists that “since the late 1980s and early 1990s, several new and some long-established journals have been becoming more important, whereas traditional elite journals, including Science and Nature, are publishing a decreasing proportion of the top-cited papers” (p.653) and it has been demonstrated that “traditional ‘elite’ journals still have the highest citation impact, but other journals are also publishing an increasingly higher proportion of top-cited papers.” (p.655) Whether JIF will lose its relevance in a new world of discovery and a more even playing field remains to be seen. The trajectory toward irrelevance for the JIF may already be happening, even though it is still a major focus of research assessment exercises and a cornerstone metric for evaluation of the journals used by faculty authors and whole departments and universities. Another Popular Metric for Evaluation of Individual Researchers and even Journal Publications: the h-index Measuring journals against each other using impact factor did not satisfy those that wanted a metric to compare productivity of individual researchers. One metric that has developed traction in many fields for evaluation of an individual scientist is the h-index, proposed as “an easily computable index, h, which gives an estimate of the importance, significance, and broad impact of a scientist’s cumulative research contributions.” (Hirsch, 2005, p.16572) The h-index is felt to be a more effective indicator of an individual scientist’s total contribution, and takes into consideration quantity of papers as well as citation activity of those papers. Although developed as a measure of impact for an individual scientist, some have used a subset of h-index to compare journals. Google has used h-index as the basis for two of its popular metrics services. Google Citations, a service where individual researchers set up citation profiles, will display the h-index of an author. Google Metrics also uses a subset of h-index to compare journals. (Antell, Foote, & Foote, 2016) Google Scholar also has developed a metrics resource where h-index is used for publications, and journals can be browsed by subject category. Google Scholar also has developed a metrics resource where h-index is used for publications, and journals can be browsed by subject category. (https://scholar.google.com/intl/en/scholar/metrics.html#overview) In Google’s Scholar Metrics, the category “Psychology” is listed as a subcategory under “Health & Medical Sciences.” Choosing the “h5-index” for any particular journal title displays highly cited papers from the last five calendar years in a publication. It remains to be seen, as time evolves, which metrics for both individuals and the journal publications that they choose will be most important to promotion and tenure committees or for university or funder reporting. For those that can use a variety of innovative metrics approaches (both inside and outside of rigid systems) there are many ways to leverage metrics in an individual’s scholarly publishing behavior. Depending on motivation, some researchers are very engaged with demonstrating impact and using a quantitative approach to show the impact of their work. Others may learn to game systems to their advantage. There are many issues with use of h-index including the importance of the genesis of the data behind the calculation. Traditional Citation Metrics and the Journal Impact Factor in Psychology JIF is still a proprietary metric and a subscription is required to do comparisons of impact factors between psychology journals. Journal websites now often list Journal Impact Factors in order to attract authors to higher impact titles. Within psychology, across the subfields a researcher would have to expect a very wide range of impact factors and promotion and tenure and research assessment exercises would need to take that into account (rather than use any one size fits all approach). With the move to measuring impact of individual articles and authors, and in this age of ramped up focus on citation rates, it is important to consider issues that may affect how frequently psychology researchers cite individual works. One example from Stevens and Duque (2018) is the possibility that APA Style’s requirement for psychology (as compared to the conventions that exist for biology and geosciences) that in-text citations be alphabetized by surname “biases citation rates.” The study, published in Psychonomic Bulletin & Review reports that “we found that surnames earlier in the alphabet were cited more often than those later in the alphabet when journals ordered citations alphabetically compared with chronologically or 88 numerically” and that “we suggest that journals using alphabetically ordered citations switch to chronological ordering to minimize this arbitrary alphabetical citation bias.” (Abstract section) Another Popular Metric for Evaluation of Individual Researchers and even Journal Publications: the h-index Strategic use of h-index by researc psychological science has been discussed, comprehensive look at 22 citation-based in concludes that “the most attractive measur outside the h square, and two variations th 2012 studies examining h-index and psych with top h-index calculations are available (but not necessarily from sources) and have begun appearing on the internet. Bishop has analyzed the use of “departmental h-index” as a funding from the UK Research Assessment Exercise (RAE). Could be a different approach to reporting impact for the next iteration of (the UK Research Excellence Framework which was to assess the q of 154 UK universities) that was proposed at that time? Bishop stu from each of the 76 psychology departments that participated in the from 2000-2007), utilizing an address search of data in the Web of this use of departmental h-index (not for every discipline, however) alternative to the use of the journal impact factor as an indicator of funder research assessment exercise. (Bishop, 2013) One complicat bibliometrics for these large assessment exercises is interdisciplinar reporting of aggregated metrics. For instance, the REF2014 has 36 including a grouping of Psychology, with an expert sub-panel work psychology grouping (UoA 4) includes Psychology, Psychiatry and areas would have different h-index profiles and other differences in bibliometrics for assessment, pointing to the value of employing ex type of evaluation that would assess impact appropriately for any ar periphery of) psychology. Use of the h-index has other benefits in e working in niche areas. Ruscio (2016) has reported on the advantag citations and productivity, stating that: in addition, h is a transparent, reproducible, and objective m This has the potential to reduce many kinds of bias that can decisions. It also affords the opportunity for systematic, qua comparisons. Unlike the more subjective reading of a CV, f select an appropriate reference group and sampling techniqu to help interpret the h-index. (p. 906) Ruscio (2016) was also able to study a grouping of social psycholo robustness of h-index when used as a citation-based metric for eval individual. Strategic use of h-index by researchers, funders and univers psychological science has been discussed, but not extensively. Rusc comprehensive look at 22 citation-based indices which might be us concludes that “the most attractive measures include h several vari with top h-index calculations are available (but not necessarily from credible or transparent sources) and have begun appearing on the internet. Another Popular Metric for Evaluation of Individual Researchers and even Journal Publications: the h-index Bishop has analyzed the use of “departmental h-index” as a predictor of eventual research funding from the UK Research Assessment Exercise (RAE). Could use of departmental h-index be a different approach to reporting impact for the next iteration of the exercise, the REF2014, (the UK Research Excellence Framework which was to assess the quality of the research output of 154 UK universities) that was proposed at that time? Bishop studied the research outputs from each of the 76 psychology departments that participated in the RAE for 2008 (using data from 2000-2007), utilizing an address search of data in the Web of Science, and concluded that this use of departmental h-index (not for every discipline, however) was acceptable as an alternative to the use of the journal impact factor as an indicator of impact for this type of UK funder research assessment exercise. (Bishop, 2013) One complication for psychology in use of bibliometrics for these large assessment exercises is interdisciplinarity and how it affects reporting of aggregated metrics. For instance, the REF2014 has 36 Units of Assessment (UoAs), including a grouping of Psychology, with an expert sub-panel working on each UoA. The psychology grouping (UoA 4) includes Psychology, Psychiatry and Neuroscience. Each of these areas would have different h-index profiles and other differences in terms of strict use of bibliometrics for assessment, pointing to the value of employing expert peer review panels in any type of evaluation that would assess impact appropriately for any area within (or on the periphery of) psychology. Use of the h-index has other benefits in evaluating research groups working in niche areas. Ruscio (2016) has reported on the advantages of h-index for analyzing citations and productivity, stating that: in addition, h is a transparent, reproducible, and objective measure of scholarly impact. This has the potential to reduce many kinds of bias that can influence judgments and decisions. It also affords the opportunity for systematic, quantitative evaluations, or comparisons. Unlike the more subjective reading of a CV, for example, one can explicitly select an appropriate reference group and sampling technique to obtain comparison data to help interpret the h-index. (p. 906) Ruscio (2016) was also able to study a grouping of social psychologists to demonstrate the robustness of h-index when used as a citation-based metric for evaluation purposes of an individual. Another Popular Metric for Evaluation of Individual Researchers and even Journal Publications: the h-index Promotion and tenure (or hiring committees) will want to make sure they understand whether the h-index was based on data from Google Scholar, for instance, which has very broad coverage but there is no transparency in what is indexed, or a curated disciplinary index such as PsycINFO, or the wide-ranging Elsevier index Scopus. Of course, the values for h- index of scholars varies greatly across the disciplines and subfields. In a cross-disciplinary study of Web of Science, Scopus and Google Scholar that includes h-index, Harzing et al. found that “in the Web of Science, the h-index of the average Life Sciences academic is nearly 8 times as high as for the average Humanities academic and nearly 3 times as high as for the average Social Scientist.” (Harzing & Alakangas, 2016, p. 797) Those using h-index should only compare within a disciplinary niche and make sure that individuals do not consider their h-index as the only measure of their impact. Like “top lists” of everything else, lists of psychology researchers 89 with top h-index calculations are available sources) and have begun appearing on the Bishop has analyzed the use of “de funding from the UK Research Assessmen be a different approach to reporting impac (the UK Research Excellence Framework of 154 UK universities) that was proposed from each of the 76 psychology departmen from 2000-2007), utilizing an address sear this use of departmental h-index (not for e alternative to the use of the journal impact funder research assessment exercise. (Bish bibliometrics for these large assessment ex reporting of aggregated metrics. For instan including a grouping of Psychology, with psychology grouping (UoA 4) includes Ps areas would have different h-index profile bibliometrics for assessment, pointing to t type of evaluation that would assess impac periphery of) psychology. Use of the h-ind working in niche areas. Ruscio (2016) has citations and productivity, stating that: in addition, h is a transparent, repro This has the potential to reduce ma decisions. It also affords the oppor comparisons. Unlike the more subj select an appropriate reference gro to help interpret the h-index. (p. 90 Ruscio (2016) was also able to study a gro robustness of h-index when used as a citat individual. Another Popular Metric for Evaluation of Individual Researchers and even Journal Publications: the h-index Strategic use of h-index by researchers, funders and university departments in areas of psychological science has been discussed, but not extensively. Ruscio et al. (2012) provides a comprehensive look at 22 citation-based indices which might be useful to psychology and concludes that “the most attractive measures include h, several variations that credit citations outside the h square, and two variations that control for career stage.” (p. 123) In two separate 2012 studies examining h-index and psychology faculty in U.S institutions, Ruscio & Prajapati (2013) present comparison studies of h-index calculations resulting from the use of citations gathered from both PsycINFO and Web of Science, and also offer a method of how one might compare an institution’s psychological sciences faculty with peers in other disciplines. In the first study of h-index results (of 204 randomly selected psychology professors from 185 U.S. 90 psychology doctoral programs) between the two indexes, it was demonstrated that similar results in terms of comparable scores could be obtained from both PsycINFO and Web of Science. In another larger study of 1750 university-affiliated U.S. psychology faculty, it was shown how one might examine norms on h-index for psychological scientists by rank (assistant, associate, full professor). Ruscio & Prajapati (2013) recommend the use of PsycINFO and Web of Science (and not Google Scholar) due to the comparatively more robust and vetted data behind these major indexes. It is likely that many agree that, at this time, while Google Scholar is convenient, the coverage and messiness around its coverage, the lack of a public API that would allow more robust analysis, and the lack of refinement of its tools does not allow replication with other data sources or trusted results in comparison studies in the case of psychology. The word “impact” has taken on various meanings when it comes to scholarly communication in any given discipline. While impact has taken on more and more of a quantitative meaning in recent years, with long lists of available metrics, and a few taking center stage (journal impact factor and h-index, for instance), it is interesting to consider which scientists have made the most impact to psychology. The impact of a person is never easy to quantify, but there are some whose reputations and work stand the test of time, with a few whose fellow scientists consider the most impactful. Another Popular Metric for Evaluation of Individual Researchers and even Journal Publications: the h-index Sternberg (2003) edited a book that serves as a reminder that there is much more to impact than sheer numbers. The Anatomy of Impact: What Makes the Great Works of Psychology Great is a work that brings together a number of experts in the philosophy and history of psychology (as well as other distinguished psychologists), each of whom contribute a chapter on a single scholarly work by a preeminent author. Each chose a work of “monumental impact” and analyzed why “the work was so successful in terms of influencing the field. (p. ix) Further, it is stated that “the ultimate goal of any publication in psychology (or anything else) is to have an impact-to make a difference to a field.” (p. ix) This book succeeds in defining impact differently than it is often discussed today through the use of examples of seminal works in psychology and what they have come to mean to the field over time. Scholarly Collaboration Networks: Featuring ResearchGate and Academia.ed The internet has also fueled the creation of the scholars’ networks that allow collaboration between researchers and combine a social networking function with availability of papers. Millions have signed on to services like ResearchGate (RG), Academia.edu and others. These services may be known as “scholarly collaboration networks” or other names like “academic or scholarly social networks.” More research is needed to ascertain how authors and researchers use these services, how they figure into the calculus of search, and whether there is a decided benefit to uploading work to these sites. These sites allow social collaboration along with access to articles, including the many publisher-branded versions that are uploaded without concern for publisher copyright. Millions of articles can be found in these multidisciplinary services, and publishers also need to understand the ramifications of the popularity of ResearchGate and Academia.edu and other similar sites. Usage statistics of works in these services are of interest to both publishers and authors. A focus on the collaboration aspects of these services (such as Q&A features, which are little used) may miss the point that the main 91 attraction may be the ability of researchers to not only connect with others, but more importantly, to upload and disseminate articles (many in proprietary publisher “version of record” format) and watch the subsequent citation and social media activity that results. A compelling aspect of these two sites is the ability to market and promote one’s work via upload to ResearchGate or Academia.edu. This “sharing of full text papers” aspect has been considered a major contributor to the success of these sites. Authors are contributing their own content, not just following others’ work. Sites like Academia.edu have some highly productive “producers” in comparison to mere “viewers” of content. (Ortega, 2016) A continuing issue is that authors continue to upload many proprietary publisher article versions, often violating the terms of the copyright agreements that they signed at the time of article submission. Major funders are now supporting these sites even though these services continue to fill with proprietary content. Academia.edu, even one with a name that evokes “academia” is in fact backed by venture capitalists mainly interested in data mining. The enormity of the Academia.edu and ResearchGate communities allows for scale of collaboration, something otherwise not easily found in academia, or via the large network of subject or institutional repositories. Scholarly Collaboration Networks: Featuring ResearchGate and Academia.ed Also, the scholarly collaboration networks often provide for researchers an invaluable collaboration platform where they may not only share papers, but ask research questions to the large audience, and receive answers that can spur new research directions or provide clarity on topics that are better discussed within a more scholarly online community. Some have likened these services to a “Facebook for academics.” (Carrigan, 2016). Others see a whole new centralized online system incorporating all of the new elements of scientific communication that the web allows, pulling everything together into something akin to a “Facebook for science.” (Buttliere, 2014) With every new system proposed, there has to be a very compelling reason for researchers to spend any time in deviating from their established disciplinary scholarly publishing practices. ResearchGate has made great inroads into the scholarly community and is not owned by any commercial entity at this point. For many, that fact makes a difference, and at this point, ResearchGate is an established and desirable service for many academics. In the case of Academia.edu, due to its name, it is possible that many of its users confuse it with an actual service based in academia. Quite the contrary, Academia.edu was founded by Richard Price in 2008, and by August, 2014, it had raised 17.7 million USD from venture capitalists and had claimed 11 million users at that time who had uploaded 3 million papers. (Van Noorden, 2014b) Academia.edu has attractive value-added services such as the practice of sending an email to an author with information about the keywords someone searched while discovering his or her papers, the search engine used, and the geographic area of the search. For some researchers this is very valuable information, for other busy authors, it may be construed as spam. In fact, one of the complaints that users have about these platforms is the constant email bombardment that ensues on registration. Some academics have warned colleagues that there are better solutions for posting academic work online, and asked others to delete their Academia.edu accounts. There was a backlash in 2016 after Academia.edu suggested that users might want to pay for a “recommender” service in which Academia.edu would “boost” certain papers on the site. Scholarly Collaboration Networks: Featuring ResearchGate and Academia.ed (Bond, 2017) Some enticing services that had once been free are no longer without cost and it is common now when hearing from Academia.edu with an enticing offer to find out 92 information about traffic to articles available there to be asked to pay for this and other services via their “Academia Premium” service (which started in December, 2016). Since Academia.edu was founded by a philosophy professor at Oxford University with the goal of connecting authors to readers, it isn’t surprising that one recent study focused on the site’s use by philosophy researchers. Academia.edu is used heavily by social sciences and humanities scholars, but at least in this study in 2013, psychology was the 5th highest (out of 39 subject areas) listed “broad research interest” of users. (Thelwall & Kousha, 2014) ResearchGate is used by many scientists and studies demonstrate that it is well known (more than 88% if scientists and engineers in a recent study were aware of it, placing the site just behind Google Scholar. Along with Academia.edu as a commercial enterprise, ResearchGate (as of June, 2014) had secured 35 million USD from investors and claimed 14 million available papers. (Van Noorden, 2014b) By the fall of 2017, ResearchGate had reached 85 million dollars of venture capital (and other investor) funding. It is the most popular scholarly collaboration network and also boasts more traffic than even some of the largest publisher platforms. (Harrington, 2017) The site “launched in 2008 with the stated aim of helping researchers to communicate, cooperate, and share information” and as of August, 2015 had a robust 7 million users. By April, 2017, the ResearchGate website boasted more than 12 million members. The site has a social networking side alongside its use as a platform from which to disseminate scholarly research articles from an author’s profile (which is a more popular use of ResearchGate). Although there are few studies of how psychology and neuroscience researchers use ResearchGate, it is clear that there is robust usage across these disciplinary areas. (Thelwall & Kousha, 2017). It would be useful to analyze, with a large scale study, how ResearchGate and other similar services are being used specifically by psychological science researchers. Where ResearchGate allows collaboration and has its Q&A service for engaging researchers, different disciplines would be expected to respond differently. Scholarly Collaboration Networks: Featuring ResearchGate and Academia.ed Publishers and vendors of psychology research literature would want to understand how ResearchGate and other services are engaging their authors, and how published papers or accepted manuscripts are being uploaded to these sites. For any discipline, it is interesting (and a value add) that DOIs are now provided by ResearchGate for any item, such as an author’s original contribution (such as a preprint), that does not already have one associated with it. (Nicholas, Clark, & Herman, 2016). ResearchGate is used by many scientists and studies demonstrate that it is well known (more than 88% if scientists and engineers in a recent study were aware of it, placing the site just behind Google Scholar. Along with Academia.edu as a commercial enterprise, ResearchGate (as of June, 2014) had secured 35 million USD from investors and claimed 14 million available papers. (Van Noorden, 2014b) By the fall of 2017, ResearchGate had reached 85 million dollars of venture capital (and other investor) funding. It is the most popular scholarly collaboration network and also boasts more traffic than even some of the largest publisher platforms. ResearchGate offers reputational metrics, 10 of which have been studied by researchers (beyond the oft-studied and well known “ResearchGate Score,” undoubtedly the most well- known of the available metrics that purport to measure a researcher’s reputation). There is a lack of information (and some say transparency) about the formulas used to calculate the various scores. (Nicholas et al., 2016) One aspect of ResearchGate that is either compelling or off- putting is the regular emails that are sent to users to enhance engagement with the site. ResearchGate offers reputational metrics, 10 of which have been studied by researchers (beyond the oft-studied and well known “ResearchGate Score,” undoubtedly the most well- known of the available metrics that purport to measure a researcher’s reputation). There is a lack of information (and some say transparency) about the formulas used to calculate the various scores. (Nicholas et al., 2016) One aspect of ResearchGate that is either compelling or off- putting is the regular emails that are sent to users to enhance engagement with the site. ResearchGate is not “out of sight, out of mind.” As for the reputational metrics and services, each discipline and university would likely view these differently. Each service a researcher joins represents a certain time sink, the most valuable commodity for most researchers. Scholarly Collaboration Networks: Featuring ResearchGate and Academia.ed After funder and institutional policy, it remains to be seen how much more time can be invested by busy authors and researchers in these dissemination, networking and reputation management sites. ResearchGate is not “out of sight, out of mind.” As for the reputational metrics and services, each discipline and university would likely view these differently. Each service a researcher joins represents a certain time sink, the most valuable commodity for most researchers. After funder and institutional policy, it remains to be seen how much more time can be invested by busy authors and researchers in these dissemination, networking and reputation management sites. 93 ResearchGate has high usage and the wide uptake across disciplines and countries may speak volumes about interest in reputational management. Another issue for these platforms is the sharing of scholarship within them, often running afoul of publisher rules. Publishers have had to grapple with the amount of sharing that goes on within these tools, and they have moved to try to regulate this somewhat by setting out rules about which versions of articles are allowed to be shared. In fact, in 2015, the International Association of STM Publishers created some general guidelines for the ResearchGate user community and has sought buy-in to these guidelines from various stakeholder groups, including libraries. (Dylla, 2016) In one case, Elsevier sent 2800 takedown notices to researchers who had publicly posted publisher versions of their articles in Academia.edu. (Reller, 2013). With the large numbers of scholars using these services, this is a trend that is not going away. In a recent study regarding copyright compliance issues with ResearchGate, it was demonstrated just how often authors upload publisher-branded PDF versions of record, even when publishers allow other earlier versions to be uploaded legally. Authors infringe copyright often in using the “wrong version” of articles on the service. This may be due to authors’ not understanding versioning issues, or it may be due to complexity and diversity of publisher policies. With ResearchGate, authors are responsible for the copyright clearance, which differs from the situation with some other less popular services, such as institutional repositories. (Jamali, 2017) Another explanation for the popularity of posting publisher PDFs in ResearchGate would be, as most would agree, that the publisher version is the one that authors want to share most often, and they do. Scholarly Collaboration Networks: Featuring ResearchGate and Academia.ed With major funders now backing ResearchGate, there is a bit of a mixed message for authors in terms of what can and should be shared. Readers also want to search for and find the publisher version. ResearchGate’s popularity speaks to the desires of researchers for broad dissemination of their work on a popular online open scholarly platform and this sharing anywhere possible will certainly continue unabated. Sharing is facilitated by the discovery of ResearchGate papers and is fueled by the use of Google Scholar for search (where ResearchGate can be indicated on papers). Previous studies have shown the importance of a rapidly growing ResearchGate corpus of papers for readers and researchers seeking accessible full-text of articles via online search. (Jamali, 2017) ResearchGate papers are identified as such in Google Scholar searches and readers know the chance is good that publisher full text is likely to be available from the site. ResearchGate, with its enormous popularity and healthy funding support, experienced some issues in 2017. It remains to be seen how the service will respond to these challenges going forward. In what may be a boon for the institutional repository (which often checks publisher permissions), ResearchGate has had a series of communications from the international publishing community which has asked it to remove proprietary material. When asking did not produce action, lawsuits went out against ResearchGate. Publishers (initially Elsevier, American Chemical Society, Wolters Kluwer, Wiley and Brill), for their part, have formed a “Coalition of Responsible Sharing” to try to promote a culture of sharing of articles legally in ResearchGate. The International Association of Scientific, Technical and Medical Publishers (STM) has repeatedly (over a period of two years) tried to work with ResearchGate on the “legal sharing” of articles and issues of collaboration with publishers and has met with rejection. Following this 94 rejection, takedown notices were imminent, and a lawsuit from Elsevier and also the American Chemical Society (ACS) was filed in Germany. (Hinchliffe, 2017) Another lawsuit was filed in the U.S. (District of Maryland) in October, 2018 by Elsevier and ACS regarding massive copyright infringement of proprietary versions of papers. (https://www.infodocket.com/wp- content/uploads/2018/10/acs_elsevier_rgate.pdf) It remains to be seen how the participating faculty and others react to these continuing issues. ResearchGate goes on with business as usual for now. Scholarly Collaboration Networks: Featuring ResearchGate and Academia.ed Authors accustomed to uploading publisher-branded PDFs in ResearchGate, and counting on ResearchGate to make the papers more discoverable while facilitating the sharing of those articles will now need to grapple with what the lawsuits and takedown threats mean. For all the authors of psychology articles, it may seem that ResearchGate may not be sustainable in the same way as it was before, in the way that it has facilitated a robust sharing and collaboration of scholars and their works across the globe. Who will win this tug of war over the sharing of scholarly information? Researchers and the reading public want seamless online access to peer reviewed (and other) literature and they will use whatever service can facilitate discovery and access, and ResearchGate is certainly one enormously popular way to access the scholarly literature. A common scenario in scholarly search increasingly seems to be starting with Google Scholar and ending up with the paper in a library, or in ResearchGate, and if some are not successful with the library or ResearchGate, it’s possible that a pirate site like Sci-Hub may be the next stop for some. All of this is a dilemma for libraries and publishers as well, both of whom want the reader to have access to essential scholarly information. Sharing Works Outside the “Formal” Scholarly Communication System, including the Sci- Hub Phenomenon Sharing Works Outside the “Formal” Scholarly Communication System, including the Sci- Hub Phenomenon This fact was surprising to some, that “everyone” is downloading articles from Sci-Hub even if they have access via other channels such as through research libraries. (John Bohannon, 2016b) Also somewhat surprisingly, Elbakyan has made available an immense data set of 28 million download requests from the server logs of Sci-Hub representing the time period Sept. 1, 2015 to Feb. 29, 2016. Using publisher DOIs prefixes with this dataset allows one to see the content of many publishers of psychological science that are included in Sci-Hub, including major players as well as smaller presses. (John Bohannon, 2016a) Sci-Hub may be considered a pirate site, but a study by Himmelstein et al. (2018) reveals a situation that is truly a game changer for scholarly communication in all fields. As of March, 2017, Sci-Hub was providing a huge number of readers and researchers with another mechanism of accessing all of the world’s scholarly papers (mainly articles, but some other content as well) that are currently behind paywalls and restricted to subscribers by their publishers. Not as concerned with providing a complete repository of all scholarship (including open access), Sci-Hub has as its focus making available all recent papers that are behind paywalls. The service is monetized through donations, especially via Bitcoin. Sci-Hub makes available 85.1% of all articles currently available only from toll access journals. Its coverage of Elsevier articles was reported at 96.9%, and more than 90% for the American Chemical Society, Wiley-Blackwell, and Taylor & Francis (all part of a group of eight publishers that have more than a million articles represented). Sci-Hub’s coverage of articles in the Psychology category (using Scopus data) was determined to be 1.3 million out of 1.6 million (or 82.9%). Clearly, Sci-Hub is making available most of the peer-reviewed paywalled psychology literature. As a benchmark, the authors compared the University of Pennsylvania’s subscription library holdings against the content available from Sci-Hub, and even though Penn had paid 13.13 million dollars USD on its electronic resources, it was determined that “Sci-Hub provided greater access to paywalled articles than a leading research university spending millions of US dollars per year on subscriptions.” (Himmelstein et al., 2018, p. Sharing Works Outside the “Formal” Scholarly Communication System, including the Sci- Hub Phenomenon 1, 2015 to Feb. 29, 2016. Using publisher DOIs prefixes with this dataset allows one to see the content of many publishers of psychological science that are included in Sci-Hub, including major players as well as smaller presses. (John Bohannon, 2016a) Sci-Hub may be considered a pirate site, but a study by Himmelstein et al. (2018) reveals a situation that is truly a game changer for scholarly communication in all fields. As of March, 2017, Sci-Hub was providing a huge number of readers and researchers with another mechanism of accessing all of the world’s scholarly papers (mainly articles, but some other content as well) that are currently behind paywalls and restricted to subscribers by their publishers. Not as concerned with providing a complete repository of all scholarship (including open access), Sci-Hub has as its focus making available all recent papers that are behind paywalls. The service is monetized through donations, especially via Bitcoin. Sci-Hub makes available 85.1% of all articles currently available only from toll access journals. Its coverage of Elsevier articles was reported at 96.9%, and more than 90% for the American Chemical Society, Wiley-Blackwell, and Taylor & Francis (all part of a group of eight publishers that have more than a million articles represented). Sci-Hub’s coverage of articles in the Psychology category (using Scopus data) was determined to be 1.3 million out of 1.6 million (or 82.9%). Clearly, Sci-Hub is making available most of the peer-reviewed paywalled psychology literature. As a benchmark, the authors compared the University of Pennsylvania’s subscription library holdings against the content available from Sci-Hub, and even though Penn had paid 13.13 million dollars USD on its electronic resources, it was determined that “Sci-Hub provided greater access to paywalled articles than a leading research university spending millions of US dollars per year on subscriptions.” (Himmelstein et al., 2018, p. 10) publishers must be stopped. Larger issues involve the library and legal issues with how the content is obtained, which is often via use of user credentials outside of normal channels. Still, where researchers need access, it has been surprising to some the extent of the access that happens outside normal channels, and especially the fact that many who access are actually at affiliated institutions that have subscriptions, via their libraries, that allow legal access to that content. Sharing Works Outside the “Formal” Scholarly Communication System, including the Sci- Hub Phenomenon Much psychology literature is available to potential readers via popular crowdsourced sharing platforms and practices. There seems no stopping (by publishers) the sharing of PDF copies of scholarly articles online by communities of researchers on a global scale. Widespread sharing of research papers takes place on social media platforms and recently there have been studies of this activity on sites like Facebook, Reddit Scholar (a subforum of Reddit), and by use of the popular Twitter hashtag #icanhazpdf. This peer to peer sharing goes above and beyond the very popular informal sharing that goes on via email, for instance. Peer to peer sharing centers around a few high volume websites that host the files, namely Avaxhome, LibGen (The Library Genesis Project) and Sci-Hub. Will readers and researchers use traditionally available channels such as interlibrary loan or will they choose convenience and just go to a crowdsourced site and get an article that’s likely been obtained illegally? (Gardner & Gardner, 2017) Often in the news, Sci-Hub, and its founder, neuroscientist Alexandra Elbakyan have created a site where much of the content of commercial and other publishers has been made available illegally since 2011 to searchers and readers worldwide. Lawsuits by Elsevier and the American Chemical Society have not been able to prevent the continued growth of Sci-Hub and its partner site, LibGen. Controversy erupts whenever discussion of the use of these methods of gaining research paper access comes up, with some feeling that papers are meant to be read and shared in the open, and others acknowledging that the illegal nature of the sharing of the property of 95 publishers must be stopped. Larger issues involve the library and legal issues with how the content is obtained, which is often via use of user credentials outside of normal channels. Still, where researchers need access, it has been surprising to some the extent of the access that happens outside normal channels, and especially the fact that many who access are actually at affiliated institutions that have subscriptions, via their libraries, that allow legal access to that content. This fact was surprising to some, that “everyone” is downloading articles from Sci-Hub even if they have access via other channels such as through research libraries. (John Bohannon, 2016b) Also somewhat surprisingly, Elbakyan has made available an immense data set of 28 million download requests from the server logs of Sci-Hub representing the time period Sept. ublic and Social Media Engagement for the Results of Research in Psychology New audiences outside the expected niches are interested in reading scholarly articles, and this includes many interested members of the public, policy makers and of course in psychology, practitioners. There have been calls for scientists to engage more with the public, and reporting of research results via the news media would be one way that funded research results could be disseminated further to taxpayers and other readers of the popular press. (Begg, 2016; Carrigan, 2016) There have been many calls for the need to translate psychological science research results, whether in journals, books or other formats to materials that can be used by the wider public. With the capacity to address many societal and medical issues, strategies for translating research results to content that is more useful to the reading public have been put forth. With the added vehicles of open access and the wide reach of the internet and mobile devices, the public has never had so much ability to take advantage of the availability of educational content. (Kaslow, 2015) For psychological science, the advantages of this added accessibility have the potential to educate many readers, to spur innovation and to further research into areas important to the health and well-being of citizens. (Kaslow, 2015) For psychological science, the advantages of this added accessibility have the potential to educate many readers, to spur innovation and to further research into areas important to the health and well-being of citizens. Research impact via open access can also happen using publicly accessible vehicles such as Wikipedia. Citations to open access research articles are an integral part of Wikipedia articles and inclusion of links to those freely available articles in Wikipedia references creates major diffusion of research information to readers worldwide. As of 2016, there were 5 million articles in English Wikipedia (and 35 million in the other hundreds of languages). Wikipedia is a first stop for millions of searchers and has become the top choice for those seeking medical information online, for instance. (Lammey, 2016) It is likely that this is the case for psychology as well and as a very heavily used open encyclopedia, Wikipedia serves as a gateway for the dissemination of scholarly information about psychological science. Sharing Works Outside the “Formal” Scholarly Communication System, including the Sci- Hub Phenomenon 10) With institutions and their libraries spending millions of dollars on access to journal subscriptions from publishers, this issue is one that will continue to be of major interest to libraries and publishers, especially as they aim to combat continuing infringement activities of sites like Sci-Hub. (Russell & Sanchez, 2016) Facilitating more availability of open access content will be one strategy that can mitigate some of the lengths that researchers need to go to in order to access articles. The research community of psychological science has everything to gain by making sure the products of research are available to every individual that needs or wants access. It is not only access that researchers want, but seamless, convenient, one-click access, which is just the type that Sci-Hub offers and publishers and many academic libraries do not. Sci-Hub appears to be an appealing “one stop shop” for convenient access to content for those that can’t get access to scholarly publications, as well as those that could use other methods. It is currently unclear how libraries and publishers will (or won’t) prevail against Sci-Hub. 96 ublic and Social Media Engagement for the Results of Research in Psychology With a lot of public reader traffic going to Wikipedia, there have been repeated calls for all academic authors (and publishers) to contribute content and to add open access links to all articles in the popular online encyclopedia. Many articles in reference lists are paywalled, creating roadblocks for information seekers. One way that the results of scientific research could be surfaced to the public would also be through inclusion of direct links to open access versions of peer reviewed articles in reference lists at the end of Wikipedia articles. Links to open content facilitates access for readers but also serves to increase visibility and resulting research impact for authors: Controlling for field and impact factor, the odds that an open access journal is referenced on the English Wikipedia are 47% higher compared to paywall journals. These findings provide evidence (is) that a major consequence of open access policies is to significantly amplify the diffusion of science, through an intermediary like Wikipedia, to a broad audience. (Teplitskiy, Lu, & Duede, 2016, p.1) Adding to the possibilities that the internet provides for enhancing citation effect via open access are the very positive uses of social media for publicizing scholarly work. (Carrigan, 2016) Many scholars may see some of the more popular social media platforms as lacking in scholarly 97 credibility, but after researchers became aware of the potential of services like Twitter to rapidly send out research results (for instance, by depositors tweeting out from the preprint server arXiv), they may not want to miss such valuable visibility. In some cases, this rapid online communication has greatly increased the wide dissemination of very current research, especially in the case of the timely articles and other outputs available from preprint servers. It has become clear that in order for the widest dissemination of research results, services like Twitter and Facebook, extremely popular among academics, are part of a mix for marketing early articles that also includes more scholarly channels. In fact, it seems many agree that “Twitter isn’t the only social media platform around, but it’s worth noting that it is a favored channel for a wide- spectrum of those working with scholarly output.” (Michael, 2016b) Scholars now have many means to self-promote and use of social media is becoming commonplace. ublic and Social Media Engagement for the Results of Research in Psychology Brief guides on getting started using Twitter in university research settings are available, and the use of these services does not require a high learning curve or much time spent in composing brief tweets in order to share current articles. (Mollett, Moran, & Dunleavy, 2011) Longer treatments, including entire books have been written on how researchers can use the power of many social media services to market and promote their work, receiving valuable feedback along the way. (Carrigan, 2016) ; (Mollett, Brumley, Gilson, & Williams, 2017) The advent and uptake of social media has been a boon to the wide sharing of research. Open access strategies facilitate this dissemination. Alongside reporting of traditional impact via established metrics, researchers are interested in the “attention” that sharing work widely can bring to published work. Studies of sharing via Twitter, Facebook and Mendeley show at least more attention to openly published articles than those that are published in a closed access manner. (Wang, Fang, & Guo, 2016) Savvy researchers promote and market their scholarly work for greater impact using proven strategies that work with various social media. (Mollett et al., 2017) In a sense, there are methods that any author can use to market a publication, drawing attention to it. These methods are not time-consuming, but can create visibility and added sharing with other scholars and with the public. Enhanced visibility may lead to invitations to present the work at a conference, may attract media attention, or could drive many more individual readers to the article, whether the article is shared as an early version online (preprint) or whether the final published version is shared in more conventional ways. Psychological scientists Weinstein and Sumeracki (2017) provide an example of the many invitations to speak (and other opportunities received) as a result of engaging on Twitter and publishing a blog. Of course, for the busy academic (especially those on the tenure track) the perennial question is one of time spent on one activity (or one platform) at the expense of more traditional scholarly activities that may be required for promotion and tenure. Strategies for author marketing of publications are very useful as a complement to the efforts of publishers. Using green or gold open access strategies have a proven track record as far as increasing research impact. Authors of scholarly monographs may also need to focus on marketing to lay audiences. ublic and Social Media Engagement for the Results of Research in Psychology Snijder (2016) concludes that studies of monographs’ increasing usage when made freely available may also be tied to increased activity on social media, particularly Twitter: 98 The results identified very little overlap between Twitter usage and citation behaviour; it seems reasonable to hypothesise that the factors affecting citations of books do not play a significant role in tweets about books. Therefore, the probable reason that open access is a significant influence on book citations does not necessarily apply to Twitter mentions. Nonetheless, it is possible to conclude that making books freely available has some positive impact on the number of tweets. Lowering the access barrier does indeed lead to more attention, in line with the effects for discoverability and online consultation found in the 2009 experiment. (p. 1871) In terms of the most popular referrers to scholarly articles, Twitter and Facebook, there is some evidence (from one study) that attention in the form of social media referrals toward scholarly articles accumulates quickly in the first week after publication, and then dissipates. This does show that Twitter and Facebook visitors to scholarly articles do result in actual clicks on those publications. (Wang et al., 2016) Wider impact of these practices is not clear at this time. Researchers are analyzing whether the wide dissemination through tweets (by authors or others) and the enhanced visibility that Twitter makes possible does actually affect citation impact, as measured by various new (alternative) metrics. More metrics are required for assessing impact of social media participation. Outside of traditional citation metrics, alternative metrics, or “altmetrics” have taken on more prominence, at least informally, with many publishers (as well as repositories and preprint servers) adding altmetrics indicators to individual articles. Altmetrics are thought to provide a much more well- rounded picture of the impact of an article, allowing for information to be presented about how readers use and engage with articles, books and other products of scholarship. Services like Plum Analytics aggregate resulting metrics from social media through measures of attention that are demonstrated as “clicks,” downloads, “likes,” “shares,” “captures to citation management services,” and more. This information allows an author to create a narrative of alternative types of impact that may tell a more complete story of a particular work’s meaning to the discipline as well as to the community and reading public. ublic and Social Media Engagement for the Results of Research in Psychology Publishers are now also using many new products and strategies to both market articles for visibility as well as provide new visualizations of impact using altmetrics. Utilizing new services for assisting authors in marketing their work online in order to reach more readers and potentially increasing impact, for example, Kudos (https://www.growkudos.com/). Kudos reaches out to authors proactively with information about an article’s traction and traffic. On its site, Kudos states in its information targeting authors: Wherever you publish or share your work, use Kudos to help achieve 23% higher growth in full-text downloads: Open up your research so new audiences can find and understand it. Track the most effective networks for getting your work read, discussed and cited. Learn where to focus your efforts to make best use of your time. Improve the metrics by which you are evaluated. In its information for publishers, Kudos states: Increase publication performance and strengthen author relationships. Authors are increasingly sharing their work, often within private networks. Publication usage is being fragmented, putting subscriptions at risk, and publishers are being cut out of the picture in terms of 99 understanding and building on new modes of scholarly communication. Kudos provides tools and intelligence to help you connect with authors after publication, collaborate with them to maximize publication usage and impact, and reclaim lost usage. It is also becoming commonplace to see visualizations of alternative metrics (altmetrics) data on articles, preprints, and entire journals. Where traditional metrics such as article citation counts or journal impact factor are not appropriate or are unavailable, the ability for authors to see the use of their research around the world has become a desirable aspect of publishing one’s work and then depositing it in repositories that offer altmetrics services. Adding altmetrics reporting to publisher services has added value to what publishers offer to their authors and readers. Publishers focus on author services in order to establish better relationships, increase the possibility of more submissions, likely enhancing brand loyalty among the pool of potential authors. With the development of altmetrics, scholars as well as promotion and tenure committees have seen new ways of demonstrating impact. A narrative about an article’s impact can be drawn by looking at the aggregated measures of attention that an individual work is attracting. Author Submission of Work to Psychology Journals and the “In Person” Conference Decision-making by authors as to choice of publication outlet of course is key. For early career scholars, learning the traditions of the corpus of literature in the field is key and advice is needed from mentors and advisors, some of whom may not be aware of new methods of marketing work or using open science strategies. It is paramount for psychological science to ensure that researchers are empowered to use all available open science strategies to make the literature more visible to other scholars and the public. Engagement with publishers on open access and other associated issues may be more effective if done by established scholars. Senior scholars with a solid knowledge of new publishing paradigms and new ways of looking at author impact are essential to upending a model that may be somehow stuck in the past. With traditional forces at play in promotion and tenure decisions (like impact factor), there may be little room for early career researchers to create change. Regarding the situation in the U.S., one study of early career researchers (ECRs) shows that: while not all ECRs knew about the scholarly communication practices of their mentors, advisors and supervisors, their assumption is that the practices of their senior counterparts are much the same as their own, except, possibly, in regard to social media and sharing. (PRC- CIBER, 2016, p.27) Today, there are many options available for early sharing of drafts of articles, even before (or alongside) first submission to a scholarly journal. It is possible to consider a range of sharing of ideas through a continuum that might include sharing tweets from a conference, sharing ideas in an online forum, participating in blog posting or commenting, presentation of initial results at a conference (in person or virtually), posting a preprint online and getting important feedback from interested scholars across the world, and finally, if appropriate, submitting to a peer reviewed journal in the field. The creation of new knowledge can form a continuum from early idea on social media to published journal article. (Daniels, 2015) The open environment of the internet breaks down barriers and allows discussion by interested people that crosses disciplinary boundaries and invites a wide conversation. Invitations to present at conferences and to submit articles can be the result of this “self-promotion” on social/digital media platforms. ublic and Social Media Engagement for the Results of Research in Psychology In 2010, members of the Association of College and Research Libraries Psychology/Psychiatry Committee combined information from the major tools, Ulrich’s 100 Periodicals Directory, Elsevier’s Scopus, and Thomson Reuters Web of Science in an attempt to create a type of “core journal list for psychology.” (Paynter, Jackson, & Mullen, 2010) Periodicals Directory, Elsevier’s Scopus, and Thomson Reuters Web of Science in an attempt to create a type of “core journal list for psychology.” (Paynter, Jackson, & Mullen, 2010) Periodicals Directory, Elsevier’s Scopus, and Thomson Reuters Web of Science in an attempt to create a type of “core journal list for psychology.” (Paynter, Jackson, & Mullen, 2010) Commercial publishers are now making tools available where an author can search by keyword, draft title, some selected article text and other factors in attempts to find potential journals across the publishers’ lists of thousands of journal titles to which to submit draft articles. Springer Journal Suggester (https://journalsuggester.springer.com/) and Wiley’s Find a Journal service (https://authorservices.wiley.com/author-resources/Journal-Authors/find-a- journal/index.html) are two such examples. These tools and others like them also help authors wade through an increasingly lengthy list of journals, whether open access, traditionally published, or those that contain a mix of both subscription and open access articles (hybrid). ublic and Social Media Engagement for the Results of Research in Psychology Whether new metrics showing internet downloads or Twitter followers, for instance, will matter to evaluators in a given university is not yet known. As authors become more savvy about marketing their publications online, those using traditional practices may miss some opportunities to reach a larger readership on a global scale. Many are using scholarly collaboration networks as well as various repository solutions for internet dissemination of their scholarship (and data) and these authors now expect and enjoy using various altmetrics to see uptake in various ways. Of course, many studies have demonstrated that open access increases research impact, and so making one’s work open access and then marketing it via popular social media would seem to be a winning strategy for dissemination of scholarly work on a global scale. (SPARC Europe, 2015) Beyond open access strategies and the use of social media, it is necessary for authors to think of all of the factors that make their work more visible and discoverable. If an article has robust and accurate metadata and a well thought out title, that article is more likely to be discoverable by search engines and indexes. As in the past, choosing the best fit between article and publication is paramount, and there are many factors to consider. Authors have many options and also can also employ a long list of strategies to aid in the discoverability of their publications. Planning for open access is necessary for the article to attain maximum readership following initial discovery. Beyond consideration of readership, open licenses like Creative Commons’ CC-BY make works more useful and impactful. Many new tools are available now to assist authors in matching their draft articles to the most appropriate journal publication outlets. Tools have been developed that are attempting to assist authors in matching papers with appropriate journals, or allowing the comparison between potential publication outlets. One tool that is building the capacity to suggest journal titles based on particular attributes chosen by the author is the Cofactor Journal Selector Tool (Sharman, 2016). Author Submission of Work to Psychology Journals and the “In Person” Conference Sharing via social media also promotes cross-disciplinary (and transdisciplinary) conversation and can lead to important new collaborations within institutions and with colleagues around the world. 101 One somewhat surprising element of scientific communication that seems here to stay is the in person annual meeting. Notwithstanding reductions in travel funding and other impediments, the annual meetings of major societies and organizations are still attracting audiences to exhibits, presentations and social events. It appears that in person networking and attending presentations in person is still important in many disciplines. (Mervis, 2013) Even though virtual conferences have sprung up and all sessions can be attended online, there is evidence that, for now, the in person meeting provides opportunities for attendees that don’t necessarily translate into the online only environment. Large major conferences in psychological science, such as the annual American Psychological Association (APA) Convention, now having been held for 125 years, continue to be a draw. In recent years, attendance at the APA convention has been holding its own, with no evidence of major drop-off even in this online age. Registration numbers for 2016 are almost identical to those for 2012, and although a bit higher, 2010 and 2014 are almost identical as well, demonstrating that the convention continues to be of interest to its many attendees. (C.Won, personal communication, August 16, 2017) Even as researchers move to online meetings, there are new and exciting in person conferences popping up that continue to attract audiences. For psychological science, there is even a new conference (which started in 2016 and grew in 2017) that focuses on many new aspects of scholarly communication and research practices in the discipline. Known as SIPS (Society for the Improvement of Psychological Science) with its latest meeting described as “SIPS 2018 is an action-oriented meeting, serving our mission to improve psychological science. There will be no symposia or keynote speakers: the meeting will focus on initiating and conducting projects.” (https://www.improvingpsych.org/SIPS2018/program/) This innovative meeting utilizes an Open Science Framework wiki at: https://osf.io/ck28s/ This dynamic forward-thinking SIPS conference includes training sessions, hack-a-thons, lightning talks, and unconference sessions that focus on topics such as metascience, improving measurement in research, replication, improving teaching and training, peer review, advancing data sharing and much more. Sustainability of the Societies; Will Open Access Harm the Societies that Serve Psychology? As the open availability of research materials grows, there have been concerns about the membership benefit of the society journal, and as the call for more openness grows, there is a concern that membership in scholarly societies may decline. For many scholars, the issue of the sustainability of the societies has been a concern. Recent reports analyzing largescale changes in how scholarship is to be monetized admit that there may be a “ripple effect for societies that subsidize other activities via their publishing revenue.” (Mellon Foundation, 2016, p.89) With other disruptions in the system due to changing modes of conference attendance to more virtual, and the lack of as much interest in receiving the society’s journal in the mail, or even online, open access is sometimes at issue. For many, the journal subscription may have been available online via the university library, further lessening the incentive of the journal subscription as membership benefit. Adding the move to an article-level discovery environment and the move of many learned society journals to the platforms of the largest commercial publishers, and it is obvious that societies had to view the increased opportunities for more visibility that are inherent in moving their publications to more open models, or to situations with limited (or no) embargoes. Ten years ago, Willinsky explored these issues when writing about the Society for Neuroscience, “that, even if no one disputes the public good represented by the greater circulation of this knowledge, how can a journal be expected to offer free access to its content and remain financially viable?” (Willinsky, 2006, p. 9078) At that time, Willinsky had also called for the societies to collaborate more with each other, and possibly with the large research libraries (many of whom became open access publishers using platforms such as Open Journal Systems) as open access was expected to move forward and journal access would not provide the same levels of sustainability. (Willinsky, 2004) The scholarly journal literature has been intertwined with the mission of the scholarly society, and the whole system is being disrupted as boundaries blur on the internet and journal publishing continues to consolidate toward a few very large publishers. Even large funder initiatives (such as the aforementioned “Plan S” currently emanating from Europe), with its lack of allowance for embargoes or closed access, will put pressure on society publishers. Author Submission of Work to Psychology Journals and the “In Person” Conference (Center for Open Science, 2017b) This is a conference that, as time goes on could attract even more scientists, librarians, and all of those interested in open science and how it is utilized in psychology. Another way to establish a scholarly presence and create visibility for one’s work is through sharing ideas on a blog. Blogging is now an established part of our digital reading and writing culture, allowing ideas to be shared with interested audiences. Separating out quality scholarly and academic blogs from the deluge of other blogs on the internet can be daunting, and many potential readers stumble upon blogs by searching the content in a hit or miss fashion using Google or Google Scholar. Outside of discovering blogs through professional associations, networking with colleagues, or links from other information sources, at least one discovery service, ACI Scholarly Blog Index (https://aci.info/scholarly-blogs/) is an aggregator of scholarly blogs across all disciplinary areas. All of the blogs included in this service are individually curated by researchers and experts in the disciplinary or topical area. Searching ACI Scholarly Blog Index, via an institutional or personal subscription, surfaces high impact blogs, and is indexed in major library discovery tools such as OCLC WorldCat, ProQuest’s Summon, EBSCO Discovery Service, and others. (ACI, 2016) Blog entries by leading scholars and thought leaders 102 are now an important part of primary source, current awareness scholarship, and are often cited in peer reviewed journal articles. Major libraries are subscribing to this resource, thereby including blogs in the search, discovery and access resources offered to researchers as part of the suite of subscription offerings. Sustainability of the Societies; Will Open Access Harm the Societies that Serve Psychology? The value of the society will in the end be what its disciplinary community decides. Whereas learned societies and their publications have represented a necessary component of networking, an aspiration for researchers to publish in the society’s journals, and a meaningful connection to the discipline, it will be interesting to see whether norms around professional membership connections for faculty, researchers, students and practitioners remain a vital and integral part of the scholarly communication landscape. The American Psychological Association (APA) is the largest professional membership organization for psychologists as well as the largest nonprofit publisher of psychology abstracting and indexing services (PsycINFO), monographs, journals, and other popular 103 publications and research tools. The APA had 77,552 full members in 2015, a 4% decline for that year, even as more focus had been put on serious outreach to new and continuing members. (American Psychological Association, 2016a) Membership losses have been reported at APA in recent years. For instance, there was a significant decline of 7.6 percent in membership from 2010-2011. APA is not alone in its membership declines; the American Psychiatric Association, for instance, had a 7% membership decline from 2009-2012. However, the Association for Psychological Science (APS), saw a 16.3 percent overall growth from 2007-2011. This may represent growth in membership of a new generation of researchers in psychological science. (Grohol, 2012) Clements, taking the example of the restricted subscriber access to articles in British Psychological Society (BPS) outlets, offers arguments for wide public access to research results, and even likely attracting more writers to BPS journals and lessening the subscription burden on libraries. If the public and even practitioners have restricted access, there is also an “ethical imperative of using psychology to help others.” (Clements, 2016) The fact the American Psychological Association recently introduced an innovative open access, open data journal, Archives of Scientific Psychology is an indication of the organization’s commitment to innovation and the wider dissemination of research results. The Role of Academic Libraries Today in Advancing Research and Scholarly Communication It is a time of transition and disruption for academic libraries. In this interconnected web of online research content, with all of it seamlessly hyperlinked with reader and researcher access as its goal, questions and challenges have emerged for another provider of current and older research material, the academic research library. The role of the brick and mortar academic library as sometimes gatekeeper, with its collection and preservation space reserved for the vast print journal literature has certainly changed and evolved. Concerns may arise around the continued availability into the future of the curated research level library collections that cover psychology from its historical roots to the present day. Electronic access to subscription literature via the libraries of institutions is today (not necessarily forever) still crucial to researchers, and all access must be remote and seamless from users’ homes, via laptops or mobile phones, as well as on site at the university. Formats such as ebooks create disruption in libraries due to sustainability of these books in comparison to the collections of hardcover print titles. Due to digital rights management (DRM) issues, psychology’s ebook collections have become less shareable between libraries via interlibrary loan. Academic libraries, stewards of the comprehensive literature of psychology, need to be concerned with the continued availability of an explosion of research literature online, including quality open access materials. Academic and research libraries struggle with redefining and prioritizing the development of collections, services and new tools to aid researchers in their efforts to pull together a targeted search result. Readers and researchers increasingly seek tools that gather together scholarship in personalized targeted ways. Whether the solution to organizing the literature and making it discoverable falls to libraries or internet search engines, readers need to separate the wheat from the chaff, and researchers (with ever higher bars to jump over for 104 promotion and tenure) need to publish more often, and often in high impact journal titles. Psychology librarians are finding important new roles as partners in the research process with departmental faculty and university research offices in providing new scholarly communication services around open access, data services, use of research tools, consultation around citation metrics, and much more. The Role of Academic Libraries Today in Advancing Research and Scholarly Communication Many academic libraries and librarians are providing a suite of new services centered around research data management, digital humanities, open access solutions for university-generated scholarship, open access policymaking, institutional repository and library publishing services, digital scholarship, citation management tools, scholarly networking services, open educational resources and open textbooks, or partnering to teach classes on reproducibility, for instance. Provision of services around increasing open access to scholarship is now an established part of the mission of university libraries, and extends the mission of librarians to connect all readers and researchers with the scholarly literature that they need. Psychology librarians will find a particular role in making sure they are connecting authors with open access services that can extend the reach of psychological science to other researchers and the public. Many librarians provide discipline-based scholarly communication information and consultation to faculty, staff and students. Many libraries have a focus on teaching scholarly communication topics such as open access strategies in their library instruction classes and in individual research consultations, even to undergraduates. Open access is now part of the library. The corpus of openly available scholarship extends and complements traditional library collections even though it may be more difficult to capture, organize and make available to library users. This open access material must be made available alongside subscription content from the library. The future of the library depends in part on the ability for it to present a relevant, useful, organized, and easily discoverable collection to library users. Items in the collection must be chosen for quality, not whether the business model for a publication is OA or subscription-based. Whether a publication is available from the institution via subscription or allowed to be accessed freely from the internet is not a necessary distinction in terms of readers’ need or interest. Open access collection development is still in its infancy and something with which libraries are grappling. For a subject specialist librarian, this leveling of the playing field between freely available scholarship and traditional subscription of purchased materials allows new opportunities to build collections without necessarily always having to pay. The challenge is in bringing all of this scholarship together for discovery by the university’s readers and researchers. The Role of Academic Libraries Today in Advancing Research and Scholarly Communication (Mullen, 2011) A new role for librarians building research-level psychology collections is to ensure that traditional as well as credible, quality, vetted scholarly open access materials are organized and made accessible in ways that are most useful to researchers. The library is still able to connect the research materials with the user in a way more effective than a search of the open web. A part of libraries’ value for the user will be their ability to present a coherent “collection” of research materials for their constituencies, keeping the user from having to dig through a massive and continually growing corpus of material out on the web. The library can make available a meaningful and useful curated global subset of the available scholarship on the web. Subject specialist librarians also offer consulting services that can convey the most current ways to search, discover, and access targeted content. Changing roles for psychology librarians afford new opportunities for them to work more closely with faculty and students on scholarly communication issues. 105 Academic and research libraries (and librarians) find a natural fit with a continuing focus on the development of a useful suite of research and open access services. Scholarly communication, broadly defined, has always been within the purview of libraries, but now has come to signify a broad range of research services promulgated by librarians in their daily work as liaisons to departments, individual faculty members and researchers. Librarians are able to synthesize knowledge of a complex basket of metrics, with information on open access and research data management issues. Many librarians work in all of these newer scholarly communication areas while maintaining their focus on traditional reference services using a distinct disciplinary focus where needed. Librarians, especially the subject specialists can contribute to the literature of the field of Library and Information Science (LIS) with scholarly communication-related studies focused on the disciplines served. Collaboration with departmental faculty will allow the conversation to resonate with disciplinary faculty and researchers. Alongside this new focus on openness and scientific communication, libraries and librarians continue their focus on development of relevant collections, using the best strategies to provide discovery and access to the research materials needed by faculty, students and the public. Collection development now does not focus on just what is purchased or subscribed, but instead libraries need to gather all relevant quality scholarly material together and organize it for their constituencies. The Role of Academic Libraries Today in Advancing Research and Scholarly Communication This access reportedly works in a way more seamless and simple than many university libraries’ web scale discovery services (and database access) currently provides. As library expenditures continue to be stressed by the costs of keeping up with commercial publisher bundles, and many potential former library users begin their research with Google Scholar or elsewhere on the open web, academic librarians seek closer relationships with their faculty, student and community constituencies, wanting to ensure that research services can be customized and targeted. Psychology librarians network nationally as members of the Association of College & Research Libraries’ Education and Behavioral Science Section’s (EBSS) Psychology Committee. Psychology/Behavioral sciences librarians interface with faculty, students, administrators, research office staff, publishers, vendors and others in order to ensure that psychology researchers have access to the most relevant and useful psychological science collections and services. Dolan’s (2018) book “A Research Guide to Psychology: Print and Electronic Sources” provides a comprehensive treatment of the research literature of the discipline likely found in libraries with research-level psychology collections. Libraries can use this resource to ensure they are providing excellent library collections in psychology. Today, psychology librarians’ roles often also expand from ensuring that the library is providing the research literature of the discipline to also include new services such as consulting on open access publication strategies, helping faculty to identify strategies for paying APCs (or BPCs), providing information on funder requirements, assisting faculty with data management planning, working on open journal publishing teams, assisting with systematic reviews or facilitating implementation of institutional open access policies for individual scholars and whole departments or schools. However, there is need for more contributions to the scholarly communication and open access literature that focus on the traditions and evolution of psychological science. Pulling this information on various scholarly communication topics together in an inclusive and accessible manner for all potential readers would create a more cohesive jumping off point for global discussions that could move the literature of psychology forward. There is no “one size fits all” when it comes to how the discipline will move forward with open access, open science, open data, metrics and how they are used for evaluation of scholars and other aspects of the complex landscape of today’s scholarly communication environment. The Role of Academic Libraries Today in Advancing Research and Scholarly Communication Psychology librarians serving research needs in the discipline and its subfields anticipate demand for services and workshops that target the current needs of researchers in scholarly communication and open access areas. The Role of Academic Libraries Today in Advancing Research and Scholarly Communication Traditional services such as interlibrary loan, circulation of books, and in person consultations with subject specialists are still important, but they exist alongside new services where departmental library liaisons now offer subject-specific advice on the use of open access strategies for faculty work and possibly participating in library-led publishing efforts, for example. Many research libraries work to develop comprehensive institutional repositories (IRs) that ingest and preserve faculty scholarship (including all of the products of scholarship such as data), electronic dissertations, and a wide variety of other digital objects created at the institution. The institutional repository is focused on openness and collaboration with faculty and other libraries, and is crawled by Google and other search engines. An institution’s IR serves as a vehicle that enables open science and open access to publications and data, and often is a valued service offered to faculty and students. Academic and research libraries are focused on the creation as well as the dissemination of scholarship. Research data management initiatives in libraries are evolving, and libraries and librarians are finding new and productive collaborations with other university offices such as the research office. Libraries, publishers, and vendors inhabit some of the same spaces and find some challenges and opportunities in collaborating with each other on open access or other important initiatives. (Mullen & Ross, 2016) Some publishers, such as the APA, have had close relationships with psychology subject specialist librarians via groups such as library advisory councils that have convened to work on information sharing and product development. There are some challenges for libraries and publishers in the areas of green and gold open access, which will in some ways be pushed toward solutions through increasing funder and reader/researcher demands for open access to taxpayer- funded research. Increasing discovery of articles via inclusion of more and more articles in Google Scholar and other search engines creates a demand for individual articles. Enhanced discovery fuels demand. All of the new publisher and library services play out against a backdrop that includes pirate sites like Sci-Hub, which shows no intention of slowing down as it 106 provides millions of users with access to proprietary subscription content worth millions of dollars. This access reportedly works in a way more seamless and simple than many university libraries’ web scale discovery services (and database access) currently provides. provides millions of users with access to proprietary subscription content worth millions of dollars. Conclusion After so many years where there was little change in the way science was communicated, the vast potential of the internet for sharing and learning has opened new opportunities for authors, publishers, funders, and universities seeking maximum impact for the work of its faculty. The issue of open access alone exemplifies the transformation and disruption of scientific communication and scholarly publishing. Often, there will seem two sides when discussing the best way forward. Whereas green open access seemed to have its beginnings as a more grass roots movement of sorts, with making their work open access left to the authors 107 themselves (with allowances from publishers in some cases), or Harvard-style open access institutional policies stating right up front that scholars’ works need to be made open to the world of potential readers, it remains only one strategy in place to increase the corpus of freely available online peer reviewed material. With gold open access, a more grass roots approach to publishing journals could be seen in university library publishing of journals using one of many open source services such as Open Journal Systems, allowing journal publishing to emanate directly from academia, not just from commercial and other traditional publishers. Currently, the commercial journal publishers are sitting right in the middle of the aforementioned “flip” of the system, offering paid open access options, with article processing charges far from standardized and all over the map, from zero to more than 5000 dollars US. The “hybrid” model also exemplifies in some ways where the system is now, with cash-strapped research libraries still negotiating complex subscription deals with commercial publishers while at the same time working to ensure that the work that their authors produce is widely disseminated. Authors at subscriber institutions are paying APCs to those same publishers, providing another revenue stream that is outside of the subscription outlay but adds to institutional costs. Megajournals have changed the landscape, where, even in psychology, many authors choose the more rapid and cross-disciplinary solutions of journals like PLOS ONE, or Springer Nature’s Scientific Reports, which has taken over the top spot as “largest journal’ with thousands of articles published in one annual issue. These megajournals help to subsidize the other high impact offerings of their publishers, and are able to offer to publish at what may be called a “reasonable” APC. Conclusion Complicating matters in the complex OA publishing landscape are the different approaches taken by various nations and funders and instead of one size fits all, the situation becomes almost dizzyingly complex. All in all, a pervasive audit culture is taking over at universities in many countries, leading to “publish or perish” scenarios and a need to maintain established high impact publication outlets, no matter the cost. At this point in time, there seems to be no sure way forward. There is talk of a “flip” of the entire system from subscription to open access, but there are still many concerns around issues like sustainability or inclusion of researchers from the Global South in this new system largely based around APCs. Too many researchers are shut out of the current system due to issues of language, resources, and other roadblocks. The library community as well as publishers and other stakeholders are currently discussing very intentionally how to increase diversity, equity and inclusion in many aspects of scholarly communication. There is a long way to go in addressing these concerns. The licensing issues get increasingly sticky, and may be confusing to many authors and others who want to legally reuse work. Copyright remains a challenging part of the system for authors of scholarly works who sign away their works to publishers without expectation of payment. Authors are unsure of their rights to share as they publish their work. The complex rules surrounding copyright are not fully understood, or are not of interest to many academic researchers. Many working on open access solutions recognize the need for liberal reuse licensing, specifically the use of CC-BY, a Creative Commons license that allows any reuse of the content (with attribution) in order to spur innovation by maximal reuse and rebuilding of published text and data. This is another vital part of the open access conversation and academic libraries and their copyright and licensing specialists may be a vital piece of moving what many 108 view as “real” open access out to a research community that needs the ability to do text and data mining of more of the research corpus. Finally, there seems a dearth of information on how psychological scientists are using and participating in all of the newer scientific or scholarly communication tools, resources and practices. Conclusion At this point, there is much speculation as to how psychology faculty, authors, researchers and graduate students are using these all of the internet-enabled scholarly networks/academic social networks. There must be a call for more studies on scholarly communication behavior based around both existing disciplinary norms as well as newly emerging practices that speak to interdisciplinary areas of interest to psychological science. 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https://openalex.org/W2613371230
https://link.springer.com/content/pdf/10.1007%2Fs00431-017-2923-y.pdf
English
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Final adult height in long-term growth hormone-treated achondroplasia patients
European journal of pediatrics
2,017
cc-by
5,058
Eur J Pediatr (2017) 176:873–879 DOI 10.1007/s00431-017-2923-y ORIGINAL ARTICLE 2 Neonatal Intensive Care Unit, Nara Prefecture General Medical Center, Nara, Japan Final adult height in long-term growth hormone-treated achondroplasia patients Daisuke Harada1 & Noriyuki Namba1 & Yuki Hanioka1 & Kaoru Ueyama1 & Natsuko Sakamoto1 & Yukako Nakano1 & Masafumi Izui1 & Yuiko Nagamatsu1 & Hiroko Kashiwagi1 & Miho Yamamuro1 & Yoshihito Ishiura1 & Ayako Ogitani2 & Yoshiki Seino1 Received: 8 September 2016 /Revised: 11 April 2017 /Accepted: 2 May 2017 /Published online: 13 May 2017 # The Author(s) 2017. This article is an open access publication Abstract The objective of this study was to evaluate the gain in final height of achondroplasia (ACH) patients with long-term growth hormone (GH) treatment. We analyzed medical data of 22 adult patients (8 males and 14 females) treated with GH at a dose of 0.05 mg/kg/day. Optionally, tibial lengthening (TL) was performed with the Ilizalov method in 15 patients and TL as well as femoral lengthening (FL) in 6 patients. Concomitant gonadal suppression therapy with buserelin acetate was applied in 13 patients. The mean treatment periods with GH were 10.7 ± 4.0 and 9.3 ± 2.5 years for males and females, respectively. GH treatment augmented the final height +0.60 ± 0.52 SD (+3.5 cm) and +0.51 ± 1.29 SD (+2.8 cm) in males and females compared to non-treated ACH patients, respectively. Final height of ACH patients that underwent GH and TL increased +1.72 ± 0.72 SD (+10.0 cm) and +1.95 ± 1.34 SD (+9.8 cm) in males and females, respectively. GH, TL, and FL increased their final height +2.97 SD (+17.2 cm) and +3.41 ± 1.63 SD (+17.3 cm) in males and females, respectively. Gonadal suppres- sion therapy had no impact on final height. py p g Conclusions: Long-term GH treatment contributes to 2.6 and 2.1% of final adult height in male and female ACH patients, respectively. Keywords Achondroplasia . Growth hormone . Limb lengthening . Gonadal suppression . Final height Abbreviations ACH Achondroplasia ACH-SD ACH-specific SD score Abbreviations ACH Achondroplasia ACH-SD ACH-specific SD score Communicated by Mario Bianchetti Patients • Average final height SD score increased +1.85 SD with GH and tibial lengthening and +3.27 SD with GH, tibial, and femoral lengthening. Fifty-two patients with ACH (23 males and 29 females) were enrolled in this study (Fig. 1). All patients had visited our hos- pital for treatment and were clinically diagnosed as ACH due to severe rhizomelic short stature, characteristic facial features, and trident hands. Bone X-ray features of all of the patients included thick and short longitudinal bones, metaphyseal cupping, narrowing of the lumber interpediculate distance, and narrow ischiatic notches. When the clinical diagnosis was uncertain, FGFR3 gene analysis was performed by direct sequencing. The typical p.Gly380Arg mutation was detected in all tested patients. Medical records and/or questionnaires from 40 patients with ACH (17 males and 23 females) that underwent GH treat- ment were obtained. Twenty-two patients (8 males and 14 fe- males) had reached final height and were included in the analy- sis. Of the 22 ACH patients, gene analysis was performed in 10 patients (45%). Annual height throughout GH treatment was available in only 16 patients (70%, 4 males and 12 females) (Fig. 2). Data at initiation of GH treatment was accessible in 19 patients (86%, 6 males and 13 females) (Fig. 3). Abbreviations Communicated by Mario Bianchetti Communicated by Mario Bianchetti Hiroko Kashiwagi kashiwagi-hiroko@osaka.jcho.go.jp Miho Yamamuro yamamuro-miho@osaka.jcho.go.jp Yoshihito Ishiura ishiura-yoshihito@minato.jcho.go.jp Ayako Ogitani ayaohgi@yahoo.co.jp Yoshiki Seino yoseino@tcct.zaq.ne.jp 1 Department of Pediatrics, Osaka Hospital, Japan Community Healthcare Organization (JCHO), 4-2-78, Fukushima, Fukushima-ku, Osaka, Osaka 553-0003, Japan 2 Neonatal Intensive Care Unit, Nara Prefecture General Medical Center, Nara, Japan * Noriyuki Namba nnamba@ped.med.osaka-u.ac.jp Daisuke Harada harada-d@nifty.com Yuki Hanioka hanioka-yuki@osaka.jcho.go.jp Kaoru Ueyama slowpoke_the_elephant@yahoo.co.jp Natsuko Sakamoto sakamoto-natsuko@osaka.jcho.go.jp Yukako Nakano yuccayuka1977@gmail.com Masafumi Izui izui-masafumi@osaka.jcho.go.jp Yuiko Nagamatsu yuiko_honda@hotmail.com 1 Department of Pediatrics, Osaka Hospital, Japan Community Healthcare Organization (JCHO), 4-2-78, Fukushima, Fukushima-ku, Osaka, Osaka 553-0003, Japan 2 Neonatal Intensive Care Unit, Nara Prefecture General Medical Center, Nara, Japan 2 Neonatal Intensive Care Unit, Nara Prefecture General Medical Center, Nara, Japan 874 Eur J Pediatr (2017) 176:873–879 FGFR3 Fibroblast growth factor receptor 3 FL Femoral lengthening GH Growth hormone SD Standard deviations SHG Standing height gain TL Tibial lengthening TLV Theoretical lengthening value by various groups [13–15]. Given the exceptional safety record of GH, it is essential that height gain achieved by these treat- ments is not inferior to that of GH. We therefore investigated the effect of long-term GH treatment in patients with ACH. Introduction Achondroplasia (ACH, MIM no. 100800) is the most com- mon form of congenital rhizomelic dwarfism characterized by severe and disproportionate short stature, macrocephaly with a prominent forehead, midface hypoplasia, and trident hands. ACH is inherited as an autosomal dominant trait and is caused by gain of function mutations in the fibroblast growth factor receptor 3 (FGFR3) gene. The final height may be as short as 118–145 cm for males and 112–136 cm for females in Caucasian patients [1]. In Japanese patients, the average final height without treatment has been reported as 130.4 cm for males (−7.0 standard deviations [SD] compared with normal Japanese children) and 124.0 cm (−6.4 SD) for females [2]. Classically, limb lengthening has been performed to amelio- rate body disproportion [3]. While individual studies suggest that tibial lengthening (TL), femoral lengthening (FL), and combined TL and FL add 4.0–10.5, 3.0–13.0, and 9.0– 24.0 cm, respectively, to bone length or standing height of patients with ACH [4–7], a recent systematic review shows that the overall height gain in ACH/hypochondroplasia patients is 6–12 cm [8]. In addition, short-term growth hormone (GH) treatment has also been shown to be effective for accelerating height velocity and improving height SD score in ACH patients [9–12]. GH treatment has been approved only in Japan since 1997. Although nearly 20 years have passed since its approval, there have been no reports on the long-term effects of GH treatment in patients with ACH. Moreover, in recent years, height-targeting novel therapies for ACH have been proposed What is New: • Long-term GH treatment increased the final height of ACH patients +0.60 ± 0.52 SD (+3.5 cm) and +0.51 ± 1.29 SD (+2.8 cm) for males and females, respectively. Study design We conducted a retrospective cohort study regarding the effect of long-term GH treatment in ACH patients. All patients were treated with subcutaneous GH injections. Some received limb lengthening and/or gonadal suppression therapy (comprehen- sive treatment) as well. The primary outcome was gain in final height due to GH. The secondary outcome was increase in final height with comprehensive treatment. What is Known: • ACH is a common form of rhizomelic dwarfism, with an average adult height of 130.4 cm for males and 124.0 cm for females in the Japanese population. • Short-term GH improves height standard deviation (SD) scores in ACH patients. What is New: • Long-term GH treatment increased the final height of ACH patients +0.60 ± 0.52 SD (+3.5 cm) and +0.51 ± 1.29 SD (+2.8 cm) for males and females, respectively. • Average final height SD score increased +1.85 SD with GH and tibial lengthening and +3.27 SD with GH, tibial, and femoral lengthening. What is Known: • ACH is a common form of rhizomelic dwarfism, with an average adult height of 130.4 cm for males and 124.0 cm for females in the Japanese population. • Short-term GH improves height standard deviation (SD) scores in ACH patients. What is New: • Long-term GH treatment increased the final height of ACH patients +0.60 ± 0.52 SD (+3.5 cm) and +0.51 ± 1.29 SD (+2.8 cm) for males and females, respectively. • Average final height SD score increased +1.85 SD with GH and tibial lengthening and +3.27 SD with GH, tibial, and femoral lengthening. Follow-up protocol Recombinant human GH was injected subcutaneously at a dose of 0.05 mg/kg/day. Physical examination and blood/ biochemical examinations were performed every 3–4 months. Limb lengthening and/or gonadal suppression therapy were added according to the expectations of the patients and/or parents. Limb lengthening was performed by the Ilizalov method [16]. For gonadal suppression therapy, a daily dose of 0.9 mg buserelin acetate was provided as a nasal spray when patients entered puberty. On every visit, standing height was measured by a single well-calibrated stadiometer. To assess the effect of limb 875 Eur J Pediatr (2017) 176:873–879 Fig. 1 Enrollment and follow-up. One hundred twelve patients were registered as Bchondrodystrophy^ in our institution. Sixty patients with hypochondroplasia and other skeletal dysplasias were excluded. A total of 52 ACH patients were enrolled in this study. No clinical data of 12 patients were available. Medical information of 40 patients with ACH who had received GH treatment was obtained through medical records and/or questionnaires. GH treatment is ongoing in 16 patients and 2 patients had discontinued GH treatment due to severe deformation of their spine and lower extremity. Twenty-two patients (8 males and 14 females) had reached final height and were included in the analysis. Pretreatment data of two males and one female were partially missing. Among these 22 patients, seven (three males and four females) were treated only with GH, nine (four males and five females) underwent TL in addition to GH, and six (one male and five females) underwent FL in addition to GH and TL. Concomitant gonadal suppression therapy was performed in 13 patients (3 males and 10 females). GH growth hormone, ACH achondroplasia, TL tibial lengthening, FL femoral lengthening the pre-lengthening height from the post-lengthening height. In this study, we focused on SHG as the actual limb length- ening value. We subtracted SHG from final height to deter- mine growth due to GH alone. Statistical analysis Height SD scores were compared with normal Japanese chil- dren (no secular trend since 1990) of the same sex and age. To further highlight treatment efficacy, SD scores were also cal- culated using the average height of non-treated patients with ACH derived from a nationwide survey of 135 ACH patients from 1991 to 1995 [2]. SDs of normal Japanese children were adopted for this purpose because SDs of non-treated Japanese ACH patients are not available. We refer to this score as ACH- specific SD score (ACH-SD). Fig. 1 Enrollment and follow-up. One hundred twelve patients were registered as Bchondrodystrophy^ in our institution. Sixty patients with hypochondroplasia and other skeletal dysplasias were excluded. A total of 52 ACH patients were enrolled in this study. No clinical data of 12 patients were available. Medical information of 40 patients with ACH who had received GH treatment was obtained through medical records and/or questionnaires. GH treatment is ongoing in 16 patients and 2 patients had discontinued GH treatment due to severe deformation of their spine and lower extremity. Twenty-two patients (8 males and 14 females) had reached final height and were included in the analysis. Pretreatment data of two males and one female were partially missing. Among these 22 patients, seven (three males and four females) were treated only with GH, nine (four males and five females) underwent TL in addition to GH, and six (one male and five females) underwent FL in addition to GH and TL. Concomitant gonadal suppression therapy was performed in 13 patients (3 males and 10 females). GH growth hormone, ACH achondroplasia, TL tibial lengthening, FL femoral lengthening Statistical analyses were performed by the Mann–Whitney U test and Pearson’s correlation coefficient using SPSS soft- ware V23.0 (IBM Japan, Tokyo). P values <0.05 were con- sidered significant. Final height attained with GH treatment Table 1 shows the background of the patients. Mean age and height SD scores did not differ significantly between males and females. The mean treatment period and age at termination were 10.7 ± 4.0 and 16.2 ± 1.3 years for males and 9.3 ± 2.5 and 14.7 ± 1.8 years for females, respectively. Growth records of 16 lengthening, we measured two values. One was the actual reading of the Ilizarov external fixator scale. We termed this value Btheoretical lengthening value (TLV).^ The other, Bstanding height gain (SHG),^ was calculated by subtracting Fig. 2 GH treatment improves final height in ACH patients. Growth curves of each patient with ACH who had long-term GH treatment. The black lines indicate the mean ± SD of the patients. The gray dotted lines show the average curves of non-treated patients with ACH according to reference 2. Following GH treatment, 69% (11/16) of the patients maintained height above average. Since the ages when GH was started differ among patients, the mean heights at age 3 years do not match the height SD scores at the start of the treatment in Table 1. GH growth hormone, ACH achondroplasia Fig. 2 GH treatment improves final height in ACH patients. Growth curves of each patient with ACH who had long-term GH treatment. The black lines indicate the mean ± SD of the patients. The gray dotted lines show the average curves of non-treated patients with ACH according to reference 2. Following GH treatment, 69% (11/16) of the patients maintained height above average. Since the ages when GH was started differ among patients, the mean heights at age 3 years do not match the height SD scores at the start of the treatment in Table 1. GH growth hormone, ACH achondroplasia Eur J Pediatr (2017) 176:873–879 876 Fig. 3 Overall effect of comprehensive treatment. a Comparison of ACH-SD scores (ΔACH-SD). GH treatment alone (n = 22) increased ACH-SD scores by +0.60 ± 0.52 SD for males (p < 0.05) and +0.51 ± 1.29 SD for females (p < 0.05). Final height ACH-SD scores attained with the combination of GH and TL (n = 15) were +1.85 ± 1.16 SD (p < 0.01) (+1.72 ± 0.72 SD and +1.95 ± 1.34 SD for males and females, respectively). Final height attained with GH treatment Comprehensive treatment with GH and limb lengthening significantly increased final height in ACH patients (Fig. 3a). The ΔACH-SD with GH and TL was +1.72 ± 0.72 SD and +1.95 ± 1.34 SD for males and females, respectively. The mean of ΔACH-SD with GH, TL, and FL was +2.97 SD and +3.41 ± 1.63 SD for males and females, respectively. According to the ΔACH-SD scores, the average final heights of male and female patients were calculated as 140.4 cm (+10.0 cm) and 133.8 cm (+9.8 cm) with GH and TL and 147.6 cm (+17.2 cm) and 141.3 cm (+17.3 cm) with GH, TL, and FL, respectively (Fig. 3b). There was no significant correlation between lengthening values and age or height at surgery. Final height attained with GH treatment The combination of GH, TL, and FL (n = 6) in- creased final height ACH-SD scores +3.27 ± 1.46 SD (p < 0.01) (+2.97 SD and +3.41 ± 1.63 SD for males and females, respectively). b Calculated final height based on ΔACH-SD scores. GH growth hormone, ACH achondroplasia, TL tibial lengthening, FL femoral lengthening females, respectively). The combination of GH, TL, and FL (n = 6) in- creased final height ACH-SD scores +3.27 ± 1.46 SD (p < 0.01) (+2.97 SD and +3.41 ± 1.63 SD for males and females, respectively). b Calculated final height based on ΔACH-SD scores. GH growth hormone, ACH achondroplasia, TL tibial lengthening, FL femoral lengthening Fig. 3 Overall effect of comprehensive treatment. a Comparison of ACH-SD scores (ΔACH-SD). GH treatment alone (n = 22) increased ACH-SD scores by +0.60 ± 0.52 SD for males (p < 0.05) and +0.51 ± 1.29 SD for females (p < 0.05). Final height ACH-SD scores attained with the combination of GH and TL (n = 15) were +1.85 ± 1.16 SD (p < 0.01) (+1.72 ± 0.72 SD and +1.95 ± 1.34 SD for males and SHG are indicated in Table 2. Although TLV and SHG were not exactly consistent, there was no statistically sig- nificant difference between TLV and SHG. patients with GH treatment show that 69% of patients (4/4 and 8/ 12 in males and females, respectively) maintained their height above the average curve of non-treated ACH patients (Fig. 2). Consequently, the increase in ACH-SD score (ΔACH-SD) with GH treatment at final height was +0.60 ± 0.52 SD for males (p < 0.05) and +0.51 ± 1.29 SD for females (p < 0.05) (Fig. 3a). The average final height attained by GH treatment was calculated as 133.9 cm (+3.5 cm) and 126.8 cm (+2.8 cm) for males and females, respectively (Fig. 3b). patients with GH treatment show that 69% of patients (4/4 and 8/ 12 in males and females, respectively) maintained their height above the average curve of non-treated ACH patients (Fig. 2). Consequently, the increase in ACH-SD score (ΔACH-SD) with GH treatment at final height was +0.60 ± 0.52 SD for males (p < 0.05) and +0.51 ± 1.29 SD for females (p < 0.05) (Fig. 3a). The average final height attained by GH treatment was calculated as 133.9 cm (+3.5 cm) and 126.8 cm (+2.8 cm) for males and females, respectively (Fig. 3b). Gonadal suppression and other considerations nificant. We therefore considered the patients in this study as a representative group. Gonadal suppression was performed in 13 of the 22 patients (59%, Table 3). The mean height ACH-SD score at GH initi- ation tended to be lower in patients who received this therapy than in patients who did not. Buserelin acetate did not statis- tically increase final height of ACH patients (p = 0.33). GH treatment increased the final height ACH-SD score +0.60 SD and +0.51 SD for males and females, respec- tively. This translates to an addition of 3.5 cm for males and 2.8 cm for females to the final height of non-treated ACH patients. Previous reports have shown that short- term GH treatment in ACH patients increases height SD scores from +0.3 to +1.6 SD during 2 to 6 years of treat- ment [9–12]. Our data shows that the gain in height SD is mostly conserved until final height. Of note, SHG inevi- tably includes GH induced growth during TL and FL. Thus, we may have underestimated final height SD attrib- uted to GH treatment despite using ACH-SD. No patients received protein anabolic hormones and/or oth- er treatments for short stature. No patients had major adverse events or worsening of complications, even after long-term GH treatment. Final height attained with comprehensive treatment (GH and limb lengthening) TL (n = 15) and FL (n = 6) were performed at ages 12.4 ± 3.2 years (range, 9.0–17.0 years) and 12.6 ± 2.4 years (range, 10.0–17.0 years), respectively. The mean TLV and Male Female Number of patients 8 14 Age at start of treatment (years) 5.2 ± 3.9 (3.0 to 14.0) 5.5 ± 2.7 (3.0 to 11.0) Height SD score at GH initiation (SD) −5.11 ± 0.84 (−5.89 to −4.46) −5.22 ± 1.33 (−7.16 to −3.42) Height ACH-SD score at GH initiation (SD) 0.05 ± 0.80 (−1.43 to 1.40) −0.28 ± 1.35 (−2.35 to 1.94) Table 1 Background of the patients Table 1 Background of the patients 877 Eur J Pediatr (2017) 176:873–879 Table 2 Effect of limb lengthening No. of patients TLV (cm) SHG (cm) Tibial lengthening Males 5 8.1 ± 1.6 (6.4 to 10.2) 6.9 ± 2.4 (5.1 to 10.2) Females 10 8.2 ± 2.2 (3.1 to 10.0) 8.9 ± 2.3 (5.0 to 13.0) Total 15 8.2 ± 2.0 8.3 ± 2.4 Femoral lengthening Males 1 10.7 7.0 Females 5 8.6 ± 1.1 (8.5 to 10.0) 6.9 ± 2.1 (3.6 to 9.0) Total 6 9.0 ± 1.3 7.0 ± 1.9 Values are mean ± SD (range) TLV theoretical lengthening value, SHG standing height gain Discussion −0.57 SD (−3.3 cm). Genetic background, treatment compli- ance, or treatment duration may have contributed to the dif- ference. Some patients tended to be less responsive and reached final height at an age slightly earlier than non- treated patients. Since GH can accelerate bone maturation in idiopathic short stature, further optimization of GH dose or duration may be necessary [18]. When new height targeting treatments that are currently under development become avail- able, it may be reasonable to use GH only in patients that respond well. Authors’ contributions All of the authors (D.H., N.N., Y.H., K.U., N.S., Y.Nk., M.I., Y.Ng., H.K., M.Y., Y.I., A.O., Y.S.) were involved in the systematic examination and clinical management of the patients. D.H., N.N., and Y.S. designed the study. D.H. compiled and analyzed the retrospective data. D.H. and N.N. wrote the paper. Limb lengthening still remains to be the most effective measure to increase final height in ACH patients. However, patients need to overcome many problems, such as stiffness of the Achilles tendon, recurrent fractures, asymmetry of the legs, focal bacterial infection, and pain [5–7, 19]. In this study, we found no correlation between surgical age and lengthening values. Interestingly, we seem to consistently achieve greater height gain with GH and limb lengthening than that achieved by limb lengthening alone [8]. This suggests that GH, at least in part, may contribute to the results, although the expertise of the orthopedic surgeons most obviously plays a major role. Compliance with ethical standards Ethical approval This study was approved by the Medical Ethic Committee of JCHO Osaka Hospital (ID 2015-19) for collection and analysis of the clinical data. All procedures performed in studies involv- ing human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. Informed consent Informed consent was obtained from all individual participants included in this study. Gonadal suppression was performed in attempt to delay epiphyseal fusion and sustain growth. The effect of gonadal suppression on final adult height is controversial. In our study, ACH-SDs at the initiation of GH treatment in patients that underwent this therapy tended to be lower than those in pa- tients that did not. Although a significant change in final height was not detected in our study, a selection bias (shorter patients) may have been present. It is also possible that buselerin acetate did not suppress gonadotropins as thorough- ly as leuprolerin depot injections. Recent studies have shown that more effective reagents (i.e., aromatase inhibitors) in combination with GH may increase height potential in puber- tal children [20]. Taken together, there still seems to be room for further exploration especially when newer height targeting therapeutic agents become available. Funding This study was founded in part by a grant from the Foundation for Growth Science 2012 (D.H.). Funding This study was founded in part by a grant from the Foundation for Growth Science 2012 (D.H.). Conflict of interest N.N. consults for Novo Nordisk Pharma Ltd. and has received honoraria as a speaker from Eli Lilly Japan K.K. All other authors have no conflicts of interest. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appro- priate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Discussion In Japanese children with GH deficiency, height gain by GH treatment corresponds to 4.1 and 3.1% of final height for males and females, respectively [17]. ACH children gained 2.6 and 2.1% for males and females, respectively. Taking into consideration that ACH is a far severer condi- tion than short stature due to GH deficiency, we consider that the effect of GH treatment is reasonable for this group of patients. However, further investigation concerning GH dose and duration, as well as other treatment options, is necessary. GH treatment for ACH patients has been approved in Japan with an eligibility criteria of (1) height shorter than −3.0 SD and (2) age older than 3 years. In some patients, GH treatment was started at ages much older than 3 years be- cause they were recruited into clinical trials before the drug was approved. Since ACH patients usually have little pu- bertal growth spurt, calculating SD scores from the mean height of normal children will attenuate the post-pubertal scores by 2 SD. Accordingly, we assessed final height using the ACH-SD score. Although there was a difference in pretreatment height ACH-SD between males and fe- males, it ranged within ±0.3 and was not statistically sig- In our study, the effect of GH varied widely. While ΔACH- SD scores of six (26%) patients were greater than +1.0 SD with a maximum of +2.84 SD (+16.5 cm), those in another six (26%) patients had scores below 0 SD and the lowest was Table 3 Effect of gonadal suppression therapy in addition to GH treatment Gonadal suppression therapy - + Number of patients 9 13 ACH-SD score at GH initiation 0.12 ± 1.23 (−1.60 to 1.46) −0.32 ± 1.20 (−2.35 to 1.94) ACH-SD score at final height 0.51 ± 1.17 (−0.89 to 2.75) 0.29 ± 1.08 (−1.40 to 2.15) Height ΔACH-SD score (SD) 0.42 ± 0.67 (−0.57 to 1.29) 0.58 ± 0.86 (−0.40 to 2.05) Values are mean ± SD (range) Table 3 Effect of gonadal suppression therapy in addition to GH treatment 878 Eur J Pediatr (2017) 176:873–879 Acknowledgments We would like to thank our patients and their fam- ilies for agreeing to participate and for providing their medical data through medical records and questionnaires. We also express our grati- tude to the clinical staff and the orthopedists in JCHO Osaka Hospital and all supporting hospitals for their efforts in improving the patients’ lives. References A limitation of this study is that data were collected retro- spectively in one institution without non-treated controls. Some difficulties were encountered while collecting data. Medical records of patients whose last visit was more than a decade ago were not available, the questionnaires were not necessarily completely filled out, and patients who reached their final height comprised 65.7% of all included patients. Due to these limitations, some data were analyzed using a small number of patients. On the other hand, since all patients in this study have been examined and treated at our institution, the advantages are the accuracy and consistency of diagnosis, data collection, and clinical management. 1. Horton WA, Rotter JI, Rimoin DL, Scott CI, Hall JG (1978) Standard growth curves for achondroplasia. J Pediatr 93:435–438 2. Tachibana K, Suwa S, Nishiyama S, Matsuda I (1997) Height of Japanese achondroplasia patients based on a nationwide investiga- tion. J Pediatr Practice 60:1363–1369 in Japanese 3. Aldegheri R, Trivella G, Renzi-Brivio L, Tessari G, Agostini S, Lavini F (1988) Lengthening of the lower limbs in achondroplastic patients: a comparative study of four techniques. J Bone Joint Surg Br 70:69–73 4. Kocaoglu M, Bilen FE, Dikmen G, Hi B, Eralp L (2014) Simultaneous bilateral lengthening of femora and tibiae in achon- droplastic patients. Acta Orthop Traumatol Turc 48:157–163 In conclusion, long-term GH treatment contributes to 2.6 and 2.1% of final adult height in male and female ACH pa- tients, respectively, without any severe side effects. Final adult height attained with GH will serve as a benchmark when eval- uating novel therapeutic agents under development. 5. Venkatesh KP, Modi HN, Devmurari K, Yoon JY, Anupama BR, Song HR (2009) Femoral lengthening in achondroplasia. J Bone Joint Surg (Br) 91B:1612–1617 6. Kim SJ, Agashe MV, Song SH, Choi HJ, Lee H, Song HR (2012) Comparison between upper and lower limb lengthening in patients with achondroplasia. J Bone Joint Surg (Br) 94B:128–133 Eur J Pediatr (2017) 176:873–879 879 7. Donaldson J, Aftab S, Bradish C (2015) Achondroplasia and limb lengthening: results in a UK cohort and review of the literature. J Orthop 12:31–34 15. Matsushita M, Kitoh H, Ohkawara B, Mishima K, Kaneko H, Ito M, Masuda A, Ishiguro N, Ohno K (2013) Meclozine facilitates proliferation and differentiation of chondrocytes by attenuating ab- normally activated FGFR3 signaling in achondroplasia. PLoS One 8:e81569 8. References Kim SJ, Pierce W, Sabhjarwal S (2014) The etiology of short stature affects the clinical outcome of lower limb lengthening using exter- nal fixation. A systematic review of 18 trials involving 547 patients. Acta Orthop 85:181–186 16. Tanaka T, Hanew K, Nishi Y, Tachibana K, Yokoya S, Igarashi Y, Hirano T, Fujita K, Saitoh T, Hizuka N, et. al. (2001) Final height of growth hormone (GH)-treated short children registered at the foun- dation for growth science in Japan: comparison between the pitui- tary human GH era and the recombinant human GH era. Clin Pediatr Endocrinol 10:53–62. 9. Tanaka H, Kubo T, Yamate T, Ono T, Kanzaki S, Seino Y (1998) Effect of growth hormone therapy in children with achondroplasia: growth pattern, hypothalamic-pituitary function, and genotype. Eur J Endocrinol 138:275–280 10. Tanaka N, Katsumata N, Horikawa R, Tanaka T (2003) The com- parison of the effects of short-term growth hormone treatment in patients with achondroplasia and hypochondroplasia. Endocr J 50: 69–75 17. Ilizarov GA, Deviatov AA (1969) Surgical lengthening of the shin with simultaneous correction of deformities. Ortop Traumatol Protez 30:32–37 18. Kamp GA, Waelkens JJ, de Muinck Keizer-Schrama SM, Delemarre-Van de Waal HA, Werhoeven-Wind L, Zwinderman AH, Wit JM (2002) High dose of growth hormone treatment in- duces acceleration of skeletal maturation and an earlier onset of puberty in children with idiopathic short stature. Arch Dis Child 87:215–220 11. Hertel NT, Eklof O, Ivarsson S, Aronson S, Westphal O, Sipila I, Kaitila I, Bland J, Veimo D, Muller J et al (2005) Growth hormone treatment in 35 prepubertal children with achondroplasia: a five- year-dose-response trial. Acta Paediatr 94:1402–1410 12. Ramaswami U, Rumsby G, Spoudeas HA, Hindmarsh PC, Brook CG (1999) Treatment of achondroplasia with growth hormone: six years of experience. Pediatr Res 46:435–439 19. Kim SJ, Balce GC, Agashe MV, Song SH, Song HR (2012) Is bilateral lower limb lengthening appropriate for achondroplasia? Clin Orthop Relat Res 470:616–621 13. 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Climate Change Projections of Potential Evapotranspiration for the North American Monsoon Region Eylon Shamir Hydrologic Research Center Lourdes Mendoza-Fierro  University of Arizona Sahar Mohsenzadeh Karimi  University of Arizona Norman Pelak  Hydrologic Research Center Hsin-I Chang  University of Arizona Christopher Castro  University of Arizona Research Article Keywords: Climate change, Potential Evapotranspiration, North American Monsoon, NA-CORDEX, Penman-Monteith Posted Date: March 6th, 2024 DOI: https://doi.org/10.21203/rs.3.rs-4009798/v1 DOI: https://doi.org/10.21203/rs.3.rs-4009798/v1 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Additional Declarations: No competing interests reported. Version of Record: A version of this preprint was published at Hydrology on June 14th, 2024. See the published version at https://doi.org/10.3390/hydrology11060083. Page 1/28 Abstract We assessed future projected changes in terrestrial evaporative demand by calculating Potential Evapotranspiration (PET) for the North American Monsoon region at the Southwest U.S. and Mexico. The PET projections were calculated using the daily Penman-Monteith equation and the terrestrial meteorological variables needed for the equation (i.e. minimum and maximum daily temperature, specific humidity, wind speed, incoming shortwave radiation, and pressure) were available from the North American – CORDEX initiative. We used six dynamically downscaled projections of three CMIP5 GCMs forced with RCP8.5 emission scenarios (i.e. HadGEM2-ES, MPI-ESM-LR, and GFDL-ESM2M), each was dynamically downscaled to ~ 25 km by two RCMs (i.e. WRF and regCM4). All terrestrial annual PET projections showed a statistically significant increase when comparing 1986–2005 to 2020–2039 and 2040–2059. The regional spatial average of the six climate models projected an increase in the annual PET of about + 4% and + 8% for 2020–2039 and 2040–2059, respectively. The projected average 20-year annual changes over the study area range respectively for the two projection periods were + 1.4%-+8.7% and + 3%-+14.2%. The projected annual PET increase trends are consistent across the entire region and for the 6 climate models. Higher annual changes are projected in the northeast part of the region, while smaller changes are projected along the pacific coast. The main drivers for the increase are the projected warming and increase in the vapor pressure deficit. The projected changes in PET, which represent the changes in the atmospheric evaporative demand, are substantial and likely to impact vegetation and the hydrometeorological regime in the area. Introduction Climate change impacts on rainfall and temperature patterns and the effect of these changes in the North American Monsoon (NAM) region (Southwest U.S. and Mexico) is an active research topic (a few examples: Wang et al., 2021; Pascale et al., 2017 and 2019; Hernandez and Chen, 2022; Shamir et al., 2015 and 2021). While the effects on precipitation is well studied, a less studied topic, which is the focus of this study, is the impact of climate change on the atmospheric evaporative demand (AED) in the NAM region. The AED represents the upper limit of actual evapotranspiration when water availability is unlimited. Changes in AED impact the hydrological cycle to alter water resources availability, soil moisture conditions, runoff production from rainfall events, water storage in surface and subsurface reservoirs, vegetative land cover, and drought severity. AED is linked to the NAM dynamics by influencing the interplay between enhancing tropospheric stability that suppress convection to increase evaporation that in turn increases moisture for convective activity (e.g., Pascale et al., 2019). Moreover, evapotranspiration in the NAM region is a major source of moisture for convective precipitation events (e.g., Hu and Dominguez, 2015; Feng and Houser, 2015). evapotranspiration in the NAM region is a major source of moisture for convective precipitation events (e.g., Hu and Dominguez, 2015; Feng and Houser, 2015). Projecting changes in future AED is a challenging task because it depends on changes of various near- surface atmospheric variables that represent the radiative and aerodynamic state of the atmosphere. The radiative state represents the energy available to vaporize water and it is estimated by temperature and net radiation. The aerodynamic state represents that capacity of the air to store and remove water Page 2/28 Page 2/28 and estimated by wind and vapor pressure deficit. A common method to assess the AED is by estimating the Potential Evapotranspiration (PET), which is the evaporation that would occur when sufficient water source at the land surface is available. A review of 55 worldwide studies of observed pan evaporation datasets pointed to declining evaporation since the second half of the 20th century (McVicar et al. 2012). This historical declining trend, as measured by pan evaporation, was also shown in several studies from the Southwest U.S and Mexico (Ruiz-Alvarez et al., 2019; Magallanes Quintanar et al., 2019; Breña-Naranjo et al., 2016; Blanco-Macías et al., 2011; Groisman et al. 2004). Introduction This reduction in evaporation demand may be seen as counterintuitive to the concurrent observed warming trend (Cuervo-Robayo et al., 2020; Magallanes Quintanar et al., 2019; Shamir et al., 2021). The causes for the decline in pan evaporation are yet inconclusive and various explanations have been provided, such as an increase in cloudiness that in conjunction of aerosols presence causing a reduction in shortwave radiation (Roderick et al. 2009; Stanhill and Cohen, 2001), changes in the aerodynamic component such as reduced wind speeds (Groisman et al., 2004; Pryor et al., 2009; Roderick et al., 2009) and decreased vapor pressure deficit (Hobbins et al., 2004); and other factors such as declines in El Nino Southern Oscillation and cyclical sunspot activity (Magallanes Quintanar et al., 2019; Blanco-Macías et al., 2011). Another possible reason for the observed historical decline may be attributed to the deficiency of pan evaporation to represent AED in water-limited environments. This is because in these water-limited regions the unused energy at the land surface increase the sensible heat flux from the ground, a process that is not being accounted for in pan evaporation (Brutsaert and Parlange, 1998). Notwithstanding the observed historical declining trend, using output from Global Climate Models (GCM), Cook et al., (2014) projected globally widespread increases in PET. The projected future PET increase was attributed to projected increases in surface net radiation and vapor pressure deficit. The highest PET increases are projected for the mid-latitudes of the Northern Hemisphere and in western North America, Europe, and southeast China. Other GCM studies for the conterminous U.S. also projected PET increases (Dewes et al., 2017; Ficklin et al., 2016). In Mexico, Martinez-Sifuentes et al., (2023) projected increase PET for northern part of the state of Durango in north-central Mexico, using a PET equation that considers only air surface temperature. Mundo-Molina (2015) estimated an increase in annual PET that can reach 8% in Northern Mexico for a climate change scenario of temperature increase by 3°C over the entire country. Since the NAM region is dominated by regional (mesoscale) processes, its representation by relatively coarse GCMs is challenging (e.g. Castro et al. 2012 and 2017; Bukovsky et al. 2013 and; 2015; Geil et al. 2013). Dynamical downscaling with regional climate models (RCMs) for longer-term climate simulations has shown skill in capturing climate variability, depending on the region of study and storm types (Prein et al., 2013; Qing and Wang, 2021). Introduction For future climate projections, RCMs with dynamical downscaling generally improve the representation of mean precipitation changes and convective precipitation (e.g. Chang et al. 2015, Kendon et al. 2017), as compared to the GCM projections. Page 3/28 In this study we assess the projected changes in annual and monthly PET in the NAM region using terrestrial meteorological variables from dynamically downscaled simulations of six Coupled Model Intercomparison Project Phase 5 (CMIP5) Representative Concentration Pathways 8.5 (RCP8.5) GCMs as input to the daily Penman-Monteith equation. In this study we assess the projected changes in annual and monthly PET in the NAM region using terrestrial meteorological variables from dynamically downscaled simulations of six Coupled Model Intercomparison Project Phase 5 (CMIP5) Representative Concentration Pathways 8.5 (RCP8.5) GCMs as input to the daily Penman-Monteith equation. PET Equation. RN Δ γ where is net daily radiation at the vegetated surface (MJ m− 2 d− 1) calculated as the difference between incoming net shortwave radiation and outgoing net longwave radiation (as described in Allen et al., 1998), G is heat flux into the ground (MJ m− 2 d− 1), which is assumed negligible at the daily time scale, is the slope of the vapor pressure as a function of temperature curve (kPa oC−1), is the psychrometric constant (kPa °C− 1), Ta is mean daily air temperature (°C), VPD is vapor pressure deficit (kPa), which is calculated as the difference between the saturated and actual vapor pressure, and u2 is average daily wind speed at 2m above ground elevation (m s− 1). The daily near-surface (i.e., 2-meter elevation above ground) atmospheric variables that are required as input for the equation are temperature, incoming short wave radiation, specific humidity, wind speed, and atmospheric pressure. The implementation of this equation followed the procedure outlined by Allen et al., (1998). RN Δ γ PET Equation. To estimate PET we used the FAO-56 reference crop PET equation that is often named the standardized reference evapotranspiration equation (Allen et al., 1998). In contrary to ET that represents an upward water flux from soil, free water, and vegetation, PET indicates the demand of water from the atmosphere and is calculated using terrestrial meteorological variables that represent the radiative and aerodynamic state of the atmosphere. The FAO-56 reference crop equation was developed to estimate evapotranspiration from a well-watered vegetated surface using the Penman-Monteith equation for a reference crop with a height of 0.12 m, surface resistance of 70 s/m− 1, and albedo of 0.23. The FAO-56 equation for daily PET in millimeters is written as follows: PET = , 0.408Δ (Rn −G) + γ u2V PD 900 Ta+273 Δ + γ(1 + 0.34u2) where is net daily radiation at the vegetated surface (MJ m− 2 d− 1) calculated as the difference between incoming net shortwave radiation and outgoing net longwave radiation (as described in Allen et al., 1998), G is heat flux into the ground (MJ m− 2 d− 1), which is assumed negligible at the daily time scale, is the slope of the vapor pressure as a function of temperature curve (kPa oC−1), is the psychrometric constant (kPa °C− 1), Ta is mean daily air temperature (°C), VPD is vapor pressure deficit (kPa), which is calculated as the difference between the saturated and actual vapor pressure, and u2 is average daily wind speed at 2m above ground elevation (m s− 1). The daily near-surface (i.e., 2-meter elevation above ground) atmospheric variables that are required as input for the equation are temperature, incoming short wave radiation, specific humidity, wind speed, and atmospheric pressure. The implementation of this equation followed the procedure outlined by Allen et al., (1998). Climate Model Projections Dynamically Downscaled climate projections of the CMIP5 GCMs are available from the North America Coordinated Regional Climate Downscaling Experiment (NA-CORDEX) program (https://na-cordex.org/; Mearns et al. 2017), an initiative sponsored by the World Climate Research Program to provide regional climate downscaling data for regional climate change adaptation and impact assessment. Although the Intergovernmental Panel on Climate Change (IPCC) has already published the Sixth Assessment Report (AR6) in 2021, as of November 2023, dynamically downscaled projections of the GCM simulations that supported the AR6 are not readily available for the study region. We retrieved six dynamically downscaled projections from the NA-CORDEX of GCMs that were forced by the Representative Concentration Pathway (RCP) 8.5 greenhouse gas and aerosol emission scenario. This set of six Page 4/28 Page 4/28 projections consists of three GCMs that were downscaled to a 25 km horizontal grid resolution by two different Regional Climate Models (RCMs). The GCMs are the HadGEM2-ES (Global Environmental Model, Version 2 from the United Kingdom Meteorological Office, the Hadley Centre); the MPI-ESM-LR (Earth System Model) running on the low resolution (LR) grid from the Max Planck Institute for Meteorology; and the GFDL-ESM2M from the NOAA Geophysical Fluid Dynamics Laboratory, U.S. using the Earth System Model version 2. Each of these three GCMs were downscaled for the domain of the NA-CORDEX program using two different RCMs. The first RCM is the Advanced Research version of the Weather Research and Forecasting (WRF) model (Version 3.4, Skamarock et al. 2005) that is supported by the National Center for Atmospheric Research, which is responsible for WRF development, management and user support. The configuration and parameterization of the WRF model is described in Chang et al. (2015) and Castro et al. (2017). The second RCM, RegCM4 is supported by the Regional Climate Research Network, a network of scientists coordinated by the Earth System Physics section of the Abdus Salam International Centre for Theoretical Physics (ICTP http://users.ictp.it/RegCNET/). Both RCMs the WRF and RegCM4 are open development community models. The NA-CORDEX experimental design can be found in Mearns et al. 2017 and Bukovsky and Mearns 2020. The three GCMs were selected to be dynamically downscaled because of their representation of a range of North America climate sensitivities (Sheffield et al., 2013a, Sheffield et al., 2013b). Climate Model Projections They were also found to represent well the global air temperature, atmospheric pressure, wind, and solar radiation patterns as well as the Western US regional temperature, precipitation, sea level pressure, and El Niño/Southern Oscillation variability (Cayan & Tyree, 2015). In addition, the selected GCMs were found to represent the large-scale synoptic features of the NAM (Geil et al., 2013). These GCMs were previously used in numerous climate impact assessments for the region (e.g., Gupta et al., 2023; Bearup and Gangopadhyay, (2021); Tapia et al., (2020); Shamir and Halper, (2019); Shamir et al., (2019); Shamir et al., (2015). In this study we used these six climate projections to assess two future horizon periods (i.e., 2020–2039 and 2040–2059). These two projected future periods were compared to the simulated historical period of 1986–2005. In this study we used these six climate projections to assess two future horizon periods (i.e., 2020–2039 and 2040–2059). These two projected future periods were compared to the simulated historical period of 1986–2005. Results Historical Data Historical Data We used data from TerraClimate to calculate the climatological PET for the NAM region (Fig. 1). TerraClimate is a ~ 4km (1/24th degree) monthly climatological dataset of global terrestrial surface meteorological fluxes (i.e., maximum and minimum temperature, vapor pressure, precipitation accumulation, downward surface shortwave radiation, wind-speed) with data updated annually and available since 1958 (Abatzoglou et al., 2018). We note that, as far as we know, this is the only observation-based climatological datasets that include all the variables needed as input for the FAO-56 equation. In Fig. 1 the PET annual climatologies were calculated using Eq. 1 with the 1986–2005 Page 5/28 monthly climatological variables as input. The 20-year average annual values range from 750 to 2436 mm/year with a regional average of 1456 mm/year. The spatial distribution shows the highest annual PET in southeastern California and western Arizona, as well as another high-evaporation region that is centered at the southeast border of New Mexico with a clear decline in the northward and eastward directions. To evaluate the annual variability of the PET estimates for the analysis period, in Fig. 2 the spatial distribution of the maximum, minimum, and the difference between these are shown. The regional average of the annual PET difference is 266 mm/year with lowest and highest differences being 69 and 397 mm/year, respectively. It can be seen that for most of Mexico the PET difference between the maximum and the minimum annual PET did not exceed 200 mm/year, while higher ranges are found north of the U.S.-Mexico border with the highest differences seen in Kansas and Northern Nevada. Although this distinct differences in the PET ranges between the two countries may be attributed to climatological differences, it may also be because of the differences between the two countries’ datasets that were used to derive the climatological dataset. Although the TerraClimate dataset is used in this study as the quantitative ground truth measure, we would like to recognize its sources of epistemic uncertainties. The main sources of uncertainties in the PET estimates are the large differences in number of observation stations among the various meteorological variables, the variety of sources of data with differences in quality and reporting times, and the uncertainties associated with the selection of the interpolating and extrapolating procedures. Results In addition, the standardized reference evapotranspiration equation used herein is a nonlinear equation and therefore the use of monthly average variables to calculate daily PET will not necessarily yield the average monthly PET values as calculated daily. The 20-year average annual climatologies of the TerraClimate meteorological variables for the 1986–2005 period that were used in Eq. 1 are shown in Fig. 3. PET Projections Quantitative historical PET simulations by climate models are often inaccurate because of biases in the meteorological variables, and consequently the PET quantitative projections of the future period are highly uncertain (e.g. Shi et al. 2020; Donohue et al. 2010). Thus, in this analysis, rather than looking at quantitative PET projections, we assessed the percent changes from the historical to the future periods of interest. The relative changes were calculated as the ratio between the difference of the future and historical periods and the historical period as expressed in the equation below: δPET (dur) = × 100 PET (dur)future −PET (dur)historical PET (dur)historical δPET (dur) = × 100 PET (dur)future −PET (dur)historical PET (dur)historical 2 where is the calculated change in percent (%), dur indicates the duration of the analysis of change (e.g. monthly, seasonal, annual), and the future and historical subscripts refer to the periods of the climate model simulations. δ where is the calculated change in percent (%), dur indicates the duration of the analysis of change (e.g. monthly, seasonal, annual), and the future and historical subscripts refer to the periods of the climate model simulations. δ Page 6/28 In the analysis presented in the upper panels of Fig. 4, the 20-year arithmetic average of the annual changes are shown for the two future projection periods (2020–2039 and 2040–2059). The average annual changes and other statistical indices were calculated for each grid cell from a statistical sample that contains 2,400 estimates of percent annual change. The 2,400 annual PET changes were calculated for each of the six climate models for 400 combinations (20 historical years x 20 projection years). It is seen in Fig. 4 that PET is projected to increase across the entire North American Monsoon region. This PET increase is projected to amplify during 2040–2059. The regions that are projected to have higher changes are the high elevation mountain ranges along the Sierra Madre Occidental and Sierra Madre del Sur and also the Sierra Madre Oriental, while smaller changes are projected in the Central Mexican Plateau and along the Pacific coast. In the lower panels of Fig. 4 the number of models (out of the six climate model projections used in this study) that projected future changes significantly different from the simulated historical period (1985– 2005). The statistical significance test is calculated from the 2-sample non-parametric Kolmogorov- Smirnov (KS) hypothesis test with α assigned to 0.05. PET Projections We note that the KS significant test results were comparable to results obtained from Student’s t-test. For the entire region of analysis, at least three of the projections showed that the projected PET was significantly different than the distribution of the simulated historical period. It is also seen that for the further away future period (2040–2059), the annual PET projections, in most of the region, were found to be significantly different than the historical period by the six climate models. It appears that the area with largest agreement among the models on the projected future being significantly different that the historical period is the longitudinal band that includes the Sierra Madre Occidental and the Sierra Madre Del Sur. In general, the 2020–2039 projections of PET annual changes have an overall west-to-east pattern. In the western coastal region, the annual PET changes are projected to be less than 5%, while farther east towards the Sierra Madre Occidental the projected changes are about 7–8%. The changes are projected to decrease moving eastward towards the Mexican Plateau and to increase again at the Sierra Madre Oriental. A similar pattern is shown for the 2040–2059 projections but with larger projected annual changes that exceed 15%. In Table 1 the annual PET regional statistics of the six climate models are summarized. It can be seen that the average projected change for 2020–2039 and 2040–2059 over the entire study area are 4.0% and 7.0%, respectively. It is interesting to note that although the signal shows projected increase in annual PET overall, an average of only 77% and 87% of the statistical samples show positive changes for 2020–2039 and 2040–2059, respectively. Page 7/28 Table 1 Areal average of PET changes statistics   2020–2039 2040–2059 Average 4.0% 7.0% Median 3.6% 6.5% 95th percentile 14.9% 18.5% Minimum 20-year average 1.4% 3.0% Maximum 20-year average 8.7% 14.2% 5th percentile -5.4% -2.6% Standard deviation 6.2% 6.5% Positive change 77% 87% Table 1 Table 1 Areal average of PET changes statistics To represent the spatial variability of the spread in the distribution of projected annual changes in PET, Fig. 5 shows the ranges between the 95th and 5th percentiles of the PET annual changes for the two projection periods. PET Projections It is seen that that although there a clear increase in annual PET changes from the near future to the far future, the spatial distribution of the PET annual change ranges are almost similar between the two projection periods. An interesting pattern seen in this plot is the generally increasing gradient from west-to-east and south-to-north. The largest ranges of annual changes, which are larger than 55%, are seen in the northeast while smaller ranges (< 10%) are seen for example along the Pacific coast. These differences of ranges can be attributed to greater inter-annual variability of the annual PET, which we attempted to capture in Fig. 2. However, these ranges may also be attributed to the uncertainty that stems from the differences among the climate projections, which is explored in the following analysis. In Fig. 6 we show scatter plots of all the climate models grid cells projected average changes in the annual PET as a function of the (a) grid cells elevation and (b) the average 6-model simulated historical average annual PET (mm/year). It is seen that the projected annual PET changes is positively correlated with the grid cell elevation (Correlation coefficients (R) of 0.62 and 0.75 for the near and far future, respectively). On the other hand the projected anuual change of PET is negatively correlated with the historical simulations of the annual PET (R -0.46 and − 0.59 for the near and far future, respectively). These two factors (elevation and historical simulations) although exhibiting substantial correlations are, as seen by the large scatter in Fig. 6, are limited predictors of the projected annual change. It is also observed the GCMs that were downscaled by the RegCM showed considerable higher correlation values than the GCMs that were downscaled by the WRF. In Fig. 6 we show scatter plots of all the climate models grid cells projected average changes in the annual PET as a function of the (a) grid cells elevation and (b) the average 6-model simulated historical average annual PET (mm/year). It is seen that the projected annual PET changes is positively correlated with the grid cell elevation (Correlation coefficients (R) of 0.62 and 0.75 for the near and far future, respectively). On the other hand the projected anuual change of PET is negatively correlated with the historical simulations of the annual PET (R -0.46 and − 0.59 for the near and far future, respectively). PET Projections These two factors (elevation and historical simulations) although exhibiting substantial correlations are, as seen by the large scatter in Fig. 6, are limited predictors of the projected annual change. It is also observed the GCMs that were downscaled by the RegCM showed considerable higher correlation values than the GCMs that were downscaled by the WRF. Page 8/28 While in the upper panels of Fig. 4 we show the average of the 6 climate models, in Figs. 7 and 8 the projected annual changes indicated by the individual models are shown for 2020–2039 and 2040–2059, respectively. All six models projected an overall positive changes in annual PET over most of the region. It can also be seen that within individual model, the annual PET increases from the early to mid 21st century (Figs. 7 and 8, respectively). However, the models do not always agree among themselves on the spatial pattern of the annual PET changes. It can also be seen that within individual model, the annual PET increases from the early to mid 21st century (Figs. 7 and 8, respectively). However, the models do not always agree among themselves on the spatial pattern of the annual PET changes. In general, it can be seen that the GCMs that were downscaled with the RegCM model show PET annual changes that are overall larger than the GCMs that were downscaled with the WRF model. It can also be seen, for instance, that while the GFDL-RegCM and MPI-WRF showed the lowest changes in southern Texas, for the same region the MPI-RegCM, Had-RegCM and GFDL-WRF showed their largest projected changes. Another example of a notable difference is seen between MPI-WRF and GFDL-WRF in the eastern region. There are noticeable differences among the GCMs and their representation of the regional atmosphere and surface meteorological variables. In this study we assumed that the 6 climate models are equally skillful in their PET simulations. Thus although all models agree that PET is projected to increase, the spatial distribution of the changes is rather uncertain. In order to assess the main causes for the projected annual PET increase, we analyzed the changes in meteorological variables considered in the PET equation (Fig. 9). As expected, both minimum and maximum temperature are showing significant projected warming. The projected annual changes in wind speed and surface radiation were found not to be significantly different than during the historical period. PET Projections Another flux that shows a clear signal of significant projected increase is the specific humidity, which is associated with temperature because warmer air can hold more water vapor. Increases in specific humidity for a given temperature decreases the Vapor Pressure Deficit (VPD), which as can be seen in Eq. 1, decreases the daily PET. The VPD (i.e. the difference between the actual specific humidity and the specific humidity at saturation) indicates the maximum amount of water that can be evaporated. The sensitivity of VPD to changes in temperature and specific humidity as calculated with the Clausius– Clapeyron equation is demonstrated in Fig. 10. It can be seen in this figure that for a given temperature, an increase in the actual specific humidity, as expected, decreases the VPD. However, increases in temperature for a given specific humidity increase the VPD, which in turn would increase the PET. Monthly Changes The regional interannual average of monthly PET as calculated using the TerraClimate variables is shown in Fig. 11. In Figs. 12 and 13 the average projected percent changes of monthly PET are shown for 2020– 2039 and 2040–2059, respectively. Table 2 provides the estimated regional average monthly PET and the regional projected changes for the two projection periods. It is interesting to note that PET is projected to increase for all months, except for a projected PET decrease in November-December for the 2020–2039 period. We note that the largest projected increases are expected during March-April and the lowest are in November-December. Evaluating the spatial extent of the projected monthly PET changes it is seen that for the near future some negative changes are projected during September-January mainly at the northern portion of the region (Fig. 12). For the far future (Fig. 13) the projected negative changes in PET are seen only for November – December and in higher latitudes. Page 9/28 Page 9/28 Table 2 Areal average monthly PET and projected changes for the two projection periods. TerraClimate 1986–2005 (mm/month) Projected Change 2020–2039 Projected Change 2040–2059 Jan 71 5.8% 7.9% Feb 91 5.7% 12.6% Mar 119 7.8% 13.9% Apr 145 9.4% 12.6% May 161 7.9% 9.5% Jun 167 4.7% 7.3% Jul 166 3.8% 6.2% Aug 156 2.6% 5.2% Sep 129 2.3% 5.3% Oct 107 1.0% 6.2% Nov 83 -2.0% 3.8% Dec 68 -1.9% 5.8% Annual 1483(mm/year) 3.9% 8.0% Table 2 Discussion In this study we projected the future changes in annual and monthly PET using terrestrial meteorological variables from six dynamically downscaled climate models as input to the daily standardized Penman- Montieth equation. In the following we discuss the potential caveats and sources of uncertainties in our analysis. First we note that the study relied on six CMIP5 RCP8.5 dynamically downscaled projections from the NA-CORDEX. Although CMIP6 GCMs are already available since 2019, at the time of writing, the NA-CORDEX are the only available community standardized dynamically downscaled regional climate model simulations for the study region. Although the analysis is limited to RCP 8.5 emission scenario and the estimated uncertainty is based on analysis of 6 ensemble members, as far as we know, these results reflects the most recently available state-of-the-art projections. As discussed in the Results section, in some cases the six climate projections disagree on the spatial variability of the projected changes. Despite these differences, overall the models are highly cross- correlated, as can be seen in Table 3. In this table the correlation coefficient of the average areal PET historical period ranges from 0.62 to 0.97. We note that lower correlation coefficients are obtained when Page 10/28 the cross-correlation is derived between GCMs that were downscaled by WRF and RegCM, while when the same RCM is used the cross-correlation coefficients are greater than 0.95. Table 3 Correlation coefficients of the average areal PET of the historical period (1985–2005) among the six climate models. Had-WRF GFDL-WRF MPI-RegCM Had-RegCM GFDL-RegCM MPI-WRF 0.96 0.95 0.68 0.70 0.62 Had-WRF   0.97 0.70 0.74 0.66 GFDL-WRF     0.69 0.74 0.70 MPI-RegCM       0.97 0.95 Had-RegCM         0.97 The PET estimates in this study are based on projected changes in terrestrial meteorological variables. These estimates neglect to consider the physiological adaption of vegetation to increased concentrations of atmospheric carbon dioxide. Studies have shown that various plant species have adapted to reduce stomatal conductance to decrease transpiration when atmospheric evaporative demand is high (e.g., Vicente-Serrano et al., 2022). However, this adaptation is highly dependent on the vegetation type and on the ecosystems’ response to elevated CO2. Notwithstanding the potential limitations described above, we believe that the approach used in this study points to a clear trend in projected monthly and annual PET changes, and that the use of six projections provides uncertainty bounds that can be used for decision making and risk analysis studies. Author Contribution E.S wrote the main manuscript text and created the figures. L.M-F collected and assembled the datasets for the analysis All authors reviewed the manuscript and provided constructive comments. Acknowledgements The project is funded by the Frasnillo Plc as part of grant titled ‘Ensemble-based Climate Assessments for Fresnillo Mining Sites in Mexico’. Spatial thanks are extended to our collaborators from Fresnillo Mr. Exequiel Rolon and Ms. Alicia del Carmen Sanchez Rangel. Exequiel Rolon and Ms. Alicia del Carmen Sanchez Rangel. Summary The projected average 20-year annual changes over the study area range respectively for the two projection periods were + 1.4%-+8.7% and + 3%-+14.2%. In general, the higher values of annual changes were found in the northeast part of the region, while smaller changes are projected along the pacific coast. The projected annual PET increase trends are consistent across the entire region and for the 6 climate models. The main drivers for the increase are the projected warming and increase in the vapor pressure deficit. The projected changes in PET, which represent the changes in the atmospheric evaporative demand, are substantial and likely to impact vegetation and the hydrometeorological regime in the area. Our analysis provides a probabilistic characterization of the PET changes that describe their interannual and spatial variability in addition to the associated uncertainties. These probabilistic indices can be used in local climate change risk analysis studies that assess the impacts of various agricultural practices and water resources management strategies. Summary In this study we assessed the climate change impacts on PET in the Southwest US and Mexico. To assess these changes we used an ensemble of daily terrestrial meteorological variables from six CMIP5 RCP8.5 dynamically downscaled climate projections that followed the standards set by the NA-CORDEX initiative. These climate projections are from three GCMs that were found to represent the study region well (HadGEM2-ES, MPI-ESM-LR and GFDL-ESM2M) and each was downscaled by two regional (mesoscale) models (WRF and RegCM). The terrestrial meteorological variables from these six models, which include minimum and maximum temperature, wind speed, specific humidity, pressure, precipitation, and incoming short-wave radiation, were used as input to the FAO-56 reference crop daily PET equation. The projected future changes in the annual and monthly PET were assessed by comparing the historical period (1986–2005) of the climate models’ simulations to simulations of two future projection periods (2020–2039 and 2040–2059). As a quantitative PET reference for the historical period (1986–2005), we used the 4km-resolution monthly climatological variables available from the TerraClimate dataset. Page 11/28 Our study provides a statistical distribution for each grid cell of the dynamically downscaled models that represents the projected changes in the annual and monthly PET for the two projection periods. Although some of the ensemble members projected a slight decline in annual PET, in general over the entire region the average 20-year annual change is + 4% and + 7% for 2020–2039 and 2040–2059 (Table 1), Our study provides a statistical distribution for each grid cell of the dynamically downscaled models that represents the projected changes in the annual and monthly PET for the two projection periods. Although some of the ensemble members projected a slight decline in annual PET, in general over the entire region the average 20-year annual change is + 4% and + 7% for 2020–2039 and 2040–2059 (Table 1), respectively. The projected average 20-year annual changes over the study area range respectively for the two projection periods were + 1.4%-+8.7% and + 3%-+14.2%. In general, the higher values of annual changes were found in the northeast part of the region, while smaller changes are projected along the pacific coast. The projected annual PET increase trends are consistent across the entire region and for the 6 climate models. The main drivers for the increase are the projected warming and increase in the vapor pressure deficit. respectively. References 1. Abatzoglou, J.T., S.Z. Dobrowski, S.A. Parks, K.C. Hegewisch, 2018, Terraclimate, a high-resolution global dataset of monthly climate and climatic water balance from 1958-2015, Scientific Data, 2. Allen, R. G., Pereira, L. S., Raes, D., and Smith, M.: Crop evapotranspiration Guidelines for computing crop water requirements, FAO Irrigation and Drainage Paper 56, Food and Agriculture Organization of the United Nations, 1998 3. Bearup, L. and S Gangopadhyay, 2021. Lower Santa Cruz River Basin Study Hydroclimate Analysis. A Technical Memorandum No. ENV-2021-35, Bureau of Reclamation. 3. Bearup, L. and S Gangopadhyay, 2021. Lower Santa Cruz River Basin Study Hydroclimate Analysis. A Technical Memorandum No. ENV-2021-35, Bureau of Reclamation. 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Climate change and water resources management in the Upper Santa Cruz River, Arizona. Journal of Hydrology. 521: 18-33. https://doi.org/10.1016/j.jhydrol.2014.11.062 44. Sheffield et al., 2013. North American Climate in CMIP5 Experiments. Part I: Evaluation of Historical Simulations of Continental and Regional Climatology J. Clim., 26 (2013), pp. 9209-9245, 10.1175/JCLI-D-12-00592.1 45. Sheffield et al. 2013. 50. Vicente-Serrano SM., DG. Miralles, N. McDowell, T. Brodribb, F. Domínguez-Castro, R. Leung, and A. Koppa. 2022 The uncertain role of rising atmospheric CO2 on global plant transpiration, Earth- Science Reviews, 230: 2022,104055, ISSN 0012-8252, https://doi.org/10.1016/j.earscirev.2022.104055. References North American Climate in CMIP5 Experiments. Part II: Evaluation of Historical Simulations of Intraseasonal to Decadal Variability J. Clim., 26 (2013), pp. 9247-9290, 10.1175/JCLI- D-12-00593. 46. Shi, L., P. Feng, B. Wang, D.L. Liu, J. Cleverly, Q. Fang, Q. Yu, (2020) Projecting potential evapotranspiration change and quantifying its uncertainty under future climate scenarios: A case study in southeastern Australia. Journal of Hydrology, 584, 124756, ISSN 0022-1694, https://doi.org/10.1016/j.jhydrol.2020.124756. 47. Skamarock WC, Klemp JB, Dudhia J, Gill DO, Barker DM, Wang W, Powers JG (2005) A description of the advanced research WRF version 2. NCAR Tech. Note NCAR/TN-468+STR 48. Stanhill, G. and S. Cohen, “Global dimming: a review of the evidence for a widespread and significant reduction in global radiation with discussion of its probable causes and possible agricultural consequences,” Agricultural and Forest Meteorology, 107: 255–278, 2001, doi:10.1016/S0168 1923(00)00241-0. 49. Tapia-Villaseñor, E.M.; Shamir, E.; Megdal, S.B.; Petersen-Perlman, J.D. Impacts of Variable Climate and Effluent Flows on the Transboundary Santa Cruz Aquifer. JAWRA J. Am. Water Resour. Assoc. 2020, 56, 409–430. 50. Vicente-Serrano SM., DG. Miralles, N. McDowell, T. Brodribb, F. Domínguez-Castro, R. Leung, and A. Koppa. 2022 The uncertain role of rising atmospheric CO2 on global plant transpiration, Earth- Science Reviews, 230: 2022,104055, ISSN 0012-8252, https://doi.org/10.1016/j.earscirev.2022.104055. Figures Figures Page 16/28 Figure 1 Annual PET calculated from the monthly data of the TerraClimate database. Figure 1 Annual PET calculated from the monthly data of the TerraClimate database. Page 17/28 Figure 2 Maximum (left), minimum (center), and the range (right) of 1986-2005 annual PET as calculated for the region from TerraClimate. Figure 2 Figure 2 Maximum (left), minimum (center), and the range (right) of 1986-2005 annual PET as calculated for the region from TerraClimate. Maximum (left), minimum (center), and the range (right) of 1986-2005 annual PET as calculated for the region from TerraClimate. Page 18/28 gure 3 nual averages (1986-2005) of precipitation, maximum and minimum daily temperature, daily incoming lar radiation, wind speed, and vapor pressure deficit as available from TerraClimate Figure 3 Figure 3 Annual averages (1986-2005) of precipitation, maximum and minimum daily temperature, daily incoming solar radiation, wind speed, and vapor pressure deficit as available from TerraClimate Annual averages (1986-2005) of precipitation, maximum and minimum daily temperature, daily incoming solar radiation, wind speed, and vapor pressure deficit as available from TerraClimate Annual averages (1986-2005) of precipitation, maximum and minimum daily temperature, daily incoming solar radiation, wind speed, and vapor pressure deficit as available from TerraClimate Page 19/28 gure 4 ojected annual changes in PET for the North American Monsoon region from 1986-2005 to eft) and to 2040-2059 (right). The upper plots are the 20-year average percent annual chang ojected the six NA-CORDEX climate models. The lower plots are the number of models (out elded a significant difference in the annual PET between the historical period and the future Figure 4 Projected annual changes in PET for the North American Monsoon region from 1986-2005 to 2020-2039 (left) and to 2040-2059 (right). The upper plots are the 20-year average percent annual changes as projected the six NA-CORDEX climate models. The lower plots are the number of models (out of 6) that yielded a significant difference in the annual PET between the historical period and the future projections using a KS test (alfa = 0.05). Figure 4 Figure 4 Projected annual changes in PET for the North American Monsoon region from 1986-2005 to 2020-2039 (left) and to 2040-2059 (right). The upper plots are the 20-year average percent annual changes as projected the six NA-CORDEX climate models. The lower plots are the number of models (out of 6) that yielded a significant difference in the annual PET between the historical period and the future projections using a KS test (alfa = 0.05). Page 20/28 Page 20/28 Figure 5 The areal statistics of the projected annual PET expressed as the range of change between the 95th and 5th percentiles Figure 5 The areal statistics of the projected annual PET expressed as the range of change between the 95th and 5th percentiles The areal statistics of the projected annual PET expressed as the range of change between the 95th and 5th percentiles Page 21/28 Figure 6 The annual PET changes as a function of elevation (a) and average simulate historical annual PET (b) Figure 6 The annual PET changes as a function of elevation (a) and average simulate historical annual PET (b). The annual PET changes as a function of elevation (a) and average simulate historical annual PET (b). Page 22/28 7 rage 2020 2039 projected annual change of PET (%) for the six climate models gure 7 Figure 7 The average 2020-2039 projected annual change of PET (%) for the six climate models. Figure 8 Figure 8 As in Figure 7 but for 2040-2059 As in Figure 7 but for 2040-2059 Page 23/28 Figure 9 Figure 9 The 2020-2039 (left) and 2040-2060 (right) annual projected changes of the average 6-climate models for the terrestrial variables that are used as input for the PET equation. The 2020-2039 (left) and 2040-2060 (right) annual projected changes of the average 6-climate models for the terrestrial variables that are used as input for the PET equation. The 2020-2039 (left) and 2040-2060 (right) annual projected changes of the average 6-climate models for the terrestrial variables that are used as input for the PET equation. Page 24/28 Page 24/28 Figure 10 The sensitivity of Vapor Pressure Deficit (VPD) to changes in temperature and specific humidity. Figure 10 The sensitivity of Vapor Pressure Deficit (VPD) to changes in temperature and specific humidity. Figure 10 The sensitivity of Vapor Pressure Deficit (VPD) to changes in temperature and specific humidity. The sensitivity of Vapor Pressure Deficit (VPD) to changes in temperature and specific humidity. Page 25/28 Figure 11 Figure 11 1986-2005 monthly average PET (mm/month) as calculated with TerraClimate terrestrial meteorological variables. 1986-2005 monthly average PET (mm/month) as calculated with TerraClimate terrestrial meteorological variables. Page 26/28 Figure 12 Average monthly changes in PET projected for 2020-2039 Page 27/28 Figure 13 Figure 13 As in Figure 12 but projected for 2040-2059. Page 28/28
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Learning Parameterized ODEs From Data
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INDEX TERMS Parameterized ordinary differential equations, neural networks, ODE solver. INDEX TERMS Parameterized ordinary differential equations, neural networks, ODE solver. The associate editor coordinating the review of this manuscript and approving it for publication was Derek Abbott . his work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons.org/licenses/by/4.0/ QING LI 1, STEINAR EVJE1, AND JIAHUI GENG 2, (Graduate Student Member, IEEE) 1Department of Energy and Petroleum Engineering, University of Stavanger, 4021 Stavanger, Norway 2Department of Electrical Engineering and Computer Science, University of Stavanger, 4021 Stavanger, Norway Corresponding author: Qing Li (qing.li@uis.no) This work was supported by the Department of Energy and Petroleum Engineering at the University of Stavanger, under Grant IN-125 QING LI 1, STEINAR EVJE1, AND JIAHUI GENG 2, (Graduate Student Member, IEEE) 1Department of Energy and Petroleum Engineering, University of Stavanger, 4021 Stavanger, Norway 2Department of Electrical Engineering and Computer Science, University of Stavanger, 4021 Stavanger, Norway Corresponding author: Qing Li (qing.li@uis.no) QING LI 1, STEINAR EVJE1, AND JIAHUI GENG 2, (Graduate Student Member, IEEE) 1Department of Energy and Petroleum Engineering, University of Stavanger, 4021 Stavanger, Norway 2Department of Electrical Engineering and Computer Science, University of Stavanger, 4021 Stavanger, Norway Corresponding author: Qing Li (qing.li@uis.no) This work was supported by the Department of Energy and Petroleum Engineering at the University of Stavanger, under Grant ABSTRACT In contemporary research, neural networks are being used to derive Ordinary Differential Equations (ODEs) from observations. However, parameterized ODEs pose a more significant challenge than non-parameterized ODEs since the networks are required to understand the roles of the parameters, i.e., the structure of the equations. This paper proposes a novel approach by combining Symbolic Neural Network (S-Net) with ODE Solver to solve this issue. First, S-Net learns the structure of the parameterized ODEs and then predicts the dynamics based on the new parameters with the new initial states. To assess its performance, we compare our approach with a widely used Ordinary Neural Network (O-Net) that directly learns and predicts ODEs. Our numerical experiments demonstrate that our approach outperforms O-Net when applied to the Lotka-Volterra and Lorenz equations. Received 18 April 2023, accepted 27 May 2023, date of publication 2 June 2023, date of current version 7 June 2023. Received 18 April 2023, accepted 27 May 2023, date of publication 2 June 2023, date of current version 7 June 2023. Digital Object Identifier 10.1109/ACCESS.2023.3282435 Learning Parameterized ODEs From Data QING LI 1, STEINAR EVJE1, AND JIAHUI GENG 2, (Graduate Student Member, IEEE) 1Department of Energy and Petroleum Engineering, University of Stavanger, 4021 Stavanger, Norway 2Department of Electrical Engineering and Computer Science, University of Stavanger, 4021 Stavanger, Norway Corresponding author: Qing Li (qing.li@uis.no) This work was supported by the Department of Energy and Petroleum Engineering at the University of Stavanger, under Grant IN-12570. VOLUME 11, 2023 This work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons I. INTRODUCTION works (PINNs) to solve data-driven solutions and data-driven discovery problems of partial differential equations (PDEs). Long et al. [6], [7] proposed PDE-Net, a feed-forward deep network that predicts the dynamics of complex systems and uncovers the underlying hidden PDE models. PDE-Net implemented Symbolic Neural Network (S-Net) to learn the structure of PDEs and demonstrated powerful learning abil- ity. Similarly, [8], [9] also proved the competitive general- ization capability of S-Net. These works show the potential of deep learning in solving PDEs and discovering hidden models. The combination of deep learning and differential equations is a highly promising research direction. Deep learning can help uncover the underlying differential equations governing the behavior of many systems, such as electromagnetism, aerodynamics, weather prediction, and geophysics. Dif- ferential equation-guided network design can significantly improve model interpretability and generalization perfor- mance. The potential impact of this approach on scientific discovery and innovation is immense. Chen et al. [1] introduced Neural Ordinary Differential Equations (NODEs), a new family of deep networks. They used a neural network to parameterize the derivative of the hidden state, serialized the neural network layers and param- eters, and used the adjoint ODE method to optimize the neural network instead of back-propagation, which saved memory. Their work inspired research on variants of NODE meth- ods, such as [2] and [3]. Other studies have also explored the potential of neural networks to learn and solve differ- ential equations. For example, Chen et al. [4] proposed the Symplectic Recurrent Neural Network (SRNN) to capture the dynamics of physical systems from regularly observed data. Raissi et al. [5] introduced physics-informed neural net- Parameterized ODEs are a class of ODEs with solutions that vary with parameters, representing multiple dynamics specified by input parameter instances. They have been extensively studied in computational science and engineering domains, such as fluid dynamics and the ideal pendulum sys- tem. In critical situations, computing high-fidelity solutions of parameterized ODEs is necessary, either for numerous input parameter instances or initial states. Data-driven meth- ods have been used in recent years to estimate the evolution of dynamical systems over time, including different initial conditions [10] and system parameters [11]. To learn the latent dynamics of complex dynamical processes in computa- tional physics, Lee and Parish [11] proposed encoder-decoder parameterized NODEs (PNODEs). I. INTRODUCTION Shimizu and Parish [12] presented the windowed space-time least-squares The associate editor coordinating the review of this manuscript and approving it for publication was Derek Abbott . 54897 Q. Li et al.: Learning Parameterized ODEs From Data Mesh-based simulations have recently shown significant progress [21], [22], surpassing grid-based convolutional neu- ral networks (CNNs) in terms of runtime and exhibiting greater adaptivity to the simulation domain. While sev- eral methods, such as AntisymmetricRNN [23] and the continuous-time Gated Recurrent Unit with a Bayesian update network [24], have leveraged the stability of underly- ing differential equations to capture long-term dependencies, they did not address the challenge of learning the expres- sion of the equation to gain a deeper understanding of the underlying mechanism behind the observed data. In another work [25], the authors learned the unknown parameters of the ODE system by constructing certain time-related features, but this method did not address the expressiveness of the equation. Petrov-Galerkin method (WST-LSPG) for model reduction of nonlinear parameterized dynamical systems. WST-LSPG divides the time simulation into several windows and sequen- tially minimizes the discrete-in-time residual within its own unique low-dimensional space-time subspace. Lee and Trask [13] introduced POUNODEs, a new variant of NODEs with evolving model parameters. They modeled the evolution using partition-of-unity networks, allowing for greater flex- ibility in capturing the dynamics of complex systems. To the best of our knowledge, the majority of existing approaches for solving parameterized ODEs rely on black- box methods, which employ neural networks directly to simulate its behavior and make predictions. Our proposed approach, on the other hand, aims to gain a deeper under- standing of the underlying mechanics of the dynamic system by first learning the structure of the ODEs. This understand- ing enables us to predict the behavior of the dynamical system more accurately and efficiently for new parameters and initial states compared to black-box methods. The contributions of this work are summarized as follows: A. NON-PARAMETERIZED AND PARAMETERIZED ODES Assume that ODEs take the following generic form, which is usually used to describe some physical dynamics with different functions f (s, p, r, α, β, γ), g(s, p, r, α, β, γ) and h(s, p, r, α, β, γ), • To evaluate our approach, we compare its performance with that of a baseline model, O-Net, which represents a black-box approach. We empirically demonstrate the advantages of our proposed framework in terms of both accuracy and interpretability.    ds dt = f (s, p, r, α, β, γ), dp dt = g(s, p, r, α, β, γ), dr dt = h(s, p, r, α, β, γ). (1) (1) The remainder of this paper is organized as follows: Section II presents related works. The considered parameter- ized ODEs problem and the ODE Solver are briefly intro- duced in Section III. Section IV illustrates the proposed approach. We evaluate the performance of our method on two case studies: the Lotka-Volterra Equation in Section V and the Lorenz Lotka-Volterra Equation in Section VI. Finally, in Section VII, we summarize our findings and discuss potential avenues for future research. Here, we consider the nonlinear ODE system with indepen- dent variables s, p, and r, and initial states s0, p0, and r0 at time t0. The system also involves parameters α, β, and γ, where t ∈(0, T] represents the time interval of interest. In non-parameterized ODEs, parameters such as α, β, and γ remain fixed during both model training and prediction, whether they are known or unknown. Thus, we assume that α = α1, β = β1, and γ = γ1, and denote the observations as: III. KNOWLEDGE In this section, we’ll define parameterized ODEs and dif- ferentiate them from non-parameterized ODEs. Additionally, we’ll introduce the ODE Solver, a crucial component in our approach. • Our proposed framework combines S-Net with an ODE solver to learn parameterized ODEs. This novel approach enables accurate and efficient modeling of the dynamics of complex systems, even when the properties of the governing equations vary across multiple input parameters. II. RELATED WORK Once we obtain the correct analytical formulas, we can accurately predict the system. In this context, the number of cars at positions x1 and x2 are represented by s and p, respectively, and the traffic flow changes over time at these locations are modeled using func- tions f and g. Here, t ∈(0, 24] denotes a day for a cycle, and the vector w represents external factors that influence traffic conditions, such as weather, temperature, and so on. We assume that the external factors w change daily, but the expressions for f and g remain constant as the mechanism by which each factor affects traffic flow remains the same. Once we obtain the correct analytical formulas, we can accurately predict the system. (3) is generated by different parameters (αk, βk, γk) at some specified time ti on different initial states (sj 0, pj 0, rj 0). Here, we define K > 0 as the number of parameters, Nobs > 0 as the number of observation time points, and M > 0 as the number of initial states. This approach is effective for discrete chaotic maps, using the Logistic map as an example. The Logistic map is a straightforward, one-dimensional discrete-time dynamical system characterized by the following equation: In the scenario of parameterized ODEs, if (s∗ 0, p∗ 0, r∗ 0 ) ∈ {(sj 0, pj 0, rj 0)|j = 1, . . . M} and (α∗, β∗, γ∗) ∈{(αk, βk, γk)| k = 1, . . . K}, we predict s(t∗; s∗ 0, p∗ 0, r∗ 0 , α∗, β∗, γ∗), p(t∗; s∗ 0, p∗ 0, r∗ 0 , α∗, β∗, γ∗), r(t∗; s∗ 0, p∗ 0, r∗ 0 , α∗, β∗, γ∗)  at t∗> tNobs. Otherwise, we predict the dynamics at t∗∈(0, T].i xn+1 = γxn(1 −xn). (5) (5) Parameterized ODEs find applications in various scenar- ios. For instance, in [26], different parameters associated with the ODEs represent distinct strategies for regulating cancer tumor progression behavior. Given patient data describing the evolution of a tumor, it would be advantageous to obtain the functional form of the ODE system underlying this complex system, both for the state variables and parameters. Subse- quently, once we have constructed the functional form of the ODE system using a neural network, we can directly compute solutions of the ODE for new initial states and parameter sets. Traffic flow problems represent another common application. II. RELATED WORK Changes in traffic flow over time at two specific locations x1, Here, x is the state variable at time step n, and γ is a parameter. We can employ the proposed method to learn the expression on the right side of (5), which means that the input of the S-Net consists of both γ and x. II. RELATED WORK Initial states s0, p0, r0 and parameters α, β, γ are fed into the ANN model to predict the derivatives of s, p, and r with respect to time. These derivatives combined with initial states s0, p0, r0 will be further fed into the ODE Solver to obtain the next state s1, p1, r1, and so on. Finally we will get the trajectories of S = {s0, s1, . . . sT }, P = {p0, p1, . . . , pT } and R = {r0, r1, . . . , rT }. FIGURE 1. Schematic diagram of the framework. Initial states s0, p0, r0 and parameters α, β, γ are fed into the ANN model to predict the derivatives of s, p, and r with respect to time. These derivatives combined with initial states s0, p0, r0 will be further fed into the ODE Solver to obtain the next state s1, p1, r1, and so on. Finally we will get the trajectories of S = {s0, s1, . . . sT }, P = {p0, p1, . . . , pT } and R = {r0, r1, . . . , rT }. Concerning the parameterized ODEs problem, the obser- vation data x2 in a city can be modeled as    ds dt = f (s, p, w), dp dt = g(s, p, w). (4) (4) Zvariable = n s(ti; sj 0, pj 0, rj 0, αk, βk, γk), p(ti; sj 0, pj 0, rj 0, × αk, βk, γk), r(ti; sj 0, pj 0, rj 0, αk, βk, γk)  i = 1, × . . . , Nobs, j = 1, . . . , M, k = 1, . . . , K} , (3) In this context, the number of cars at positions x1 and x2 are represented by s and p, respectively, and the traffic flow changes over time at these locations are modeled using func- tions f and g. Here, t ∈(0, 24] denotes a day for a cycle, and the vector w represents external factors that influence traffic conditions, such as weather, temperature, and so on. We assume that the external factors w change daily, but the expressions for f and g remain constant as the mechanism by which each factor affects traffic flow remains the same. II. RELATED WORK Zfixed = n s(ti; sj 0, pj 0, rj 0, α1, β1, γ1), p(ti; sj 0, pj 0, rj 0, α1, β1, × γ1), r(ti; sj 0, pj 0, rj 0, α1, β1, γ1)  i = 1, . . . , Nobs, × j = 1, . . . , M} . (2) Several studies have explored the use of Gaussian process regression to develop tailored functional representations for a given linear operator [14], [15], [16]. However, the local linearization of nonlinear terms in time and prior assump- tions of Gaussian process regression limit the representation capacity of the model. Sparse regression, discussed in [17], [18], [19], and [20], overcomes this limitation by developing a dictionary of basic functions and partial derivatives that can accurately represent the data using sparsity-promoting tech- niques. However, the predictive and expressive capabilities of the dictionary are restricted since the sparse regression method necessitates predefining specific numerical approx- imations for spatial differentiation. (2) The observations are denoted by a set of Nobs > 0 time points, and the number of initial states is denoted by M > 0. If (s∗ 0, p∗ 0, r∗ 0 ) ∈ {(sj 0, pj 0, rj 0)|j = 1, . . . M}, we predict s(t∗; s∗ 0, p∗ 0, r∗ 0 , α1, β1, γ1), p(t∗; s∗ 0, p∗ 0, r∗ 0 , α1, β1, γ1), r(t∗; s∗ 0, p∗ 0, r∗ 0 , α1, β1, γ1)  at t∗> tNobs. Other- wise, we predict the dynamics at t∗ ∈ (0, T]. The non-parameterized ODEs problem has been widely studied in [2], [3], and [4]. 54898 54898 VOLUME 11, 2023 VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data FIGURE 1. Schematic diagram of the framework. Initial states s0, p0, r0 and parameters α, β, γ are fed into the ANN model to predict the derivatives of s, p, and r with respect to time. These derivatives combined with initial states s0, p0, r0 will be further fed into the ODE Solver to obtain the next state s1, p1, r1, and so on. Finally we will get the trajectories of S = {s0, s1, . . . sT }, P = {p0, p1, . . . , pT } and R = {r0, r1, . . . , rT }. FIGURE 1. Schematic diagram of the framework. Algorithm 1 Algorithm for Solving the Parameter- ized ODEs Problem Algorithm 1 Algorithm for Solving the Parameter- ized ODEs Problem Input: Nobs: the number of observation time points; Integrator: ODE Solver; Z0: initial state set; W: parameter set; Fθ(s, p, r, α, β, γ): neural network; θ0: initial parameters of neural network; Z: observed trajectories of initial state Z0 and parameters W; nepochs: the number of epoch; 1t: time step; L: loss function Output: ˆZ: estimated trajectories of initial state Z0 and parameters W; Fθ∗: the trained neural network θ = θ0 for i = 1, . . . , nepochs do ˆZ = [] for j = 1, . . . , M do Select one element (sj 0, pj 0, rj 0) from Z0 for k = 1, . . . , K do Select one element (αk, βk, γk) from W for i = 1, . . . , Nobs do ( ds dt , dp dt , dr dt ) = Fθ(sj i−1, pj i−1, rj i−1, αk, βk, γk) sj i = integrator(sj i−1, 1t, ds dt ) pj i = integrator(pj i−1, 1t, dp dt ) rj i = integrator(rj i−1, 1t, dr dt ) Add (sj i, pj i, rj i) to ˆZ. end end end Loss = L( ˆZ, Z) Update parameters θ based on Loss end In this paper, we begin with Euler integrator [29], a popular choice due to its simplicity, as demonstrated in previous works [1], [2], [13]. Euler method also facilitates a fair com- parison with black-box methods. Given the state zn at time point tn = t0 + n1t, the state at the next time point can be computed using the following formula: zn+1 = zn + 1tF(zn, tn, α, β, γ). (6) (6) zn+1 = zn + 1tF(zn, tn, α, β, γ). The time step size, denoted by 1t, is a crucial parameter in numerical methods for solving ODEs. Specifically, Euler method can generate unstable solutions for stiff ODE sys- tems unless a very small 1t is employed, as noted in [30]. To maintain solution stability in our experiments, we metic- ulously select an appropriate value for 1t. In Appendix A, we present a rigorous proof of the convergence of Euler method, which is essential for understanding the accuracy of numerical solutions. Our approach can also be adapted to learn unknown functions using semi-implicit solvers with appropriate modifications. Algorithm 1 Algorithm for Solving the Parameter- ized ODEs Problem In Appendix B, we provide a brief explanation of how to make the necessary adjustments to fit semi-implicit solvers. IV. OUR APPROACH A. PIPELINE −z(ti; zj 0, αk, βk, γk)}∥2. (8) (8) We use initial states Z0 = n zj 0|j = 1, . . . , M o and parameters W = {(αk, βk, γk)|k = 1, . . . , K} for the training process. Following the work [1], we let the right side of ODEs be a parametric function Fθ(z, α, β, γ), where z = (s, p, r) and θ is the vector of parameters of the neural network. After train- ing, trajectories ˆZ = n ˆzθ(ti; zj 0, αk, βk, γk) oNobs i=1 are generated based on initial state zj 0 ∈Z0, parameters (αk, βk, γk) ∈W and θ, i.e., Inspired by [7], we also add the regularization term LS-Net to the loss function to avoid overfitting and enhance the gener- alization capability of the model. LS-Net is defined as (9), Inspired by [7], we also add the regularization term LS-Net to the loss function to avoid overfitting and enhance the gener- alization capability of the model. LS-Net is defined as (9), LS-Net = X p∈θLS-Net ls 1(p), (9) (9) p∈θLS-Net where ls 1(x) =    |x| −s 2, if |x| > s 1 2sx2, otherwise and s = 0.001. ˆzθ(ti; zj 0, αk, βk, γk) = ˆzθ(ti−1; zj 0, αk, βk, γk) + 1tFθ  ˆzθ(ti−1; zj 0, αk, βk, γk), × αk, βk, γk) , (7) 2s Ldata and LS-Net constitute the loss function L, that is 2s et constitute the loss function L, that is L = Ldata + LS-Net. (10) (10) (7) Figure 1 provides a detailed illustration of how to generate a trajectory based on the initial state z0 = (s0, p0, r0) ∈ Z0 and parameters (α, β, γ) ∈ W. Herein, we denote si = s(ti; z0, α, β, γ), pi = p(ti; z0, α, β, γ) and ri = r(ti; z0, α, β, γ) to represent the states of s, p and r at time ti. Algorithm 1 illustrates the pipeline for solving the param- eterized ODE problem. We back-propagate the loss and use it to update the parameter θ, which allows us to obtain the best θ∗. This value represents the ODE system and enables us to predict the dynamics based on new initial states and parameters. where i = 1, . . . , Nobs. B. ODE SOLVER The ODE Solver, also known as a numerical integrator, iterates a numerical scheme to obtain improved approxima- tions of the solution. There exist works dedicated to design- ing numerical integrators that produce more accurate solu- tions [27], [28]. Typically, the ODE Solver is employed to VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data Algorithm 1 Algorithm for Solving the Parameter- ized ODEs Problem Input: Nobs: the number of observation time points; Integrator: ODE Solver; Z0: initial state set; W: parameter set; Fθ(s, p, r, α, β, γ): neural network; θ0: initial parameters of neural network; Z: observed trajectories of initial state Z0 and parameters W; nepochs: the number of epoch; 1t: time step; L: loss function Output: ˆZ: estimated trajectories of initial state Z0 and parameters W; Fθ∗: the trained neural network θ = θ0 for i = 1, . . . , nepochs do ˆZ = [] for j = 1, . . . , M do Select one element (sj 0, pj 0, rj 0) from Z0 for k = 1, . . . , K do Select one element (αk, βk, γk) from W for i = 1, . . . , Nobs do ( ds dt , dp dt , dr dt ) = Fθ(sj i−1, pj i−1, rj i−1, αk, βk, γk) sj i = integrator(sj i−1, 1t, ds dt ) pj i = integrator(pj i−1, 1t, dp dt ) rj i = integrator(rj i−1, 1t, dr dt ) Add (sj i, pj i, rj i) to ˆZ. end end end Loss = L( ˆZ, Z) Update parameters θ based on Loss end approximate the true solution of the form dz dt = F(z, t) based on the initial state z0, where F(z, t) is a vector func- tion. Considering the parameters are variable, parameters α, β, and γ can not be embedded in F in our problem. So F can be expressed in the form of F(z, t, α, β, γ) = (f (z, t, α, β, γ), g(z, t, α, β, γ), h(z, t, α, β, γ)) and z(t; z0, α, β, γ) ={s(t; z0, α, β, γ), p(t; z0, α, β, γ), r(t; z0, α, β,γ)}. Algorithm 1 Algorithm for Solving the Parameter- ized ODEs Problem 2) S-NET S-Net possesses the ability to learn analytical expressions that can generalize to new domains effectively. The primary distinction between O-Net and S-Net lies in their layer-unit mapping, where S-Net is designed to capture the interaction between various variables and parameters efficiently. This is accomplished through two types of transformations: identity and linear combination maps, which enable S-Net to learn the underlying dynamics of the system accurately. Algorithm 2 O-Net Input: s, p, r, α, β, γ ∈R Output: ds dt , dp dt , dr dt y1 = relu(wT 1 (s, p, r, α, β, γ)T + b1), w1 ∈R6×512, b1 ∈R512×1; y2 = relu(wT 2 y1 + b2), w2 ∈R512×512, b2 ∈R512×1; y3 = relu(wT 3 y2 + b3), w3 ∈R512×512, b3 ∈R512×1; y4 = relu(wT 4 y3 + b4), w4 ∈R512×512, b4 ∈R512×1; y51 = tanh(wT 51y4 + b51), w51 ∈R512×512, b51 ∈R512×1; y52 = tanh(wT 52y4 + b52), w52 ∈R512×512, b52 ∈R512×1; y53 = tanh(wT 53y4 + b53), w53 ∈R512×512, b53 ∈R512×1; ds dt = wT 61y51 + b61, w61 ∈R512×1, b61 ∈R; dp dt = wT 62y52 + b62, w62 ∈R512×1, b62 ∈R; dr dt = wT 63y53 + b63, w63 ∈R512×1, b63 ∈R; Algorithm 2 O-Net Input: s, p, r, α, β, γ ∈R Output: ds dt , dp dt , dr dt y1 = relu(wT 1 (s, p, r, α, β, γ)T + b1), w1 ∈R6×512, b1 ∈R512×1; y2 = relu(wT 2 y1 + b2), w2 ∈R512×512, b2 ∈R512×1; y3 = relu(wT 3 y2 + b3), w3 ∈R512×512, b3 ∈R512×1; y4 = relu(wT 4 y3 + b4), w4 ∈R512×512, b4 ∈R512×1; y51 = tanh(wT 51y4 + b51), w51 ∈R512×512, b51 ∈R512×1; y52 = tanh(wT 52y4 + b52), w52 ∈R512×512, b52 ∈R512×1; y53 = tanh(wT 53y4 + b53), w53 ∈R512×512, b53 ∈R512×1; ds dt = wT 61y51 + b61, w61 ∈R512×1, b61 ∈R; dp dt = wT 62y52 + b62, w62 ∈R512×1, b62 ∈R; dr dt = wT 63y53 + b63, w63 ∈R512×1, b63 ∈R; As an example, consider a two-layer S-Net that aims to learn the function f ∈F in (1), as illustrated in Figure 3. With the appropriate number of layers, S-Net can represent all polynomials of the variables (s, p, r, α, β, γ). Herein, we only use addition and multiplication operators in S-Net. If neces- sary, we can add more operations to the S-Net to increase the capacity of the network. B. ARTIFICIAL NEURAL NETWORKS:O-NET AND S-NET In Algorithm 1, we can use any form of the neural net- work, but we adopt the O-Net as our baseline, which is commonly used for regression tasks without exploring the underlying mechanism connecting inputs and outputs. How- ever, to learn the combinations of different variables and parameters, we design S-Net, inspired by [6], [7], [8], and [9]. Unlike O-Net, S-Net first learns the analytic expression of ODEs and then predicts the dynamics. Notably, S-Net has no activation functions, and the most significant difference between O-Net and S-Net is the mapping between units in the layers. (12) 2) S-NET To better understand S-Net, we present an example in Algorithm 3 showing how S-Net is constructed. Particularly, we illustrate the learning process of αs −βr using S-Net in (11), (12), (13), (14) , and (15). y53 = tanh(wT 53y4 + b53), dt 61 dp dt = wT 62y52 + b62, w62 ∈R512×1, b62 ∈R; d (δ1, ε1)T = w1 ×  s, p, r, α, β, γ T =  1 0 0 0 0 0 0 0 0 1 0 0  ×   s p r α β γ   , (11) f1 = δ1ε1 = αs, (12) (δ2, ε2)T = w2 ×  s, p, r, α, β, γ, αs T =  0 0 1 0 0 0 0 0 0 0 0 1 0 0  ×   s p r α β γ αs   , (13) f2 = δ2ε2 = βr, (14) w3 ×  s, p, r, α, β, γ, αs, βr T 54901 , ε1)T = w1 ×  s, p, r, α, β, γ T =  1 0 0 0 0 0 0 0 0 1 0 0  ×   s p r α β γ   , (11) f1 = δ1ε1 = αs, (12) (δ1, ε1)T = w1 ×  s, p, r, α, β, γ T dt 62 dr dt = wT 63y53 + b63, w63 ∈R512×1, b63 ∈R; (11) IV. OUR APPROACH A. PIPELINE The input vector goes through a four-layer network structure. Each layer has 512 units and a relu function. There are three parts for ds dt , dp dt and dr dt respectively after four layers. Each part has two layers: the first layer has 512 units with the tanh activation function, and the second layer outputs the derivatives of ds dt , dp dt and dr dt . IV. OUR APPROACH A. PIPELINE Each layer has 512 units and a relu function. There are three parts for ds dt , dp dt and dr dt respectively after four layers. Each part has two layers: the first layer has 512 units with the tanh activation function, and the second layer outputs the derivatives of ds dt , dp dt and dr dt . FIGURE 2. Schematic diagram of the O-Net. States of s, p, and r and parameters of α, β, γ are the input vector. The input vector goes through a four-layer network structure. Each layer has 512 units and a relu function. There are three parts for ds dt , dp dt and dr dt respectively after four layers. Each part has two layers: the first layer has 512 units with the tanh activation function, and the second layer outputs the derivatives of ds dt , dp dt and dr dt . four shared layers and two unique layers for ds dt , dp dt and dr dt , as illustrated in Figure 2. To better understand O-Net, which is usually used for regression, we present a mathe- matical description in Algorithm 2 showing how O-Net is constructed. O-Net is ineffective in solving variable parameters ODEs problems as it fails to capture the role of parameters. Although both parameters and variables are treated as input features, they behave differently. Specifically, at each time point, the input vector is (z, α, β, γ), where z changes over time while (α, β, γ) do not. As a result, it is challenging for α, β, γ to find appropriate weights in a fully connected neural network, making it difficult for O-Net to effectively learn the underlying dynamics of the system. FIGURE 2. Schematic diagram of the O-Net. States of s, p, and r and parameters of α, β, γ are the input vector. The input vector goes through a four-layer network structure. Each layer has 512 units and a relu function. There are three parts for ds dt , dp dt and dr dt respectively after four layers. Each part has two layers: the first layer has 512 units with the tanh activation function, and the second layer outputs the derivatives of ds dt , dp dt and dr dt . FIGURE 2. Schematic diagram of the O-Net. States of s, p, and r and parameters of α, β, γ are the input vector. IV. OUR APPROACH A. PIPELINE Given a series of observations Z = n z(ti; zj 0, αk, βk, γk)|i ∈ {1, . . . , Nobs}, j ∈{1, . . . , M}, k ∈{1, . . . , K}}, we esti- mate the parameter θ by minimizing the error between the observed trajectories Z and predicted trajectories ˆZ, denoted as Given a series of observations Z = n z(ti; zj 0, αk, βk, γk)|i ∈ {1, . . . , Nobs}, j ∈{1, . . . , M}, k ∈{1, . . . , K}}, we esti- mate the parameter θ by minimizing the error between the observed trajectories Z and predicted trajectories ˆZ, denoted as Ldata = Nobs X i=1 M X j=1 K X k=1 ∥ˆzθ(ti; zj 0, αk, βk, γk)} 54900 VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data FIGURE 2. Schematic diagram of the O-Net. States of s, p, and r and parameters of α, β, γ are the input vector. The input vector goes through a four-layer network structure. Each layer has 512 units and a relu function. There are three parts for ds dt , dp dt and dr dt respectively after four layers. Each part has two layers: the first layer has 512 units with the tanh activation function, and the second layer outputs the derivatives of ds dt , dp dt and dr dt . Algorithm 2 O-Net Input: s, p, r, α, β, γ ∈R Output: ds dt , dp dt , dr dt y1 = relu(wT 1 (s, p, r, α, β, γ)T + b1), w1 ∈R6×512, b1 ∈R512×1; y2 = relu(wT 2 y1 + b2), w2 ∈R512×512, b2 ∈R512×1; y3 = relu(wT 3 y2 + b3), w3 ∈R512×512, b3 ∈R512×1; y4 = relu(wT 4 y3 + b4), w4 ∈R512×512, b4 ∈R512×1; y51 = tanh(wT 51y4 + b51), w51 ∈R512×512, b51 ∈R512×1; y52 = tanh(wT 52y4 + b52), w52 ∈R512×512, b52 ∈R512×1; y53 = tanh(wT 53y4 + b53), w53 ∈R512×512, b53 ∈R512×1; ds dt = wT 61y51 + b61, w61 ∈R512×1, b61 ∈R; dp dt = wT 62y52 + b62, w62 ∈R512×1, b62 ∈R; dr dt = wT 63y53 + b63, w63 ∈R512×1, b63 ∈R; FIGURE 2. Schematic diagram of the O-Net. States of s, p, and r and parameters of α, β, γ are the input vector. The input vector goes through a four-layer network structure. A. RESULTS AND DISCUSSIONS Our study shows that S-Net is able to effectively recover the ODEs for the unknown variables of x and y, as well as the parameters α, β, δ, and γ. We use the notation MNobs to represent the model trained on training data with Nobs time points. The results, summarized in Table 1, demonstrate that we are able to accurately recover the terms of (16). We observe that increasing the number of time points within a specific range results in higher model accuracy. Specifically, we find that when MNobs = 25, the coefficients of αx, βxy, δy, and γxy match those of the true equation. Additionally, we find that the terms not included in (16) have relatively small coefficients. Our analysis of αs −βr reveals that the sparsity of S-Net is a critical factor. Therefore, we introduced a regularization term into the loss function to promote model sparsity, as dis- cussed in section IV-A. 1) O-NET Apart from s, p, r, α, β and γ gotten by the identity map, f1 will also be input to the second hidden layer. Similar to the first hidden layer, we get the further combination f2 = δ2ε2 by w2 and b2. Finally, we obtain the analytic expression of function f . It is necessary to enforce the sparsity of S-Net since it helps reduce overfitting and enables more robust predictions. The performance of O-Net and S-Net could get improved with a reasonable increase in the number of time points, i.e., Nobs, in the training data. We set four group experiments on training data with Nobs = 10, 15, 20, and 25. If the number of observation points is too large, it will also hurt the effec- tiveness of the model. Once there are too many observations, the accumulated error will be too large for one trajectory, which is not conducive to model training. We train S-Net with the L-BFGS optimizer [32] and use maximum iterations of 30000, a batch size of 150. We train O-Net with ADAM optimizer [33] for 5000 epochs using a batch size of 50, and a learning rate of 5e-3. We predict trajectories based on various initial states and parameters on t ∈(0, 10]. =  0 0 0 0 0 0 1 −1  ×   s p r α β γ αs βr   = αs −βr. (15) (15) V. NUMERICAL STUDIES: LOTKA-VOLTERRA EQUATION The Lotka-Volterra model is frequently used to describe the dynamics of ecological systems where two species inter- act. [31] shows that cannibalism has both positive and nega- tive effects on the stability of the Lotka-Volterra predator-prey model. It depends on the dynamic behaviors of the original system. To evaluate the ability of the models to generate correct trajectories for new initial states and parame- ters, we feed 33 testing trajectories into the well-trained models and obtained predicted trajectories. Figure 4 shows the results of S-Net and O-Net with Nobs = 10, 15, 20, 25 for a specific test example (x0, y0, α, β, δ, γ) = (0.71468, 1.01860, 1.10023, 1.17939, 2.78173, 1.18328). We find that S-Net can accurately predict the trajectory in the period of t ∈[0, 801t] = (0, 8], but its accuracy decreases when t ∈ (8, 10]. However, we observe that increasing the number of time points used in the training process improves the prediction of the S-Net of long-time dynamics. Specifically, S-Net trained on MNobs = 25 predicts with higher accuracy for t ∈(8, 10] than S-Net trained on MNobs = 10. On the other hand, O-Net performs poorly in all four cases, even though it performs well in the early stages To evaluate the ability of the models to generate correct trajectories for new initial states and parame- ters, we feed 33 testing trajectories into the well-trained models and obtained predicted trajectories. Figure 4 shows the results of S-Net and O-Net with Nobs = 10, 15, 20, 25 for a specific test example (x0, y0, α, β, δ, γ) = (0.71468, 1.01860, 1.10023, 1.17939, 2.78173, 1.18328).i In this section, we consider Lotka-Volterra Equation (16), where different ecological systems have different parameters of α, β, δ and γ and initial states of x0 and y0,    dx dt = αx −βxy, dy dt = −δy + γxy. (16) (16) We find that S-Net can accurately predict the trajectory in the period of t ∈[0, 801t] = (0, 8], but its accuracy decreases when t ∈ (8, 10]. However, we observe that increasing the number of time points used in the training process improves the prediction of the S-Net of long-time dynamics. Specifically, S-Net trained on MNobs = 25 predicts with higher accuracy for t ∈(8, 10] than S-Net trained on MNobs = 10. 1) O-NET O-Net uses fully connected layers to learn the mapping from low to high-dimensional space and uses activation functions to learn the nonlinear relationship. Consider an O-Net with VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data FIGURE 3. Schematic diagram of the S-Net. The identity map directly transfers s, p, r, α, β, γ from input layer to the first hidden layer. The linear combination chooses two elements remarked by δ1 and ε1 from the input vector using w1 and b1. The expressions f1 = δ1ε1and f1 = δ1 ε1 correspond to the multiplication and division of two elements, respectively. We only implement the multiplication operation in this work. Apart from s, p, r, α, β and γ gotten by the identity map, f1 will also be input to the second hidden layer. Similar to the first hidden layer, we get the further combination f2 = δ2ε2 by w2 and b2. Finally, we obtain the analytic expression of function f . It is necessary to enforce the sparsity of S-Net since it helps reduce overfitting and enables more robust predictions. Algorithm 3 S-Net Input: s, p, r, α, β, γ ∈R Output: F (δ1, ε1)T = w1(s, p, r, α, β, γ)T + b1, w1 ∈R2×6, b1 ∈R2×1; f1 = δ1ε1; (δ2, ε2)T = w2(s, p, r, α, β, γ, f1)T + b2, w2 ∈R2×7, b2 ∈R2×1; f2 = δ2ε2; F = w3(s, p, r, α, β, γ, f1, f2)T + b3, w3 ∈R1×8, b3 ∈R; Algorithm 3 S-Net Input: s, p, r, α, β, γ ∈R Output: F (δ1, ε1)T = w1(s, p, r, α, β, γ)T + b1, w1 ∈R2×6, b1 ∈R2×1; f1 = δ1ε1; (δ2, ε2)T = w2(s, p, r, α, β, γ, f1)T + b2, w2 ∈R2×7, b2 ∈R2×1; f2 = δ2ε2; F = w3(s, p, r, α, β, γ, f1, f2)T + b3, w3 ∈R1×8, b3 ∈R; FIGURE 3. Schematic diagram of the S-Net. The identity map directly transfers s, p, r, α, β, γ from input layer to the first hidden layer. The linear combination chooses two elements remarked by δ1 and ε1 from the input vector using w1 and b1. The expressions f1 = δ1ε1and f1 = δ1 ε1 correspond to the multiplication and division of two elements, respectively. We only implement the multiplication operation in this work. V. NUMERICAL STUDIES: LOTKA-VOLTERRA EQUATION On the other hand, O-Net performs poorly in all four cases, even though it performs well in the early stages The Euler integrator simulates ground truth trajectories in both training and testing stages with the time step 1t = 0.1, which empirically meets the stability requirements. The train- ing and testing data consist of 150 and 33 trajectories, respec- tively, each of which starts from random initial state (x0, y0) in the interval [0.6, 1.4] and parameters of (α, β, δ, γ) in the interval ([1.0, 2.0], [0.5, 1.5], [2.5, 3.5], [0.5, 1.5]) respec- tively. There is no overlap between the training and test data. 54902 VOLUME 11, 2023 VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data FIGURE 4. Lotka-Volterra: Testing results on (x0, y0, α, β, δ, γ) = (0.71468, 1.01860, 1.10023, 1.17939, 2.78173, 1.18328) by S-Net and O-Net with time points 10, 15, 20 and 25 for the x-component (left) and y-component (right). In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 10], and the vertical axis shows the values. The solid red line is the ground truth. The blue and orange dashed lines show the O-Net and S-Net results, respectively. FIGURE 4. Lotka-Volterra: Testing results on (x0, y0, α, β, δ, γ) = (0.71468, 1.01860, 1.10023, 1.17939, 2.78173, 1.18328) by S-Net and O-Net with time points 10, 15, 20 and 25 for the x-component (left) and y-component (right). In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 10], and the vertical axis shows the values. The solid red line is the ground truth. The blue and orange dashed lines show the O-Net and S-Net results, respectively. FIGURE 4. Lotka-Volterra: Testing results on (x0, y0, α, β, δ, γ) = (0.71468, 1.01860, 1.10023, 1.17939, 2.78173, 1.18328) by S-Net and O-Net with time points 10, 15, 20 and 25 for the x-component (left) and y-component (right). In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 10], and the vertical axis shows the values. The solid red line is the ground truth. The blue and orange dashed lines show the O-Net and S-Net results, respectively. FIGURE 5. Lotka-Volterra: Prediction errors of the O-Net(orange) and S-Net(green) with different training time points 20 and 25. V. NUMERICAL STUDIES: LOTKA-VOLTERRA EQUATION L-BFGS optimizer with a maximum of 50,000 iterations and a batch size of 150. For training O-Net, we use the ADAM optimizer with a learning rate of 5e-3, a batch size of 100, and 5,000 epochs. We predict trajectories for various initial states and parameters on the time interval t ∈(0, 1]. that of S-Net when MNobs is 10 or 25, respectively. Clearly, S-Net performs significantly better than O-Net, suggesting that proper discretization is crucial when the ODE structure is unknown. Appendix C presents the findings of three other cases using different models obtained by MNobs = 10, 15, 20, and 25, respectively. A. RESULTS AND DISCUSSIONS Table 3 presents the capability of the trained S-Net to identify the underlying ODE model, showing the top five terms of coefficient weights recovered by S-Net with certain accuracy. Notably, when MNobs = 20, the coefficients of σy, σx, and xρ match those of the true equation with high precision. The coefficients of the remaining four terms, namely xz, y, xy, and βz, deviate only slightly from the true values, with a maximum difference of 0.01. These results demonstrate the effectiveness of S-Net in recovering the underlying ODE model. V. NUMERICAL STUDIES: LOTKA-VOLTERRA EQUATION In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 10], and the vertical axis shows the errors. The banded curves indicate the 25% −100% percentile of the relative errors among 33 test samples. The dark regions indicate the 25% −75% percentile of the relative error, which shows that S-Net performs significantly better than O-Net. The upper row is for variable x and the bottom low is for variable y. FIGURE 5. Lotka-Volterra: Prediction errors of the O-Net(orange) and S-Net(green) with different training time points 20 and 25. In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 10], and the vertical axis shows the errors. The banded curves indicate the 25% −100% percentile of the relative errors among 33 test samples. The dark regions indicate the 25% −75% percentile of the relative error, which shows that S-Net performs significantly better than O-Net. The upper row is for variable x and the bottom low is for variable y. Figure 5 for two different time points, 20 and 25. In both cases, the error of O-Net is significantly larger than that of S-Net. For example, in Figure 5(c), we can observe that the error of O-Net sharply increases over time and soon reaches 500. In contrast, the error of S-Net increases at a relatively slower rate and reaches a maximum of approximately 100. Specifically, Table 2 shows the error of S-Net and O-Net for different models. The error of O-Net can be five or six times for a short period, its predictions often deviate significantly from the actual trajectory. In some cases, O-Net even predicts trends that are opposite to the actual situation. Therefore, we conclude that S-Net has a stronger generalization ability than O-Net. We define the error between observations Z and predic- tions ˆZ as ϵ = q ||Z −ˆZ||2. The error plots are shown in 54903 VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data TABLE 3. Lorenz identification with different models. TABLE 1. Lotka-Volterra identification with different time points. TABLE 3. Lorenz identification with different models. TABLE 1. Lotka-Volterra identification with different time points. TABLE 2. MSE of S-Net and O-Net for equations of different models. TABLE 2. MSE of S-Net and O-Net for equations of different models. VI. NUMERICAL STUDIES: LORENZ EQUATION of time points increased, the performance of S-Net improvei significantly larger errors than S-Net. For instance, consider FIGURE 6. Lorenz: Testing results on (x0, y0, z0, σ, ρ, β) = (0.82841, 0.14785, 0.17099, 12.39551, 32.03720, 2.67205) by S-Net and O-Net with time points 4, 6, 10 and 20 for the x-component (left), y-component (middle) and z-component (right). In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 1], and the vertical axis shows the values. The solid red line is the ground truth. The blue and orange dashed lines show the O-Net and S-Net results, respectively. FIGURE 6. Lorenz: Testing results on (x0, y0, z0, σ, ρ, β) = (0.82841, 0.14785, 0.17099, 12.39551, 32.03720, 2.67205) by S-Net and O-Net with time points 4, 6, 10 and 20 for the x-component (left), y-component (middle) and z-component (right). In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 1], and the vertical axis shows the values. The solid red line is the ground truth. The blue and orange dashed lines show the O-Net and S-Net results, respectively. FIGURE 7. Lorenz: Prediction errors of the O-Net(orange) and S-Net(green) with different training time points 4, 6, 10, and 20. In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 1], and the vertical axis shows the errors. The banded curves indicate the 25% −100% percentile of the relative errors among 60 test samples and the dark regions indicate the 25% −75% percentile of the relative error. FIGURE 7. Lorenz: Prediction errors of the O-Net(orange) and S-Net(green) with different training time points 4, 6, 10, and 20. In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 1], and the vertical axis shows the errors. The banded curves indicate the 25% −100% percentile of the relative errors among 60 test samples and the dark regions indicate the 25% −75% percentile of the relative error. of time points increased, the performance of S-Net improve significantly, but the performance of O-Net remain almost unchanged, as shown in Figures 6(b), 6(c), and 6(d). Even in the initial stages of each subfigure, O-Net was unable to perform well. significantly larger errors than S-Net. For instance, consider Figure 7(l). VI. NUMERICAL STUDIES: LORENZ EQUATION In this section, we consider Lorenz Equations (17) where different ecological systems have different parameters σ, ρ and β and initial states x0, y0 and z0.    dx dt = σ(y −x), dy dt = x(ρ −z) −y, dz dt = xy −βz. (17) (17) We evaluate the predictive performance of S-Net and O-Net on (17) using 60 testing trajectories and obtain corresponding predictions from the trained models. Fig- ure 6 shows the results of S-Net and O-Net with Nobs = 4, 6, 10, 20 for a specific test example (x0, y0, z0, σ, ρ, β) = (0.82841, 0.14785, 0.17099, 12.39551, 32.03720, 2.67205). We predict the trajectories of x, y and z on t ∈(0, 1001t] = (0, 1] using the learned models. When MNobs = 4, both O-Net and S-Net predictions are very poor. As the number Both the training and testing data consist of 150 and 60 tra- jectories, respectively, simulated by the Euler integrator with a time step of 1t = 0.01. The initial states and parameters are randomly selected from the intervals [0.8, 1.2], [0, 0.2], [0, 0.3], [5, 15], [23, 33], and [2, 3], respectively, without any overlap between the two sets. We conduct four group experiments on the training data with different numbers of time points: 4, 6, 10, and 20. For training S-Net, we use the 54904 VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data FIGURE 6. Lorenz: Testing results on (x0, y0, z0, σ, ρ, β) = (0.82841, 0.14785, 0.17099, 12.39551, 32.03720, 2.67205) by S-Net and O-Net with time points 4, 6, 10 and 20 for the x-component (left), y-component (middle) and z-component (right). In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 1], and the vertical axis shows the values. The solid red line is the ground truth. The blue and orange dashed lines show the O-Net and S-Net results, respectively. FIGURE 7. Lorenz: Prediction errors of the O-Net(orange) and S-Net(green) with different training time points 4, 6, 10, and 20. In each plot, the horizontal axis indicates the time of prediction in the interval (0, 1001t] = (0, 1], and the vertical axis shows the errors. The banded curves indicate the 25% −100% percentile of the relative errors among 60 test samples and the dark regions indicate the 25% −75% percentile of the relative error. VI. NUMERICAL STUDIES: LORENZ EQUATION The error of O-Net increases sharply with time and soon reaches 1400, while the error of S-Net increases relatively slowly with time and reaches a maximum of about 100. Table 2 shows the errors of S-Net and O-Net of various time points. The error of O-Net can be up to a thousand times larger than that of S-Net. Clearly, S-Net outperforms The error plots for four different time points (4, 6, 10, and 20) are presented in Figure 7. In each case, O-Net exhibits VOLUME 11, 2023 54905 Q. Li et al.: Learning Parameterized ODEs From Data FIGURE 8. Testing results on (x0, y0, α, β, δ, γ) ∈{(1.03591, 0.71055, 1.64399, 0.73789, 2.63207, 0.58110), (1.34048, 1.08388, 1.29828, 1.44437, 3.24866, 0.58960), (1.39070, 1.15958, 1.20000, 1.01820, 3.32212, 0.93040)} by S-Net and O-Net with time points 10, 15, 20 and 25 for the x-component (left) and y-component (right). FIGURE 8. Testing results on (x0, y0, α, β, δ, γ) ∈{(1.03591, 0.71055, 1.64399, 0.73789, 2.63207, 0.58110), (1.34048, 1.08388, 1.29828, 1.44437, 3.24866, 0.58960), (1.39070, 1.15958, 1.20000, 1.01820, 3.32212, 0.93040)} by S-Net and O-Net with time points 10, 15, 20 and 25 for the x-component (left) and y-component (right). FIGURE 8. Testing results on (x0, y0, α, β, δ, γ) ∈{(1.03591, 0.71055, 1.64399, 0.73789, 2.63207, 0.58110), (1.34048, 1.08388, 1.29828, 1.44437, 3.24866, 0.58960), (1.39070, 1.15958, 1.20000, 1.01820, 3.32212, 0.93040)} by S-Net and O-Net with time points 10, 15, 20 and 25 for the x-component (left) and y-component (right). O-Net significantly. We provide the findings of two other cases using different models obtained by Nobs = 4, 6, 10, and 20, respectively, in Appendix D. The proposed framework marks a significant advancement in studying parameterized ODEs in computational science and engineering. However, there are several limitations to address in future research. Firstly, the current version of S-Net only supports basic operators such as addition, subtraction, and multi- plication, which limits its application to complex systems. To broaden its applicability, it is necessary to incorporate more advanced operators such as division, trigonometric functions, powers, and fractional calculation operators. Sec- ond, enhancing simulation accuracy requires implementing other ODE Solvers. Thirdly, the present approach is not applicable to arbitrary order systems, which present a more complex challenge. The combinatorial relationship between variables and parameters must be known, and the observa- tions are supplied based on the information on variables. VI. NUMERICAL STUDIES: LORENZ EQUATION An additional step may be required to predict the number of variables or parameters based on the current method. Finally, while S-Net has proven resilient against noisy data in [9], testing with real data is necessary to establish its applicability to diverse domains. VII. CONCLUSION Exploring parameterized ODEs is a broad area in computa- tional science and engineering. Parameterized ODEs prob- lems are particularly challenging to solve because the solu- tions to these problems can vary with the parameters used. Black-box methods offer some insights, but their general- ization performance is often subpar due to a limited under- standing of underlying mechanisms. To address this issue, we propose a novel framework that combines the S-Net with an ODE Solver to learn parameterized ODEs. Unlike the black-box O-Net method that simply fits the observed data, S-Net learns the expressions of the equations based on the observed data. We use the Euler method as the ODE Solver due to its simplicity. Experiments show the S-Net framework surpasses the O-Net method in learning parame- terized ODEs, evidenced by superior efficiency and accuracy in tests involving the Lotka-Volterra and Lorenz Equations. 54906 VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data FIGURE 9. Testing results on (x0, y0, z0, σ, ρ, β) ∈{(0.84731, 0.11332, 0.24186, 5.24679, 29.69917, 2.26212), (0.92617, 0.04462, 0.21900, 14.47371, 27.97391, 2.57754)} by S-Net and O-Net with time points 4, 6, 10 and 20 for the x-component (left), y-component (middle) and z-component (right). FIGURE 9 Testing results on (x0 y0 z0 σ ρ β) ∈{(0 84731 0 11332 0 24186 5 24679 29 69917 2 26212) (0 92617 0 04462 0 21900 FIGURE 9. Testing results on (x0, y0, z0, σ, ρ, β) ∈{(0.84731, 0.11332, 0.24186, 5.24679, 29.69917, 2.26212), (0.92617, 0.04462, 0.21900, 14.47371, 27.97391, 2.57754)} by S-Net and O-Net with time points 4, 6, 10 and 20 for the x-component (left), y-component (middle) and z-component (right) Theorem 1: Assume the following one-step method cor- responding to the initial value problem (18) be the p-order accuracy [1] R. T. Q. Chen, Y. Rubanova, J. Bettencourt, and D. K. Duvenaud, ‘‘Neural ordinary differential equations,’’ in Proc. Adv. Neural Inf. Process. Syst., vol. 31, Dec. 2018, pp. 6572–6583. APPENDIX C LOTKA-VOLTERRA In Figure 8, we present the outcomes of three distinct models obtained by utilizing Nobs = 10, 15, 20, and 25, respec- tively. The rows indicate the prediction results of the dif- ferent models for three test samples. The first two columns in each row demonstrate the evolution of the two vari- ables x and y for the first test sample (x0, y0, α, β, δ, γ) = (1.03591, 0.71055, 1.64399, 0.73789, 2.63207, 0.58110). i.e., en+1 = en + h[φ(xn, y(xn), h) −φ(xn, yn, h)] + Tn+1. Since the one-step method is the p-order accuracy, then ∃h0, 0 < h ≤h0, satisfy |Tn+1| ≤Chp+1 where C is a constant. That is The center two columns illustrate the changes in the variables x and y over time for the second test sample (x0, y0, α, β, δ, γ) = (1.34048, 1.08388, 1.29828, 1.44437, 3.24866, 0.58960). Finally, the last two columns show how the variables x and y varied over time for the third test sample (x0, y0, α, β, δ, γ) = (1.39070, 1.15958, 1.20000, 1.01820, 3.32212, 0.93040). |en+1| ≤|en| + hL|en| + Chp+1 = α|en| + β, where α = 1 + hL, β = Chp+1. So we can get |en+1| ≤|en| + hL|en| + Chp+1 = α|en| + β, where α = 1 + hL, β = Chp+1. So we can get |en| ≤α|en−1| + β ≤α2|en−2| + αβ + β ≤α3|en−3| + β(1 + α + α2) ≤. . . ≤. (19) |en| ≤α|en−1| + β ≤α2|en−2| + αβ + β ≤α3|en−3| + β(1 + α + α2) ≤. . . ≤. (19 (19) Each subplot displays the time of prediction on the horizontal axis within the interval (0, 1001t] = (0, 10], while the ver- tical axis indicates the corresponding values. The solid red line represents the ground truth, while the orange and blue dashed lines show the O-Net and S-Net prediction results, respectively. Notably, within a specific range, the prediction accuracy of the model increases with a higher number of observation points used to train the model. From the known conditions, we get From the known conditions, we get |en| ≤exp (L(xn −x0))|e0| + ChpL−1(exp (L(xn −x0)) −1) = ChpL−1(exp (L(xn −x0)) −1). (20) From (20), we know when h →0, then |en| →0. From (20), we know when h →0, then |en| →0. [2] Y. Rubanova, R. T. Chen, and D. K. Duvenaud, ‘‘Latent ordinary differ- ential equations for irregularly-sampled time series,’’ in Proc. Adv. Neural Inf. Process. Syst., vol. 32, Dec. 2019, pp. 5321–5331. [4] Z. Chen, J. Zhang, M. Arjovsky, and L. Bottou, ‘‘Symplectic recur- rent neural networks,’’ in Proc. 8th Int. Conf. Learn. Represent. (ICLR), Addis Ababa, Ethiopia, Apr. 2020, pp. 1–23. [Online]. Available: https://openreview.net/forum?id=BkgYPREtPr CONVERGENCE OF THE EULER METHOD Our subsequent analysis establishes the convergence of the Euler method when solving the initial-value problem of a first-order differential equation, as stated in (18) yn+1 = yn + hφ(xn, yn, h) and the function φ satisfies the Lipschitz condition for y, i.e., ∃L > 0, and the function φ satisfies the Lipschitz condition for y, i.e., ∃L > 0,    dy dx = f (x, y), x > x0, y(x0) = y0. (18) ∃L > 0, (18) |φ(x, y1, h) −φ(x, y2, h)| ≤L|y1 −y2|, ∀y1, y2 Here, the unknown function is denoted by y(x), the known function by f (x, y), and the initial data by y0. and y0 = y(x0), then the one-step method is convergent and y(xn) −yn = O(hp). 54907 VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data Proof: Let en = y(xn) −yn, then y(xn+1) = y(xn) + hφ(xn, y(xn), h) + Tn+1, APPENDIX D LORENZ Notably, the prediction accuracy of the model improves with an increase in the number of observation points used to train the model. (22) where 1t is the time step. The difference with the standard Euler method is that the semi-implicit Euler method uses yn+1 in the equation for xn+1, while the standard Euler method uses yn. Given that the expressions for f and g are represented by S-Nets, S-Netf and S-Netg, it is necessary to provide them with known information. In the semi-implicit Euler method, we use a positive time step to compute xn+1 from yn+1 generated by S-Netg based on starting points x0, y0, that is [3] C. Herrera, F. Krach, and J. Teichmann, ‘‘Neural jump ordinary differ- ential equations: Consistent continuous-time prediction and filtering,’’ in Proc. Int. Conf. Learn. Represent. (ICLR), Austria, May 2021, pp. 1–44. [Online]. Available: https://openreview.net/forum?id=JFKR3WqwyXR REFERENCES [1] R. T. Q. Chen, Y. Rubanova, J. Bettencourt, and D. K. Duvenaud, ‘‘Neural ordinary differential equations,’’ in Proc. Adv. Neural Inf. Process. Syst., vol. 31, Dec. 2018, pp. 6572–6583. [2] Y. Rubanova, R. T. Chen, and D. K. Duvenaud, ‘‘Latent ordinary differ- ential equations for irregularly-sampled time series,’’ in Proc. Adv. Neural Inf. Process. Syst., vol. 32, Dec. 2019, pp. 5321–5331. [3] C. Herrera, F. Krach, and J. Teichmann, ‘‘Neural jump ordinary differ- ential equations: Consistent continuous-time prediction and filtering,’’ in Proc. Int. Conf. Learn. Represent. (ICLR), Austria, May 2021, pp. 1–44. [Online]. Available: https://openreview.net/forum?id=JFKR3WqwyXR [4] Z. Chen, J. Zhang, M. Arjovsky, and L. Bottou, ‘‘Symplectic recur- rent neural networks,’’ in Proc. 8th Int. Conf. Learn. Represent. (ICLR), Addis Ababa, Ethiopia, Apr. 2020, pp. 1–23. [Online]. Available: https://openreview.net/forum?id=BkgYPREtPr APPENDIX D LORENZ Our approach can be adapted to learn unknown functions utilizing semi-implicit solvers with suitable modifications. For instance, consider the semi-implicit Euler method, which can be employed for a pair of differential equations with the form In Figure 9, we present the outcomes of two examples utilizing distinct models derived from Nobs = 4, 6, 10, and 20, respectively. Each row represents the prediction results of different models on two test samples. The first three columns of each row demonstrate the progression of the three variables x, y, and z for the first test sample (x0, y0, z0, σ, ρ, β) = (0.84731, 0.11332, 0.24186, 5.24679, 29.69917, 2.26212), In Figure 9, we present the outcomes of two examples utilizing distinct models derived from Nobs = 4, 6, 10, and 20, respectively. Each row represents the prediction results of different models on two test samples. The first three columns of each row demonstrate the progression of the three variables x, y, and z for the first test sample (x0, y0, z0, σ, ρ, β) = (0.84731, 0.11332, 0.24186, 5.24679, 29.69917, 2.26212), while the last three columns depict how the three vari- ables x, y, and z evolve over time for the third test sample (x0, y0, z0, σ, ρ, β) = (0.92617, 0.04462, 0.21900, 14.47371, 27.97391, 2.57754). Each plot shows the predic- tion time in the interval (0, 1001t] = (0, 1] on the horizontal axis and the corresponding values on the vertical axis. The solid red line in each subplot represents the actual ground truth, while the orange and blue dashed lines show the O-Net and S-Net prediction results, respectively. Notably, the prediction accuracy of the model improves with an increase in the number of observation points used to train the model. dx dt = f (t, y), dy dt = g(t, x), (21) (21) where f and g are unknown functions that we want to learn. The semi-implicit Euler method produces an approximate discrete solution by iterating yn+1 = yn + g(tn, xn)1t, xn+1 = xn + f (tn, yn+1)1t, (22) tion time in the interval (0, 1001t] = (0, 1] on the horizontal axis and the corresponding values on the vertical axis. The solid red line in each subplot represents the actual ground truth, while the orange and blue dashed lines show the O-Net and S-Net prediction results, respectively. QING LI QING LI received the B.S. degree in applied math- ematics from Qingdao University, China, in 2015, with a focus on solid foundation in mathemat- ical theory and its practical applications, and the M.S. degree in mathematics from the South China University of Technology, China, with a focus on advanced mathematical concepts and numerical methods. She is currently pursuing the Ph.D. degree with the Department of Energy and Petroleum Technology, University of Stavanger, Norway, with a focus on developing novel machine learning algorithms that leverage her expertise in differential equations, both ordinary and partial, and numerical calculation. Her research interests include the intersection of these fields, with a particular emphasis on developing innovative solutions to complex problems in energy and petroleum technology. [11] K. Lee and E. J. Parish, ‘‘Parameterized neural ordinary differential equa- tions: Applications to computational physics problems,’’ Proc. Roy. Soc. A, Math., Phys. Eng. Sci., vol. 477, no. 2253, Sep. 2021, Art. no. 20210162. [12] Y. S. Shimizu and E. J. Parish, ‘‘Windowed space–time least-squares Petrov–Galerkin model order reduction for nonlinear dynamical systems,’’ Comput. Methods Appl. Mech. Eng., vol. 386, Dec. 2021, Art. no. 114050. [13] K. Lee and N. Trask, ‘‘Parameter-varying neural ordinary differential equations with partition-of-unity networks,’’ 2022, arXiv:2210.00368. [14] H. Owhadi, ‘‘Bayesian numerical homogenization,’’ Multiscale Model. Simul., vol. 13, no. 3, pp. 812–828, Jan. 2015. [15] M. Raissi, P. Perdikaris, and G. E. Karniadakis, ‘‘Inferring solutions of differential equations using noisy multi-fidelity data,’’ J. Comput. Phys., vol. 335, pp. 736–746, Apr. 2017. [16] M. Raissi, P. Perdikaris, and G. E. Karniadakis, ‘‘Machine learning of linear differential equations using Gaussian processes,’’ J. Comput. Phys., vol. 348, pp. 683–693, Nov. 2017. [17] S. L. Brunton, J. L. Proctor, and J. N. Kutz, ‘‘Discovering governing equa- tions from data by sparse identification of nonlinear dynamical systems,’’ Proc. Nat. Acad. Sci. USA, vol. 113, no. 15, pp. 3932–3937, Mar. 2016. STEINAR EVJE received the M.S. and Ph.D. degrees in applied mathematics from the Univer- sity of Bergen, in 1992 and 1998, respectively. He is currently a Professor in applied and com- putational mathematics with the Department of Energy and Petroleum Engineering, University of Stavanger. QING LI With more than two decades of experi- ence in the field, he has developed a keen interest in the development of mathematical models that can be used to gain insight into fundamental mech- anisms for various multiphase transport and reaction processes within fluid mechanics and medical engineering. In addition to his work on mathemat- ical modeling, he has also focused on leveraging the power of data-driven modeling, including machine learning methods to solve problems related to partial differential equations. He has published numerous papers and articles that have helped advance the state of the art in both machine learning and mathematical modeling. [18] H. Schaeffer, ‘‘Learning partial differential equations via data discovery and sparse optimization,’’ Proc. Roy. Soc. A, Math., Phys. Eng. Sci., vol. 473, no. 2197, Jan. 2017, Art. no. 20160446. [19] S. H. Rudy, S. L. Brunton, J. L. Proctor, and J. N. Kutz, ‘‘Data-driven dis- covery of partial differential equations,’’ Sci. Adv., vol. 3, no. 4, Apr. 2017, Art. no. e1602614. [20] Z. Wu and R. Zhang, ‘‘Learning physics by data for the motion of a sphere falling in a non-Newtonian fluid,’’ Commun. Nonlinear Sci. Numer. Simul., vol. 67, pp. 577–593, Feb. 2019. [21] V. Iakovlev, M. Heinonen, and H. Lähdesmäki, ‘‘Learning continuous-time PDEs from sparse data with graph neural networks,’’ in Proc. Int. Conf. Learn. Represent. (ICLR), Austria, May 2021, pp. 1–15. [22] T. Pfaff, M. Fortunato, A. Sanchez-Gonzalez, and P. W. Battaglia, ‘‘Learn- ing mesh-based simulation with graph networks,’’ in Proc. Int. Conf. Learn. Represent. (ICLR), Austria, May 2021, pp. 1–18. [23] B. Chang, M. Chen, E. Haber, and E. H. Chi, ‘‘AntisymmetricRNN: A dynamical system view on recurrent neural networks,’’ in Proc. Int. Conf. Learn. Represent. (ICLR), New Orleans, LA, USA, May 2019, pp. 1–15. [24] E. D. Brouwer, J. Simm, A. Arany, and Y. Moreau, ‘‘GRU-ODE-Bayes: Continuous modeling of sporadically-observed time series,’’ in Proc. Adv. Neural Inf. Process. Syst., Vancouver, BC, Canada, Dec. 2019, pp. 7377–7388. JIAHUI GENG (Graduate Student Member, IEEE) received the B.S. degree from the School of Automation, Southeast University, China, in 2015, and the M.S. degree from the Department of Computer Science, RWTH Aachen University, Germany, in 2018. He is currently pursuing the Ph.D. degree with the Department of Computer Science and Computer Engineering, University of Stavanger, Norway. REFERENCES (23) xn+1 = xn + S-Netf (tn, S-Netg(tn, xn)1t). (23) In this context, y is not utilized as an observable variable; instead, it serves as a component to generate the observable variable x. With this approach, as the expression for g must be learned through the x variable, we require additional observa- tions on the x variable and no longer need observations on the y variable. 54908 54908 VOLUME 11, 2023 Q. Li et al.: Learning Parameterized ODEs From Data [5] M. Raissi, P. Perdikaris, and G. E. Karniadakis, ‘‘Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations,’’ J. Comput. Phys., vol. 378, pp. 686–707, Feb. 2019. [30] J. D. Lambert, Numerical Methods for Ordinary Differential Systems, vol. 146. New York, NY, USA: Wiley, 1991. [31] H. Deng, F. Chen, Z. Zhu, and Z. Li, ‘‘Dynamic behaviors of Lotka–Volterra predator–prey model incorporating predator cannibalism,’’ Adv. Difference Equ., vol. 2019, no. 1, pp. 1–17, Dec. 2019. [6] Z. Long, Y. Lu, X. Ma, and B. Dong, ‘‘PDE-Net: Learning PDEs from data,’’ in Proc. Mach. Learn. Res., Jul. 2018, pp. 3208–3216. [32] D. C. Liu and J. Nocedal, ‘‘On the limited memory BFGS method for large scale optimization,’’ Math. Program., vol. 45, nos. 1–3, pp. 503–528, Aug. 1989. [7] Z. Long, Y. Lu, and B. Dong, ‘‘PDE-Net 2.0: Learning PDEs from data with a numeric-symbolic hybrid deep network,’’ J. Comput. Phys., vol. 399, Dec. 2019, Art. no. 108925. [33] D. P. Kingma and J. Ba, ‘‘Adam: A method for stochastic optimization,’’ 2014, arXiv:1412.6980. [8] S. Sahoo, C. Lampert, and G. Martius, ‘‘Learning equations for extrapola- tion and control,’’ in Int. Conf. Mach. Learn., Jul. 2018, pp. 4442–4450. [9] Q. Li and S. Evje, ‘‘Learning the nonlinear flux function of a hidden scalar conservation law from data,’’ Netw. Heterogeneous Media, vol. 18, no. 1, pp. 48–79, 2022. [10] R. Maulik, K. Fukami, N. Ramachandra, K. Fukagata, and K. Taira, ‘‘Probabilistic neural networks for fluid flow surrogate modeling and data recovery,’’ Phys. Rev. Fluids, vol. 5, no. 10, Oct. 2020, Art. no. 104401. QING LI His research interests include robustness, privacy, and security, as well as the development of blockchain systems and the application of dynamic systems in machine learning. With a passion for exploring the cutting edge of his field, he is committed to making meaningful contributions to the development of robust, secure, and privacy-preserving machine learning systems that can be used to drive innovation and progress in a wide range of industries and applications. [25] A. Yazdani, L. Lu, M. Raissi, and G. E. Karniadakis, ‘‘Systems biology informed deep learning for inferring parameters and hidden dynamics,’’ PLOS Comput. Biol., vol. 16, no. 11, Nov. 2020, Art. no. e1007575. [26] C. K. Buhler, R. S. Terry, K. G. Link, and F. R. Adler, ‘‘Do mecha- nisms matter? Comparing cancer treatment strategies across mathemati- cal models and outcome objectives,’’ Math. Biosci. Eng., vol. 18, no. 5, pp. 6305–6327, 2021. [27] K. Ohta and H. Ishida, ‘‘Comparison among several numerical integration methods for Kramers–Kronig transformation,’’ Appl. Spectrosc., vol. 42, no. 6, pp. 952–957, Aug. 1988. [28] G. R. W. Quispel and D. I. McLaren, ‘‘A new class of energy-preserving numerical integration methods,’’ J. Phys. A, Math. Theor., vol. 41, no. 4, Feb. 2008, Art. no. 045206. [29] K. Atkinson, An Introduction to Numerical Analysis. Hoboken, NJ, USA: Wiley, 2008. 54909 VOLUME 11, 2023 VOLUME 11, 2023 VOLUME 11, 2023
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Increased incidence of giant cell arteritis and associated stroke during the COVID-19 pandemic in Spain: A nation-wide population study
Autoimmunity reviews
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Increased incidence of giant cell arteritis and associated stroke during the COVID-19 pandemic in Spain: A nation-wide population study Víctor Moreno-Torres a,b,*, Vicente Soriano a, Jorge Calder´on-Parra c, María Martínez-Urbistondo b, Ana Trevi˜no a, Zayrho de San Vicente d,e, Carmen de Mendoza c,f, Guillermo Ruiz-Irastorza g,h a UNIR Health Sciences School, Madrid, Spain b Systemic Autoimmune Diseases Unit, Internal Medicine Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain c Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain d Neurology Department, Hospital Universitario HM Puerta del Sur, M´ostoles, Madrid, Spain e Neurology Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain f Basic Medical Sciences, Faculty of Medicine, Universidad CEU San Pablo, Madrid, Spain g Universidad del País Vasco / Euskal Herriko Unibertsitatea, Bizkaia, The Basque Country, Spain h Autoimmune Diseases Research Unit, Biocruces Bizkaia Health Research Institute, Bizkaia, The Basque Country, Spain Contents lists available at ScienceDirect Contents lists available at ScienceDirect Autoimmunity Reviews 22 (2023) 103341 Autoimmunity Reviews 22 (2023) 103341 Autoimmunity Reviews journal homepage: www.elsevier.com/locate/autrev Abbreviations: AION, Anterior ischemic optic neuropathy; CI, Confidence interval; CRF, Cardiovascular risk factors; GCA, Giant cell arteritis; ICD, International Classification of Diseases; ICU, Intensive care Unit; SNHDD, Spanish Hospital Discharge Database; TIA, transient ischemic attack. * Corresponding author at: Systemic Autoimmune Diseases Unit, Internal Medicine Department, Hospital Universitario Puerta de Hierro Majadahonda, C/ Joaquín Rodrigo n◦2 28222 Majadahonda, Madrid, Spain. E mail addresses: victor moreno torres 1988@gmail com victor morenotorres@unir net (V Moreno Torres) Available online 14 April 2023 1568-9972/© 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). https://doi.org/10.1016/j.autrev.2023.103341 Received 26 March 2023; Accepted 13 April 2023 A R T I C L E I N F O Keywords: Giant cell arteritis Stroke COVID-19 SARS-CoV-2 vaccine Introduction: SARS-CoV-2 infection and COVID-19 vaccines might have increased the incidence of giant-cell arteritis (GCA) and the risk of associated stroke in Spain. Methods: Retrospective nation-wide observational analysis of all adults hospitalized with GCA in Spain during 5 years (Jan-2016 and Dec-2021). The incidence and proportion of admissions with or because of GCA and GCA- associated stroke were compared between pre-pandemic (2016–2019) and pandemic (2020 and 2021) years. Sensitivity analyses were conducted for the different COVID-19 waves and vaccine timing schedules. i Results: A total of 17,268 hospital admissions in patients diagnosed with GCA were identified. During 2020 there were 79.3 and 8.1 per 100,000 admissions of GCA and GCA-associated stroke, respectively. During 2021 these figures were 80.8 and 7.7 per 100,00 admissions, respectively. As comparison, yearly admissions due to GCA and GCA-associated stroke were 72.4 and 5.7 per 100,00, respectively, during the pre-pandemic period (p < 0.05). Coincident with the third wave of COVID-19 (and first vaccine dosing), the rate of GCA-associated stroke ad­ missions increased significantly (from 6.7 to 12%; p < 0.001). Likewise, there was an increase in GCA-associated stroke (6.6% vs 4.1%, p = 0.016) coincident with the third dose vaccination (booster) in patients older than 70 at the end of 2021. In multivariate analysis, only patients admitted during the third COVID-19 wave (and first vaccine dosing) (OR = 1.89, 95% CI 1.22–2.93), and during the third vaccination dosing in patients older than 70 (booster) (OR = 1.66, CI 1.11–2.49), presented a higher GCA-associated stroke risk than the same months of previous years after adjustment by age, sex, classical cardiovascular risk factors and COVID-19 diagnosis. Conclusions: The COVID-19 pandemic led to an increased incidence of GCA during 2020 and 2021. Moreover, the risk of associated stroke significantly risen accompanying times of COVID-19 vaccine dosing, hypothetically linked to an increased thrombotic risk of mRNA-SARS-CoV-2 vaccines. Hence, forthcoming vaccine policies and indications must weigh the risk of severe COVID-19 with the risk of flare or stroke in patients with GCA. p y j y g g Conclusions: The COVID-19 pandemic led to an increased incidence of GCA during 2020 and 2021. Moreover, the risk of associated stroke significantly risen accompanying times of COVID-19 vaccine dosing, hypothetically linked to an increased thrombotic risk of mRNA-SARS-CoV-2 vaccines. 1. Introduction Giant-cell arteritis (GCA) is a chronic granulomatous vasculitis involving large and medium sized arteries [1]. Although GCA can potentially occur any time after 50 years of age, the disease typically affects elderly patients, with the peak incidence being between 70 and 80 years [2,3]. Clinically, GCA usually presents with an insidious course with general manifestations including fever, asthenia or weight-loss, along with local symptoms due to arterial inflammation and vascular deficits such as headache or jaw claudication [2]. When the arterial compromise is severe enough, GCA might lead to ischemic phenomena, such as acute ischemic optic neuropathy (AION), transient ischemic attack (TIA) or even established stroke, frequently in the carotid or vertebrobasilar territories [3,4]. These severe complications can occur in up to 20–50% of patients with GCA and usually appear within the period of active disease [4]. GCA pathogenesis is yet practically un­ known [5]. However, some reports have pointed out the potential role of certain viruses, such as cytomegalovirus or varicella zoster, as well as influenza vaccines, as triggers for GCA in predisposed individuals [6–8]. Demographics and outcome data, including age, sex, ethnicity, length of admission, intensive care unit (ICU) admission or in-hospital mortality was retrieved from the database. Besides, considering that the main diagnosis was the defining reason for admission, all main di­ agnoses were decodified and four primary outcomes were analyzed: total number of admissions in patients with GCA, admissions attribut­ able to GCA (being GCA the main diagnosis), admissions with GCA- associated stroke and admissions attributable to GCA-associated stroke (being stroke the main diagnosis). GCA-associated stroke was defined by both the presence of stroke (codes I61, I62.9 and I63), AION (code H47.01) or TIA (code G45) in GCA patients. These outcomes were compared between the years of the pandemic (2020 and 2021) and the most recent pre-pandemic period (2016–2019). Furthermore, to evaluate the incidence and distribution of GCA and GCA-associated stroke during the different stages of the pandemic, seven periods were considered: the first wave (March–April 2020), the post-lockdown period (June–July 2020), the second wave (October–November 2020), the third wave, coexisting with the first and second vaccine dosing in the elderly population (January–February 2021), the fourth wave (March–April 2021), the fifth wave (June–July 2021) and the third vaccination period in patients older than 70 years (October–November 2021). 1. Introduction These intervals and dates were defined ac­ cording to the COVID-19 epidemiology and the waves described in Spain, as well as according to the national vaccine policy implemented during 2020 and 2021 [31–33]. l The surge of SARS-CoV-2 infection by the end of 2019 in China and its rapid spread worldwide is an unprecedented medical phenomenon. Millions of deaths have occurred during the three years since the pandemic onset [9]. However, COVID-19 is clinically very heteroge­ neous [10]. On the one hand, a majority of patients present an asymp­ tomatic or oligo-symptomatic illness whilst other might suffer an interstitial pneumonia and even an acute respiratory distress syndrome (ARDS), the main cause of death in these patients. In addition, a subset of patients develops what has been called a ‘cytokine storm’, a syndrome of systemic hyperinflammatory dysregulation with coagulation disor­ ders, thromboembolic events, myocarditis, acute kidney injury, hepati­ tis and multi-organ failure [11]. The cytokine storm has been compared to catastrophic antiphospholipid syndrome (CAPS), Still's disease or hemophagocytic lymphohistiocytosis, all severe hyperinflammatory conditions strongly associated with autoimmunity [12]. Altogether, the similarities between severe COVID-19 and certain autoimmune diseases could explain why both SARS-CoV2 infection and COVID-19 vaccines have been related to autoimmune disease onset, disease flares and more severe inflammatory activity during the pandemic [13–15]. Indeed, small-size and/or monocenter reports have claimed an increase of cases of GCA and/or associated ischemic events following COVID-19 disease and/or vaccination, although this observation has not been confirmed by others [16–30]. Finally, the ICD-10 coding was also used to analyze CRF. Patients were tagged as hypertensive if they had a diagnosis of primary hyper­ tension (code I10), hypertensive cardiac disease (I11), hypertensive chronic kidney disease (I12), hypertensive cardiac and chronic kidney disease (I13) or secondary hypertension (I15). Diabetes included type 1 diabetes mellitus (E10), type 2 diabetes mellitus (E11) and other types of diabetes mellitus (E12). High cholesterol was defined by pure hyper­ cholesterolemia (E78) or hyperlipidemia (E78.2 and E78.5) and obesity by the homonymous code E66. Smoking was classified according to tobacco consumption (Z72.0) or nicotine dependence (F17) and alcohol according to alcohol related disorders (F10). 2. Methods First, we compared the annual incidence and the proportion of ad­ missions with or because of GCA and GCA-associated stroke between the pre-pandemic years (2016–2019) and 2020 or 2021, respectively. Sec­ ond, we analyzed the distribution of GCA and GCA-associated stroke admissions for each pandemic period, considering the subsequent waves and the third vaccination period in patients older than 70 years. Herein, and to determine the impact of COVID-19 disease and vaccine on the epidemiology of GCA, the different periods were compared with the same months in 2016–2019. Finally, we performed a binary logistic regression analysis to determine if each of these bi-monthly intervals were associated with a higher GCA-associated stroke risk. For adjust­ ment, age, male sex, baseline CRF and COVID-19 diagnosis during admission were considered. 2.3. Statistical analysis Categorical variables were reported as frequencies and percentages while continuous variables were presented as mean and standard devi­ ation. Bivariate comparisons of quantitative and qualitative variables were performed using the Kruskal-Wallis test, U Mann-Whitney test, and the Chi2 test. Incidence was expressed by 100,000 national admissions and rates or proportions of GCA and GCA-associated stroke as percent­ ages of the overall admissions in patients with GCA. In the light of the aforementioned considerations, the aim of the present study was to assess the impact of COVID-19 pandemic and SARS- CoV-2 vaccines on the incidence of GCA and the development of GCA- associated stroke in a nation-wide analysis conducted in Spain, a 47 million population country. A R T I C L E I N F O Hence, forthcoming vaccine policies and indications must weigh the risk of severe COVID-19 with the risk of flare or stroke in patients with GCA. Abbreviations: AION, Anterior ischemic optic neuropathy; CI, Confidence interval; CRF, Cardiovascular risk factors; GCA, Giant cell arteritis; ICD, International Classification of Diseases; ICU, Intensive care Unit; SNHDD, Spanish Hospital Discharge Database; TIA, transient ischemic attack. * Corresponding author at: Systemic Autoimmune Diseases Unit, Internal Medicine Department, Hospital Universitario Puerta de Hierro Majadahonda, C/ Joaquín Rodrigo n◦2 28222 Majadahonda, Madrid, Spain. E mail addresses: victor moreno torres 1988@gmail com victor morenotorres@unir net (V Moreno Torres) g j p E-mail addresses: victor.moreno.torres.1988@gmail.com, victor.morenotorres@unir.net (V. Moreno-Torres). p 1568-9972/© 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). V. Moreno-Torres et al. Autoimmunity Reviews 22 (2023) 103341 3.2. Differences in the incidence of GCA and GCA-associated stroke during the pandemic Compared with the same months in 2016–2019, the incidence of admissions in GCA patients decreased during the first wave (62.3 vs 78.1 per 100,000 national admissions, p < 0.001). On the contrary, the incidence of admissions in patients with GCA was higher in the second wave (82.9 vs 70.5 per 100,000 national admissions, p < 0.001), in the fifth wave (85.2 vs 71.9 per 100,000 national admissions, p < 0.001) and in the period coinciding with the third vaccine dose in elderly pa­ tients (90.8 vs 70.5 per 100,000 national admissions, p < 0.001), (Table 3, Fig. 1.A). Table 2 illustrates epidemiological data of admissions related with GCA in Spain from 2016 to 2021. The incidence of admissions associated with GCA was higher in 2020 (79.3 per 100,000 national admissions) and in 2021 (80.8 per 100,000 national admissions) than in the pre- pandemic period (mean 72.4 per 100,000 national admissions, p < 0.001). By contrast, the admissions attributable to GCA itself were lower in 2020 than in the previous years (19.7% vs 21.7% of total admissions in GCA cases; p = 0.003). In addition, several differences with the pre-pandemic period were found when the rates of admissions attributable to GCA and the pro­ portions of admissions with or because of stroke were compared (Table 3, Fig. 1.B, 1. C and 1.D). The proportion of admissions with GCA- associated stroke in the post-lockdown period was higher than in pre­ vious years (12.6% vs 9.1% of all admissions in patients with GCA, p = 0.023). In the second wave, when a 16% of GCA patients were admitted with COVID-19, the proportion of admissions attributable to GCA was lower than other years (17.1% vs 22.1% of all admissions in GCA pa­ tients, p = 0.017). Likewise, during the third wave, when 18.2% of pa­ tients presented COVID-19, less patients were admitted because of GCA itself (14.9% vs 19.2% of all admissions in GCA patients, p = 0.037). On the other hand, both a higher rate of GCA-associated stroke (12% vs 6.7% of all admissions in GCA patients, p < 0.001) and more admissions attributable to GCA-associated stroke (6.7% vs 3.6% of all admissions in GCA patients, p = 0.006) were reported in this period compared with 2016–2019. 3.3. Differences in GCA and GCA-associated stroke incidence within pandemic periods Since the epidemiology of GCA, including the rate of stroke, varied during 2020 and 2021, a bi-monthly-analysis of both GCA admissions and GCA-associated stroke incidence was performed to clarify the impact of the different COVID-19 waves and the potential influence of the SARS-CoV-2 vaccine (Table 3, Fig. 1). 2.1. Study population We performed an analysis of data extracted from the Spanish Hos­ pital Discharge Database (SNHDD), a registry belonging to the Spanish Ministry of Health. The SNHDD includes demographic and epidemio­ logical data and up to 20 discharge diagnoses carried out during admission and defined by the International Classification of Diseases (ICD-10) from January 1st, 2016. We selected hospital admissions from 2016 to 2021 for patients with a diagnosis within the ICD-10 code M31.5 (giant cell arteritis with polymyalgia rheumatica) and M31.6 (other giant cell arteritis) at any position in the list. The study complies with the Declaration of Helsinki and was approved by the local research ethics committee (PI 68–23). The database was provided after all po­ tential patient identifiers were deleted ensuring the anonymity of data. All statistical analyses were performed using IBM SPSS for Windows (IBM Corp, Armonk, NY). All tests were two-tailed and only p values <0.05 were considered as significant. 2 V. Moreno-Torres et al. Autoimmunity Reviews 22 (2023) 103341 3.1. Population characteristics 3.1. Population characteristics Between 2016 and 2021,17,268 hospital admissions in patients diagnosed with GCA were reported in the SNHDD registry. The popu­ lation characteristics are shown in Table 1. The mean age was 80.9 years and 63.5% of the patients were female. Regarding classical CRF, 65.6% of the patients were identified as hypertensive, 31.4% as diabetic, 38.8% as hypercholesterolemic and 7.5% as obese. Smoking was reported in 4.3% and alcohol consumption in 2.7%. GCA was the cause of admission in 21.2% of the patients, and 8.6% were consistent with stroke (ischemic stroke 3.6%, TIA 1.7%, AION 2.8% and hemorrhagic stroke 0.5%). Stroke was the cause of admission in 4.8% of the cases overall. The mean average in-hospital stay was 9.3 days and the global mortality was 7% (1206 deaths). 3. Results admissions in GCA patients and 7.7 per 100,000 national admissions, respectively) than in the 2016–2019 period (7.9% of all admissions in GCA patients and 5.7 per 100,000 national admissions, respectively, p = 0.05). Likewise, the rate of admissions attributable to GCA-associated stroke was higher during 2020 (5.5% of all admissions in GCA pa­ tients and 4.4 per 100,000 national admissions, respectively) and during 2021 (5.6% and 4.5 per 100,000 national admissions in 2021, respec­ tively) compared with the pre-pandemic period (4.5% of all admissions in GCA patients and 3.2 per 100,000 admissions in 2016–2019, respectively, p = 0.01). Table 1 Population characteristics. Admissions in patients with Giant Cell Arteritis (N = 17,268) Female N (%) 10,966 (63.5) Age (years) (Mean, SD) 80.9 (8.7) Cardiovascular risk factors Hypertension N (%) 11,318 (65.6) Diabetes N (%) 5416 (31.4) Cholesterol N (%) 6714 (38.8) Obesity N (%) 1292 (7.5) Smoking habit N (%) 734 (4.3) Alcohol consumption N (%) 468 (2.7) Diagnoses or events during admission GCA as admission cause 3659 (21.2) GCA-associated stroke 1477 (8.6) Ischemic stroke 619 (3.6) TIA 288 (1.7) AION 478 (2.8) Hemorrhagic stroke 92 (0.5) GCA-associated stroke as admission cause 829 (4.8) Outcomes ICU admission N (%) 590 (3.4) Mortality N (%) 1206 (7) Admission- length stay (days) mean (SD) 9.3 (9.5) ICU admission- length stay (days) mean (SD) 4.8 (7.9) SD: Standard deviation, GCA: Giant cell arteritis, Cerebrovascular accident related to Giant cell arteritis, TIA: Transient ischemic attack, AION: Anterior ischemic optic neuropathy, ICU: Intensive Care Unit. 3.2. Differences in the incidence of GCA and GCA-associated stroke during the pandemic Finally, it should be highlighted that a higher proportion of patients during October–November 2021 (third vaccine in patients older than 70 years) were admitted because of GCA-associated stroke (6.6% vs 4.1% of all admissions in patients with GCA, p = 0.016). Regarding ischemic events, both the proportion of admissions with GCA-associated stroke and the incidence of GCA-associated stroke were higher in 2020 (10.2% of all admissions in GCA patients and 8.1 per 100,000 national admissions, respectively) and in 2021 (9.5% of all Table 3 On the other hand, it has been shown that general health care and, particularly, the diagnosis and outpatient management of autoimmune diseases, including GCA, has been greatly influenced by the pandemic [30,34]. Accordingly, the incidence, clinical onset and severity of the disease may have changed during this period not only by COVID-19 itself, but also influenced by a more difficult access to health facilities for clinical conditions other than COVID-19. Altogether, we believe that this large study can help clarify the epidemiology of GCA and the impact of COVID-19 waves and vac­ cines during the first two years of the pandemic. vascular complications [19,20,25,26,28]. However, all these assump­ tions should be interpreted cautiously, since these data are mostly based on case reports, small series or single-center studies. Moreover, other authors have not confirmed a significantly higher incidence of GCA during the COVID-19 pandemic [18,29,30]. For example, Kaulen et al. only found one case of GCA in >200,000 inhabitants who received SARS-CoV-2 vaccinations in Germany [22]. On the other hand, it has been shown that general health care and, particularly, the diagnosis and outpatient management of autoimmune diseases, including GCA, has been greatly influenced by the pandemic [30,34]. Accordingly, the incidence, clinical onset and severity of the disease may have changed during this period not only by COVID-19 itself, but also influenced by a more difficult access to health facilities for clinical conditions other than COVID-19. Altogether, we believe that this large study can help clarify the epidemiology of GCA and the impact of COVID-19 waves and vac­ cines during the first two years of the pandemic. Table 3 Table 3 GCA and GCA-associated stroke epidemiology during the COVID-19 pandemic periods in Spain. First wave (March–April 2020) Post-lockdown period (June–July 2020) Second wave (October–November 2020) Third wave (January–February 2021) Fourth wave (March–April 2021) Fifth wave (June–July 2021) Third vaccine (October–November 2021) Admissions in patients with GCA (Incidence per 100,000 admissions) 369 (62.3) 507 (86.5) 486 (82.9) 451 (73) 502 (81.3) 526 (85.2) 561 (90.8) Admissions with COVID-19 N (%) – 4 (0.8) 78 (16) 82 (18.2) 20 (4) 12 (2.3) 13 (2.3) Admissions attributable to GCA N (%) 66 (17.9) 124 (24.5) 83 (17.1) 67 (14.9) 109 (21.7) 132 (25.1) 116 (20.7) Admissions with GCA-associated stroke N (%) 28 (7.6) 64 (12.6) 47 (9.7) 54 (12) 41 (8.2) 52 (9.9) 53 (9.4) Admissions attributable to GCA-associated stroke N (%) 16 (4.3) 35 (6.9) 19 (3.9) 30 (6.7) 25 (5) 31 (5.9) 37 (6.6) GCA: Giant cell arteritis. Percentages are related to the number of admissions in patients with GCA, while the incidence is expressed in number of admissions per 100,000 national admissions. Statistically significant differences when compared to the incidence of previous years (p < 0.05) are highlighted in bold. GCA and GCA-associated stroke epidemiology during the COVID-19 pandemic periods in Spain. and GCA-associated stroke epidemiology during the COVID-19 related to the number of admissions in patients with GCA, while the incidence is expressed in number of admissions per significant differences when compared to the incidence of previous years (p < 0.05) are highlighted in bold. GCA: Giant cell arteritis. Percentages are related to the number of admissions in patients with GCA, while the incidence is expressed in number of admissions per 100,000 national admissions. Statistically significant differences when compared to the incidence of previous years (p < 0.05) are highlighted in bold. GCA: Giant cell arteritis. Percentages are related to the number of admissions in patients with GCA, while the incidence 100,000 national admissions. Statistically significant differences when compared to the incidence of previous years (p < vascular complications [19,20,25,26,28]. However, all these assump­ tions should be interpreted cautiously, since these data are mostly based on case reports, small series or single-center studies. Moreover, other authors have not confirmed a significantly higher incidence of GCA during the COVID-19 pandemic [18,29,30]. For example, Kaulen et al. only found one case of GCA in >200,000 inhabitants who received SARS-CoV-2 vaccinations in Germany [22]. 3.4. Impact of pandemic waves and vaccination periods on GCA- associated stroke In order to determine whether the different periods related to COVID-19 waves and/or SARS-CoV-2 vaccines, entailed a higher risk of stroke in the setting of GCA, a binary logistic regression analysis considering age, sex, CRF and COVID-19 during admission, for each bi- monthly period, was performed (Fig. 2, Table 4). Only patients admitted during the third wave, concurring with the first and second vaccine in the elderly (OR = 1.89, 95% CI 1.22–2.93), and during the third vaccination period in patients older than 70 years (OR = 1.66, CI 1.11–2.49), presented a higher GCA-associated stroke risk compared with the same months in previous years. No similar increased risk was seen among patients admitted during other periods of the study. 3 Autoimmunity Reviews 22 (2023) 103341 V. Moreno-Torres et al. V. Moreno-Torres et al. Table 2 Epidemiology of GCA and GCA-associated stroke between 2016 and 2021 in Spain. Epidemiology of GCA and GCA-associated stroke between 2016 and 2021 in Spain. Epidemiology of GCA and GCA-associated stroke between 2016 and 2021 in Spain. 2016 (N = 3,895,317) 2017 (N = 3,972,586) 2018 (N = 4,026,251) 2019 (N = 3,971,324) 2020 (N = 3,516,107) 2021 (N = 3,706,163) Admissions in patients with GCA N 2757 2844 2822 3052 2788 2.995 Incidence per 100,000 admissions 70.1 71.6 70.1 76.9 79.3 80.8 Admissions attributable to GCA N (%) 621 (22.5) 605 (21.3) 598 (21.2) 659 (21.6) 548 (19.7) 628 (21) Incidence per 100,000 admissions 15.9 15.2 14.9 16.6 15.6 16.9 Admissions with GCA-associated stroke N (%) 214 (7.8) 219 (7.7) 242 (8.6) 233 (7.6) 285 (10.2) 284 (9.5) Incidence per 100,000 admissions 5.5 5.5 6 5.9 8.1 7.7 Admissions attributable to GCA-associated stroke N (%) 120 (4.4) 138 (4.9) 123 (4.4) 127 (4.2) 153 (5.5) 168 (5.6) Incidence per 100,000 admissions 3.1 3.5 3.1 3.2 4.4 4.5 GCA: Giant cell arteritis. Percentages are related to the number of admissions in patients with GCA, while the incidence is expressed in number of admissions per 100,000 national admissions. Statistically significant differences when compared to the incidence of previous years (p < 0.05) are highlighted in bold. : Giant cell arteritis. Percentages are related to the number of admissions in patients with GCA, while the incidence is expre 000 national admissions. 3.4. Impact of pandemic waves and vaccination periods on GCA- associated stroke Statistically significant differences when compared to the incidence of previous years (p < 0.05) are related to the number of admissions in patients with GCA, while the incidence is expressed in number of admissions per significant differences when compared to the incidence of previous years (p < 0.05) are highlighted in bold. GCA: Giant cell arteritis. Percentages are related to the number of admissions in patients with GCA, while the incidence is expressed in number of admissions per 100,000 national admissions. Statistically significant differences when compared to the incidence of previous years (p < 0.05) are highlighted in bold. 4. Discussion This nation-wide epidemiological study explores the incidence of GCA and the risk of GCA-associated stroke during the COVID-19 pandemic. Our results suggest that COVID-19 disease and, especially, SARS-CoV-2 vaccine, might be responsible for the higher rate of GCA- associated stroke reported in this period, leading to the increased inci­ dence of admissions among patients with GCA during 2020 and 2021. i Previous works have already identified that COVID-19 disease and immunization, especially with mRNA-vaccines, can trigger the onset of GCA and GCA flares [16,17,19,24,25,27,28]. An analysis based on the WHO safety report database by Mettler et al. found that COVID-19 vaccines might be actually associated with an increased number of diagnosis of GCA, identifying a potential safety signal and raising con­ cerns about repeated vaccinations [24]. In addition, some authors have proposed that after SARS-CoV-2 vaccination, GCA can present with atypical features, including a higher rate of neuro-ophthalmological and i Overall, our results show that the incidence of GCA rose during 2020 4 Autoimmunity Reviews 22 (2023) 103341 Fig. 1. Incidence of GCA and GCA-associated stroke in Spain during the COVID-19 pandemic in Spain. Footnote: The figure represents the monthly incidence of GCA (A) and GCA-associated stroke (B) admissions during the COVID-19 pandemic in Spain. Incidence is expressed by 100,000 annual national admissions. V. Moreno-Torres et al. Autoimmunity Reviews 22 (2023) 103341 V. Moreno-Torres et al. Autoimmunity Reviews 22 (2023) 103341 V. Moreno-Torres et al. V. Moreno-Torres et al. Fig. 1. Incidence of GCA and GCA-associated stroke in Spain during the COVID-19 pandemic in Spain. Footnote: The figure represents the monthly incidence of GCA (A) and GCA-associated stroke (B) admissions during the COVID-19 pandemic in Spain. Incidence expressed by 100,000 annual national admissions. Fig. 1. Incidence of GCA and GCA-associated stroke in Spain during the COVID-19 pandemic in Spain. Footnote: The figure represents the monthly incidence of GCA (A) and GCA-associated stroke (B) admissions during the COVID-19 pandemic in Spain. Incidence is expressed by 100,000 annual national admissions. Fig. 1. Incidence of GCA and GCA-associated stroke in Spain during the COVID-19 pandemic in Spain. Footnote: The figure represents the monthly incidence of GCA (A) and GCA-associated stroke (B) admiss expressed by 100,000 annual national admissions. Fig. 2. Factors related to GCA-associated stroke during the COVID-19 pandemic in Spain. 4. Discussion Footnote: The figure represents the binary logistic regression analysis to determine factors related to GCA-associated stroke risk during the pandemic, including the seven periods of the COVID-19 pandemic. For adjustment, age, male sex, baseline CRF and COVID-19 diagnosis during admission were considered. Table 4 Adjusted risk of GCA-associated stroke per study periods. OR 95% CI First wave 1.10 0.63–1.90 Post-lockdown period 0.73 0.49–1.09 Second wave 1.10 0.65–1.89 Third wave 1.89 1.22–2.93 Fourth wave 1.20 0.76–1.91 Fifth wave 1.16 0.76–1.76 Third vaccine in elderly 1.66 1.11–2.49 Each period was adjusted by age, male sex, hypertension, diabetes, hypercho­ lesterolemia, obesity, smoking, alcohol consumption and COVID 19. Table 4 Adjusted risk of GCA-associated stroke per study periods. Each period was adjusted by age, male sex, hypertension, diabetes, hypercho­ lesterolemia, obesity, smoking, alcohol consumption and COVID 19. and 2021, as previously noticed [16,24,27,28]. These figures seem to be mostly determined by admissions associated with COVID-19 and by the higher incidence and proportion of admissions with or because ischemic events, supporting the hypothesized effect of both, the virus and the vaccine, on vascular events in GCA patients (19,25,26,28). Besides, this effect has not been uniform in our population during the different pe­ riods of the pandemic. In the first place, the dramatic reduction of GCA admissions during March and April 2020, when COVID-19 was not yet included in the ICD-10 coding, was followed by an increase of cere­ brovascular events in the post-lockdown period. Therefore, the diag­ nostic and therapeutic delay during the first wave, with a collapsed emergency system nationwide, probably led to a higher rate of subse­ quent complications, as other authors have already described [30,34]. On the other hand, the higher incidence of GCA admissions identified in our study during the second COVID-19 outbreak following summer 2020 was mostly related to COVID-19, and not to GCA or GCA-CVA themselves. Fig. 2. Factors related to GCA-associated stroke during the COVID-19 pandemic in Spain. i Footnote: The figure represents the binary logistic regression analysis to determine factors related to GCA-associated stroke risk during the pandemic, including the seven periods of the COVID-19 pandemic. For adjustment, age, male sex, baseline CRF and COVID-19 diagnosis during admission were considered. 5 5 Autoimmunity Reviews 22 (2023) 103341 V. Moreno-Torres et al. In Spain, the national SARS-CoV-2 vaccination campaign began at the end of December of 2020 [31]. 4. Discussion The vaccine policies were initially focused on the elderly and on those living in nursery homes, who were particularly vulnerable to COVID-19 during the first two waves [10,32,33]. Accordingly, the protective effect was not evident until the fourth and fifth waves, as seen in our population and as reported by Barandalla et al [31]. However, a significant increase in ischemic events was identified in January–February 2021 and October–November 2021, in close temporal coincidence with the first two doses of the vaccine in patients older than 80 and the third dose in patients older than 70, respectively. Therefore, the rising rates of GCA-associated stroke iden­ tified in patients with GCA during these periods, as confirmed in the multivariate analysis, supports the role of mRNA-vaccine on the subse­ quent risk of ischemic phenomena in GCA [5,17,19,35]. repeated doses does not seem that clear [10,31,33]. A third dose of the vaccine has been advocated to confer adequate immunization in GCA patients, many of them under methotrexate and glucocorticoid treat­ ment which may results in lower neutralizing activity and cellular im­ mune protection than healthy controls [40]. However, the inclusion of GCA among the potential conditions associated with the Autoimmune/ inflammatory syndrome induced by adjuvants (ASIA), and, particularly, with post-COVID-19 vaccination ASIA [41,42], should be also taken into account. Moreover, according to our results, the future vaccine policies must weigh the risk of severe COVID-19 against the risk of flare and, especially, of stroke in patients with GCA. Therefore, knowing the actual immunological status of the patients -probably including cellular im­ munity in the equation in patients with insufficient humoral response-, their baseline cardiovascular risk and also the virulence of the pre­ dominant variant of the coronavirus would help individualize the indi­ cation of future subsequent doses. Despite the many uncertainties in the pathophysiology of GCA, the association of the disease with certain infectious agents has been pre­ viously reported [5–8]. Analogous to other autoimmune or rheumatic diseases, the current pathogenic model accepts that GCA develops in genetically predisposed individuals exposed to a number of triggers, including infections. This hypothesis is well-accepted in other condi­ tions such as CAPS or polyarteritis nodosa, where infections have shown to be strongly associated with the disease onset [6,36]. Both bacteria and virus has been implicated. Submission declaration and authorship The present work has not been published previously, it is not under consideration for publication elsewhere and, if accepted, will not be published elsewhere. The work has been approved by all author, who have made substantial contribution to the manuscript. We should acknowledge several limitations of the present study. Due to the database structure, essential information such as antiplatelet, anticoagulant, tocilizumab or glucocorticoid treatment before and dur­ ing admission, and more detailed data about the diagnosis and clinical course of GCA, including the extent of the disease and the number or type of vessels involved, was lacking. Secondly, we were not able to retrieve information about COVID-19 infection prior to vaccination, immunological status and, importantly, about the specific vaccine given. However, despite these limitations, we believe that the size of the study population, the nationwide spectrum of the study and the statistical power of the analysis make our data clinically relevant. Moreover, the proportion of individuals effectively vaccinated within the analyzed periods, particularly within older people, was very high in Spain, most of them receiving mRNA-based vaccines [31,38]. Therefore, the assump­ tion that most of the population of the study received such vaccines during the presumed periods of vaccination analyzed is likely to be correct. Thirdly, given the need to fit yearly time periods, the first two months of 2020 preceded the major COVID-19 outbreak in Spain. Therefore, counting these two months within the pandemic period should have provided an underestimation of the proportion of cases of GCA and GCA-associated stroke collected in this timeframe. Trends in Fig. 2 support this observation. Another caveat is the complex interac­ tion over two years between older age, COVID-19 severity, COVID-19 vaccination, COVID-19 mortality, and GCA higher incidence. In Spain, 98,900 deaths due to COVID-19 were reported during 2020 and 2021. However, estimates derived from the excess mortality data during the same period are of 162,000 (1.64-fold greater) [39]. This huge and disproportionate high mortality mostly occurred among the elderly, the population at higher risk for of developing GCA. i 4. Discussion Escherichia coli, Propionibacterium acnes, Coxiella burnetti, Parvovirus B19, Cytomegalovirus and Varicella zoster, have all been associated with GCA or granulomatous angiitis of the CNS [5–8]. The association between SARS-CoV-2 infection and/or COVID-19 vaccines and GCA or subsequent CVA, as seen in our population, seems also plausible given the proinflammatory and prothrombotic character of both the infection and the vaccine [16,17,19,37]. Declaration of Competing Interest The authors declare the following financial interests/personal re­ lationships which may be considered as potential competing interests: i Victor Moreno-Torres reports financial support was provided by Academia M´edico-Quirúrgica Espa˜nola. Guillermo Ruiz-Irastorza re­ ports financial support was provided by Department of Education of the Basque Government. Funding Víctor Moreno-Torres received a grant from the Academia Medico- Quirúrgica Espa˜nola. Guillermo Ruiz-Irastorza was supported by the Department of Education of the Basque Government, research grant IT 1512–22. References COVID-19 recombinant mRNA vaccines and serious ocular inflammatory side effects: real or coincidence? J Ophthalmic Vis Res 2021. https://doi.org/10.18502/jovr.v16i3.9443. p p g j [27] Parreau S, Liozon E, Ly K-H, Fauchais A-L, Hantz S. High incidence of giant cell arteritis during the COVID-19 pandemic: no causal relationship but possible involvement of stress. 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References [1] Mukhtyar C, Guillevin L, Cid MC, Dasgupta B, de Groot K, Gross W, et al. EULAR recommendations for the management of large vessel vasculitis. Ann Rheum Dis 2009;68:318–23. https://doi.org/10.1136/ard.2008.088351. [1] Mukhtyar C, Guillevin L, Cid MC, Dasgupta B, de Groot K, Gross W, et al. EULAR recommendations for the management of large vessel vasculitis. Ann Rheum Dis 2009;68:318–23. https://doi.org/10.1136/ard.2008.088351. [2] Gonzalez-Gay MA, Vazquez-Rodriguez TR, Lopez-Diaz MJ, Miranda-Filloy JA, Gonzalez-Juanatey C, Martin J, et al. Epidemiology of giant cell arteritis and polymyalgia rheumatica. Arthritis Rheum 2009;61:1454–61. https://doi.org/ 10.1002/art.24459. [3] Samson M, Jacquin A, Audia S, Daubail B, Devilliers H, Petrella T, et al. Stroke associated with giant cell arteritis: a population-based study. J Neurol Neurosurg Psychiatry 2015;86:216–21. https://doi.org/10.1136/jnnp-2014-307614. [4] Gonzalez-Gay MA, Vazquez-Rodriguez TR, Gomez-Acebo I, Pego-Reigosa R, Lopez- Diaz MJ, Vazquez-Tri˜nanes MC, et al. Strokes at time of disease diagnosis in a series of 287 patients with biopsy-proven Giant cell arteritis. Medicine 2009;88:227–35. https://doi.org/10.1097/MD.0b013e3181af4518. p g [5] Weyand CM, Goronzy JJ. Immunology of Giant cell arteritis. Circ Res 2023;132: 238–50. https://doi.org/10.1161/CIRCRESAHA.122.322128. In conclusion, this nationwide epidemiological study confirms a higher risk of CVA in patients with GCA during the pandemic, probably related, at least in part, to mRNA-SARS-CoV-2 vaccines. Therefore, our findings rise concerns about the potential risk of vascular complications after SARS-CoV-2 vaccination in patients with GCA, as already sug­ gested [16,18]. Whilst the initial indication and benefit of SARS-CoV-2 immunization in this population was obvious, given the favorable ef­ fect in terms of COVID-19 severity among elderly patients, the need for [6] Teng GG, Chatham WW. Vasculitis related to viral and other microbial agents. Best Pract Res Clin Rheumatol 2015;29:226–43. https://doi.org/10.1016/j. berh.2015.05.007. [7] Quartuccio L, Treppo E, Dejaco C. The pre-clinical phase of giant cell arteritis: new clues in the pathogenesis of giant cell arteritis supporting emerging targets. Rheumatology 2022. https://doi.org/10.1093/rheumatology/keac697. [8] Bhatt AS, Manzo VE, Pedamallu CS, Duke F, Cai D, Bienfang DC, et al. Brief report: in search of a candidate pathogen for giant cell arteritis: sequencing-based characterization of the giant cell arteritis microbiome. Arthritis Rheum 2014;66: 1939–44. https://doi.org/10.1002/art.38631. 6 V. Moreno-Torres et al. Autoimmunity Reviews 22 (2023) 103341 [9] Wang H, Paulson KR, Pease SA, Watson S, Comfort H, Zheng P, et al. Estimating excess mortality due to the COVID-19 pandemic: a systematic analysis of COVID- 19-related mortality, 2020–21. Lancet 2022;399:1513–36. https://doi.org/ 10.1016/S0140-6736(21)02796-3. [26] Maleki A, Look-Why S, Manhapra A, Stephen Foster C. References Neurological autoimmune diseases following vaccinations against SARS-CoV-2: a case series. Eur J Neurol 2022;29:555–63. https://doi.org/10.1111/ene.15147. [39] Wang H, Paulson KR, Pease SA, Watson S, Comfort H, Zheng P, et al. Estimating excess mortality due to the COVID-19 pandemic: a systematic analysis of COVID- 19-related mortality, 2020–21. Lancet 2022;399:1513–36. https://doi.org/ 10.1016/S0140-6736(21)02796-3. [23] Delvino P, Bartoletti A, Cassaniti I, Bergami F, Lilleri D, Baldanti F, et al. Impact of immunosuppressive treatment on the immunogenicity of mRNA COVID-19 vaccine in vulnerable patients with giant cell arteritis. Rheumatology 2022;61:870–2. https://doi.org/10.1093/rheumatology/keab776. [40] Monti S, Fornara C, Delvino P, Bartoletti A, Bergami F, Comolli G, et al. Immunosuppressive treatments selectively affect the humoral and cellular response to SARS-CoV-2 in vaccinated patients with vasculitis. Rheumatology 2023;62: 726–34. https://doi.org/10.1093/rheumatology/keac365. p g gy [24] Mettler C, Jonville-Bera A-P, Grandvuillemin A, Treluyer J-M, Terrier B, Chouchana L. Risk of giant cell arteritis and polymyalgia rheumatica following COVID-19 vaccination: a global pharmacovigilance study. Rheumatology 2022;61: 865–7. https://doi.org/10.1093/rheumatology/keab756. g gy [41] Tervaert JWC, Martinez-Lavin M, Jara LJ, Halpert G, Watad A, Amital H, et al. Autoimmune/inflammatory syndrome induced by adjuvants (ASIA) in 2023. Autoimmun Rev 2023;22:103287. https://doi.org/10.1016/j.autrev.2023.103287. [25] Jonathan GL, Scott FM, Matthew KD. A case of post-COVID-19–associated paracentral acute middle maculopathy and Giant cell arteritis-like Vasculitis. J Neuroophthalmol 2021;41:351–5. https://doi.org/10.1097/ WNO.0000000000001348. [42] Jara LJ, Vera-Lastra O, Mahroum N, Pineda C, Shoenfeld Y. Autoimmune post- COVID vaccine syndromes: does the spectrum of autoimmune/inflammatory syndrome expand? Clin Rheumatol 2022;41:1603–9. https://doi.org/10.1007/ s10067-022-06149-4.
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Isolated thumb carpometacarpal joint dislocation: a case report and review of the literature
Journal of orthopaedic surgery and research
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* Correspondence: fotiad-e@otenet.gr 1Orthopaedic Department, General Hospital of Veria, (Verias-Asomaton), Veria, (59100), Greece © 2010 Fotiadis et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Introduction reported in the literature and a universally accepted pro- tocol has not been developed yet [3]. Isolated dislocation of the carpometacarpal (CMC) joint of the thumb is an uncommon upper limb and hand injury. The lesion is usually the consequence of an axial transmitted force through a partially flexed thumb. Due to thick and strong volar ligamentous complex the dislo- cation occurs in dorsal direction through the thin dorsal capsule [1,2]. We report a case with an acute isolated thumb carpo- metacarpal dislocation that was treated with reconstruc- tion of the dorsal capsuloligamentous structures. The three-year follow up outcome, as well as review of the literature for similar cases are presented. This study was approved by the scientific review board at our hospital and was conducted in accordance with the World Medical Association Declaration of Helsinki of 1964, as revised in 1983. Written informed consent was obtained from the patient for publication of this case report and accompanying images. The optimal treatment strategy for the acute thumb CMC joint dislocation remains a subject of debate. Closed reduction and casting, closed or open reduction along with transfixion with Kirschner wires and recon- struction of dorsal ligament and capsuloraphy have been performed so far according to joint stability and sur- geon’s preference. However, only few cases have been Abstract Background: Isolated thumb carpometacarpal dislocation is a rare injury pattern and the optimal treatment option is still controversial. Case Description: We present a 27-year-old basketball player who underwent an isolated dorsal dislocation of the thumb carpometacarpal joint after a fall. The dislocation was successfully reduced by closed means but the joint was found to be grossly unstable. Due to inherent instability, repair of the ruptured dorsoradial ligament and joint capsule was performed. p p The ligament was detached from its proximal insertion into trapezium and subsequently stabilized via suture anchors. The torn capsule was repaired in an end-to-end fashion and immobilization of the joint was applied for 6 weeks. Results: At 3-year follow up evaluation the patient was pain free and returned to his previous level of activity. No restriction of carpometacrpal movements or residual instability was noticed. Radiographic examination showed normal joint alignment and no signs of subluxation or early osteoarthritis. Conclusion: Surgical stabilization of the dorsal capsuloligamentous complex may be considered the selected treatment option in isolated carpometacarpal joint dislocations, that remain unstable after closed reduction in young and high demand patients. Level of Clinical Evidence: Level IV Isolated thumb carpometacarpal joint dislocation: a case report and review of the literature Elias Fotiadis1*, Theodoros Svarnas1, Christos Lyrtzis1, Alexis Papadopoulos1, Panagiotis Akritopoulos2, Byron Chalidis3 Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 Open Access Case Description A 27-year-old, right-hand dominant basketball player was admitted on emergency department of our hospital, after a fall during a basketball game and injury of the right hand. Clinical examination revealed a deformity and Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 Pa Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 Page 2 of 5 swelling at the dorsoradial side of the hand in association with tenderness and pain in thumb movements. Antero- posterior and oblique hand and thumb radiographs demonstrated an isolated dorsal dislocation of the CMC joint. No fracture signs were identified (Figure 1). Figure 2 Intraoperative photograph of the dorsal aspect of carpometacarpal joint. The dorsoradial ligament (black arrow) has been detached from its attachment to trapezium. The capsule (double white arrow) has been also transversely torn exposing the joint and the base of 1st metacarpal (white arrow). Intra-articular injection of local anaesthetic (xylocaine 2%) was followed by closed reduction of the carpometacar- pal joint dislocation. However, the joint found to be grossly unstable and reconstruction of the dorsal capsulo- ligamentous complex occurred. The procedure was per- formed within few hours of the injury under regional anaesthesia using a dorsoradial approach. The dorsoradial ligament of CMC joint was found to be completely torn from its proximal insertion leaving a small cuff attached on the trapezium. The joint capsule was also transversely torn in its mid-substance but no articular cartilage lesions in both joint sides were evident. (Figure 2). The volar liga- ment was remained also intact. After debridement of the dorsal surface of the trapezium the dorsoradial ligament was stabilized onto trapezium using a Mini-Mitec suture anchor loaded with a 2-0 suture material (Ethibond). Furthermore, the CMC joint capsule was repaired in an Figure 2 Intraoperative photograph of the dorsal aspect of carpometacarpal joint. The dorsoradial ligament (black arrow) has been detached from its attachment to trapezium. The capsule (double white arrow) has been also transversely torn exposing the joint and the base of 1st metacarpal (white arrow). end-to-end fashion with 3-0 Vicryl interrupted stitches. Wound closure was followed by application of a short-arm spica cast for approximately 6 weeks. Afterwards, active and passive movements in the joint were commenced but any hand-played sports were prohibited for another 6 weeks. Figure 1 Anteroposterior radiograph of the right hand. Case Description Isolated thumb CMC joint dislocation is evident. Discussion The curved articular surfaces of CMC joint provide only limited stability, compared to the ligaments embedded within the joint capsule. Ligaments do not only repre- sent the primary source of joint stability, but also set the limits of motion in conjunction with the passive ten- sion of muscles [4]. Therefore, their integrity is essential to maintain the static and dynamic stability between the 1st metacarpal bone and trapezium. Excessive laxity of the ligaments, such as after CMC dislocation, may lead to joint instability and subsequently to degeneration of the articular cartilage [4]. The healing potential of dorsal elements without any surgical intervention is still a controversial issue and the indications for performing early ligament reconstruction have not been clearly defined. Conservative or minimally invasive methods (percutaneous pinning) have been applied by some authors. (Table 1) Watt and Hooper [8] described the result of closed reduction and cast or cast and K-wire fixation in 12 patients. One third of patients who treated with cast only and two thirds of patients who treated with cast and K-wire fixation had an unstable and dorsally subluxating joint, which caused weakness and discomfort on hand gripping. Jacobsen and Elberg [3] reported a case with isolated thumb CMC dislocation that was treated with closed reduction and K-wire fixation. Eighteen months post-injury, slight instability and radial subluxation of the first metacarpal bone was found. In the latter scenario, ligament recon- struction by using the Eaton and Littler technique can be applied. The operation has offered good functional results and adequate pain relief in patients with chronic CMC instability after traumatic dislocation of the thumb [9]. Isolated CMC dislocation is associated with various degrees of joint capsule and ligament damage. The volar or anterior oblique ligament is a short and strong struc- ture that was considered for many years the basic key stabilizer for preventing dorsal dislocation of the joint [1]. Bettinger et al. [5] were further reported that the anterior oblique as well as the radial collateral and the ulnar collateral ligaments should be considered the main dynamic stabilizers of the thumb. However, Strauch et al [6] in a cadaveric found that the dorsoradial ligament complex was the primary restraint to dorsal dislocation and responsible for Figure 4 Anteroposterior radiograph of the right hand 3 years post-operatively. Good joint congruency without signs of instability or osteoarthritis are seen. Results At 3-year follow-up, the patient was pain free and returned to the pre-injury level of activity. No limitation of thumb carpometacarpal joint mobility or residual instability was observed (Figure 3). Radiographic exami- nation revealed normal joint anatomy without any signs of subluxation or early osteoarthritis (Figure 4). Figure 3 Appearance of the right hand 3 years post- operatively. The patient had normal and painless thumb movement. Figure 3 Appearance of the right hand 3 years post- operatively. The patient had normal and painless thumb movement. Figure 1 Anteroposterior radiograph of the right hand. Isolated thumb CMC joint dislocation is evident. Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 Page 3 of 5 obtaining joint stability in thumb opposition. Moreover, the authors found that it could be also responsible for joint stability in thumb opposition. This finding was confirmed clinically from Shah and Patel [7] who noticed no disruption of volar capsule or ligament in 4 cases with thumb CMC dislocation. Conversely, the dor- sal capsule and ligament found to be avulsed or torn. In our patient, we similarly observed that the dorsal capsu- loligamentous complex was completely ruptured but the integrity of volar ligament was well preserved. Discussion On the other hand, Bosmans et al [1] obtained good result in 2 patients with isolated thumb CMC joint dis- location after closed reduction and cast. Three year post-injury the patients were pain free and had normal range of motion. Similarly, a very satisfactory outcome was noticed by Khan et al [10] in another patient with bilateral thumb CMC dislocation that treated with closed reduction and cast. Kural et al [11] achieved also good result after closed reduction and cast of a unilat- eral thumb CMC dislocation. Simonian and Trumble [12] compared early ligamen- tous reconstruction with closed reduction and pinning. Four out of 8 patients who initially treated with closed reduction and percutaneous pinning showed recurrent instability. In reconstructive group (minimum follow-up period of 2 years), painless full range of motion and nor- mal grip strength were observed. A good result was seen also from Chen VT [2] in a patient who treated with dorsal ligament reconstruction. Shah and Patel [7] advo- cated that open reduction and K-wire fixation without ligament reconstruction might not be adequate for this type of injury. In their series 2 patients had dorsal Figure 4 Anteroposterior radiograph of the right hand 3 years post-operatively. Good joint congruency without signs of instability or osteoarthritis are seen. Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 Page 4 of 5 Table 1 Published cases with isolated thumb CMC dislocation in English literature Study Year Number of cases Treatment Result Shah J and Patel7 Clin Orthop Relat Res 1983 4 A. Open reduction + pinning (2 patients) B. Closed reduction pinning (1 patient) C. Open reduction + cast in (1 patient) A. Dorsal subluxation, mild arthritic changes. B and C. No subluxation - Normal range of motion Watt N and Hooper G8 J Hand Surg 1987 12 A. Closed reduction + cast (6 patients) B. Closed reduction + cast after 3-21 days (3 patients) C. Closed reduction + pinning + cast (3 patients) A. Asymptomatic instability B. Pain and instability C. No pain or instability Chen VT2 J Hand Surg (Br) 1987 1 Ligament reconstruction Good functional result Jacobsen CW and Elberg JJ3 Scand J Plast Reconstr Surg Hand Surg 1988 1 Closed reduction + pinning Slight instability Simonian PT and Trumble TE12 J Hand Surg (Am) 1996 17 A. Author details 1 1Orthopaedic Department, General Hospital of Veria, (Verias-Asomaton), Veria, (59100), Greece. 21st Orthopaedic Department, Aristotle University of Thessaloniki, (Ag. Dimitriou), Thessaloniki, (54622), Greece. 3Orthopaedic Department, Avenue Hospital, Melbourne, Australia. The above cases point out the unpredictable outcome of conservative or minimally operative treatment modal- ities in stability of thumb CMC joint. Inadequate treat- ment may increase the incidence of recurrent instability, joint degeneration and chronic pain and negatively affect the long-term functional result[11]. Bosmans et al [1] suggested that a nonoperative protocol should be fol- lowed in case of joint congruency after successful closed reduction. The authors mentioned that ligament recon- struction was not clearly justified and should be avoided in acute cases. However, it seems that closed or open reduction and percutaneous pinning can not always guarantee an optimum result and ligament reconstruc- tion should not be considered a superfluous treatment option. References 1. Bosmans B, Verhofstad MHJ, Gosens T: Traumatic thumb carpometacarpal joint dislocations. J Hand Surg 2008, 33A:438-441. 1. Bosmans B, Verhofstad MHJ, Gosens T: Traumatic thumb carpometacarpal joint dislocations. J Hand Surg 2008, 33A:438-441. 2. Chen VT: Dislocation of the carpometacarpal joint of the thumb. J Hand Surg (Br) 1987, 12(2):246-51. 3. Jacobsen CW, Elberg JJ: Isolated carpometacarpal dislocation of the thumb. Scand J Plast Reconstr Surg 1988, 22:185-186. Competing interests The authors declare that they have no competing interests. The authors declare that they have no competing interests. Received: 30 November 2009 Accepted: 10 March 2010 Published: 10 March 2010 Acknowledgements Authors state that no funds have received for this study. subluxation of thumb metacarpal bone after application of the above technique. The remaining patients who underwent open reduction and K-wire fixation or closed reduction and percutaneous pinning respectively had congruent joints. Authors’ contributions E. F. was a major contributor in writing the manuscript while B. C. was a major contributor in writing and in editing the manuscript, as well. C. L. and T.S. analyzed and interpreted the patient data regarding the injury. A. P. and P.A. have been involved in drafting the manuscript. Discussion Closed reduction + pinning (8 patients) B. Early ligamentous reconstruction (9 patients) A. Revision surgery for recurrent instability in 4 patients (50%) B. Normal grip strength and range of motion Kural C et al11 Acta Orthop Traum Turc 2002 1 Closed reduction + cast No pain or instability Khan AM et al10 Am J Orthop 2003 1 Closed reduction + cast Good functional result Bosmans et al. 1 J Hand Surg (Am) 2008 2 Closed reduction + cast No instability-Normal range of motion Table 1 Published cases with isolated thumb CMC dislocation in English literature Conclusion Acta Orthop Traumatol Turc 2002, 36(5):446-8. 12. Simonian PT, Trumble TE: Traumatic dislocation of the thumb carpometacarpal joint: early ligamentous reconstruction versus closed reduction and pinning. J Hand Surg [Am] 1996, 21(5):802-6. doi:10.1186/1749-799X-5-16 Cite this article as: Fotiadis et al.: Isolated thumb carpometacarpal joint dislocation: a case report and review of the literature. Journal of Orthopaedic Surgery and Research 2010 5:16. 8. Watt N, Hooper G: Dislocation of the trapezio-metacarpal joint. J Hand Surg [Br] 1987, 12B:242-245. 9. Akmaz I, Kiral A, Pehlivan O, Solakoglu C: Ligament reconstruction for the chronic instability of the traumatic thumb carpometacarpal joint. Acta Orthop Traumatol Turc 2003, 37(3):237-43. 10. Khan AM, Ryan MG, Teplitz GA: Bilateral carpometacarpal dislocations of the thumb. Am J Orthop 2003, 32:38-41. 11. Kural C, Malkoc M, Ugras AA, Sen A: Isolated carpometacarpal dislocation of the thumb: a case report. Acta Orthop Traumatol Turc 2002, 36(5):446-8. 12. Simonian PT, Trumble TE: Traumatic dislocation of the thumb carpometacarpal joint: early ligamentous reconstruction versus closed reduction and pinning. J Hand Surg [Am] 1996, 21(5):802-6. doi:10.1186/1749-799X-5-16 Cite this article as: Fotiadis et al.: Isolated thumb carpometacarpal joint dislocation: a case report and review of the literature. Journal of Orthopaedic Surgery and Research 2010 5:16. 8. Watt N, Hooper G: Dislocation of the trapezio-metacarpal joint. J Hand Surg [Br] 1987, 12B:242-245. 9. Akmaz I, Kiral A, Pehlivan O, Solakoglu C: Ligament reconstruction for the chronic instability of the traumatic thumb carpometacarpal joint. Acta Orthop Traumatol Turc 2003, 37(3):237-43. 10. Khan AM, Ryan MG, Teplitz GA: Bilateral carpometacarpal dislocations of the thumb. Am J Orthop 2003, 32:38-41. 11. Kural C, Malkoc M, Ugras AA, Sen A: Isolated carpometacarpal dislocation of the thumb: a case report. Acta Orthop Traumatol Turc 2002, 36(5):446-8. 12. Simonian PT, Trumble TE: Traumatic dislocation of the thumb carpometacarpal joint: early ligamentous reconstruction versus closed reduction and pinning. J Hand Surg [Am] 1996, 21(5):802-6. doi:10.1186/1749-799X-5-16 Cite this article as: Fotiadis et al.: Isolated thumb carpometacarpal joint dislocation: a case report and review of the literature. Journal of Orthopaedic Surgery and Research 2010 5:16. doi:10.1186/1749-799X-5-16 Cite this article as: Fotiadis et al.: Isolated thumb carpometacarpal joint dislocation: a case report and review of the literature. Journal of Orthopaedic Surgery and Research 2010 5:16. Conclusion 4. Neumann DA, Bielefeld T: The carpometacarpal joint of the thumb: Stability, deformity and therapeutic intervention. J Orthop Sports Phys Ther 2003, 33(7):386-399. 4. Neumann DA, Bielefeld T: The carpometacarpal joint of the thumb: Stability, deformity and therapeutic intervention. J Orthop Sports Phys Ther 2003, 33(7):386-399. 5. Bettinger PC, Linscheid RL, Berger RA, Cooney WP, An KN: An anatomic study of the stabilizing ligaments of the trapezium and trapeziometacarpal joint. J Hand Surg [Am] 1999, 24(4):786-798. 6. Strauch RJ, Behrman MJ, Rosenwasser MP: Acute dislocation of the carpometacarpal joint of the thumb: an anatomic and cadaver study. J Hand Surg 1994, 19A:93-98. We believe that an unstable thumb CMC joint after closed reduction of dorsal dislocation probably illus- trates a more serious damage in dorsal ligament and joint capsule. In this case, dorsal capsuloraphy and liga- ment repair may be of clear benefit particularly in young athletes with high upper extremity demand. 5. Bettinger PC, Linscheid RL, Berger RA, Cooney WP, An KN: An anatomic study of the stabilizing ligaments of the trapezium and trapeziometacarpal joint. J Hand Surg [Am] 1999, 24(4):786-798. 6. Strauch RJ, Behrman MJ, Rosenwasser MP: Acute dislocation of the carpometacarpal joint of the thumb: an anatomic and cadaver study. J Hand Surg 1994, 19A:93-98. 5. Bettinger PC, Linscheid RL, Berger RA, Cooney WP, An KN: An anatomic study of the stabilizing ligaments of the trapezium and trapeziometacarpal joint. J Hand Surg [Am] 1999, 24(4):786-798. trapeziometacarpal joint. J Hand Surg [Am] 1999, 24(4):786 798. 6. Strauch RJ, Behrman MJ, Rosenwasser MP: Acute dislocation of the carpometacarpal joint of the thumb: an anatomic and cadaver study. J Hand Surg 1994, 19A:93-98. 7. Shah J, Patel M: Dislocation of the carpometacarpal joint of the thumb. A report of four cases. Clin Orthop Relat Res 1983, 175:166-169. Page 5 of 5 Page 5 of 5 Fotiadis et al. Journal of Orthopaedic Surgery and Research 2010, 5:16 http://www.josr-online.com/content/5/1/16 8. Watt N, Hooper G: Dislocation of the trapezio-metacarpal joint. J Hand Surg [Br] 1987, 12B:242-245. 9. Akmaz I, Kiral A, Pehlivan O, Solakoglu C: Ligament reconstruction for the chronic instability of the traumatic thumb carpometacarpal joint. Acta Orthop Traumatol Turc 2003, 37(3):237-43. 10. Khan AM, Ryan MG, Teplitz GA: Bilateral carpometacarpal dislocations of the thumb. Am J Orthop 2003, 32:38-41. 11. Kural C, Malkoc M, Ugras AA, Sen A: Isolated carpometacarpal dislocation of the thumb: a case report. 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ANALYSIS OF THE USE OF MINERAL AND SECONDARY RAW RESOURCES OF UZBEKISTAN IN ELECTROCERAMIC COMPOSITE MATERIALS
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IJER, ISSN: 2799-1873 IJER, ISSN: 2799-1873 Vol 03, Issue1 (2024) ANALYSIS OF THE USE OF MINERAL AND SECONDARY RAW RESOURCES OF UZBEKISTAN IN ELECTROCERAMIC COMPOSITE MATERIALS. Valieva Gulshan Fayzimuradovna Namangan institute of engineering-construction PhD. E-mail: gulshanvaliyeva@mail.ru, phone number:+99(893) 266 7671 International Journal of Engineering Research ANNOTATION International Journal of Engineering Research 17 IJER, ISSN: 2799-1873 Vol 03, Issue1 (2024) Products made from aluminosilicate ceramics are widely used in electronics, communications technology, electrical engineering, vacuum technology, mechanical engineering, etc. A limited number of grades of corundum materials are produced and there is practically no strict classification of them. Mass production of products of various shapes and sizes from corundum ceramics with its valuable properties is possible only if the initial ceramic mass is obtained in a plastic state, which allows the use of a high-performance extrusion method. In recent years, our republic has achieved certain results in modernizing light industry enterprises, expanding the types and sizes of competitive products, and developing technologies for the production of ceramic materials from local raw materials and waste from enterprises. The ceramic-technological and dielectric properties of electroceramics depend on many factors and, first of all, on the density, structure, phase composition and heat treatment mode. Therefore, first of all, it is necessary that the raw materials used for the production of electroceramic products are homogeneous, i.e. did not contain any inclusions or impurities that would form a fly, smelting, swelling or other defects during the firing process. For electroceramic production, elutriated kaolins are mainly used. In Uzbekistan, kaolin from the Angren deposit is of great practical interest. The reserves of primary kaolins approved by the State Reserves Committee amount to 51.2 million tons, the forecast reserves of secondary kaolins are estimated at 940 million tons of kaolins and talc, 150 thousand tons of the total production are used by ACC and construction materials enterprises of the republic. The obtained data on the chemical-mineralogical composition and technological properties of Angren primary enriched kaolin of the AKS-30 grade is of significant interest as a raw material for the production of electroceramic materials. Bentonite clay is a very important type of mineral raw material, widely used in most sectors of the national economy. Bentonite clays have fairly good properties: hydrophilicity - high dispersity, plastic ability for adsorption and swelling, thixotropy), etc. These properties make it possible to widely use bentonite in the production of ceramic products as plasticizing additives that improve the molding properties of masses and increase the strength of products in air. -dry condition. ANNOTATION The article provides an analysis of the use of local mineral and secondary raw materials for the production of electroceramic composite materials. Keywords: kaolin, leucocratic granite, bentonite, alumina-containing waste, properties, electroceramics. Today, electroceramic materials are widely used in the world in energy, mechanical engineering, electrical engineering, petrochemical, metallurgical and other industries. In this regard, the development of the electroceramic industry in the world is of particular economic importance, and the demand for composite electroceramic materials and products used in electrical engineering is growing rapidly. In this aspect, the development of energy- and resource-saving technology for producing composite electrical insulating ceramic materials of effective composition for the working parts of electric machines and mechanisms is important. Research work is being carried out on a global scale to develop electroceramic materials with high physical, mechanical and dielectric properties and high-frequency insulating properties. In this aspect, the creation of methods for obtaining effective compositions of electroceramic composite materials and products based on them, the development of resource-saving technology and the improvement of existing technologies are of great importance. Fine technical ceramics - ceramic materials synthesized from high-purity substances, are promising for the manufacture of special products, mechanisms and devices with high performance characteristics (mechanical, magnetic, optical, etc.) that are not available when using traditional materials. In the USA, Japan, Germany and other developed countries, intensive research into fine technical ceramics on a large scale has been carried out since the 70 %, mainly in two types - electronic and structural [1]. In the field of structural ceramics, progress has been less significant. Particular interest in these materials is caused by the possibility of using them in heat engines, especially gas turbine engines, as well as in diesel and conventional gasoline internal combustion engines. The creation of ceramic engines promises a qualitative leap in engine building: a significant increase in efficiency, suitability for operation in various types of fuel, reduction in fuel consumption, engine weight, exhaust gas toxicity and noise. The creation of such engines is still an unsolved problem, although a diesel engine made almost entirely of ceramics has already been tested in Japan for advertising purposes. The main difficulty hindering the industrial production of ceramic engines remains obtaining parts that are affordable and of uniform quality. So far, none of the developed methods guarantees the production of defect- free products with the required viscosity. ANNOTATION Analysis of the literature data on the study and use of bentonite clays in the composition of electroceramics allows us to conclude that bentonite clays, and in general bentonites of Uzbekistan, in particular, have not been studied as components for their use in the production of the insulator industry. In this regard, this work conducts research into the properties and technological qualities of the most promising bentonite deposits in Uzbekistan in order to determine the possibility of their use in various electroceramics. It is known from literary sources that instead of feldspars, nepheline syenites, alaskites, leucocratic granites, etc. can be used in the production of porcelain and sanitary construction products [1]. In this work, we selected leucocratic granites from the Vysotnoye deposit as the object of study in order to establish the possibility of their use in the production of electroceramic materials. With the increase in production volumes of the ceramic industry, the need for natural materials increases: conditioned clays, quartz and feldspathic materials, alumina-containing materials International Journal of Engineering Research 18 IJER, ISSN: 2799-1873 Vol 03, Issue1 (2024) and others. An effective way to save mineral resources is to use waste from various industries - secondary production [2]. The rational use of industrial waste also helps to reduce the cost of production without compromising its basic physical and mechanical properties. Electroceramic products obtained from traditional raw materials meet the requirements of GOST in their properties for their use in very important units of the national economy. In order to further improve the quality of these materials, it is necessary to find new ways to improve the quality of products, new energy-fuel- raw materials-saving technology. Thus, most researchers share a common point of view regarding the influence of alumina on the physical and mechanical properties of porcelain and indicate that with increasing alumina content, the mechanical strength of porcelain increases due to an increase in the number of crystalline components in the phase composition of the material. Moreover, the strength of aluminous porcelain depends on the dispersion of alumina, the shape and size of the crystals, the amount of the crystalline phase, as well as the degree of enrichment of the glassy phase with alumina. In this work [2], the object of study was alumina-containing industrial waste. ANNOTATION Every year, this plant produces alumina-containing waste in the amount of 25-30 thousand tons per year, as well as the plant of LLC GKhK Shurtangaz. As is known, alumina is a valuable raw material in the production of ceramic materials with high physical and technical properties. These types of products include electroceramic products. In this regard, the study of alumina-containing waste is of great interest. Based on these considerations, the goal was set to study the chemical-mineralogical composition, physical-chemical and technological properties of the initial components, study the physical-chemical processes occurring when heating each component and calculating the compositions of mixtures, as well as physical-chemical processes occurring during firing of mixtures of various compositions and creation of physical and chemical foundations for obtaining the technology of electroceramic materials. International Journal of Engineering Research Literatures: 1. Maslennikova G.N., Bezhentsev V.D., Orlova R.G., Bogdanis E.P. Ways to increase the strength of porcelain // Glass and Ceramics, 1984, No. 11, pp. 17-19. 2. Tulyaganova V.S., Abdullaeva R.I., Negmatov S.S., Valieva G.F. Composition and properties of electroceramic compositions based on industrial waste // Composite materials, No. 3, 2021, -P. 179-181. International Journal of Engineering Research 19
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Reproductive factors and breast cancer risk in Palestine: A case control study
Cancer epidemiology
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Reproductive Factors and Breast Cancer Risk in Palestine: A Case Control Study Nuha El Sharif (  nsharif@staff.alquds.edu ) Al-Quds University Imtithal Khatib Al-Quds University Research Article Keywords: Breast cancer, Palestine, reproductive factors, consanguinity, family history Posted Date: May 24th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-122076/v2 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/20 Abstract Background: Early age at menarche, late age at menopause, and late age at first full-term pregnancy are linked to a modest increase in the risk of developing breast cancer (breast ca). This study aims to investigate the reproductive determinants of breast cancer among women in the West Bank of Palestine. A structured questionnaire was used to collect data in a case-control study (237 registered cases and 237 controls). A multivariate analysis model was used to adjust for the association between women’s reproductive factors and breast ca risk. This study was approved by Al Quds University Ethical Research Committee and the Ministry of Health research unit. Results: In the multivariate analysis, menarche after 13 years of age, use of oral contraceptives for more than two months, hormonal contraceptives use, and becoming pregnant at an early age (≤18 years) significantly doubled the risk for breast ca. Women who used hormone replacement therapy (HRT) were significantly associated with higher odds (6 times) of having breast ca versus those who did not use them (p <0.05). Similarly, nulliparous women showed 6 times the odds of breast ca compared with women with one or more children (p = 0.005). Also, parental consanguinity marriage and positive family history of the condition can be strong determinants for breast ca in this study. Conclusion: This study provides clear evidence that the use of reproductive hormones, whether as a birth control tool or for therapeutic purposes, must be rationalized worldwide and in Palestine in particular. Introduction Breast cancer (breast ca) is the most common form of cancer mortality among women in the world1.Breast cancer is a multi-factorial type of cancer. Being genetically predisposed or having a family history of a first-degree relative with breast ca was shown to increase the cancer incidence 2-4. Parental marriage to a relative was also shown to increase the risk 5. Among women aged 40 years or more, breast ca is related to increased risk 6,7. Modifiable risk factors such as obesity, physical inactivity, sedentary behavior, and poor dietary patterns were also shown to be related to breast cancer risk 8-10. The effect of reproductive factors strongly supports a hormonal role in its aetiology 11-14. Early age at menarche, late age at menopause, and late age at first full-term pregnancy are linked to a modest increase in the risk of developing breast cancer 14,15. However, multiple full-term pregnancies and longterm breastfeeding decrease the risk of breast cancer16,17. Reproductive surgeries such as ovariectomy, tubal sterilization, and hysterectomy may also affect the breast cancer risk by altering hormone levels before menopause or by bringing forward the age at menopause 18,19 . Long-term use of hormone replacement therapy (HRT) 20, but not long-term use of oral contraceptives (OC), was also related to an increased risk of breast ca 21 . Moreover, it was noted that the Page 2/20 time elapsed since last oral contraceptive use was associated with a higher risk of breast ca than recent use 22. Breast cancer is the most common and widespread type of cancer in Palestine, and ranks as the third cancer that causes death. It constitutes 17% of all cancer cases. At the end of 2017, there were 503 new cases documented in the West Bank and 327 new cases recorded in the Gaza Strip. The rate was 33.1 new cases per 100,000 females annually 23 . Few studies have tackled the risk factors of breast ca in Palestine 2,24. In Gaza, a study among women aged 18 to 60 years suggested that a positive family history of breast ca, high body mass index, and some common diseases (hypertension, diabetes mellitus) maybe epigenetic factors that promote the occurrence of breast ca 2. The reproductive determinants of breast cancer among women in the southern region of the West Bank will be presented here. The study findings may help to clarify the interaction of these factors in the development of breast cancer among Palestinian women. Study context The cancer burden in Palestine is expected to increase and will pose a substantial challenge for the healthcare system. The limited financial and infrastructural resources, plus political uncertainty, exacerbate the problem 25. Cancer care, diagnosis and treatment services are provided in four West Bank hospitals. However, isotope scans like PET-CT are not available and all such cases are referred to Israeli hospitals. The shortage of specialized physicians and of drugs, chemotherapy, and radiation therapy present a challenge in providing proper care for cancer patients 26 . This study was conducted at the major governmental hospital: BeitJala hospital in the southern West Bank. BeitJala hospital has an oncology department and daycare clinic that offers daycare medical services for cancer patients in the central and southern areas of the West Bank. Therefore, this study aimed to explore the various reproductive risk factors for breast cancer in the West Bank of Palestine. Material And Methods Study design This case-control study was conducted at Beit Jala governmental hospital in the West Bank of Palestine over the period 2016 to 2017. Study cases and control selection Based on hospital chart number, 237 women were selected at random as study cases from those attending the daycare oncology department or the chemotherapy unit of BeitJala hospital. These women had a pathologically confirmed breast carcinoma and were aged 40 years or more at the time of interview. Page 3/20 To serve as a comparable and representative control group, 237 women of the same age distribution and geographic area were randomly recruited from the screening program for breast ca. The subjects in the control group were confirmed as free from breast ca and had never been suspected of having any previous neoplastic disease or any other cancer. Their medical records were checked to include a normal (BIRADS 1) mammography. Those referred by a physician for a suspected history of breast problems were excluded. Only a very low proportion (2%) of selected women (study cases and controls) refused to participate in this study. This study was approved by Al Quds University Ethical Review Committee. Written approval was obtained from the Ministry of Health to access the patients' records from the oncology department and cancer registry. All women provided written informed consent. Data collection The medical records of cancer patients were used to retrieve information related to the breast ca: date of diagnosis, stage at diagnosis, type of cancer, and therapy strategy. Trained female interviewers administered an in-person structured questionnaire during the patient visit to the oncology department. Controls were contacted by a nurse from the mammography department and were invited to participate. If a control refused to come to the clinic, the interview was conducted via a phone call. The questionnaire included questions on demographic and lifestyle factors; parental consanguinity marriage; contraceptive history; use of hormone therapy; menstrual history; pregnancy and breastfeeding history; medical history, including cancer and mammogram history; and family history of malignancy. Women were also asked whether they had undergone surgery to remove one or both ovaries partially or fully. Women were also asked whether they had undergone a hysterectomy or tubal sterilization, and the approximate month and year of the procedure(s). Statistical analysis SPSS version 23 (IBM Corp., Chicago, IL, USA) was used for the data analysis. Bivariate and multivariate unconditional logistic regressions were used to assess the association of breast ca with independent variables. Crude and adjusted odds ratio (AOR) and 95% confidence intervals (CIs) were calculated to determine the precision of the estimates. The level of significance used was 5%. The p-value < 0.05 indicated significance. Results In total, 237 cases and 237 age-matched controls were included. The mean age of those in the study was 54.6 (SD=10.9) years and 54 (SD= 9.9) years for the control group (p>0.05). Page 4/20 Most of the study cases were diagnosed at stage 2 and 3 of cancer (35% and 30% respectively). Most of the study cases (83%) discovered that they had cancer after they noticed a mass and only 17% were diagnosed by screening. More than half of the study cases had ductal carcinoma (n=138, 58%); 19 women had lobular carcinoma (8%); 5 women had follicular carcinoma (2.1%); 4 had mixed type (ductal lobular 1.7%); and 30% did not have a documented type in their files. Almost all cases had undergone chemotherapy treatment (98%). About 83% of cases had undergone partial mastectomy and half of them had undergone a full mastectomy. Furthermore, 75% of cases had surgery as the first-line treatment and did not receive neo-adjuvant therapy. Socio-demographic factors Table 1 shows the socio-demographic characteristics for cases and controls. Study cases and controls had significantly different distributions for multiple characteristics such as educational level, home type, family size, and parental consanguinity, but not for others (Table 1). Study cases had higher levels of education than those in the control group (41%) had more than 10 years of education versus 24.5%). Controls had larger families than study cases (mean 6.35, SD 2.6 versus mean 5.61, SD 2.96 respectively) but lived in smaller residences than the study cases. About 43% of study cases had married a first-degree relative compared with 21% in the control group. Table 1: Socio-demographic characteristic of study participants Page 5/20 Characteristics Controls Study cases N=237 =237 Frequency (%) Frequency (%) P-value -- Age groups 39-44 50 (21.1) 50 (21.1) (years) 45-49 40 (16.9) 40 (16.9) 50-54 37 (15.6) 37 (15.6) 55-59 40 (16.9) 40 (16.9) 60-64 19 (8.0) 19 (8.0) 65-69 27 (11.4) 27 (11.4) More than 70 24 (10.1) 24 (10.1) 1-6 117 (49.3) 81 (34.2) 7-9 62 (26.2) 59 (24.9) 10-12 44 (18.6) 49 (20.7) >12 14 (5.9) 48 (20.2) Separate house 147 (62) 198 (83.5) Apartment 90 (38) 39 (16.5) Less than 1000 55 (23.2) 78 (32.9) 1000 to 2000 182 (76.8) 159 (67.1) Yes (now or then) 23 (9.7) 35 (14.8) No 214 (90.3) 202 (85.2) Less than 15 15 (65.3) 16 (45.7) 15-30 7 (30.4) 15 (42.9) More than 30 1 (4.3) 4 (11.4) Single 10 (4.2) 19 (8.0) Married 189 (79.7) 185 (78.1) Divorced or widowed 38 (16.1) 33 (13.9) No 12 (5.1) 36 (15.2) Yes 225 (94.9) 201 (84.8) 1-5 93 (39.2) 108 (45.6) Educational level (years) Home type Family monthly income** Working status Period of work (years) Marital status Parity Family size Page 6/20 Chi square 0.001 0.001 0.012 0.09 0.31 0.20 0.000 0.16 (persons) 6 or more 144 (60.8) 129 (54.4) Parental consanguinity No Relation 123 (51.9) 100 (42.2) relation 1st degree 52 (21.9) 102 (43.0) 2nd degree 62 (26.2) 35 (14.8) 0.001 *p-value was calculated by using Pearson’s chi square test ** NIS: new Israeli Shekels: 1000 NIS is about 300 dollars Socio-demographic factors and their association with breast cancer The odds ratio between socio-demographic factors and breast ca are summarised in Table 2. The odds of breast ca were higher among women with more than 12 years of education versus those with less education. The odds of breast ca were 3.87 times higher among women living in separate houses compared with those living in apartments (95% CI: 2.36-6.33, p =0.00). Women with no children were 2.5 times more likely to get breast ca versus women with children. Interestingly, the odds of breast ca were 2.5 times higher among women married to a first cousin (consanguinity marriage) compared with those whose spouse was not related or were married to a second-degree relative (95% CI: 1.60-4.08, p=000). Table 2: Socio-demographic factors and their association with breast cancer Page 7/20 Characteristics Controls N=237 Frequency (%) Study cases Univariate analysis Multivariate analysis OR AOR N=237 Frequency (%) 95% CI L-U Educational level (years) 95% CI P value L-U 1-6 117 (49.3) 81 (34.2) 0.20 0.100.39 0.14 0.070.30 .000 7-9 62 (26.2) 59 (24.9) 0.28 0.140.56 0.27 0.130.57 .001 10-12 44 (18.6) 49 (20.7) 0.33 0.160.67 0.32 0.140.69 .004 >12 14 (5.9) 48 (20.2) 1.0 (Ref) 1.0 (Ref) Family monthly income Less than 1000 55 (23.2) 78 (32.9) 1.62 1.082.43 1.80 1.132.90 (NIS)** 1000 to 2000 182 (76.8) 159 (67.1) 1.0 (Ref) 1.0 (Ref) Home type Separate house 147 (62) 198 (83.5) 3.1 2.024.79 3.87 2.366.33 Apartment 90 (38) 39 (16.5) 1.0 (Ref) 1.0 (Ref) Yes 225 (94.9) 201 (84.8) 0.30 0.150.59 0.39 0.190.80 NO 12 (5.1) 36 (15.2) 1.0 (Ref) 1.0 (Ref) Parental consanguinity 2nd degree 62 (26.2) 35 (14.8) 0.69 0.431.13 0.68 0.391.16 0.16 relation 1st degree 52 (21.9) 102 (43.0) 2.41 1.583.69 2.56 1.604.08 .000 No Relation 123 (51.9) 100 (42.2) 1.0 (Ref) 1.0 (Ref) Parity 0.012 .000 .010 Legend: L lower, U upper, COR crude odds ratio, AOR adjusted odds ratio, Ref reference, CI confidence interval OR was calculated by using logistic regression, p-value < 0.05. NIS: new Israeli Shekels Reproductive factors and their association with breast cancer A woman’s age at menarche was significantly higher among the control group compared with study cases mean 13.2 (SD=1.01) years versus 13.6 (SD=1.08) years in the study cases, T-test significance Page 8/20 <0.001. The odds of breast ca were 2.6 times higher among women with late menarche (≥ 13 years) versus those who got their menarche earlier (< 13 years old) (95% CI: 1.44–4.69, p value=0.002) (Table 3). More than half of both study cases and controls were postmenopausal women with no significant difference in the age of menopause (mean 49.21 (SD=3.55) years versus 48.5 (SD=4.38) years, T-test significance>0.05. The mean age for use of OC in the control group was 29.28 years (SD=6.02) and 28.91 years (SD=5.96) in the study cases (T-test significance >0.05).Ceasing use of OC was also not significantly different between the two groups 34.38 years (SD=6.61) in control group and 33.91 years (SD=7.68) in study, T-test significance >0.05). Women who used hormonal contraceptives and hormone replacement therapy (HRT) were significantly associated with higher odds of having breast ca at 2.09 (95% CI: 1.10-3.95, p <0.001) and 6.37 (95% CI: 2.40-16.9, p = 0.002) respectively, compared for those who did not use them. Similarly, nulliparous women showed 6 times the odds of breast ca (95% CI: 1.71-20, p = 0.005) compared with women with one or more children. Women who became pregnant at an early age (≤18 years) were also at higher risk of breast cancer than women who became pregnant later (>18 years) (AOR 2.09, CI: 1.30-6.55, p=0.01) (Table 3). Breastfeeding showed fewer odds for breast ca but the association was not statistically significant (AOR 0.59, CI: 0.32-1.58).The longer the duration of breastfeeding, the lower the odds for breast ca (Table 3). Table 3: Reproductive factors and their association with breast cancer Page 9/20 characteristic Controls N= 237 Freq (%) Study cases N= 237 Freq (%) Age at menarche * ≥13 179 (75.5) 205 (86.5) (years) <13 58 (24.5) 32 (13.5) Yes 25 (10.5%) 47 (19.8%) ≥ 2 months* No 212 (89.5) 190 (80.2) Use of HRT* Yes 8 (3.4) 36 (15.2) No 229 (96.6) 201 (84.8) Age at first marriage (years) ** ≤18 124 (54.4) 95 (43.6) >18 104 (45.6) 123 (56.4) Parity ** No 12 (5.1) 36 (15.2) Yes 225 (94.9) 201 (84.8) Age at first pregnancy (years)† ≤18 105 (46.5) 63 (30.9) >18 121 (53.5) 141 (69.1) Age at first ≤18 81 (36) 54 (26.9) >18 144 (64) 147 (73.1) >5 children 177 (74.7) 140 (59.1) 1-4 children 49 (20.7) 64 (27) Ever OC use for Delivery (years)† Number of full term pregnancies† Univariate Multivariate analysis analysis P- OR value 0.002 0.005 00 0.02 0.00 0.001 0.045 0.001 Page 10/20 95% CI AOR L-U 95% CI P value L-U 2.07 1.293.34 2.6 1.444.69 .002 1.0 (Ref) 1.0 (Ref) 2.09 1.243.52 2.09 1.103.95 0.01 1.0 (Ref) 5.13 2.3311.2 6.37 2.4016.9 0.002 1.0 (Ref) 1.0 (Ref) 1.54 1.062.24 1.48 1.012.16 1.0 (Ref) 1.0 (Ref) 3.36 1.716.63 5.90 1.7120 1.0 (Ref) 1.0 (Ref) 1.94 1.312.89 2.90 1.306.55 1.0 (Ref) 1.0 (Ref) 1.0 (Ref) 1.0 (Ref) 0.65 0.430.99 0.56 0.241.29 0.17 1.61 1.042.49 1.35 0.852.14 0.20 1.0 (Ref) 1.0 (Ref) 0.042 0.005 0.01 Ever breastfeeding† Yes 217 (95.2) 187 (85.8) No 11 (4.8) 13 (12.4) Age at first breastfeeding ≤18 77 (35.5) 48 (25.7) (years)† † >18 140 (64.5) 139 (74.3) Total breastfeeding durations (all children) (years) †† ≤3 12 (5.5) 28 (15) 4-6 32 (15.2) 7-9 >9 0.001 0.31 0.250.63 0.59 0.321.58 1.0 (Ref) 1.0 (Ref) 1.59 1.042.45 1.17 0.731.86 1.0 (Ref) 1.0 (Ref) 1.0 (Ref) 1.0 (Ref) 58 (31) 0.75 0.341.67 0.75 0.341.67 0.49 59 (27.0) 48 (25.7) 0.35 0.160.76 0.35 0.110.76 0.008 113 (52.1) 53 (28.3) 0.20 0.090.43 0.21 0.060.45 0.000 0.034 00 0.26 0.51 Legend Hormone Replacement Therapy (HRT), Chi square p value *Among all participating women ** Age of marriage and parity calculations were based on number of non single women †Age at first pregnancy, at first delivery, and number of full pregnancy calculations were based on married women with children †† Age of first breastfeeding and duration were calculated bases on the number of breastfeeding Discussion The reason for international variations in the incidence of breast ca remains unclear. These variations can be seen between both high and low-income countries. Many of the risk factors for breast ca have been investigated but require further examination in individual nations. In this study, we examined a broad spectrum of risk factors for breast ca, including female reproductive factors. The reproductive risk factors for breast ca identified in Palestinian women are similar to those observed in other studies. This study provides clear evidence that late menarche poses an additional risk for breast ca. Early marriage and having children early in life, both popular in the Palestinian community, were shown to increase the odds of breast ca. The role of oral contraceptives and hormonal replacement therapy on women’s health was also clearly shown and there should be rational use of hormones, whether as a birth control tool or for therapeutic purposes. Having children proved to be protective Page 11/20 against breast ca but as most married women in Palestine breastfeed their children, we could not show that breastfeeding is a protective factor for breast cancer among the study group. However, we can still highlight the role of breastfeeding in breast ca protection. More in-depth investigations are needed to identify the relationship between various factors, especially the protective role of having children and breastfeeding practices on breast ca in Palestine. Special attention should be devoted to the particular social and cultural factors related to sexual and reproductive issues among women in Palestine. Several studies have indicated that women with high socioeconomic status (SES) are at risk for breast ca with an overall estimate of 20% increased risk 27. This positive association was clearer among Hispanic and Asian women 28, and not only for breast ca but for other cancers such as colon, ovary, and melanoma cancers 29. Our study found that breast ca was more common among more educated rather than less educated women, and in women with a lower family income rather than women with a higher family income. In the north of Palestine, a previous study showed that there was a four-fold increase in the risk of breast ca among highly educated women 24; this was also reported among Egyptian women 30. In European women, a direct dose-response relationship was seen between educational level and postmenopausal breast ca incidence 31. Our results found that women living in an apartment had a significantly lower risk of getting breast ca compared with those living in a separate home; this was assumed to be due to a higher SES. Several studies showed that lower SES increased the risk of breast ca because women were less aware of screening techniques and diagnosis 32. Our results could be explained by the fact that women with a higher family income can afford health insurance and are more willing to spend money on their health and better medical care access. Greater awareness among educated women about mammography screening tests is very clear in Palestine. It is worth mentioning that screening in Palestine is free of charge for all women over 40 years of age. Another possible explanation is that the more a woman is educated, the later she marries, the later the age of pregnancy, the shorter the period of breastfeeding, and the lower parity is characteristic of women from higher SES. Indeed, socio-economic inequalities could affect the time of diagnosis, survival or mortality due to cancer despite improved knowledge, reduction of risk factors for cancer, early diagnosis, and treatment 33. Consanguinity is becoming a very strong factor for cancers and other genetic diseases in many countries 34,35. Our study showed that daughters of unrelated parents had a decreased breast ca risk, whereas the risk increased 2.5-fold for those with first-degree related parents. A similar finding was reported in the United Arab of Emirates (UAE) in which having unrelated parents halved the risk (RR=0.5, 95%CI: 0.270.93) 35. A study among Israeli Arabs of Palestinian origin showed an increase in diabetes and duodenal ulcers 34. Consanguineous practices in populations might affect the gene frequency in these populations, which could have a major effect on the carrier rate of such genes. Therefore, in countries with high consanguinity, the incidence of diseases and syndromes should be monitored with caution. Page 12/20 It is believed that up to 10% of breast ca cases in Western countries were due to genetic predisposition with a threefold increase in the risk of breast ca among those with a family history of breast ca 36. In our study, women with a family history of breast cancer had a fourfold increased risk of breast ca. In Qatar, a country with high consanguinity marriage, a study showed that consanguinity was lower in breast cancer patients than in controls, but a family history of breast cancer was significantly more prevalent in breast cancer patients 37. The risk of breast ca ranged from 1.5 to 3.6 in a pooled analysis depending on the relative in question, with the highest risk reported among women who had a mother or a sister with breast ca 38. Furthermore, women living in the Gaza Strip and who had a positive family history of breast ca showed an increased risk of breast ca (OR=2.7, 95%CI: 1.04-7.20). Similar results were reported among Algerian women, where the odds for breast cancer were four times higher among those with a family history of the disease (95% CI: 2.22-7.77) 39. These two factors, i.e. consanguinity and family history of breast cancer, may have a synergistic effect in such studies and the risk might be greater if combined in these women. Early age at menarche, late age at menopause, and late age at first full-term pregnancy are linked to a modest increase in the risk of developing breast cancer 14-16. Also, parity and age of marriage are among the most common extrinsic factors that modulate breast cancer risk. It is well documented that parity has a dual effect on breast cancer risk, with an increased risk during 5 to 10 years after pregnancy, followed by a strong and life-long protective effect 15. In several studies, older age at menarche was inversely associated with breast ca risk. The high-risk groups were females with menarche before the age of 11 years 4 . Around 117 studies showed that the breast ca risk increased by a factor of 1.050 for every year less at menarche 15, and a delay of two years at menarche led to a 10% reduction in breast ca worldwide 40. In our study, older age at menarche was shown to be associated with an increased risk of breast ca. The risk increased three-fold with menarche at the age of 13 or more. In the north of the West Bank, the estimated risk was 6.5 which also showed an increase the risk for breast ca 24 . The protective result of menarche at an older age was explained by the lower cumulative number of ovulatory cycles, which is negatively associated with the risk, younger age at menarche, and older age at menopause, means a female would have more cycles and an increased risk 41,42 . According to the Palestinian Central Bureau of Statistics (2016), the mean age of first marriage was 19.8 years in the southern region of Palestine 43. Consequently, many women may have their first pregnancy and first delivery at a young age (below 18 years). Women with breast ca in our study had a mean age of marriage of 20.4 years (SD=5.44). Our multivariate results showed an inverse association between age at first marriage and age of first pregnancy for breast ca. We could not see any difference according to whether a woman had her first child before the age of 18 years or after. In contrast, a study in the north of the West Bank showed that there was a 10% increase in the risk of breast ca when the first marriage was below 20 years of age 24. Another study in the Gaza Strip showed that women who had their first pregnancy after the age of 35 years had an 11-fold increase in breast cancer risk 2. Page 13/20 Our results revealed no significant association between full-term pregnancies and the risk of breast ca. However, the number of full-term pregnancies was negatively associated with breast ca risk in almost all studies, even in the Western world. This result was consistent for not only one type but for all subtypes of breast ca in pre- and post-menopausal women. The reduction in the risk ranged from 18% to 60% 44. In the north of Palestine, a 50% decrease in risk was reported among women with four full-term pregnancies or more 24. One of the well-established protective factors against breast ca is breastfeeding. In our results, almost all women who had children had engaged in breastfeeding, but the protective effect in our analysis was not in the breastfeeding itself but in its duration. Previous studies found that breastfeeding itself was protective. A Saudi study reported that never having breastfed doubled the risk (OR=1.89, 95%CI: 1.192.94) 45. Furthermore, breastfeeding decreased the risk of having breast ca by almost 60% in an Israeli study in our region (OR=0.39, 95%CI: 0.26-0.59) 46. Breastfeeding is assumed to protect against breast ca through hormonal mechanisms that include postponing the resumption of ovulatory menstrual cycles after pregnancy, reducing estrogen levels in the breast, and having fully differentiated breast tissue that is less susceptible to hormones 47. The results of studies about the duration of breastfeeding have been inconsistent. A study that summarized findings from developed countries showed that for every year a woman breastfed, her risk of developing breast ca was reduced by 4.3% 48. Similar results were reported in an American study for different age and ethnic groups 49. In our study, a very clear inverse dose-response relationship was found with AOR=0.39 for the group of 9 years or more of breastfeeding versus those who had never breastfed, with a decrease in risk of 25-30% for an additional three years of breastfeeding. Among Palestinian women in the north, the risk for those who had never breastfed was doubled compared with those who had lactated for four years or more 24 . No association was found between breastfeeding duration and the risk of breast ca in either developed or developing countries 48. Regarding the use of hormonal contraceptive pills (OCP) and their association with breast ca, our study showed that previous oral OCP use for more than two months significantly doubled the risk of breast ca (AOR=2.22), but failed to show any link to the duration of using OCP. Similar results were revealed among Jordanian females 50,51. Regular use of OCPs in Jordanian women was shown to be associated with an increased risk of breast cancer (OR = 2.25, 95% CI 1.34-2.79; p = 0.002), although the duration of use was not associated with an increased risk of breast cancer (p > 0.05) 51. However, many studies found a slight increase in the risk 52. Other studies reported that the increased risk was only for the 10 years that followed the last OCP use 31. Other studies have found a decreased risk among women, but at least 10 years after the last use of OCPs 53. A study in Iran showed that long term OCP use (>/=10 years) (OR = 3.17, 95% CI: 1.27-7.95, P = 0.01) increased the risk of breast ca 54. On the contrary, some studies showed that OCP played a protective role against breast ca. A study in the Central African Republic showed a decrease in the risk for breast ca (0.62) 55. In Palestine, 54.8% of married women aged 15-49 years reported using contraception and 44.0% of women of reproductive age used modern contraceptives 56. Page 14/20 Hormone replacement therapy (HRT) was very strongly associated with the risk of breast ca in our results (AOR=3.97). Similar results were reported among Saudi and Jordanian women, (OR=2.25, 95%CI: 1.653.08) 45,50. A population-based study in Korea showed that the risk of breast cancer in HRT users was 1.25 95% CI, 1.22-1.29 compared with non-HRT users. As the duration of use increased, so did the adjusted hazard ratio (HR) (adjusted HR for 2 to <5 years was 1.33 and was 1.72 for ≥ 5 years) 8. In our study, 77% of women used HRT for less than 5 years (mean 3 years, standard deviation 2.61 years) with no significant difference between the study cases and control group. An increased risk among HRT users was shown in most studies. Martino et al. showed a 30% increase in risk of breast ca in past users compared with 60% in current users, revealing a dose-response relationship with duration of use 57. Nevertheless, it was reported that HRT therapy using estrogen alone had a reduced breast ca risk in young women but increased the risk in older women 58. In our study, women could not tell us which type of HRT they used and the exact duration of its use. Some limitations must be taken into consideration to explain the findings of this study. Firstly, the study was carried out on patients living in the south of Palestine. Thus, known risk factors may be different in the general population. Secondly, there could be information (recall) bias from the self-reporting of information of some variables such as the age of menarche, age of menopause, breastfeeding practices, and abortion experiences. Also, women were not able to report which type of OCP and HRT they used and the duration of its use. Thirdly, the use of women who came for screening of breast ca as the control group introduced some selection bias in the study. Nevertheless, the results and limitations of the study contribute to the ongoing research in the field of breast ca among Palestinian women. Also, this study was conducted in an Arab developing country where lifestyle changes can provide other important information about breast ca risk factors. Conclusions This is the first epidemiological study in Palestine to investigate the risk for breast ca based on women’s reproductive factors. Significant differences in breast ca were found between the study cases and control group: age at puberty, use of OCP and HRT, nullparity, early marriage, early pregnancy, and early delivery. All these factors indicated a higher risk of breast ca alongside being from a family with a history of breast cancer and married to a first cousin. In Palestine, most women breastfeed so more in-depth investigations are needed to identify the protective role of having children and breastfeeding practices on breast ca protection. Moreover, the Palestinian community must be aware of the effect of early marriage and parental consanguinity on the risk of breast cancer. These results are very important in clinical practice and women must be aware of the results on their health of the use of OCP and HRT. The use of reproductive hormones whether as a birth control tool or for therapeutic reasons must be rationalized. We encourage more studies to be conducted on breast cancer to tackle the specific types of breast ca in all areas of Palestine and other unknown determinants. Special attention should be given to the particular social and cultural factors related to sexual and reproductive issues among women in Palestine. Page 15/20 Declarations Ethics approval and consent to participate This study was approved by Al Quds University Ethical Research Committee, which is based on the Helsinki declarations. Therefore, all study methods were performed following the Helsinki guidelines and regulations. Al Quds University ethical research regulations adhere to Helsinki regulations Written approval was obtained from the Ministry of Health to access patient records from the oncology department and cancer registry. All women provided written informed consent. Consent for publication NA Availability of data and materials The datasets used and/or analysed during the current study are available from the corresponding author upon reasonable request. Competing interests: The authors declare that they have no competing interests. Funding This study was funded by Al Quds University research funds. Author contributions NS and IK designed the survey and developed the study tool. IK was responsible for data collection, data entry, and primary analysis. NS and IK participated in the study of advanced analysis and the development of study tables. NS was responsible for writing the manuscript. All authors read and approved the final manuscript. Acknowledgements The authors wish to thank all participants for their willingness to participate and the Ministry of Health teams for facilitating the study implementation. Also, the authors wish to express their gratitude to Al Quds University for funding this research. Author details Nuha El Sharif and Imtithal Khatib, AlQuds University School of Public Health, Abu Dis Campus, Jerusalem, Occupied Palestinian Authority. Page 16/20 References 1. Ghoncheh M, Pournamdar Z, Salehiniya H: Incidence and Mortality and Epidemiology of Breast Cancer in the World. Asian Pacific Journal of Cancer Prevention: APJCP 2016, 17:43-46. 2. 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The Multidisciplinary Virtual Product Development Integrates the Influence of Die Casting Defects in the Mechanical Response
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The Multidisciplinary Virtual Product Development Integrates the Influence of Die Casting Defects in the Mechanical Response Nicola Gramegna, Iñigo Loizaga, Susana Berrocal, Franco Bonollo, Giulio Timelli, Stefano Ferraro To cite this version: Nicola Gramegna, Iñigo Loizaga, Susana Berrocal, Franco Bonollo, Giulio Timelli, et al.. The Multi- disciplinary Virtual Product Development Integrates the Influence of Die Casting Defects in the Me- chanical Response. 19th Advances in Production Management Systems (APMS), Sep 2012, Rhodes, Greece. pp.502-509, ￿10.1007/978-3-642-40352-1_63￿. ￿hal-01472283￿ Distributed under a Creative Commons Attribution 4.0 International License The multidisciplinary virtual product development integrates the influence of die casting defects in the mechanical response Nicola Gramegna1,*, Iñigo Loizaga2, Susana Berrocal2, Franco Bonollo3, Giulio Timelli3, Stefano Ferraro3 1 ENGINSOFT S.p.A., Padova, Italy n.gramegna@enginsoft.it 2 FUNDACION CIE, Bilbao (Vizcaya), Spain {iloizaga, sberrocal}@cieautomotive.com 3 University of Padova - DTG, Vicenza, Italy {bonollo,timelli,ferraro}@gest.unipd.it Abstract. The performance of an Al alloy component when tested under dy- namic conditions is defined on the basis of the amount of the absorbed energy during impact and the dampening rate of the striker. These tests can be complex and costly, and sometimes difficult to be realized for some specific components. Abstract. The performance of an Al alloy component when tested under dy- namic conditions is defined on the basis of the amount of the absorbed energy during impact and the dampening rate of the striker. These tests can be complex and costly, and sometimes difficult to be realized for some specific components. An useful and “ideal” approach could be the use of numerical simulation tools for virtually testing, but this objective actually remains an ambitious approach, since it requires a deep research of the factors that determine the elasto-plastic material behavior up to fracture. Even more difficult is the characterization of the material in the case of Al alloy diecastings, where the mechanical properties strongly depend on casting defects. An useful and “ideal” approach could be the use of numerical simulation tools for virtually testing, but this objective actually remains an ambitious approach, since it requires a deep research of the factors that determine the elasto-plastic material behavior up to fracture. Even more difficult is the characterization of the material in the case of Al alloy diecastings, where the mechanical properties strongly depend on casting defects. By linking mechanical results with numerical simulation data of filling and so- lidification, a through-process model is developed to predict the defects’ loca- tion and amount, thus the structural behavior of die cast components. Further- more, with particular reference to one demonstrator component, an high pres- sure die cast steering housing, the innovative correlation between defects (e.g. air inclusion, shrinkage porosity etc.) and mechanical properties has been im- plemented in MAGMASOFT® simulation tool in order to transfer the realistic local ultimate tensile strength to LS-Dyna FEM code. The multi-objective op- timization strategy has been applied to minimize the air entrapment and maxim- ize the local mechanical properties of Al alloy. HAL Id: hal-01472283 https://inria.hal.science/hal-01472283v1 Submitted on 20 Feb 2017 L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. Distributed under a Creative Commons Attribution 4.0 International License Keywords. Numerical simulation, HPDC, casting defects, mechanical proper- ties, integrated approach, process optimization 1 Introduction In the automotive sector, high-pressure die-casting (HPDC) is the preferred foun- dry process; it is versatile and appropriate for highly engineered components. Unfor- tunately, a limit to large diffusion of HPDC remains the final integrity of castings. The high injection rate of the metal causes turbulences, which form internal and sur- face defects, such as gas entrapment, and the variable thicknesses of the component itself can lead to a reduced effect of the intensification pressure on the solidification shrinkage [1-3]. Although the classification of diecasting defects is clear, an advanced study is required to understand the correlations between the type, dimension and form of defects and the mechanical properties of diecastings. The first model from this study is described elsewhere [1, 2]. In the present paper, the final quality model is described and applied to a Steering Pinion, i.e. a safety component requiring high quality standards in order to guarantee that it stays oil tight under pressure, and to assure proper fatigue resistance and ductile behavior in case of impact. The multidisciplinary virtual product development integrates the influence of die casting defects in the mechanical response The final full integrated, and more realistic, approach permits to estimate the single effect of proper Al di- ecasting design, remaining defects and residual stress on the absorbed energy under impact condition. Keywords. Numerical simulation, HPDC, casting defects, mechanical proper- ties, integrated approach, process optimization 2 Simulation and optimization of the die casting process The design and review of the die cast steering pinion followed the work-flow re- ported below and acting on a virtual level, before the final physical dynamic testing: 1. process simulation of the existing version of the pinion, and optimization of the HPDC process in order to enhance the quality of the component; 2. identification of the local mechanical properties and residual stresses, and transfer of these information to FEA code for impact analysis; 3. impact simulation using the new model, the pre-stress condition due to residual stresses, and the local mechanical properties at the end of the manufacturing process, in order to determine the most realistic amount of absorbed energy. 2.1 Process simulation of the original version of the casting The first virtual analysis was performed by using the actual manufacturing parame- ters and the operating thermal regime of the die. This evidenced the possible causes of filling and solidification defects, with the resulting localized reduction of the mechan- ical properties. The CAD models, the materials, the lubrication and the movement of the die parts in the production cycle were imported in the software to simulate the thermal behavior of the die. The virtual results were compared with thermal maps acquired by IR camera. In particular, the analysis showed that the most evident porosity in the casting is due to air/gas entrapped in the center of the area with the greatest thickness. Cross- sections made of the parts and X-ray NDT investigations identify the defect distribu- tion and morphology. The experimental results were in accordance with numerical simulation ones (Fig. 1). Despite a noticeable variation of thicknesses in the original casting design, the cen- tral area of the component, which undergoes the maximum stresses under impact testing, showed some minor interdendritic porosity, mainly located far from the bene- ficial compacting action resulting from the applied overpressure. An accurate simula- tion of the cooling rate and the prediction of positions and dimensions of the afore- mentioned defects represent the basis for working out the local mechanical properties, as further explained. Fig. 1. a) X-ray image in comparison with b) defect prediction by numerical simulation Fig. 1. a) X-ray image in comparison with b) defect prediction by numerical simulation 2.2 Optimization of the die casting The initial objective of optimizing the mechanical properties of the component can be achieved by modifying the geometry of the component or by varying the diecasting system and the process parameters. Firstly, the thickness of the central cylindrical area was reduced. Furthermore, by using an automatic optimization technique, which allows an advanced research of a multi-objective problem [4, 5], the effect of a single geometric modification to the component was analyzed. The approach adopted is divided into two optimization steps: • the first step considers the variations of the section of the two gates without any change in the shape of the existing gating and using the original process parameters (solution named ID241); • the second step analyzes a wide range of all possible modifications and variants in order to search out the highest possible quality of the die-casting component (solu- tion named ID882) while respecting the constraints imposed by the already exist- ing die, i.e. extractors, orientation, cooling channels, etc.. Fig. 2. Possible designs for steering pinion plotted as function of the critical overpressure in the casting and the maximum overpressure in the gating system Fig. 2. Possible designs for steering pinion plotted as function of the critical overpressure in the casting and the maximum overpressure in the gating system The design configurations close to the axis of origin minimize even more the aforementioned objectives, but do not respect the minimum temperature of the molten metal at the gate. Fig. 2 evidences the substantial improvement obtained both in com- parison with the original version and with the introduction of the new component with a thickness reduction in the central area (green point in Fig. 2). Fig. 3. Integration of the optimized configurations, ID882 and ID241, in the existing die Fig. 3. Integration of the optimized configurations, ID882 and ID241, in the existing die The two main objectives of the optimization process are the minimum quantity and pressure of gas entrapped in the casting, and the reduction of the gating system vo- lume, with the simultaneous reduction or absence of turbulence in the same gating. Among the possible designs analyzed by numerical simulation, the design identified as ID882 was chosen, being the best compromise between the dimension and concen- tration of the residual gas bubbles in the component (measured by the critical volume of the overpressure) and the maximum pressure and dimension of these (the air over- pressure) (see Fig. 2.2 Optimization of the die casting 2). The suggested configurations, namely ID882 and ID241, were integrated in the same die as shown in Fig. 3. The experimental investigations carried out on the castings confirmed the results expected from numerical simulation. 3 Determination of the local mechanical properties and residual stresses The effects of process parameters on material properties were experimentally eva- luated by using a multicavity die, which enables to cast specimens for mechanical testing. The multicavity die was used to produce castings with different injection pa- rameters and constant geometry model. Microstructural analysis of cross sections shows the presence of several defects, such as cold shut, segregation bands, oxide films, iron-bearing phases and air/gas bubbles entrapped during mold filling. These defects are typical of the high pressure die casting process, and all specimens contain them, but the amount and distribution vary with the process parameters used [2, 6]. Fig. 4. a) Sketch of three point bend test adopted in this work; b) experimental measurements of force (F) versus displacement (W) obtained in bending tests Fig. 4. a) Sketch of three point bend test adopted in this work; b) experimental measurements of force (F) versus displacement (W) obtained in bending tests The bending tests were performed on specimens drawn from a plate produced by the above-described multi-cavity die and the mechanical results were directly corre- lated with numerical simulations without performing any determination of defect amount. The configuration for the three point bending test is schematized in Fig. 4a., according to ASTM E290-09. As observed in Fig. 4b, the process condition named P5 produced the worst mechanical properties. This is due to the highest metal velocity produced, which causes a turbulent flow and greater gas entrapment. The same varia- tion of process parameters has been applied at virtual level by using the MAG- MAhpdc module in order to simulate the filling and solidification behavior of multi- cavity die. Fig. 5 shows air-pressure and air-entrapment images of a region of the plate diecast with P5 process parameters. The X-ray image, acquired from the same location, evidences a good agreement between numerical simulations and experimen- tal data. Fig. 5. Coherence verification of the numerical simulations of process P5 : a) X-ray images of diecast plate; b) air-pressure criteria; c) air-entrapment criteria; d) air-pressure representation with a value greater than 1850 mbar Fig. 5. Coherence verification of the numerical simulations of process P5 : a) X-ray images of diecast plate; b) air-pressure criteria; c) air-entrapment criteria; d) air-pressure representation with a value greater than 1850 mbar For each specimen the simulations results were correlated each other. The aim was to find an empirical relationship between them and the mechanical properties (particu- larly UTS). 3 Determination of the local mechanical properties and residual stresses The final suggested model, with normalized coefficients, is: UTS = A – B×meanairp – C×meanflowlen – D×meanaircontact –E×diffcoolrate UTS = A – B×meanairp – C×meanflowlen – D×meanaircontact –E×diffcoolrate (1) where UTS is Ultimate Tensile Strength [MPa]; meanairp is the mean value of air pressure [mbar] and it identifies the position, severity and dimension of gas entrap- ment; meanflowlen is the path length of the melt [mm] and it shows the possible cool- ing of the alloy and the impurities due to a less homogeneous fluid-dynamic behavior; meanaircontact is the time of metal front in contact with air [sec] and it indicates the degree of risk of oxide formation; diffcoolrate is difference between maximum and minimum value of cooling rate in the thickness [°C/s] and it identifies the possible regions of shrinkage porosity. A “quality mapping” approach [2] was then applied to the steering pinion in order to support advanced design (Fig. 6). By means of a proper tool, this approach can elaborate results from numerical simulation (mold filling, thermal field, defect predic- tion criteria), with the aim of visualizing the final quality of the casting in terms of defect localization and criticality, local distribution of residual stress and mechanical properties. In comparison to the original cast component which was used as a refer- ence, the last optimization of the shape and process parameters shows that the maxi- mum value of ultimate tensile strength of the material is always in the range of 296- 298 MPa. Fig. 6. Mechanical properties (UTS) and residual stresses transferred from a CV to a FEM program: a,b) local UTS properties prediction; c,d) residual stress distribution Fig. 6. Mechanical properties (UTS) and residual stresses transferred from a CV to a FEM program: a,b) local UTS properties prediction; c,d) residual stress distribution 4 The innovative integrated approach In order to appreciate the effect of the methodology of integration of process simu- lation and impact simulation, the results of the impact simulation, performed using original geometry and process (curve A) and assuming homogeneous mechanical properties and no residual stress, are compared in Fig. 7a with three different design approaches: Fig. 7. a) Comparison between the results of different impact simulations; b) result of impact test simulation Fig. 7. a) Comparison between the results of different impact simulations; b) result of impact test simulation ─ curve B) represents the modified model along with the optimized die casting process, without applying the integrated approach; ─ curve B) represents the modified model along with the optimized die casting process, without applying the integrated approach; ─ curve B) represents the modified model along with the optimized die casting process, without applying the integrated approach; ─ curve C) represents the original model and die casting system, but considering the prediction of the localized mechanical properties and the residual stress state; ─ curve D) represents the modified model and optimized die casting system, using the integrated approach. In other terms, the similarity of curves B and D (+3% energy absorbed) is backed up by the local UTS values which are very close to the values normally used in “sound” material. In other terms, the similarity of curves B and D (+3% energy absorbed) is backed up by the local UTS values which are very close to the values normally used in “sound” material. 5 Conclusions The present work describes an integrated approach between process simulation and impact test evaluation of a diecast component, in order to perform a virtual, but reali- able, verification of the life of the component from the production stage up to the impact test. The methodology illustrated is specifically directed at the die casting field of light alloys, as it was demonstrated in the practical application on the component studied, and addresses particularly the stages of product design and development which take place in engineering and design offices, in die casting foundries and in end-users industrial companies. The innovative aspect of the proposed method does not consist in the use of simula- tion software for the process or the mechanical response, both highly adopted in their fields of application. It consists in the prediction of the mechanical properties as a function of the process, in the prediction of the quality distribution in diecastings and finally in the communication between the different software applications. This makes possible to visualize the realistic mechanical behavior of the cast product and conse- quently allows the validation and prediction of the mechanical response of the die- cast component at in-service conditions. Acknowledgements. This work was developed with the financial support of the Eu- ropean Project NADIA (New Automotive components Designed for and manufac- tured by Intelligent processing of light Alloys, NMP-2004-SME 3.4.4.5, contract n.026563-2). References 1. Apelian, D., Makhlouf, M.M.: High Integrity Aluminum Die Casting: Alloys, Processes and Melt Preparation. North American Die Casting Association, Des Plaines, IL, (2004) 2. Timelli, G., Bonollo, F.: Quality mapping of Aluminium alloy diecastings, Metal. Sci. Tech. 26, 2–8 (2008) 3. Gariboldi E., Bonollo F., Parona P.: Handbook of defects in high pressure diecastings, As- sociazione Italiana di Metallurgia, Milano (2010) 4. Gramegna, N., Baumgartner, P., Kokot, V.: Capabilities of new multi-objective Casting Process Optimisation tool. In: IDEAL International Conference, Lecce (2005) 5. Linares, F., Gramegna, N., Furlan, L., Zamperin, L.: iDP approach to quality assessment and improvement of a diecasting process. In: TCN CAE International Conference, Italy (2003) 6. Timelli, G., Grosselle, F., Voltazza, F., Della Corte, E.: A new reference die for mechani- cal properties evaluation in die-casting. In: 4rd International Conference High Tech Die Casting, paper no. 35. AIM, Milano (2008)
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Madagascan Day Geckos (<i>Phelsuma</i>spp.) Exhibit Differing Responses Along a Gradient of Land-Use Change
Tropical conservation science
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Short Communication Tropical Conservation Science Volume 11: 1–10 ! The Author(s) 2018 DOI: 10.1177/1940082918760282 journals.sagepub.com/home/trc Keywords y land-use change, deforestation, habitat disturbance, gecko, conservation agriculture is regarded as the country’s main driver of deforestation and habitat disturbance (Irwin et al., 2010; Waeber, Wilme, Mercier, Camara, & Lowry, 2016). Creative Commons CC-BY: This article is distributed under the terms of the Creative Commons Attribution 4.0 License (http://www.creativecommons.org/ licenses/by/4.0/) which permits any use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). 1Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Australia 2Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, UK Received 31 October 2017; Revised 24 January 2018; Accepted 25 January 2018 Madagascan Day Geckos (Phelsuma spp.) Exhibit Differing Responses Along a Gradient of Land-Use Change Jacinta E. Humphrey1 and Caroline F. M. Ward2 Abstract Madagascar is a key priority for global conservation efforts, as much of its diverse and highly endemic biota is threatened by deforestation. Despite this threat, there are limited data on the responses and tolerances of herpetofaunal species to landscape change. This study investigated the response of Madagascan day geckos (Phelsuma spp.) to deforestation in Nosy Be, Madagascar. We selected six sites along a gradient of land-use change: two in Sambirano rainforest (‘‘Forest’’), two in secondary, fragmented forest (‘‘Fragment’’), and two in agricultural plantations (‘‘Orchard’’ and ‘‘Cropland’’). We conducted a series of time-constrained searches at each site. The mean encounter rate of Phelsuma geckos (geckos detected per person/hour) was greater in agricultural sites than Forest sites, but no difference was detected between Forest and Fragment or Fragment and agricultural areas. Three species were encountered more frequently in agricultural land than forested sites, but this was not true for Phelsuma seippi, an endangered species on the IUCN Red List. These results suggest that adaptive, generalist species may benefit from anthropogenic land-use change, whereas specialist species will suffer. Our study emphasizes the importance of extending research beyond the borders of protected forests to include anthropo- genically disturbed areas. Introduction Deforestation for agriculture is a key driver of species extinctions worldwide (de Almeida-Rocha, Peres, & Oliveira, 2017; Harper, Steininger, Tucker, Juhn, & Hawkins, 2007). It has negative impacts on biodiversity via direct habitat loss and fragmentation (de Almeida- Rocha et al., 2017; Smith, Horning, & Moore, 1997). Such change is particularly concerning in tropical rain- forests, which provide habitat for a significant proportion of terrestrial species (Harper et al., 2007). It is estimated that 90% of Madagascan endemic spe- cies rely solely on forest habitats (Dufils, 2003). Previous studies indicate that Malagasy fauna exhibit a negative response to land clearing and burning; however, this response is poorly understood (Gardner, 2009; Irwin et al., 2010). This issue is particularly pressing for Madagascar is a key priority for global conservation efforts due to its diverse and highly endemic biota, coupled with the ongoing threat of habitat loss (Goodman & Benstead, 2005; Harper et al., 2007; Jenkins et al., 2014; van Heygen, 2004; White, 1983). Native vegetation in Madagascar is removed via slash and burn techniques, which destroy all above-ground foliage, resulting in the transition of primary rainforest to secondary bamboo forest (van Heygen, 2004). As such, slash and burn Corresponding Author: Jacinta E. Humphrey, Department of Ecology, Environment and Evolution, La Trobe University, Melbourne 3086, Australia. Email: J.Humphrey@latrobe.edu.au Corresponding Author: 2 Tropical Conservation Science Madagascar’s unique herpetofauna which, despite their high diversity, have received little attention (D’Cruze, Henson, Olsson, & Emmett, 2009; Jenkins et al., 2014; Lehtinen & Ramanamanjato, 2006; Raxworthy & Nussbaum, 2000). 2003). Sambirano rainforests have a closed canopy 25 to 30 m in height, with few emergent trees (White, 1983). These forests are highly diverse and dominated by species of palms, bamboo, and epiphytes (White, 1983). The island has a mean annual rainfall of 2,000 to 2,250 mm and a mean annual temperature of 26C (Battistini, 1960). This study was conducted during the wet season, throughout January and February, to coincide with peak levels of herpetofaunal activity (Glaw & Vences, 2007). 2003). Sambirano rainforests have a closed canopy 25 to 30 m in height, with few emergent trees (White, 1983). These forests are highly diverse and dominated by species of palms, bamboo, and epiphytes (White, 1983). The island has a mean annual rainfall of 2,000 to 2,250 mm and a mean annual temperature of 26C (Battistini, 1960). This study was conducted during the wet season, throughout January and February, to coincide with peak levels of herpetofaunal activity (Glaw & Vences, 2007). The gecko genus Phelsuma (Gray, 1825) has the high- est diversity of any Malagasy lizard genus, and is esti- mated to contain 44 species (D’Cruze, Sabel, Dawson, & Kumar, 2009; Ikeuchi, Mori, & Hasegawa, 2005; Rocha, Posada, Carretero, & Harris, 2007; Rocha et al., 2010). Many species have successfully colonized Madagascar’s neighboring islands, including the Comoros, Mascarenes, and Seychelles, as well as more distant locations (Rocha et al., 2007, 2010). Relatively, little is known of the current distribution of Phelsuma spp. or the impact of land-use change on their patterns of occurrence (Ikeuchi et al., 2005); but they are believed to be more tolerant of habitat modification than other related genera (Raxworthy & Nussbaum, 2000; van Heygen, 2004). Phelsuma spp. have been recorded in a range of habitats, including human-modified areas such as agricultural plantations and infrastructure (Augros, Fabulet, & Hawlitschek, 2017a; Augros et al., 2017; Bauer, 2003; D’Cruze, Sabel, et al., 2009; Gardner & Jasper, 2009; Glaw & Vences, 2007). Several Phelsuma species are recognized on the IUCN Red List, including Phelsuma seippi (Meier, 1987) which is currently classified as Endangered (IUCN, 2017; Ratsoavina, Glaw, Rabibisoa, & Rakotondrazafy, 2011). Corresponding Author: Much of the primary rainforest on Nosy Be has been cleared for agricultural crops (including rice, sugar cane, coffee, ylang-ylang, and fruits), timber harvesting, zebu grazing, roads, and tourism infrastructure (Andreone et al., 2003, 2005). Patches of remnant forest still persist along creek lines and roadsides (Andreone et al., 2005). Most of the primary forest (862 ha) is now included within the Strict Nature Reserve: La Re´ serve Naturelle Inte´ grale de Lokobe (Madagascar National Parks, 2015; United Nations Environment World Conservation Monitoring Centre, 2017). Methods Study Area This study was undertaken on Nosy Be (13.317S, 48.259E; Figure 1), the largest offshore-island in Madagascar, located 12 km from the northwest coast. Measuring 25,200 ha, Nosy Be is situated within the Sambirano Domain, a transitional zone between the dry, deciduous forest of the west and the wet rainforest of the east (Andreone et al., 2003; van Heygen, 2004). It is char- acterized by a humid, tropical climate and vegetation simi- lar to the lowland rainforests of the mainland (Andreone, Guarino, & Randrianirina, 2005; Goodman & Benstead, Study Sites Six sites were chosen around the village of Ambalahonko, Nosy Be (Figure 1). Sites were selected to represent a temporal gradient of forest recovery following clearance for agriculture (Table 1). Two sites were sampled in each of the following land-use categories: Sambirano rainfor- est, free from any recent human-disturbance (‘‘Forest’’); and fragmented, secondary forest frequently visited by humans (‘‘Fragment’’). In addition, one site was sampled in a banana and ylang-ylang plantation (‘‘Orchard’’) and another in a pineapple plantation (‘‘Cropland’’; Table 1). The Forest category consisted of a primary rainforest site at the border of La Re´ serve Naturelle Inte´ grale de Lokobe and a 30-year-old forest site recovering from past clearance. Only interior forested areas were selected to avoid any edge effects. Fragment sites were located in the Ministere des Eaux et Forests managed buffer zone and consisted of a 20-year-old site and a 10-year-old site, both of which were still utilized for timber extraction and stock grazing. These sites were adjacent to cleared areas and fragmented by walking tracks. Finally, both the Orchard and Cropland sites were located in degraded, cleared agricultural areas. It was necessary to separate these two sites due to differences in vegetation structure and the presence of remnant native vegetation. All sites were located within 1,500 m of the center of Ambalahonko village. Sites were separated by a mean distance of 300 m and a minimum of 130 m (Figure 1). The majority of herpetological research in Madagascar has occurred in primary habitats within protected area networks (D’Cruze, Henson, et al., 2009; Gardner & Jasper, 2009). As such, there is limited knowledge of the distributions, responses, and tolerances of species in anthropogenically disturbed areas (Gardner & Jasper, 2009). As deforestation continues throughout Madagascar, this information will be crucial for future conservation efforts. The aim of this study was to assess and quantify the response of Phelsuma geckos to land-use change in Nosy Be, Madagascar. Survey Methods A series of time-constrained searches (Corn & Bury, 1990), also known as active searches or visual encounter 3 Humphrey and Ward Figure 1. (a) A satellite image of Madagascar indicating the island of Nosy Be off the northwest coast. (b) The white cross indicates the village of Ambalahonko (13.405˚S, 48.345˚E). (c) Squares indicate Forest sites, triangles indicate Fragment sites, and circles indicate Orchard and Cropland sites. Figure 1. (a) A satellite image of Madagascar indicating the island of Nosy Be off the northwest coast. (b) The white cross indicates the village of Ambalahonko (13.405˚S, 48.345˚E). (c) Squares indicate Forest sites, triangles indicate Fragment sites, and circles indicate Orchard and Cropland sites. Table 1. Summary of Land-Use Information for Each of the Six Study Sites. Site no. Land cover Current human land-use Forest extent Time since clearance Category 1 Primary rainforest None Continuous Never cleared Forest 2 Recovering rainforest None Continuous 30 years Forest 3 Secondary forest Travel between villages and timber extraction Fragmented 20 years Fragment 4 Secondary forest Abandoned farm land and zebu grazing Fragmented 10 years Fragment 5 Agriculture Ylang-ylang and banana plantation Cleared 0 years Orchard 6 Agriculture Pineapple plantation Cleared 0 years Cropland Note. Time since clearance was estimated from local knowledge. Table 1. Summary of Land-Use Information for Each of the Six Study Sites. defined site area of 50  50 m. Survey duration was cal- culated by dividing 180 minutes by the number of sur- veyors present. During each search, the team spread out across the survey area and moved through the site at a steady pace, searching all appropriate microhabitat sites to a height of approximately 4 m above the ground. surveys, were undertaken at each site. Each search was conducted by a team of four to seven trained volunteers and at least one experienced researcher. Wherever pos- sible, the same volunteers and researcher assisted with every search. Each search represented 180 observer min- utes of opportunistic searching for herpetofauna within a Tropical Conservation Science 4 richness of Phelsuma geckos between Forest, Fragment, Orchard, and Cropland sites. richness of Phelsuma geckos between Forest, Fragment, Orchard, and Cropland sites. Due to logistical, timing, and funding constraints, sur- veyors could not cover the forest strata above 4 m in height. Surveyors remained separated throughout the entire search to avoid double counting individuals. Results Time-constrained searches detected a total of 97 Phelsuma geckos from five species (Figure 2). The giant Madagascar day gecko (Phelsuma grandis; Gray, 1870) was the most frequently detected species, while Seipp’s day gecko (Phelsuma seippi; Meier, 1987) and the Zanzibar day gecko (Phelsuma dubia; Boettger, 1881) were the two rarest encountered species (Table 2). The Orchard and Cropland sites had the greatest relative abundance of Phelsuma geckos, while the Forest sites had the lowest relative abundance (Table 2). Survey Methods All Phelsuma species encountered during surveys were visually identified in the field to limit disturbance. Three searches, equating to 540 observer minutes, were conducted at each of the six sites. All active searches took place between 0900 and 1100 hours and 1400 and 1600 hours, from 2 January to 5 February 2012. Data Analysis Common name Scientific name Forest Fragment Orchard Cropland Total Abbott’s day gecko Phelsuma abbotti (Stejneger, 1893) 0 2 6 12 20 Zanzibar day gecko Phelsuma dubia (Boettger, 1881) 0 0 3 0 3 Giant Madagascar day gecko Phelsuma grandis (Gray, 1870) 1 14 20 15 50 Broad-tailed day gecko Phelsuma laticauda (Boettger, 1880) 2 0 8 6 16 Seipp’s day gecko Phelsuma seippi (Meier, 1987) 3 4 1 0 8 Total 6 20 38 33 97 Table 2. A Summary of the Relative Abundance of Phelsuma Species Detected in Forest, Fragment, Orchard, and Cropland Sites on Nosy Be, Madagascar. Common name Scientific name Forest Fragment Orchard Cropland Total Abbott’s day gecko Phelsuma abbotti (Stejneger, 1893) 0 2 6 12 20 Zanzibar day gecko Phelsuma dubia (Boettger, 1881) 0 0 3 0 3 Giant Madagascar day gecko Phelsuma grandis (Gray, 1870) 1 14 20 15 50 Broad-tailed day gecko Phelsuma laticauda (Boettger, 1880) 2 0 8 6 16 Seipp’s day gecko Phelsuma seippi (Meier, 1987) 3 4 1 0 8 Total 6 20 38 33 97 0 1 2 3 4 5 0 1 2 3 4 5 Forest Fragment Orchard Cropland Mean species richness Mean encounter rate (geckos pp/hr) Land-use type Forest Fragment Orchard Cropland A B B AB a a a a 0 1 2 3 4 5 0 1 2 3 4 5 Forest Fragment Orchard Cropland Mean species richness Mean encounter rate (geckos pp/hr) Land-use type Forest Fragment Orchard Cropland A B B AB a a a a Figure 3. Mean encounter rate (detections per person/hour; black) and species richness (gray) of Phelsuma geckos recorded for each land-use type in Nosy Be, Madagascar. Error bars denote standard error of the mean. Encounter rates for Forest sites (A) were significanlty different to Orchard (B) and Cropland sites (B). Fragment sites (AB) did not differ from Forest, Orchard, or Cropland sites. There was no significant difference in species richness between the four land-use types (a). Figure 3. Mean encounter rate (detections per person/hour; black) and species richness (gray) of Phelsuma geckos recorded for each land-use type in Nosy Be, Madagascar. Error bars denote standard error of the mean. Encounter rates for Forest sites (A) were significanlty different to Orchard (B) and Cropland sites (B). Fragment sites (AB) did not differ from Forest, Orchard, or Cropland sites. Data Analysis There was no significant difference in species richness between the four land-use types (a). Table 3. Summary Data of the Dunn’s Test With Bonferroni Adjustment Method for Both the Relative Abundance and Species Richness of Phelsuma Geckos. Forest Fragment Orchard Relative abundance Fragment 1.52 (p >.1) Orchard 2.51 (p <.05)* 1.25 (p >.5) Cropland 2.68 (p <.05)* 1.42 (p >.1) 0.15 (p >.5) Species richness Fragment 1.26 (p >.5) Orchard 2.17 (p >.05) 1.13 (p >.5) Cropland 1.95 (p >.1) 0.91 (0 > .5) 0.19 (p >.5) Data Analysis We collated all occurrences of Phelsuma geckos and cal- culated the relative abundance and species richness for each land-use type (Forest, Fragment, Orchard, and Cropland). A Kruskal–Wallis test and a post hoc Dunn’s test (with the Bonferroni adjustment method) were undertaken in RStudio (R version 3.3.1; R Core Team, 2016) to compare the mean encounter rate (geckos detected per person/hour) and mean species Species richness of Phelsuma geckos varied from one to five species per site. The Orchard had the highest rich- ness with all five Phelsuma species recorded. The primary forest adjacent to La Re´ serve Naturelle Inte´ grale de Lokobe had the lowest species richness, with only one species encountered (Phelsuma laticauda; Boettger, 1880). Figure 2. Examples of all five Phelsuma gecko species detected in this study. (a) Broad-tailed day gecko (Phelsuma laticauda; Boettger, 1880), (b) Abbott’s day gecko (Phelsuma abbotti; Steineger, 1893), (c) Giant Madagascar day gecko (Phelsuma grandis; Gray, 1870), (d) Seipp’s day gecko (Phelsuma seippi; Meier, 1987), and (e) Zanzibar day gecko (Phelsuma dubia; Boettger, 1881). All photographs by Jacinta Humphrey, January 2012. Figure 2. Examples of all five Phelsuma gecko species detected in this study. (a) Broad-tailed day gecko (Phelsuma laticauda; Boettger, 1880), (b) Abbott’s day gecko (Phelsuma abbotti; Steineger, 1893), (c) Giant Madagascar day gecko (Phelsuma grandis; Gray, 1870), (d) Seipp’s day gecko (Phelsuma seippi; Meier, 1987), and (e) Zanzibar day gecko (Phelsuma dubia; Boettger, 1881). All photographs by Jacinta Humphrey, January 2012. 5 Humphrey and Ward 0 1 2 3 4 5 0 1 2 3 4 5 Forest Fragment Orchard Cropland Mean species richness Mean encounter rate (geckos pp/hr) Land-use type Forest Fragment Orchard Cropland A B B AB a a a a Figure 3. Mean encounter rate (detections per person/hour; black) and species richness (gray) of Phelsuma geckos recorded for each land-use type in Nosy Be, Madagascar. Error bars denote standard error of the mean. Encounter rates for Forest sites (A) were significanlty different to Orchard (B) and Cropland sites (B). Fragment sites (AB) did not differ from Forest, Orchard, or Cropland sites. There was no significant difference in species richness between the four land-use types (a). Table 2. A Summary of the Relative Abundance of Phelsuma Species Detected in Forest, Fragment, Orchard, and Cropland Sites on Nosy Be, Madagascar. Comparison of Land-Use Types Table 3. Summary Data of the Dunn’s Test With Bonferroni Adjustment Method for Both the Relative Abundance and Species Richness of Phelsuma Geckos. Table 3. Summary Data of the Dunn’s Test With Bonferroni Adjustment Method for Both the Relative Abundance and Species Richness of Phelsuma Geckos. There was a significant difference in the relative abundance of Phelsuma species recorded at sites in different land-use types (H ¼ 10.37, df ¼ 3, p < .05; Figure 3). This difference was found between Forest and Orchard sites (Dunn’s test, Z ¼  2.51, p < .05) and Forest and Cropland sites (Dunn’s test, Z ¼  2.68, p < .05). There was no discernable differ- ence between the other remaining sites surveyed (Table 3). The species richness of Phelsuma geckos also differed between land-use types; however, this difference was not significant (H ¼ 6.59, df ¼ 3, p > .05; Figure 3; Table 3). Tropical Conservation Science 6 Species-Specific Responses species richness in disturbed, agricultural land than in primary rainforest. These results indicate that agricul- tural land can provide habitat for Malagasy species; hence, future research should extend beyond the borders of protected forests into anthropogenically disturbed areas. Phelsuma species responded differently to the gradient of land-use change (Figure 4). The mean encounter rate for the giant Madagascar day gecko (P. grandis), the broad- tailed day gecko (Phelsuma laticauda; Boettger, 1880), and Abbott’s day gecko (Phelsuma abbotti; Stejneger, 1893) increased in more recently disturbed sites (Figure 4). In contrast, the mean encounter rate for Seipp’s day gecko (P. seippi) declined with recent human disturbance (Figure 4). No conclusions could be drawn about the Zanzibar day gecko (P. dubia) as this species was only detected at one site (Figure 4). Trends of Individual Species Phelsuma geckos are likely attracted to areas with a greater number of arboreal perch sites, egg laying sites, and higher food availability (Augros et al., 2017; D’Cruze, Sabel, et al., 2009; Ineich, 2010), such as agri- cultural plantations and human settlements. These spe- cies may also favor human-modified habitats because they offer increased cover and protection from predators (D’Cruze, Sabel, et al., 2009). Our results indicated three species of Phelsuma geckos were more readily encountered in human-modified habitats than forested Discussion There was a significant difference in the relative abun- dance of Madagascan day geckos (Phelsuma spp.) between Forest and Orchard and Forest and Cropland sites. Surveys recorded a greater mean encounter rate and Figure 4. Species-specific responses to a gradient of land-use change. Each figure represents the mean encounter rate (detec person/hour) for a single Phelsuma species across the four land-use types. Error bars denote standard error of the mean. Figure 4. Species-specific responses to a gradient of land-use change. Each figure represents the mean encounter rate (detections per person/hour) for a single Phelsuma species across the four land-use types. Error bars denote standard error of the mean. 7 Humphrey and Ward Methodological Considerations sites: the giant Madagascar day gecko (Phelsuma grandis; Gray, 1870), the broad-tailed day gecko (Phelsuma lati- cauda; Boettger, 1880), and Abbott’s day gecko (Phelsuma abbotti; Stejneger, 1893). Previous studies in Madagascar have identified P. grandis and P. laticauda as adaptive generalists, as they are often recorded in dis- turbed areas (D’Cruze, Sabel, et al., 2009; Roberts & Daly, 2014). Further studies on neighboring islands have indicated similar distributions (Hawlitschek, Bruckmann, Berger, Green, & Glaw, 2011), with urban or agricultural areas found to provide habitat for up to five coexisting species (Augros, Fabulet, & Hawlitschek, 2017b). Some authors have proposed that Phelsuma geckos may benefit from ongoing deforestation in Madagascar (Glaw & Vences, 2007; van Heygen, 2004), as they are able to use open, cultivated areas and are often more abundant in such sites compared with their natural forested habitats (Bauer, 2003). Overall, our results support existing evidence that P. grandis, P. laticauda, and P.abbotti may be less vulner- able to habitat destruction than other Malagasy reptiles due to their ability to utilize disturbed forests and agricultural plantations. The detectability of reptiles is highly variable and depends on the degree of species crypsis (both in appear- ance and behavior) (Hampton, 2007; Marzerolle et al., 2007), survey technique used (Ribeiro-Junior, Gardner, & Avila-Pires, 2008), sampling effort (Garden, McAlpine, Jones, & Possingham, 2007), weather condi- tions (Crosswhite, Fox, & Thill, 1999), and the habitat type (Ribeiro-Junior et al., 2008). Large, brightly colored species, such as the giant Madagascar day gecko (P. grandis), are often easier to detect than dull, cryptic spe- cies in forested habitats (D’Cruze, Sabel, et al., 2009). Discussion In addition, previous studies in tropical regions have indi- cated that the detectability of wildlife is heavily influ- enced by forest structural complexity (Jenkins, Brady, Bisoa, Rabearivony, & Griffiths, 2003; Smith et al., 1997). Secondary forest is comparatively more open, enabling researchers to detect target species at a greater distance or encounter cryptic species more frequently (Smith et al., 1997). These factors, habitat structure and vegetation density, may have influenced our ability to detect geckos in primary rainforest habitats. Furthermore, due to logistical, timing, and funding con- straints, we were unable to survey for Phelsuma geckos above a height of 4 m during this study. The detection success of small arboreal species from the ground, espe- cially in tall-canopy forest, is likely to be low (Imlay, Dale, Buckland, Jones, & Cole, 2012). It is therefore important to note that agricultural sites, especially those devoid of tall trees such as the pineapple plantation, would have been surveyed more thoroughly in this study when com- pared with forested sites. For future surveys, we recom- mend conducting stationary vantage point surveys with binoculars (Augros et al., in press), or if possible, following the method outlined by Imlay et al. (2012): elevated point count surveys with distance sampling. In contrast, Seipp’s day gecko (Phelsuma seippi; Meier, 1987) is classified as Endangered by the IUCN (2017) due to its restricted range within a fragmented habitat, which is undergoing continued conversion into agricultural land (Ratsoavina et al., 2011; Roberts & Daly, 2014). Current research suggests that P. seippi may depend on bamboo forest, as it is often detected on the fringes of rainforest in stands of bamboo (van Heygen, 2004). Phelsuma seippi is likely a habitat specialist, and therefore it is more sensitive to forest degradation, loss, and frag- mentation than other congeners (Irwin et al., 2010; Raxworthy & Nussbaum, 2000). Our results, with most records in Forest and Fragment sites, support the view that this species is less tolerant to land-use change than the other Phelsuma geckos detected in our study. Further research is needed on the habitat requirements of this species to aid future conservation planning (Ratsoavina et al., 2011). Collection of data in this study was largely undertaken by volunteers. References Andreone, F., Glaw, F., Nussbaum, R. A., Raxworthy, C. J., Vences, M., & Randrianirina, J. E. (2003). The amphibians and reptiles of Nosy Be (NW Madagascar) and nearby islands: A case study of diversity and conservation of an insular fauna. Journal of Natural History, 37(17): 2119–2149. doi:10.1080/ 00222930210130357 Andreone, F., Guarino, F. M., & Randrianirina, J. E. (2005). Life history traits, age profile, and conservation of the panther cha- meleon, Furcifer pardalis (Cuvier 1829), at Nosy Be, NW Madagascar. Tropical Zoology, 18(2): 209–225. doi:10.1080/ 03946975.2005.10531221 Augros, S., Fabulet, P.-Y., & Hawlitschek, O. (2017a). New pattern of distribution for Phelsuma nigristriata (Meier 1984), endemic to the department of Mayotte (976), in anthropogenic areas. Bulletin de la Societe Herpetologique de France, 162, 113–116. Acknowledgments Bauer, A. M. (2003). Gekkonidae, Geckos. In: S. M. Goodman, & J. P. Benstead (Eds.). The natural history of Madagascar (pp. 973–977). Chicago, IL: The University of Chicago Press. The authors acknowledge the Ministe`re de l’Environnement et des Eaux et Foreˆts for providing the necessary research permits. They also thank the staff and students of the Frontier Madagascar Forest Research Project (Phase 121) for their assistance with fieldwork—Olivia Haggis, Petros Persad, Andy Ferris, Rachael Castle, Alex Harding, Georgia Hinkley, Tom Holland, Shelagh Taggart, Rowan Young, and Vera Ziltener. Finally, they thank Dr. Angie Haslem and Professor Andrew Bennett for their com- ments on a draft of this article, and the two anonymous reviewers who provided valuable feedback. Bird, T. J., Bates, A. E., Lefcheck, J. S., Hill, N. A., Thomason, R. J., Edgar, G. J., & Frusher, S. (2014). Statistical solutions for error and bias in global citizen science datasets. Biological Conservation, 173, 144–154. Corn, P. S., & Bury, R. B. (1990). Sampling methods for terrestrial amphibians and reptiles (General Technical Report, PNW- GTR-256). Portland, Oregon: U.S. Department of Agriculture. Crall, A. W., Newman, G. J., Stohlgren, T. J., Holfelder, K. A., Graham, J., & Waller, D. M. (2011). Assessing citizen science data quality: An invasive species case study. Conservation Letters, 4, 433–442. Funding The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: Funding for this project was provided by the Society for Environmental Exploration and the Nature Environment Research Council (NERC). ORCID iD Madagascan day geckos (Phelsuma spp.) display differing responses to landscape change. Several adaptive, generalist species are tolerant of land clearing as they are capable of using cleared agricultural areas and human infrastructure (Glaw & Vences, 2007; van Heygen, 2004); but others are sensitive to anthropogenic disturbance (Irwin et al., 2010). Phelsuma seippi, the only species detected in this study that is currently recognized on the IUCN Red List (2017), appears to be sensitive to land-use change (Irwin et al., 2010; Raxworthy & Nussbaum, 2000). Further research is required to broaden the understanding of the responses of these species, and common native fauna, to landscape change in order to face the ongoing threat of deforestation. Jacinta E. Humphrey http://orcid.org/0000-0002-4334-7018 Discussion Individuals may vary in their level of com- mitment, experience, and skill, and there is a risk that volunteers may introduce bias by recording false absences or via uneven sampling effort within or between sites (Bird et al., 2014; Crall et al., 2011). Recent research, however, suggests that volunteer data is often just as accurate as data collected by experienced professionals (Lewandowski & Specht, 2015). To reduce the potential for bias in our study, volunteers were trained in species identification and were required to pass a short test prior to participating in surveys. In addition, all volunteers in this study were current research assistants with the Society of Environmental Exploration and possessed fauna surveying experience and a relevant tertiary quali- fication. We therefore consider it unlikely that volunteer bias would have affected our findings. The Zanzibar day gecko (Phelsuma dubia) was only detected in the banana plantation (‘‘Orchard’’). As such, no conclusions could be drawn regarding its response to land-use change on Nosy Be. Phelsuma dubia is believed to be a highly adaptable species and is often found in anthropogenically modified habitats including fruit plantations (Hawlitschek et al., 2011; van Heygen, 2004). Previous studies have suggested that P.dubia may be rare in the region (van Heygen, 2004), which could account for our sparse detections. Conversely, recent research has indicated that P. dubia is likely to be underestimated in surveys as it favors high perches which are difficult to detect from ground level (Augros et al., 2018). The authors wish to acknowledge that this is only a small pilot study. Our understanding of the response of 8 Tropical Conservation Science Phelsuma geckos to land-use change would benefit from more in-depth research, particularly with the addition of a greater number of replicate sites and a broader range of survey methods to cover all forest strata, such as elevated point count surveys with distance sampling. Implications for Conservation Knowledge of the distributions, responses, and tolerances of species to anthropogenic land-use change will be cru- cial for future conservation efforts in Madagascar (Gardner & Jasper, 2009; Raxworthy & Nussbaum, 2000). Our understanding of the conservation value of secondary forest and agricultural land is limited, although unprotected forests and disturbed habitats are known to possess considerable biodiversity (Andreone et al., 2003; Gardner, 2009; Ingram & Dawson, 2006). Furthermore, as evidenced in this study, modified habi- tats can support populations of some adaptive, generalist species. We therefore recommend that future research extends beyond the borders of protected areas to include anthropogenically disturbed areas such as secondary regenerating forest and agricultural landscapes. Augros, S., Fabulet, P.-Y., & Hawlitschek, O. (2017b). First report of the co-existence of the three endemic Phelsuma species of Mayotte Island (Indian Ocean) in anthropogenic habitats. The Herpetological Bulletin, 140, 20–22. Augros, S., Faipoux, L., Bodin, M., Le Goff, A., Sanchez, M., & Clemencet, J. (2017). Evidence for colonisation of anthropo- genic habitats by the Reunion day gecko Phelsuma borbonica (Mertens, 1966) (Reunion Island, France): Conservation impli- cations. Herpetology Notes, 10, 563–571. Augros, S., Scherz, M. D., Wang-Claypool, C. Y., Montfort, L., Glaw, F., & Hawlitschek, O. (2018). Comparative perch heights and habitat plant usage of day geckos (Phelsuma) in the Comoros Archipelago (Squamata: Gekkonidae). Salamandra. Battistini, R. (1960). Description geomorphologique de Nosy Be, du delta du Sambirano et de la baie d’Ampasindava. Memoires de l’Institut Scientifique de Madagascar, Serie F, 3, 1–343. Declaration of Conflicting Interests The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article. Crosswhite, D. L., Fox, S. F., & Thill, R. E. (1999). Comparison of methods for monitoring reptiles and amphibians in upland Humphrey and Ward 9 forests of the Ouachita Mountains. Proceedings of the Oklahoma Academy of Science, 79, 45–50. forests of the Ouachita Mountains. Proceedings of the Oklahoma Academy of Science, 79, 45–50. Irwin, M. T., Wright, P. C., Birkinshaw, C., Fisher, B. L., Gardner, C. J., Glos, J., & Ganzhorn, J. U. (2010). Patterns of species change in anthropogenically disturbed forests of Madagascar. Biological Conservation, 143, 2351–2362. D’Cruze, N., Henson, D., Olsson, A., & Emmett, D. (2009). The importance of herpetological survey work in conserving Malagasy biodiversity: Are we doing enough? Herpetological Review, 40(1): 19–25. IUCN. (2017). IUCN Red List of Threatened Species (ver.2017.1). IUCN Red List of Threatened Species. Retrieved from http:// www.iucnredlist.org/ D’Cruze, N., Sabel, J., Dawson, J., & Kumar, S. (2009). The influence of habitat type and structure on the abundance of Phelsuma madagascarensis grandis (Gekkoninae) in northern Madagascar. Herpetological Conservation and Biology, 4(1): 55–61. Jenkins, R., Brady, L. D., Bisoa, M., Rabearivony, J., & Griffiths, R. A. (2003). Forest disturbance and river proximity influence chameleon abundance in Madagascar. Biological Conservation, 109, 407–415. de Almeida-Rocha, J. M., Peres, C. A., & Oliveira, L. C. (2017). Primate responses to anthropogenic habitat disturbance: A pantropical meta-analysis. Biological Conservation, 215, 30–38. Jenkins, R., Tognelli, M. F., Bowles, P., Cox, N., Brown, J. L., Chan, L., & Vences, M. (2014). Extinction risks and the con- servation of Madagascar’s reptiles. PLoS One, 9(8): e100173. doi:10.1371/journal.pone.0100173 Dufils, J. M. (2003). Remaining forest cover. In: S. M. Goodman, & J. P. Benstead (Eds.). The natural history of Madagascar (pp. 88–96). Chicago, IL: University of Chicago Press. Lehtinen, R. M., & Ramanamanjato, J.-B. (2006). Effects of rainforest fragmentation and correlates of local extinction in a herpetofauna from Madagascar. Applied Herpetology, 3, 95–110. Garden, J., McAlpine, C., Jones, D., & Possingham, H. (2007). Using multiple survey methods to detect terrestrial reptiles and mammals: What are the most successful and cost efficient combinations? Wildlife Research, 34, 218–227. Lewandowski, E., & Specht, H. (2015). Influence of volunteer and project characteristics on data quality of biological surveys. Conservation Biology, 29(3): 713–723. doi:10.1111/cobi.12481 Gardner, C. J. (2009). Declaration of Conflicting Interests A review of the impacts of anthropogenic habitat change on terrestrial biodiversity in Madagascar: Implications for the design and management of new protected areas. Malagasy Nature, 2, 2–29. Madagascar National Parks. (2015). Parc National Lokobe. Madagascar National Parks. Retrieved from http://www.parcs- madagascar.com/aire-prot%C3%A9g%C3%A9e/parc-national- lokobe# Gardner, C. J., & Jasper, L. (2009). The urban herpetofauna of Toliara, southwest Madagascar. Herpetology Notes, 2, 239–242. Marzerolle, M. J., Bailey, L. L., Kendall, W. L., Royle, A., Converse, S. J., & Nichols, J. D. (2007). Making great leaps forward: Accounting for detectability in herpetological field studies. Journal of Herpetology, 41(4): 672–689. Glaw, F., & Vences, M. (2007). A field guide to the amphibians and reptiles of Madagascar (3rd ed.). Verlag, Koln: Vences and Glaw. R Core Team R: A language and environment for statistical com- puting (Version R version 3.3.1). Vienna, Austria: R Foundation for Statistical Computing. Retrieved from http://www.R- project.org/ Goodman, S. M., & Benstead, J. P. (2003). The natural history of Madagascar. Chicago, IL: The University of Chicago Press. Goodman, S. M., & Benstead, J. P. (2005). Updated estimates of biotic diversity and endemism for Madagascar. Oryx, 39(01): 73–77. doi:10.1017/s0030605305000128 Ratsoavina, F. M., Glaw, F., Rabibisoa, N. H., & Rakotondrazafy, N. A. (2011). Phelsuma seippi. The IUCN red list of threatened species 2011. Retrieved from http://dx.doi.org/10.2305/ IUCN.UK.2011-2.RLTS.T172829A6925888.en Hampton, P. (2007). A comparison of the success of artificial cover types for capturing amphibians and reptiles. Amphibia-Reptilia, 28, 433–437. Raxworthy, C. J., & Nussbaum, R. A. (2000). Extinction and extinction vulnerability of amphibians and reptiles in Madagascar. Amphibian and Reptile Conservation, 2(1): 15–23. Harper, G. J., Steininger, M. K., Tucker, C. J., Juhn, D., & Hawkins, F. (2007). Fifty years of deforestation and forest frag- mentation in Madagascar. Environmental Conservation, 34(04): 1–9. doi:10.1017/s0376892907004262 Ribeiro-Junior, M. A., Gardner, T. A., & Avila-Pires, T. C. S. (2008). Evaluating the effectiveness of herpetofaunal sampling techniques across a gradient of habitat change in a tropical forest landscape. Journal of Herpetology, 42(4): 733–749. Hawlitschek, O., Bruckmann, B., Berger, J., Green, K., & Glaw, F. (2011). Integrating field surveys and remote sensing data to study distribution, habitat use and conservation status of the herpetofauna of the Comoro Islands. Zookeys, 144, 21–78. doi:10.3897/zookeys.144.1648 Roberts, S. H., & Daly, C. (2014). A rapid herpetofaunal assess- ment of Nosy Komba Island, northwestern Madagascar, with new locality records for seventeen species. Salamandra, 50(1): 18–26. Ikeuchi, I., Mori, A., & Hasegawa, M. (2005). Declaration of Conflicting Interests Natural history of Phelsuma madagascariensis kochi from a dry forest in Madagascar. Amphibia-Reptilia, 26, 475–483. Rocha, S., Posada, D., Carretero, M. A., & Harris, D. J. (2007). Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): Multiple natural colonisations, intro- ductions and island radiations. Molecular Phylogenetics and Evolution, 43(2): 685–692. doi:10.1016/j.ympev.2006.07.010 Imlay, T., Dale, R., Buckland, S., Jones, C. G., & Cole, N. (2012). 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Forest cover, condition, and ecology in human-impacted forests, south-eastern Madagascar. Conservation and Society, 4(2): 194–230. Tropical Conservation Science 10 Waeber, P. O., Wilme, L., Mercier, J. R., Camara, C., & Lowry, P. P. 2nd (2016). How effective have thirty years of internationally driven conservation and development efforts been in Madagascar? PLoS One, 11(8): e0161115. doi:10.1371/ journal.pone.0161115 Smith, A. P., Horning, N., & Moore, D. (1997). Regional biodiver- sity planning and lemur conservation with GIS in western Madagascar. Conservation Biology, 11(2): 498–512. United Nations Environment World Conservation Monitoring Centre. (2017). Lokobe in Madagascar. Protected Planet. Retrieved from https://protectedplanet.net/lokobe-strict-nature- reserve White, F. (1983). The vegetation of Africa: A descriptive memoir of accompany the UNESCO/AETFAT/UNSO vegetation map of Africa. 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https://openalex.org/W4379802361
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Assessment of a Parachor Model for the Surface Tension of Binary Mixtures
International journal of thermophysics
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* Alexandra Metallinou Log alexandra.m.log@ntnu.no; Alexandra.Log@hotmail.com Assessment of a Parachor Model for the Surface Tension of Binary Mixtures Alexandra Metallinou Log1 · Vladimir Diky2 · Marcia L. Huber2 Received: 25 April 2023 / Accepted: 12 May 2023 / Published online: 7 June 2023 © The Author(s) 2023 1 Department of Energy and Process Engineering, Faculty of Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway 2 Applied Chemicals and Materials Division, National Institute of Standards and Technology, 325 Broadway, Boulder, CO 80305, USA Keywords  Binary mixtures · Parachor · Surface tension International Journal of Thermophysics (2023) 44:110 https://doi.org/10.1007/s10765-023-03216-z International Journal of Thermophysics (2023) 44:110 https://doi.org/10.1007/s10765-023-03216-z 1  Introduction Surface tension is an important physical property that has long had significance in the oil and gas industry, and is also of interest in applications as varied as phar- maceuticals [1, 2], heat transfer in low-global warming potential (GWP) refriger- ants [3], ink-jet printing [4, 5] and diesel engine design [6]. Specific examples in the pharmaceutical industry include [2] the importance of controlling the surface tension of coating solutions of tablets to improve product appearance and con- trol the rate of drug release, the effect of surface tension on the size of drop- lets in a nebulizer, and control of the size of eye drops. In addition, fluorocarbon based fluids with low surface tension are being investigated as blood substitutes for oxygen delivery [1]. In the refrigeration industry, new low-GWP refrigerant blends are being proposed. In order to evaluate the performance of heat exchang- ers, accurate knowledge of the surface tension is needed to model the bubble behavior in pool boiling [3]. In ink-jet printing, From [5] analyzed the fluid flow behavior of impulsively driven laminar jet flow in terms of dimensionless param- eters involving the surface tension, density, viscosity, and a characteristic dimen- sion, and made recommendations for when the fluid has stable drop formation. In order to optimize engine performance to reduce soot emissions, there is a need for surface tension data at high pressures and high temperatures [6]. Accurate property values for surface tension are necessary for successful analysis of all these processes. p In 1923, Macleod proposed a simple empirical relationship between surface tension σ and the density of the liquid and vapor phases ρL and ρV (1) P = 휎1∕4 휌L −휌V , (1) where P is a temperature-independent parameter called the parachor by Sugden [7]. Other practical engineering methods for predicting surface tension can be found in handbooks such as Ref. [8]. In addition, there are numerous theoretically based approaches to predicting the surface tension such as density gradient theory [9, 10], density functional theory [11], hard-sphere fluid scaled particle theory [12], pertur- bation theory [13] and friction theory [14]. The parachor approach can also be applied to mixtures, as was demonstrated by Weinaug and Katz [15] and Hugill et al. [16]. Abstract We compiled an experimental database for the surface tension of binary mixtures containing a wide variety of fluids, from the chemical classes (water, alcohols, amines, ketones, linear and branched alkanes, naphthenes, aromatics, refrigerants, and cryogens). The resulting data set includes 65 pure fluids and 154 binary pairs with a total of 8205 points. We used this database to test the performance of a para- chor model for the surface tension of binary mixtures. The model uses published correlations to determine the parachors of the pure fluids. The model has a single, constant binary interaction parameter for each pair that was found by fitting experi- mental mixture data. It can be also used in a predictive mode when the interaction parameters are set to zero. We present detailed comparisons on the performance of the model for both cases. In general, the parachor model in a predictive mode without fitted interaction parameters can predict the surface tension of binary mix- tures of non-polar mixtures such as linear and branched alkanes, linear and branched alkanes with naphthenes, aromatics with aromatics, aromatics with naphthenes, and mixtures of linear alkanes of similar sizes with an average absolute percentage deviation of about 3 % or less. Polar mixtures of halocarbons with other halocar- bons and also polar/nonpolar mixtures of alkanes with halocarbons could be mod- eled with an average absolute deviation of less than 0.35 mN·m−1 with the use of a binary interaction parameter. The parachor model even with a fitted binary interac- tion parameter performs poorly for mixtures of water and organic compounds and is not recommended. Keywords  Binary mixtures · Parachor · Surface tension 456789) 3 110  Page 2 of 46 International Journal of Thermophysics (2023) 44:110 1  Introduction Although the parachor method has been used for many years in the petrochemical industry, is in active use now [17], is the recommended approach in the API Technical Databook [18], and is discussed in reference books for engineers [8] there has not been a comprehen- sive evaluation of the performance of this type of model with respect to mixtures using a large database of binary data in the open literature. It is the goal of this work to provide an evaluation of the parachor model to a wide variety of binary mixtures, including not only common hydrocarbons involved in the petrochemical industry, but also recent low-GWP fluids of interest to the refrigeration industry and to indicate expected performance and limitations of this model for a wide variety of mixtures. 1 3 1 3 International Journal of Thermophysics (2023) 44:110 Page 3 of 46  110 110 2  The Parachor Model The parachor model that we will apply to mixtures was originally presented by Wein- aug and Katz [15] and later modified by Hugill et al. [16] to allow for the use of binary interaction parameters. For a mixture, (2) 휎mix = (PL휌L −PV휌V )m (2) with mixing and combining rules (3) PL = n ∑ i=1 n ∑ j=1 xixjPij and PV = n ∑ i=1 n ∑ j=1 yiyjPij (3) (4) Pij = (1 −훿ij) Pi + Pj 2 , (4) where δij is an optional binary interaction parameter, and xi and yi are the molar compositions of the liquid and gas phases, respectively. Historically [15, 16, 19] the exponent m has been set to 4, but here we use m = 3.87 based on theoretical consid- erations as presented by Garrabos et al. [20]. In addition, it also is common to use a fixed value of the parachor obtained from compilations such as that of Quayle [21]. Zhelezny et al. [22] has studied the temperature dependence of the parachor. Mulero and coworkers [23–31] developed an extensive body of work on correlations for the surface tension of many important industrial fluids that can be used to compute the pure fluid parachors ­Pi as a function of temperature. These correlations are very accurate and can represent the data to within experimental uncertainty. We primar- ily use these correlations as implemented in the computer program REFPROP v10 [32] for pure fluid surface tension σi. The parachors are evaluated at the temperature of interest for the binary mixture, however for temperatures greater than or equal to 0.9Tc,i, where Tc,i is the pure fluid critical temperature, the parachor is calculated at 0.9Tc,i. It also is necessary to have the saturation densities and compositions xi and yi of the liquid and vapor phases. If the compositions and densities from the VLE calculations are inaccurate this will increase the uncertainty in the surface tension calculations, so care should be used in the selection of the VLE model. We obtain these compositions and densities from the default equations of state and models implemented in REFPROP v10 [32]; a description of these can be found in [33]. 1  Certain equipment, instruments, software,  or materials,  commercial or non-commercial, are identi- fied in this paper to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement of any product or service by NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. 2  The Parachor Model A few changes were made in the models of REFPROP v10 that enabled calculation for some mixtures not permitted in the original version, as well as some changes in mix- ture parameters that are summarized in the Supplementary Information in Appendix where δij is an optional binary interaction parameter, and xi and yi are the molar compositions of the liquid and gas phases, respectively. Historically [15, 16, 19] the exponent m has been set to 4, but here we use m = 3.87 based on theoretical consid- erations as presented by Garrabos et al. [20]. In addition, it also is common to use a fixed value of the parachor obtained from compilations such as that of Quayle [21]. Zhelezny et al. [22] has studied the temperature dependence of the parachor. Mulero and coworkers [23–31] developed an extensive body of work on correlations for the surface tension of many important industrial fluids that can be used to compute the pure fluid parachors ­Pi as a function of temperature. These correlations are very accurate and can represent the data to within experimental uncertainty. We primar- ily use these correlations as implemented in the computer program REFPROP v10 [32] for pure fluid surface tension σi. The parachors are evaluated at the temperature of interest for the binary mixture, however for temperatures greater than or equal to 0.9Tc,i, where Tc,i is the pure fluid critical temperature, the parachor is calculated at 0.9Tc,i. It also is necessary to have the saturation densities and compositions xi and yi of the liquid and vapor phases. If the compositions and densities from the VLE calculations are inaccurate this will increase the uncertainty in the surface tension calculations, so care should be used in the selection of the VLE model. We obtain these compositions and densities from the default equations of state and models implemented in REFPROP v10 [32]; a description of these can be found in [33]. A few changes were made in the models of REFPROP v10 that enabled calculation for some mixtures not permitted in the original version, as well as some changes in mix- ture parameters that are summarized in the Supplementary Information in Appendix A A. 1 3 110  Page 4 of 46 International Journal of Thermophysics (2023) 44:110 3  Experimental Data We extracted experimental data for the surface tension of binary mixtures for liquid–gas interfaces from the NIST TDE database [34] for which the pure fluid components are available, the composition of the liquid is explicitly specified, and also for which there are reliable models for the vapor–liquid equilibrium and thermodynamic properties in the REFPROP database [32]. We excluded HCl/water and benzene/water due to the lack of a good mixture model for thermodynamic properties in REFPROP. The resulting data set includes 65 pure fluids and 154 binary pairs with a total of 8205 points. Table  1 provides a list of the pure components along with information for compound identification, along with a reference for the pure fluid surface tension correlation implemented in REFPROP v10 [32] used to evaluate pure fluid surface tension in this work. A summary of the binary mixture data is given in Table 2 including a reference code (starting with the publication year), the experimental method, an uncertainty estimate, the fluids in the binary mixture, the number of data points, temperature range, and composition in terms of the mole fraction of the first component. The full data set is available in the supplementary information in the file InputData.txt. A discussion of experimental methods for obtaining surface tension can be found in Ref. [35]. The estimated uncertainties (at a k = 2 level) are those as assessed by the NIST TDE database and may not be the same as those stated by the original authors. As part of the data capture process, software [36] is used that assesses the uncertainty of the data taking into account factors such as the experimental method, the sample purity, property precision, precision of independent variables. However, the reader should consult the original data reference for complete details of the measurement technique and uncertainty analysis for assessment of the quality of an individual data set. 4  Results Evaluations were first made with the interaction parameter in Eq. 4 set to zero (δij = 0) for all the mixtures. All properties such as the pure fluid surface tensions and the mixture densities and compositions required in Eqs. 1–4 were obtained using the REFPROP v10 [32] computer program, with additional changes that are detailed in the supplementary information, Appendix A. A second set of evaluations was made after fitting the binary interaction parameter δij to the experimental data with a trust- region reflective least squares algorithm in Python, scipy.optimize.curve_fit [198].1 A single binary interaction parameter was fit for each fluid mixture pair, including all data sets for any given pair. For discussion of the results, we define AAPD as the average absolute percentage deviation, where PCTDEV = 100(σcalc − σexp)/σexp, and AAPD = (∑│PCTDEV│)/n, and the summation is over all n points. AAD is 1 3 International Journal of Thermophysics (2023) 44:110 Page 5 of 46  110 l Name Full name Formula Family CAS no. Standard InChI key References Acetone Propanone C3H6O Ketone 67-64-1 CSCPPACGZOOCGX-UHFFFAOYSA-N [26] Argon Argon Ar Cryogen 7440-37-1 XKRFYHLGVUSROY-UHFFFAOYSA-N [26] Benzene Benzene C6H6 Aromatic 71-43-2 UHOVQNZJYSORNB-UHFFFAOYSA-N [26] Butane n-Butane C4H10 n-Alkane 106-97-8 IJDNQMDRQITEOD-UHFFFAOYSA-N [26] Carbon dioxide Carbon dioxide CO2 Other 124-38-9 CURLTUGMZLYLDI-UHFFFAOYSA-N [26] Carbon monoxide Carbon monoxide CO Cryogen 630-08-0 UGFAIRIUMAVXCW-UHFFFAOYSA-N [26] Chlorobenzene Chlorobenzene C6H5Cl Halocb 108-90-7 MVPPADPHJFYWMZ-UHFFFAOYSA-N [37] Cyclohexane Cyclohexane C6H12 Naphthene 110-82-7 XDTMQSROBMDMFD-UHFFFAOYSA-N [26] Cyclopentane Cyclopentane C5H10 Naphthene 287-92-3 RGSFGYA​AUT​VSQA-UHFFFAOYSA-N [24] D4 Octamethylcyclotetrasiloxane C8H24O4Si4 Siloxane 556-67-2 HMMGMWAXVFQUOA-UHFFFAOYSA-N [24] D5 Decamethylcyclopentasiloxane C10H30O5Si5 Siloxane 541-02-6 XMSXQFUHVRWGNA-UHFFFAOYSA-N [24] DEA Diethanolamine C4H11NO2 Amine 111-42-2 ZBCBWPMODOFKDW-UHFFFAOYSA-N [37] Decane n-Decane C10H22 n-Alkane 124-18-5 DIOQZVSQGTUSAI-UHFFFAOYSA-N [26] Deuterium Deuterium D2 Cryogen 7782-39-0 UFHFLCQGNIYNRP-VVKOMZTBSA-N [26] Dichloroethane 1,2-Dichloroethane C2H4Cl2 Halocb 107-06-2 WSLDOOZREJYCGB-UHFFFAOYSA-N [37] Diethyl ether Diethyl ether C4H10O Ether 60-29-7 RTZKZFJDLAIYFH-UHFFFAOYSA-N [24] Dimethyl carbonate (DMC) Dimethyl ester carbonic acid C3H6O3 Other 616-38-6 IEJIGPNLZYLLBP-UHFFFAOYSA-N [24] Dimethyl ether Methoxymethane C2H6O Ether 115-10-6 LCGLNKUTAGEVQW-UHFFFAOYSA-N [26] Docosane n-Docosane C22H46 n-Alkane 629-97-0 HOWGUJZVBDQJKV-UHFFFAOYSA-N [37] Dodecane n-Dodecane C12H26 n-Alkane 112-40-3 SNRUBQQJIBEYMU-UHFFFAOYSA-N [26] Ethane Ethane C2H6 n-Alkane 74-84-0 OTMSDBZUPAUEDD-UHFFFAOYSA-N [26] Ethanol Ethyl alcohol C2H6O Alcohol 64-17-5 LFQSCWFLJHTTHZ-UHFFFAOYSA-N [27] Ethylene glycol 1,2-Ethandiol C2H6O2 Glycol 107-21-1 LYCAIKOWRPUZTN-UHFFFAOYSA-N [37] Ethylbenzene Phenylethane C8H10 Aromatic 100-41-4 YNQLUTRBYVCPMQ-UHFFFAOYSA-N [24] Heavy water Deuterium oxide D2O Water 7789-20-0 XLYOFNOQVPJJNP-ZSJDYOACSA-N [38] Helium Helium-4 He Cryogen 7440-59-7 SWQJXJOGLNCZEY-UHFFFAOYSA-N [26] 3 110  Page 6 of 46 International Journal of Thermophysics (2023) 44:110 1 3 Table 1   (continued) Name Full name Formula Family CAS no. 4  Results Standard InChI key References Heptane n-Heptane C7H16 n-Alkane 142-82-5 IMNFDUFMRHMDMM-UHFFFAOYSA-N [26] Hexadecane n-Hexadecane C16H34 n-Alkane 544-76-3 DCAYPVUWAIABOU-UHFFFAOYSA-N [37] Hexane n-Hexane C6H14 n-Alkane 110-54-3 VLKZOEOYAKHREP-UHFFFAOYSA-N [26] Hydrogen (normal) Hydrogen (normal) H2 Cryogen 1333-74-0 UFHFLCQGNIYNRP-UHFFFAOYSA-N [26] Isooctane 2,2,4-Trimethylpentane C8H18 br-Alkane 540-84-1 NHTMVDHEPJAVLT-UHFFFAOYSA-N [24] Krypton Krypton Kr Cryogen 7439-90-9 DNNSSWSSYDEUBZ-UHFFFAOYSA-N [26] MD2M Decamethyltetrasiloxane C10H30Si4O3 Siloxane 141-62-8 YFCGDEUVHLPRCZ-UHFFFAOYSA-N [24] MD3M Dodecamethylpentasiloxane C12H36Si5O4 Siloxane 141-63-9 FBZANXDWQAVSTQ-UHFFFAOYSA-N [24] MD4M Tetradecamethylhexasiloxane C14H42O5Si6 Siloxane 107-52-8 ADANNTOYRVPQLJ-UHFFFAOYSA-N [24] Monoethanolamine (MEA) Ethanolamine C2H7NO Amine 141-43-5 HZAXFHJVJLSVMW-UHFFFAOYSA-N [37] Methane Methane CH4 n-Alkane 74-82-8 VNWKTOKETHGBQD-UHFFFAOYSA-N [26] Methanol Methanol CH4O Alcohol 67-56-1 OKKJLVBELUTLKV-UHFFFAOYSA-N [26] Methyl palmitate Methyl hexadecanoate C17H34O2 FAME 112-39-0 FLIACVVOZYBSBS-UHFFFAOYSA-N [24] Methylcyclohexane Methylcyclohexane C7H14 Naphthene 108-87-2 UAEPNZWRGJTJPN-UHFFFAOYSA-N [24] m-Xylene 1,3-Dimethylbenzene C8H10 Aromatic 108-38-3 IVSZLXZYQVIEFR-UHFFFAOYSA-N [24] Neon Neon Ne Cryogen 7440-01-9 GKAOGPIIYCISHV-UHFFFAOYSA-N [26] Nitrogen Nitrogen N2 Cryogen 7727-37-9 IJGRMHOSHXDMSA-UHFFFAOYSA-N [26] Nonane n-Nonane C9H20 n-Alkane 111-84-2 BKIMMITUMNQMOS-UHFFFAOYSA-N [26] Octane n-Octane C8H18 n-Alkane 111-65-9 TVMXDCGIABBOFY-UHFFFAOYSA-N [26] Oxygen Oxygen O2 Cryogen 7782-44-7 MYMOFIZGZYHOMD-UHFFFAOYSA-N [26] o-Xylene 1,2-Dimethylbenzene C8H10 Aromatic 95-47-6 CTQNGGLPUBDAKN-UHFFFAOYSA-N [24] Pentane n-Pentane C5H12 n-Alkane 109-66-0 OFBQJSOFQDEBGM-UHFFFAOYSA-N [26] Propane Propane C3H8 n-Alkane 74-98-6 ATUOYWHBWRKTHZ-UHFFFAOYSA-N [26] Propylene Propene C3H6 n-Alkene 115-07-1 QQONPFPTGQHPMA-UHFFFAOYSA-N [26] p-Xylene 1,4-Dimethylbenzene C8H10 Aromatic 106-42-3 URLKBWYHVLBVBO-UHFFFAOYSA-N [24] R1123 Trifluoroethylene C2HF3 Halocb 359-11-5 MIZLGWKEZAPEFJ-UHFFFAOYSA-N [37] [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] 1 3 Page 7 of 46  110 International Journal of Thermophysics (2023) 44:110 Table 1   (continued) Name Full name Formula Family CAS no. Standard InChI key References R115 Chloropentafluoroethane C2ClF5 Halocb 76-15-3 RFCAUADVODFSLZ-UHFFFAOYSA-N [26] R1234yf 2,3,3,3-Tetrafluoroprop-1-ene C3F4H2 Halocb 754-12-1 FXRLMCRCYDHQFW-UHFFFAOYSA-N [26] R1234ze(E) trans-1,3,3,3-Tetrafluoropropene C3F4H2 Halocb 29,118-24-9 CDOOAUSHHFGWSA-OWOJBTEDSA-N [24] R125 Pentafluoroethane C2HF5 Halocb 354-33-6 GTLACDSXYULKMZ-UHFFFAOYSA-N [26] R134a 1,1,1,2-Tetrafluoroethane C2H2F4 Halocb 811-97-2 LVGUZGTVOIAKKC-UHFFFAOYSA-N [26] R143a 1,1,1-Trifluoroethane C2H3F3 Halocb 420-46-2 UJPMYEOUBPIPHQ-UHFFFAOYSA-N [24] R152a 1,1-Difluoroethane C2H4F2 Halocb 75-37-6 NPNPZTNLOVBDOC-UHFFFAOYSA-N [26] R22 Chlorodifluoromethane CHClF2 Halocb 75-45-6 VOPWNXZWBYDODV-UHFFFAOYSA-N [26] R227ea 1,1,1,2,3,3,3-Heptafluoropropane C3HF7 Halocb 431-89-0 YFMFNYKEUDLDTL-UHFFFAOYSA-N [26] R32 Difluoromethane CH2F2 Halocb 75-10-5 RWRIWBAIICGTTQ-UHFFFAOYSA-N [26] RC318 Octafluorocyclobutane C4F8 Halocb 115-25-3 BCCOBQSFUDVTJQ-UHFFFAOYSA-N [26] Toluene Methylbenzene C7H8 Aromatic 108-88-3 YXFVVABEGXRONW-UHFFFAOYSA-N [26] Water Water H2O Water 7732-18-5 XLYOFNOQVPJJNP-UHFFFAOYSA-N [39] 1 3 110  Page 8 of 46 International Journal of Thermophysics (2023) 44:110 Table 2   Summary of surface tension binary mixture data Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 1974 jai sin 0 [40] DROPW 0.6–0.7 Ethylbenzene Cyclohexane 28 298–308 0.0–1.0 2014 pra cow 0 [41] DROPSH 0.4 Ethylbenzene Hexadecane 9 294 0.0–1.0 1978 dhi mah 0 [42] CAPRISE 0.7–0.8 p-Xylene Chlorobenzene 18 293–303 0.1–0.9 1972 mah cho 0 [43] CAPRISE 0.1–0.2 p-Xylene Pentane 7 288 0.14–0.82 2010 dom ril 0 [44] DROPV 0.1–0.2 p-Xylene Hexane 16 298 0.12–0.95 1974 jai sin 0 [40] DROPW 0.6–0.7 p-Xylene Cyclohexane 28 298–308 0.0–1.0 2013 gay cas 0 [45] DROPV 0.2–0.3 p-Xylene Octane 12 308 0.05–0.95 2009 mos cas 0 [46] DROPV 0.3 p-Xylene Decane 11 298 0.10–0.95 2013 gay cas 0 [45] DROPV 0.3 p-Xylene Decane 11 308 0.10–0.95 2004 ouy lu 3 [47] DROPSH 0.3 p-Xylene Ethanol 11 298 0.0–1.0 1992 wan nar 1 [48] CAPRISE 0.6–0.7 p-Xylene Methanol 44 293–318 0.0–1.0 2004 ouy yan 0 [49] DROPSH 0.3 p-Xylene Acetone 9 298 0.10–0.90 2013 gay cas 0 [45] DROPV 0.3 p-Xylene DMC 10 308 0.06–0.95 1978 cal mcl 0 [50] CAPRISE 0.1 Butane RC318 24 234–254 0.0–1.0 1985 hsu nag 0 [51] DROPSH 0.1–0.2 Butane Carbon dioxide 42 319–378 0.15–0.91 2005 goz dan 0 [52] OTHER 0.02 Butane methane 1 311 0.49 1914 wor & 1 [53] UNKN 0.5–0.6 Dichloroethane Benzene 13 286–343 0.0–1.0 1978 dhi mah 0 [42] CAPRISE 0.7–0.8 m-Xylene Chlorobenzene 18 293–303 0.1–0.9 1972 mah cho 0 [43] CAPRISE 0.1–0.2 m-Xylene Pentane 9 288 0.12–0.89 2017 tah & 0 [54] DROPSH 0.3–0.4 m-Xylene Pentane 11 293 0.0–1.0 2006 dom seg 0 [55] DROPV 0.1–0.2 m-Xylene Hexane 18 298 0.04–0.95 2017 tah & 0 [54] DROPSH 0.3–0.4 m-Xylene Hexane 11 293 0.0–1.0 1974 jai sin 0 [40] DROPW 0.6–0.7 m-Xylene Cyclohexane 28 298–308 0.0–1.0 2017 tah & 0 [54] DROPSH 0.3–0.4 m-Xylene Octane 11 293 0.0–1.0 2017 tah & 0 [54] DROPSH 0.3–0.4 m-Xylene Heptane 11 293 0.0–1.0 2004 ouy lu 3 [47] DROPSH 0.3 m-Xylene Ethanol 11 298 0.0–1.0 2004 ouy yan 0 [49] DROPSH 0.3 M-Xylene Acetone 9 298 0.10–0.90 International Journal of Thermophysics (2023) 44:110 Page 9 of 46  110 able 2   (continued) eference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 929 ham and 0 [56] CAPRISE 0.2 m-Xylene Benzene 5 298 0.40–1.0 917 mor gri 0 [57] DROPW 0.2 Toluene Chlorobenzene 6 283–313 0.26–0.81 972 mah cho 0 [43] CAPRISE 0.1 Toluene Pentane 8 288 0.18–0.79 970 lam ben 0 [58] BUBBLEP 0.7 Toluene Cyclohexane 11 298 0.11–0.90 958 lin van 1 [59] OTHER 8–10 Toluene Octane 17 303–398 0.0–1.0 021 vak alw 0 [60] RINGTE 0.5 Toluene Nonane 44 298–313 0.0–1.0 003 kah wad 0 [61] DROPSH 0.2–0.3 Toluene Heptane 34 288–328 0.0–1.0 970 lam ben 0 [58] BUBBLEP 0.6–0.7 Toluene Cyclopentane 10 298 0.10–0.89 014 pra cow 0 [41] DROPSH 0.4 Toluene Hexadecane 8 294 0.0–1.0 021 vak alw 0 [60] RINGTE 0.5 Toluene Hexadecane 44 298–313 0.0–1.0 974 mye cle 0 [62] BUBBLEP 0.3 Toluene Ethanol 10 303 0.0–1.0 993 sha muk 0 [63] DROPW 0.8–1.1 Toluene Ethanol 5 298 0.1–0.9 982 sin lar 0 [64] CAPRISE 0.1 Toluene Methanol 11 308 0.0–1.0 992 wan nar 1 [48] CAPRISE 0.5–0.7 Toluene Methanol 44 293–318 0.0–1.0 003 kah wad 1 [65] DROPSH 0.2–0.3 Toluene Acetone 55 288–328 0.0–1.0 007 end kah 0 [66] DROPSH 0.5–0.6 Toluene Acetone 55 288–328 0.0–1.0 917 mor gri 0 [57] DROPW 0.3–0.6 Toluene Benzene 6 284–313 0.22–0.72 970 kon lya 1 [67] BUBBLEP 0.3–0.4 Toluene Benzene 21 293–333 0.0–1.0 972 mah cho 0 [43] CAPRISE 0.1–0.2 Chlorobenzene Pentane 7 288 0.18–0.84 978 dhi mah 0 [42] CAPRISE 0.6–0.8 Chlorobenzene Cyclohexane 18 293–303 0.1–0.9 917 mor gri 0 [57] DROPW 0.2 Chlorobenzene Acetone 1 288 0.34 917 mor gri 0 [57] DROPW 0.4–0.6 Chlorobenzene Benzene 6 283–313 0.21–0.62 978 dhi mah 0 [42] CAPRISE 0.7–0.8 Chlorobenzene Benzene 17 293–303 0.1–0.9 978 dhi mah 0 [42] CAPRISE 0.7–0.8 Chlorobenzene o-Xylene 18 293–303 0.1–0.9 972 mah cho 0 [43] CAPRISE 0.1–0.2 Pentane Cyclohexane 7 288 0.15–0.81 992 abd ada 0 [68] CAPRISE 0.1–1.2 Pentane Heptane 61 303–538 0.0–1.0 3 110  Page 10 of 46 International Journal of Thermophysics (2023) 44:110 able 2   (continued) Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 010 moh ras 0 [69] BUBBLEP 0.2 Pentane Heptane 38 293–323 0.17–0.97 011 moh & 0 [70] CAPRISE 0.1–0.2 Pentane Hexadecane 35 293–323 0.2–0.9 972 mah cho 0 [43] CAPRISE 0.1–0.2 Pentane Benzene 7 288 0.09–0.81 018 sat coo 0 [71] DROPSH 0.1–0.2 Pentane Methane 7 313 0.50–0.95 963 cle cha 0 [72] BUBBLEP 0.2–0.3 Hexane Cyclohexane 19 298–308 0.0–1.0 967 rid but 0 [73] RINGTE 0.6–0.7 Hexane Cyclohexane 8 293 0.0–1.0 968 sch cle 1 [74] BUBBLEP 0.5–0.7 Hexane Dodecane 21 298–313 0.0–1.0 019 kol yan 0 [75] SLS 0.1–0.2 Hexane Carbon dioxide 5 303 0.25–1.0 994 pap pan 1 [76] CAPRISE 0.1 Hexane Ethanol 20 298 0.0–1.0 000 jim cas 0 [77] DROPV 0.1 Hexane Ethanol 17 298 0.04–0.93 007 gin vil 1 [78] DROPV 0.3 Hexane Ethanol 77 283–313 0.07–0.91 935 tri & 0 [79] UNKN 0.1 Hexane Methanol 4 295 0.0–1.0 970 ram pat 0 [80] UNKN 0.5–0.7 Hexane Methanol 22 303–318 0.0–1.0 966 sch ran 0 [81] BUBBLEP 0.5–0.6 Hexane Benzene 23 298–313 0.0–1.0 967 rid but 0 [73] RINGTE 0.6–0.8 Hexane Benzene 8 293 0.0–1.0 002 gom mej 0 [82] DROPW 0.6 Cyclohexane Decane 6 298 0.0–1.0 003 kah wad 1 [65] DROPSH 0.2–0.3 Cyclohexane Heptane 55 288–328 0.0–1.0 001 gom mej 0 [83] RINGTE 0.4–0.5 Cyclohexane Isooctane 126 298–323 0.0–1.0 935 tri & 0 [79] UNKN 0.1 Cyclohexane Ethanol 6 295 0.0–1.0 974 mye cle 0 [62] BUBBLEP 0.3 Cyclohexane Ethanol 11 303 0.0–1.0 003 kah wad 1 [65] DROPSH 0.2–0.3 Cyclohexane Acetone 44 288–318 0.0–1.0 008 mej seg 1 [84] BUBBLEP 0.3 Cyclohexane Acetone 10 303 0.06–0.95 929 ham and 0 [56] CAPRISE 0.2 Cyclohexane Benzene 5 298 0.30–0.62 967 rid but 0 [73] RINGTE 0.7–0.8 Cyclohexane Benzene 9 293 0.0–1.0 968 sur ram 0 [85] CAPRISE 0.1 Cyclohexane Benzene 15 293–303 0.09–0.87 970 kon lya 1 [67] BUBBLEP 0.3–0.4 Cyclohexane Benzene 39 293–333 0.0–1.0 International Journal of Thermophysics (2023) 44:110 Page 11 of 46  110 able 2   (continued) Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 970 lam ben 0 [58] BUBBLEP 0.6–0.8 Cyclohexane Benzene 28 293–303 0.10–0.89 974 jai sin 0 [40] DROPW 0.6–0.8 Cyclohexane o-Xylene 28 298–308 0.0–1.0 019 abr bag 0 [86] RINGTE 0.5–0.7 DEA Ethanol 13 313 0.0–1.0 019 abr bag 0 [86] RINGTE 0.5–0.7 DEA Methanol 14 313 0.0–1.0 994 rin oel 0 [87] RINGTE 1.5–1.7 DEA Water 12 293–353 0.02–0.07 996 vaz alv 0 [88] OTHER 0.3–0.5 DEA Water 66 298–323 0.0–1.0 998 alv ren 0 [89] DROPW 0.8 DEA Water 6 298–323 0.15 001 agu tre 0 [90] DROPSH 1.3–1.5 DEA Water 21 293–363 0.02–0.07 003 alv can 0 [91] DROPSH 0.5 DEA Water 6 298–323 0.15 014 fu du 0 [92] OTHER 2.0 DEA Water 12 293–323 0.04–0.07 018 dey das 0 [93] DROPSH 0.8 DEA Water 9 313–333 0.02–0.07 018 fu xie 0 [94] OTHER 0.6 DEA Water 15 303–323 0.0–1.0 018 sho & 0 [95] RINGTE 0.6–0.9 DEA Water 65 298–348 0.0–1.0 015 lop igl 0 [96] DROPV 0.1 Octane Isooctane 55 293–313 0.0–1.0 003 seg del 0 [97] DROPV 0.2 Octane Ethanol 17 298 0.07–0.92 011 mej car 0 [98] BUBBLEP 0.3 Octane Ethanol 31 298–318 0.04–0.90 016 and mar 0 [99] DROPSH 0.3 Octane o-Xylene 11 298 0.05–0.95 013 gay cas 0 [45] DROPV 0.2–0.3 Octane DMC 12 308 0.05–0.95 021 vak alw 0 [60] RINGTE 0.4–0.5 Nonane Benzene 44 298–313 0.0–1.0 016 and mar 0 [99] DROPSH 0.3–0.4 Nonane o-Xylene 11 298 0.05–0.95 020 ond sar 0 [100] DROPV 0.3 Methyl palmitate Ethanol 1 298 0.04 964 eva cle 0 [101] BUBBLEP 0.2–0.3 Dodecane Isooctane 9 303 0.0–1.0 022 yan wu 0 [102] DROPSH 0.2–0.4 Dodecane Hexadecane 36 298–573 0.31–0.80 011 mej car 0 [98] BUBBLEP 0.3 Dodecane Ethanol 22 298–303 0.05–0.95 966 sch ran 0 [81] BUBBLEP 0.5–0.6 Dodecane Benzene 23 298–313 0.0–1.0 018 pra mun 0 [103] DROPSH 0.3 Dodecane Methylcyclohexane 9 293 0.1–0.9 110  Page 12 of 46 International Journal of Thermophysics (2023) 44:110 able 2   (continued) Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 010 bi li 0 [104] CAPRISE 0.4 Dimethyl ether Propane 114 243–333 0.29–0.69 986 nag rob 0 [105] DROPW 0.1–0.7 Decane Carbon dioxide 41 344–378 0.10–0.51 001 sha rob 0 [106] DROPSH 0.1–0.7 Decane Carbon dioxide 23 344 0.10–0.89 002 rol cac 0 [107] RINGTE 0.3–0.4 Decane Heptane 25 293–333 0.0–1.0 002 gom mej 0 [82] DROPW 0.6 Decane Isooctane 6 298 0.0–1.0 002 rol cac 0 [107] RINGTE 0.4 Decane Hexadecane 25 293–333 0.0–1.0 005 que cac 0 [108] OTHER 0.3–0.4 Decane Docosane 19 313–343 0.2–0.8 011 mej car 0 [98] BUBBLEP 0.3 Decane Ethanol 32 303–318 0.02–0.97 016 and mar 0 [99] DROPSH 0.4 Decane o-Xylene 11 298 0.05–0.95 013 gay cas 0 [45] DROPV 0.3 Decane DMC 11 308 0.05–0.95 964 gri rud 0 [109] CAPRISE 0.1 Hydrogen Deuterium 67 16–20 0.30–0.96 967 bla kro 0 [110] CAPRISE 0.1 Hydrogen Argon 21 87–140 0.0–0.05 019 abr bag 0 [86] RINGTE 0.5–0.7 MEA Ethanol 14 313 0.0–1.0 020 abr bag 0 [111] RINGTE 0.5–0.7 MEA Ethanol 12 303 0.27–0.98 019 abr bag 0 [86] RINGTE 0.5–0.7 MEA Methanol 12 313 0.0–1.0 020 abr bag 0 [111] RINGTE 0.5–0.7 MEA Methanol 10 303 0.28–0.99 981 ano & 5 [112] CAPRISE 0.9–1.1 MEA Water 20 303–393 0.03–0.05 997 vaz alv 0 [113] OTHER 0.4–0.6 MEA Water 83 298–323 0.0–1.0 998 alv ren 0 [89] DROPW 1.5–1.6 MEA Water 5 298–323 0.23 012 han jin 0 [114] DROPSH 0.6–0.8 MEA Water 44 303–333 0.0–1.0 013 jay jay 0 [115] DROPV 1.8 MEA Water 4 313–343 0.54 013 jay wee 0 [116] DROPV 2.5–2.9 MEA Water 24 303–333 0.07–0.41 014 fu du 0 [92] OTHER 2.0 MEA Water 12 293–323 0.07–0.11 018 fu xie 0 [94] OTHER 0.6 MEA Water 15 303–323 0.0–1.0 018 sho & 0 [95] RINGTE 0.6–0.9 MEA Water 66 298–348 0.0–1.0 014 lun cow 0 [117] DROPSH 0.3–0.4 Heptane Isooctane 4 294 0.0–1.0 International Journal of Thermophysics (2023) 44:110 Page 13 of 46  110 Table 2   (continued) Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 2015 lop igl 0 [96] DROPV 0.1 Heptane Isooctane 55 293–313 0.0–1.0 958 koe vil 0 [118] CAPRISE 0.1–0.7 Heptane Hexadecane 6 293–303 0.0–1.0 2002 rol cac 0 [107] RINGTE 0.3–0.4 Heptane Hexadecane 25 293–333 0.0–1.0 2011 moh & 0 [70] CAPRISE 0.2 Heptane Hexadecane 35 293–323 0.2–0.9 2003 que sil 0 [119] RINGTE 0.6–0.8 Heptane Docosane 12 313–343 0.25–0.75 994 pap pan 1 [76] CAPRISE 0.1 Heptane Ethanol 22 298 0.0–1.0 2016 yue liu 0 [120] OTHER 0.2 Heptane Ethanol 66 293–318 0.0–1.0 970 kon lya 1 [67] BUBBLEP 0.3–0.4 Heptane Benzene 27 293–333 0.0–1.0 993 zho zhu 0 [121] BUBBLEP 0.5–0.7 Heptane Benzene 20 293–303 0.08–0.90 970 lam ben 0 [58] BUBBLEP 0.6–0.7 Cyclopentane Benzene 9 298 0.11–0.90 996 hei sch 0 [122] CAPRISE 0.-0.2 R125 R143a 21 223–333 0.28–0.79 999 oka shi 0 [123] CAPRISE 0.2 R125 R143a 7 273–303 0.41 2001 fro wil 1 [124] OTHER 0.2 R125 R143a 10 243–333 0.41 996 hei sch 0 [122] CAPRISE 0–0.2 R125 R32 8 223–333 0.27–0.77 999 oka shi 0 [123] CAPRISE 0.2 R125 R32 18 273–313 0.31–0.35 2003 dua lin 0 [125] CAPRISE 0.2 R125 R32 236 253–333 0.18–0.58 996 hei sch 0 [122] CAPRISE 0.1–0.2 R125 R152a 21 223–333 0.16–0.69 2009 bi zha 1 [126] CAPRISE 0.4 R125 R152a 54 243–328 0.06–0.19 996 hei sch 0 [122] CAPRISE 0–0.2 R125 R134a 21 223–333 0.24–0.75 996 hei sch 0 [122] CAPRISE 0.1–0.2 R143a R134a 21 223–333 0.23–0.72 2004 lin dua 0 [127] CAPRISE 0.2 R143a R134a 105 257–329 0.29–0.79 2003 lin dua 2 [128] CAPRISE 0.1 R143a R227ea 241 253–333 0.39–0.85 2016 yue liu 0 [120] OTHER 0.2 Isooctane Ethanol 44 288–318 0.0–1.0 964 eva cle 0 [101] BUBBLEP 0.2–0.3 Isooctane Benzene 9 303 0.0–1.0 2015 zha li 3 [129] DROPV 0.2 Isooctane Methylcyclohexane 44 293–308 0.0–1.0 2021 vak alw 0 [60] RINGTE 0.5 Hexadecane Benzene 44 298–313 0.0–1.0 110  Page 14 of 46 International Journal of Thermophysics (2023) 44:110 able 2   (continued) Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 018 pra mun 0 [103] DROPSH 0.3 Hexadecane Methylcyclohexane 9 293 0.1–0.90 969 mye cle 0 [130] BUBBLEP 0.2–0.3 Hexadecane D4 9 303 0.0–1.0 929 ham and 0 [56] CAPRISE 0.1–0.2 Diethyl ether Benzene 4 298 0.24–1.0 965 spr pra 1 [131] CAPRISE 0.2 Carbon monoxide Nitrogen 10 84 0.0–1.0 970 kon lya 1 [67] BUBBLEP 0.3 Ethanol Methanol 39 293–333 0.0–1.0 929 ham and 0 [56] CAPRISE 0.1 Ethanol Acetone 5 298 0.0–1.0 902 ram ast 0 [132] CAPRISE 0.2–0.8 Ethanol Benzene 39 283–351 0.0–1.0 907 rit & 0 [133] UNKN 0.1 Ethanol Benzene 5 298 0.0–1.0 917 mor sca 0 [134] UNKN 0.1–0.2 Ethanol Benzene 13 298–318 0.0–1.0 929 ham and 0 [56] CAPRISE 0.1–0.2 Ethanol Benzene 4 298 0.42–1.0 935 tri & 0 [79] UNKN 0.1 Ethanol Benzene 8 295 0.0–1.0 974 mye cle 0 [62] BUBBLEP 0.3 Ethanol Benzene 7 303 0.0–1.0 885 tra & 0 [135] UNKN 0.1 Ethanol Water 7 288 0.01–1.0 903 des & 0 [136] UNKN 0.2–0.7 Ethanol Water 11 288 0.0–1.0 913 mor nei 0 [137] DROPW 0.1–0.5 Ethanol Water 36 273–303 0.0–1.0 922 bir & 0 [138] DROPW 0.3–0.6 Ethanol Water 15 298 0.0–1.0 936 ern wat 0 [139] CAPRISE 0.1–0.2 Ethanol Water 9 298 0.04–0.78 937 val hoh 0 [140] UNKN 0.1–0.5 Ethanol Water 44 293–323 0.0–0.88 940 bon bym [141] CAPRISE 0.2–0.5 Ethanol Water 42 293–362 0.01–0.83 950 sta guy 0 [142] RINGTE 1 Ethanol Water 11 298 0.0–0.85 951 tei gor 0 [143] BUBBLEP 0.2–0.8 Ethanol Water 200 263–333 0.0–1.0 968 efr & 1 [144] BUBBLEP 0.5–1.4 Ethanol Water 54 283–333 0.02–1.0 986 wan jey 0 [145] RINGTE 0.5–1.2 Ethanol Water 5 303 0.0–1.0 988 kal bid 0 [146] BUBBLEP 0.2–0.4 Ethanol Water 12 351–369 0.01–0.90 995 vaz alv 0 [147] RINGTE 0.3–0.9 Ethanol Water 98 293–323 0.0–1.0 005 bel her 0 [148] DROPW 0.2–0.3 Ethanol Water 11 298 0.0–1.0 International Journal of Thermophysics (2023) 44:110 Page 15 of 46  110 able 2   (continued) eference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 009 max & 0 [149] DROPV 0.2–0.3 Ethanol Water 13 298 0.0–1.0 016 lud kus 0 [150] BUBBLEP 0.3 Ethanol Water 1 293 0.04 018 gon pal 0 [151] RINGTE 2 Ethanol Water 6 298 0.27–0.60 019 raz hal 0 [152] RINGTE 0.5–0.9 Ethanol Water 10 298–313 0.0–0.09 020 gon pan 0 [153] OTHER 0.4 Ethanol Water 4 298 0.28–0.61 020 kho rah 0 [154] DROPSH 0.8 Ethanol Water 10 298 0.0–0.002 021 gom nav [155] OTHER 0.3 Ethanol Water 16 293–323 0.04–0.16 012 bag ami 0 [156] RINGTE 0.5–1.0 Ethanol Heavy water 84 288–318 0.001–0.86 004 ouy lu 3 [47] DROPSH 0.3 Ethanol o-Xylene 11 298 0.0–1.0 974 mye cle 0 [62] BUBBLEP 0.3 Ethanol Methylcyclohexane 10 303 0.0–1.0 003 azi hem 0 [157] RINGTE 0.3–0.7 Ethanol Ethylene glycol 56 293–323 0.0–1.0 973 cam kar 0 [158] UNKN 0.7 Methanol Acetone 12 298 0.0–1.0 982 sin lar 0 [64] CAPRISE 0.1 Methanol Acetone 8 308 0.0–1.0 917 mor sca 0 [134] UNKN 0.2 Methanol Benzene 14 273–303 0.0–1.0 933 sha muk 0 [63] DROPW 0.9–1.1 Methanol Benzene 5 298 0.1–0.9 885 tra & 0 [135] UNKN 0.1 Methanol Water 6 288 0.01–1.0 913 mor nei 0 [137] DROPW 0.5–0.6 Methanol Water 26 273–303 0.0–1.0 937 val hoh 0 [140] UNKN 0.1–0.4 Methanol Water 31 291–323 0.05–1.0 951 tei gor 0 [143] BUBBLEP 0.2–0.7 Methanol Water 110 263–323 0.0–1.0 958 uch mat 0 [159] OTHER 0.5–1.8 Methanol Water 76 303–363 0.0–1.0 968 efr & 1 [144] CAPRISE 0.5–1.0 Methanol Water 30 283–333 0.17–1.0 988 kal bid 0 [146] BUBBLEP 0.3–0.5 Methanol Water 11 339–356 0.17–0.95 995 vaz alv 0 [147] RINGTE 0.3–0.9 Methanol Water 98 293–323 0.0–1.0 009 max & 0 [149] DROPV 0.2–0.3 Methanol Water 13 298 0.0–1.0 012 bag ami 0 [156] RINGTE 0.5–0.9 Methanol Heavy water 64 288–318 0.00–0.82 929 ham and 0 [56] CAPRISE 0.1–0.2 Acetone Benzene 5 298 0.30–1.0 3 110  Page 16 of 46 International Journal of Thermophysics (2023) 44:110 able 2   (continued) Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 970 shi & 1 [160] CAPRISE 4.7–5.7 Acetone Benzene 10 298 0.0–1.0 988 ron lu 0 [161] BUBBLEP 0.6–0.7 Acetone Benzene 18 303 0.0–1.0 917 mor sca 0 [134] UNKN 0.2–0.3 Acetone Water 78 273–318 0.0–1.0 932 ern lit 0 [162] CAPRISE 0.2 Acetone Water 9 298 0.03–0.74 951 tei gan 0 [163] BUBBLEP 0.2–0.6 Acetone Water 81 273–313 0.0–1.0 957 how mca [164] CAPRISE 0.1–0.4 Acetone Water 81 288–343 0.0–1.0 970 kon lya 1 [67] BUBBLEP 0.3–0.9 Acetone Water 17 293 0.0–1.0 976 tor pog 0 [165] BUBBLEP 0.2–0.5 Acetone Water 48 298–343 0.0–1.0 988 ron lu 0 [161] BUBBLEP 0.6–1.9 Acetone Water 19 303 0.0–1.0 007 end kah 0 [66] DROPSH 0.3–0.7 Acetone Water 70 288–328 0.0–1.0 004 ouy yan 0 [49] DROPSH 0.3 Acetone o-Xylene 8 298 0.10–0.80 970 lam ben 0 [58] BUBBLEP 0.8 Benzene o-Xylene 8 298 0.10–0.79 013 bai kav 0 [166] CAPRISE 0.1–1.7 Methane Ethane 70 93–283 0.0–1.0 017 sen hug 0 [167] CAPRISE 0.7 Methane Propane 27 272–303 0.0–0.55 960 bla & 0 [168] CAPRISE 0.3–0.5 Methane Nitrogen 33 76–90 0.29–0.91 965 spr pra 1 [131] CAPRISE 0.2–0.5 Methane Nitrogen 12 91 0.0–1.0 966 fuk bel 0 [169] CAPRISE 0.1–0.6 Methane Krypton 35 110–118 0.18–0.67 960 bla & 0 [168] CAPRISE 0.4–0.6 Methane Argon 28 84–111 0.29–1.0 009 tan hig 2 [170] CAPRISE 0.4 Propane R32 99 280–300 0.00–1.00 010 zha bi 0 [171] CAPRISE 0.2 Propane R152a 51 248–328 0.27–0.59 996 hei sch 0 [122] CAPRISE 0.1–0.2 R32 R134a 17 223–333 0.23–0.72 003 yua hon 0 [172] CAPRISE 0.2 R32 R134a 300 254–334 0.35–0.86 021 liu kon 0 [173] CAPRISE 0.2–0.3 R32 R1123 37 266–307 0.48–0.87 005 lin dua 0 [174] CAPRISE 0.3 R32 R227ea 412 252–334 0.54–0.90 016 cui bi 0 [175] SLS 0.1 R32 R1234yf 24 293–348 0.52–1.0 021 liu kon 0 [173] CAPRISE 0.1–0.2 R32 R1234yf 36 267–333 0.27–0.89 International Journal of Thermophysics (2023) 44:110 Page 17 of 46  110 Table 2   (continued) Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 2013 tan hig 0 [176] CAPRISE 0.6 R32 R1234ze(E) 26 273–323 0.69 2016 cui bi 0 [175] SLS 0.1 R32 R1234ze(E) 26 293–348 0.30–1.0 996 hei sch 0 [122] CAPRISE 0.1–0.2 R152a R134a 21 223–333 0.24–0.71 969 ano & 2 [177] OTHER 1.0 R22 R115 1 298 0.63 959 bla rud 0 [178] CAPRISE 0.3–0.6 Nitrogen Oxygen 34 61–88 0.1–0.9 994 ost ost 1 [179] CAPRISE 0.3–0.5 Nitrogen Oxygen 88 55–78 0.0–1.0 2008 bai kav 0 [180] CAPRISE 0.1–0.2 Nitrogen Oxygen 61 80–132 0.0–1.0 2006 kav and 0 [181] CAPRISE 0.05–1.3 Helium Argon 33 108–140 0.0–0.01 2006 kav and 0 [181] CAPRISE 0.05–0.2 Neon Argon 27 111–140 0.0–0.04 2004 bai kav 0 [182] CAPRISE 0.1–0.3 Nitrogen Helium 38 90–118 0.97–1.0 960 bla & 0 [168] CAPRISE 0.3–0.4 Nitrogen Argon 21 69–86 0.02–0.7 965 spr pra 1 [131] CAPRISE 0.2–0.3 Nitrogen Argon 19 84 0.0–1.0 946 cle & 0 [183] RINGTE 1 Water Ethylene glycol 2 298 0.0–1.0 971 nak mat 0 [184] CAPRISE 0.3 Water Ethylene glycol 18 303 0.0–1.0 981 won chu [185] RINGTE 1–1.2 Water Ethylene glycol 4 298 0.8–1.0 991 hok che 0 [186] BUBBLEP 0.4–0.6 Water Ethylene glycol 174 295–471 0.0–0.95 996 hor fuk 0 [187] CAPRISE 0.5–0.8 Water Ethylene glycol 44 253–298 0.0–1.0 998 tsi mol 0 [188] RINGTE 1.6–2.4 Water Ethylene glycol 64 283–323 0.0–1.0 2004 hab hov 0 [189] RINGTE 1.4–2.0 Water Ethylene glycol 15 298 0.80–0.99 2008 zha zha 2 [190] DROPV 1.1–1.4 Water Ethylene glycol 48 308–323 0.0–1.0 2011 raf bag 0 [191] RINGTE 0.6–0.9 Water Ethylene glycol 54 283–308 0.10–0.99 2014 tiw son 0 [192] OTHER 0.4 Water Ethylene glycol 4 298 0.88–1.0 959 bla rud 0 [178] BUBBLEP 0.4–1.0 Oxygen Argon 28 69–88 0.19–0.9 965 saj oku 0 [193] RINGTE 0.3 Oxygen Argon 36 79–88 0.0–1.0 2016 bi cui 0 [194] SLS 0.1 R134a R1234yf 23 293–363 0.32–0.81 2016 bi cui 0 [194] SLS 0.1 R134a R1234ze(E) 9 293–369 0.44 3 International Journal of Thermophysics (2023) 44:110 110  Page 18 of 46 p y 1987 nad & 0 [196] UNKN 0–0.4 Krypton Argon 60 120–200 0.0–1.0 1994 sul bai 0 [197] CAPRISE 0.1–0.8 Krypton Argon 40 120–193 0.0–1.0 1958 wat van 0 [195] RINGTE 0.5 MD4M D5 3 293 0.26–0.66 1958 wat van 0 [195] RINGTE 0.5 MD3M D5 1 293 0.5 2021 liu kon 0 [173] CAPRISE 0.2 R1123 R1234yf 39 234–312 0.11–0.73 BUBBLEP maximum bubble pressure; CAPRISE capillary rise; DROPSH pendant drop shape; DROPV drop volume; DROPW drop weight; OTHER other; RINGTE ring tensiometer; SLS surface light scattering; UNKN unknown 1 3 Table 2   (continued) Reference code Method Unc. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 1958 wat van 0 [195] RINGTE 0.5 D4 MD4M 2 293 0.39–0.78 1958 wat van 0 [195] RINGTE 0.5 D4 MD2M 3 293 0.3–0.7 1987 nad & 0 [196] UNKN 0–0.4 Krypton Argon 60 120–200 0.0–1.0 1994 sul bai 0 [197] CAPRISE 0.1–0.8 Krypton Argon 40 120–193 0.0–1.0 1958 wat van 0 [195] RINGTE 0.5 MD4M D5 3 293 0.26–0.66 1958 wat van 0 [195] RINGTE 0.5 MD3M D5 1 293 0.5 2021 liu kon 0 [173] CAPRISE 0.2 R1123 R1234yf 39 234–312 0.11–0.73 BUBBLEP maximum bubble pressure; CAPRISE capillary rise; DROPSH pendant drop shape; DROPV drop volume; DROPW drop weight; OTHER other; RINGTE ring tensiometer; SLS surface light scattering; UNKN unknown 2021 liu kon 0 [173] CAPRISE 0.2 R1123 R1234yf 39 234–312 0.11–0.73 BUBBLEP maximum bubble pressure; CAPRISE capillary rise; DROPSH pendant drop shape; DROPV drop volume; DROPW drop weight; OTHER other; RINGTE ring tensiometer; SLS surface light scattering; UNKN unknown 1 Table 2   (continued) Reference code Method Unc. (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 1958 wat van 0 [195] RINGTE 0.5 D4 MD4M 2 293 0.39–0.78 1958 wat van 0 [195] RINGTE 0.5 D4 MD2M 3 293 0.3–0.7 1987 nad & 0 [196] UNKN 0–0.4 Krypton Argon 60 120–200 0.0–1.0 1994 sul bai 0 [197] CAPRISE 0.1–0.8 Krypton Argon 40 120–193 0.0–1.0 1958 wat van 0 [195] RINGTE 0.5 MD4M D5 3 293 0.26–0.66 1958 wat van 0 [195] RINGTE 0.5 MD3M D5 1 293 0.5 2021 liu kon 0 [173] CAPRISE 0.2 R1123 R1234yf 39 234–312 0.11–0.73 BUBBLEP maximum bubble pressure; CAPRISE capillary rise; DROPSH pendant drop shape; DROPV drop volume; DROPW drop weight; OTHER other; RINGTE ring tensiometer; SLS surface light scattering; UNKN unknown 1 Table 2   (continued) Reference code Method Unc. 4.1  Mixtures with n‑Alkanes Table  3 summarizes the results for mixtures with n-alkanes, presenting results both for binary interaction parameters set to zero and for fitted binary interaction parameters. Figure 1 displays these results graphically. The mixtures considered in this section contain n-alkanes mixed only with nonpolar fluids (branched alkanes, naphthenes, cryogens, and ­CO2) except for four mixtures with polar aprotic fluids dimethyl ether, acetone, dimethyl carbonate, and octamethylcyclotetrasiloxane (D4). Excluded from these results are mixtures of n-alkanes with hydrogen bonding flu- ids, aromatics, or halocarbons; these mixtures are treated separately in later sections. The results in Table 3 are arranged by mixture classes. g y Overall, Fig. 1 and Table  3 show that without the use of binary interaction parameters, non-polar mixtures such as linear and branched alkanes, and linear and branched alkanes with naphthenes have average absolute percentage deviations of about 3 % or less. The propane/dimethyl ether mixture and the cyclohexane/acetone mixture also are represented very well without an interaction parameter. Mixtures of linear alkanes show increasing deviations as the mixtures become more asymmetric with respect to size, as has been discussed previously [199]. Figure 2 shows that the deviations of the parachor model for a series of mixtures of components of varying chain lengths (pentane, heptane, decane, and dodecane). Note that the full citations for the reference codes used in the figures are given in Table 2. The pentane/hexade- cane mixture has the largest size difference, and the largest deviation, reaching 2.5 mN·m−1, and this deviation can be reduced with the use of a fitted binary interaction parameter to 1 mN·m−1 indicating that even mixtures of linear alkanes that only have size differences can benefit from the use of a binary interaction parameter. The tem- peratures of the data covered 293 K to 598 K, the details for each data set are given in Table 2. Although we used a simple constant binary interaction parameter, Hugill and Van Welsenes [16] and Gasem et al. [200] pointed out that the binary interac- tion parameters are temperature dependent, and introducing temperature dependence in the interaction parameters could further reduce the deviations. [37] [26] [26] [24] [26] [24] [24] [24] [37] [26] [26] [24] [24] [24] [26] [26] [26] [26] [26] [24] [26] [26] [26] [24] [37] (mN·m−1) Fluid 1 Fluid 2 Npts T range (K) x1 range 1958 wat van 0 [195] RINGTE 0.5 D4 MD4M 2 293 0.39–0.78 1958 wat van 0 [195] RINGTE 0.5 D4 MD2M 3 293 0.3–0.7 1987 nad & 0 [196] UNKN 0–0.4 Krypton Argon 60 120–200 0.0–1.0 1994 sul bai 0 [197] CAPRISE 0.1–0.8 Krypton Argon 40 120–193 0.0–1.0 1958 wat van 0 [195] RINGTE 0.5 MD4M D5 3 293 0.26–0.66 1958 wat van 0 [195] RINGTE 0.5 MD3M D5 1 293 0.5 2021 liu kon 0 [173] CAPRISE 0.2 R1123 R1234yf 39 234–312 0.11–0.73 BUBBLEP maximum bubble pressure; CAPRISE capillary rise; DROPSH pendant drop shape; DROPV drop volume; DROPW drop weight; OTHER other; RINGTE ring tensiometer; SLS surface light scattering; UNKN unknown International Journal of Thermophysics (2023) 44:110 Page 19 of 46 110 the average absolute deviation, AAD = (∑│σcalc − σexp │)/n, expressed in mN·m−1, and AADMAX is the maximum value of the AAD. We do not include in the sta- tistics any points where the REFPROP program had convergence errors. Since the surface tension is zero at the critical point, some points near the critical region may have unusually large percentage deviations and it is more informative to examine the absolute deviation instead. Detailed results for each data set listed in Table 2 are pre- sented in the supplemental information in Appendix B, Table B1. The data are also provided in the supplemental information. Here we will discuss the results in terms of chemical families. 4.1  Mixtures with n‑Alkanes Mixtures of n-alkanes with dimethyl carbonate and hexadecane with a siloxane have larger deviations with the maximum absolute deviation of approximately 2 mN·m−1, and although the use of an interaction parameter can reduce the deviations, the parachor model does not perform quite as well for these systems (with a max AD of ~ 1 mN·m−1) as it does for the n-alkane/n-alkane systems that often have max 3 3 3 110  Page 20 of 46 International Journal of Thermophysics (2023) 44:110 able 3   Summary of results for alkane mixtures Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij -Alkane/br-alkane Decane/isooctane 6 3.68 0.79 0.96 1.37 0.29 0.65 − 0.026 -Alkane/br-alkane Dodecane/isooctane 9 1.22 0.26 0.47 0.16 0.03 0.08 − 0.010 -Alkane/br-alkane Heptane/isooctane 59 1.32 0.24 0.41 0.53 0.10 0.33 − 0.010 -Alkane/br-alkane Octane/isooctane 55 1.41 0.27 0.38 0.46 0.09 0.33 − 0.010 -Alkane/cryogen Methane/argon 28 2.72 0.42 1.22 2.34 0.36 0.85 0.017 -Alkane/cryogen Methane/krypton 35 1.30 0.19 0.31 0.35 0.05 0.18 0.008 -Alkane/cryogen Methane/nitrogen 45 9.71 1.08 2.24 3.68 0.42 0.88 0.067 -Alkane/ether Propane/dimethyl ether 114 1.37 0.11 0.36 1.38 0.11 0.37 0.001 -Alkane/n-alkane Butane/methane 1 18.18 0.15 0.15 0.00 0.00 0.00 − 0.089 -Alkane/n-alkane Decane/docosane 19 6.23 1.51 2.00 0.68 0.17 0.46 0.036 -Alkane/n-alkane Decane/heptane 25 1.86 0.39 0.61 0.90 0.19 0.61 − 0.012 -Alkane/n-alkane Decane/hexadecane 25 1.10 0.27 0.61 0.86 0.21 0.61 0.005 -Alkane/n-alkane Dodecane/hexadecane 36 3.04 0.40 0.92 2.86 0.28 0.74 0.011 -Alkane/n-alkane Heptane/docosane 12 5.72 1.27 2.13 2.03 0.49 1.70 0.030 -Alkane/n-alkane Heptane/hexadecane 66 2.22 0.50 0.91 0.98 0.22 0.91 0.015 -Alkane/n-alkane Hexane/dodecane 21 0.82 0.18 0.42 0.56 0.12 0.28 0.006 -Alkane/n-alkane Methane/ethane 70 8.05 0.56 2.47 3.29 0.19 1.70 0.074 -Alkane/n-alkane Methane/propane 27 5.69 0.12 0.24 5.67 0.12 0.24 − 0.001 -Alkane/n-alkane Pentane/heptane 99a 8.80 0.11 0.67 8.80 0.11 0.67 0.000 -Alkane/n-alkane Pentane/hexadecane 35 8.07 1.58 2.45 1.67 0.31 1.05 0.045 -Alkane/n-alkane Pentane/methane 7 54.34 1.35 1.70 10.43 0.16 0.36 0.227 -Alkane/naphthene Decane/cyclohexane 6 2.68 0.66 0.70 1.14 0.28 0.68 − 0.017 -Alkane/naphthene Dodecane/methylcyclohexane 9 2.52 0.62 0.88 0.46 0.11 0.37 − 0.018 -Alkane/naphthene Heptane/cyclohexane 55 1.44 0.30 0.64 0.56 0.12 0.35 0.011 Page 21 of 46  110 International Journal of Thermophysics (2023) 44:110 aSix points omitted from statistics due to REFPROP calculation problems Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij n-Alkane/naphthene Hexadecane/methylcyclohexane 9 0.67 0.18 0.57 0.72 0.19 0.54 0.002 n-Alkane/naphthene Hexane/cyclohexane 27 0.96 0.20 0.54 0.75 0.16 0.54 0.007 n-Alkane/naphthene Pentane/cyclohexane 7 2.02 0.42 0.62 0.45 0.09 0.16 0.013 n-Alkane/other Butane/carbon dioxide 42b 28.99 0.38 1.18 20.98 0.17 0.67 − 0.178 n-Alkane/other Hexane/carbon dioxide 5 28.23 2.62 5.28 1.37 0.15 0.33 0.186 n-Alkane/other Decane/carbon dioxide 64 468.69 0.82 1.97 358.68 0.49 1.08 0.081 n-Alkane/other Decane/DMC 11 3.40 0.78 1.62 2.04 0.47 0.91 0.023 n-Alkane/other Octane/DMC 12 5.22 1.11 2.22 2.41 0.52 1.23 0.036 n-Alkane/siloxane Hexadecane/D4 9 5.39 1.13 2.12 1.90 0.39 0.72 0.045 Naphthene/br-alkane Cyclohexane/isooctane 126 1.38 0.27 0.68 0.60 0.12 0.68 0.010 Naphthene/br-alkane Methylcyclohexane/isooctane 44 0.56 0.12 0.25 0.53 0.11 0.25 0.001 Naphthene/ketone Cyclohexane/acetone 54 0.94 0.21 0.48 0.83 0.19 0.51 0.002 1 3 International Journal of Thermophysics (2023) 44:110 110  Page 22 of 46 Fig. 1 3 4.1  Mixtures with n‑Alkanes 1   Summary of results for mixtures with alkanes Fig. 1   Summary of results for mixtures with alkanes AD of 0.7 mN·m−1 or less with an interaction parameter. There are three mixtures of methane with cryogens; methane/argon and methane/krypton were represented to within 3 % without an interaction parameter, but methane/nitrogen required a binary interaction parameter to achieve an AAPD of less than 4 %. Finally, the parachor model without interaction parameters does not adequately capture the mixture composition behavior of n-alkanes with carbon dioxide, and an interaction parameter is needed. This is illustrated in Fig. 3. The temperatures of the data covered 303 K to 378 K, the details for each data set are given in Table 2. Similar to what is indicated in Fig. 2, Fig. 3 shows the largest deviations occur for systems with the largest size differences, with decane/CO2 showing larger deviations 1 3 International Journal of Thermophysics (2023) 44:110 Page 23 of 46  110 Fig. 2   Deviations between the model and experimental data for mixtures of a series of n-alkanes with hexadecane Fig. 2   Deviations between the model and experimental data for mixtures of a series of n-alkanes with hexadecane than hexane/CO2 and butane/CO2. For the hexane/CO2 mixture without interac- tion parameters, the AAPD is near 30 % but can be reduced to less than 2 % (0.3 mN·m−1) with a binary interaction parameter. Note that the percentage deviations for decane/CO2 and butane/CO2 are still large even with a binary interaction param- eter, but this is because the data sets contain points approaching the critical region where the values of the surface tensions are small and the resulting percentage devi- ations are very large. 4.2  Mixtures with Alcohols Table 4 summarizes the results for mixtures with alcohols, and Fig. 4 displays these results graphically. We include only mixtures with methanol and ethanol; larger alcohols are not presently available in REFPROP. This group of mixtures includes alcohols with a variety of fluid types [alcohols, n-alkanes, branched alkanes, amines, aromatics, glycols, ketones, naphthenes, and a fatty acid methyl ester (FAME)]. Mixtures with water are excluded and treated in Sect. 4.3. For the binary mixture of methanol and ethanol, the parachor method represents the 3 3 International Journal of Thermophysics (2023) 44:110 110  Page 24 of 46 Fig. 3   Deviations between the model and experimental data for mixtures of a series of n-alkanes with carbon dioxide Fig. 3   Deviations between the model and experimental data for mixtures of a series of n-alkanes with carbon dioxide surface tension to essentially within experimental uncertainty, and an interaction parameter is unnecessary. Similarly, mixtures of methanol and ethanol with ace- tone are represented very well without an interaction parameter. Mixtures of alco- hols with aromatics and alcohols with linear alkanes have AAPD’s without binary interaction parameters ranging from roughly 1 % to 5 %, which can be reduced to less than 3 % with binary interaction parameters. In Fig. 4, for mixtures without binary interaction parameters, mixtures of alcohols with the amines MEA and DEA, and with ethylene glycol show large deviations. Of the components in mix- tures with methanol and ethanol, pure MEA, DEA, and ethylene glycol have the largest values of surface tension (approximately 45 mN·m−1 at 313 K) compared to less than about 27 mN·m−1 for the other fluids in Table 4, and approximately 21 mN·m−1 for pure methanol and ethanol. Maximum deviations can be as large as 7 mN·m−1 for the mixtures with these three fluids and the parachor model is not recommended without a binary interaction parameter. With a binary interac- tion parameter, the maximum deviations can be reduced to 1–2 mN·m−1. surface tension to essentially within experimental uncertainty, and an interaction parameter is unnecessary. Similarly, mixtures of methanol and ethanol with ace- tone are represented very well without an interaction parameter. Mixtures of alco- hols with aromatics and alcohols with linear alkanes have AAPD’s without binary interaction parameters ranging from roughly 1 % to 5 %, which can be reduced to less than 3 % with binary interaction parameters. In Fig. 4.2  Mixtures with Alcohols 4, for mixtures without binary interaction parameters, mixtures of alcohols with the amines MEA and DEA, and with ethylene glycol show large deviations. Of the components in mix- tures with methanol and ethanol, pure MEA, DEA, and ethylene glycol have the largest values of surface tension (approximately 45 mN·m−1 at 313 K) compared to less than about 27 mN·m−1 for the other fluids in Table 4, and approximately 21 mN·m−1 for pure methanol and ethanol. Maximum deviations can be as large as 7 mN·m−1 for the mixtures with these three fluids and the parachor model is not recommended without a binary interaction parameter. With a binary interac- tion parameter, the maximum deviations can be reduced to 1–2 mN·m−1. 4.2  Mixtures with Alcohols 4   Summary of results for mixtures with alcohols 4.2  Mixtures with Alcohols 3 International Journal of Thermophysics (2023) 44:110 Page 25 of 46  110 1 Table 4   Summary of results for alcohol mixtures Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Alcohol/alcohol Ethanol/methanol 39 0.37 0.08 0.18 0.21 0.04 0.18 − 0.002 Alcohol/amine Ethanol/DEA 13 4.78 1.47 3.67 1.83 0.64 1.44 0.046 Alcohol/amine Ethanol/MEA 26 10.65 3.55 5.45 1.47 0.52 1.17 0.089 Alcohol/amine Methanol/DEA 14 1.97 0.66 2.68 1.80 0.63 2.00 0.013 Alcohol/amine Methanol/MEA 22 7.43 2.62 4.84 1.23 0.47 1.06 0.063 Alcohol/aromatic Ethanol/benzene 76 2.71 0.64 1.59 1.53 0.36 1.16 0.020 Alcohol/aromatic Ethanol/m-xylene 11 1.07 0.27 0.52 0.79 0.20 0.32 0.006 Alcohol/aromatic Ethanol/o-xylene 11 0.83 0.21 0.45 0.56 0.15 0.21 0.005 Alcohol/aromatic Ethanol/p-xylene 11 0.99 0.24 0.55 0.79 0.20 0.33 0.006 Alcohol/aromatic Ethanol/toluene 15 2.60 0.60 2.25 2.95 0.69 1.90 0.015 Alcohol/aromatic Methanol/benzene 19a 5.00 1.25 2.04 1.42 0.35 0.92 0.033 Alcohol/aromatic Methanol/p-xylene 44 5.42 1.30 2.58 1.42 0.35 1.39 0.040 Alcohol/aromatic Methanol/toluene 55 2.32 0.55 1.17 2.06 0.50 1.38 0.007 Alcohol/br-alkane Ethanol/isooctane 44 0.86 0.16 0.45 0.66 0.13 0.32 − 0.005 Alcohol/FAME Ethanol/methyl palmitate 1 8.08 1.80 1.80 0.00 0.00 0.00 0.089 Alcohol/glycol Ethanol/ethylene glycol 56 11.44 3.26 7.09 1.67 0.47 1.40 0.100 Alcohol/ketone Ethanol/acetone 5 1.08 0.25 0.56 0.82 0.19 0.36 − 0.008 Alcohol/ketone Methanol/acetone 20 0.52 0.12 0.32 0.44 0.10 0.32 0.001 Alcohol/n-alkane Ethanol/decane 32 0.88 0.19 0.53 0.76 0.16 0.40 0.004 Alcohol/n-alkane Ethanol/dodecane 22 1.43 0.33 0.85 0.92 0.21 0.42 0.010 Alcohol/n-alkane Ethanol/heptane 88 5.81 1.14 2.15 1.82 0.36 0.66 0.045 Alcohol/n-alkane Ethanol/hexane 114 1.80 0.34 0.79 0.99 0.19 0.41 0.013 Alcohol/n-alkane Ethanol/octane 48 1.14 0.23 0.77 0.78 0.16 0.61 0.008 3 International Journal of Thermophysics (2023) 44:110 110  Page 26 of 46 1 a One point omitted from statistics due to REFPROP calculation problems Table 4   (continued) Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Alcohol/n-alkane Methanol/hexane 26 8.21 1.47 3.89 3.16 0.56 1.51 0.073 Alcohol/naphthene Ethanol/cyclohexane 17 1.98 0.44 0.83 0.82 0.18 0.43 0.015 Alcohol/naphthene Ethanol/methylcyclohexane 10 1.82 0.39 0.83 1.07 0.23 0.41 0.015 1 aOne point omitted from statistics due to REFPROP calculation problems Table 4   (continued) Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Alcohol/n-alkane Methanol/hexane 26 8.21 1.47 3.89 3.16 0.56 1.51 0.073 Alcohol/naphthene Ethanol/cyclohexane 17 1.98 0.44 0.83 0.82 0.18 0.43 0.015 Alcohol/naphthene Ethanol/methylcyclohexane 10 1.82 0.39 0.83 1.07 0.23 0.41 0.015 International Journal of Thermophysics (2023) 44:110 Page 27 of 46  110 Fig 4 Summary of results for mixtures with alcohols Fig. 4.3  Mixtures with Water Table 5 summarizes the results for mixtures with water, and Fig. 5 displays these results graphically. The mixtures of water and heavy water with methanol and etha- nol, and those with water and acetone show extremely large deviations, with a maxi- mum AAD reaching 15–41 mN·m−1. The parachor model completely fails to rep- resent the surface tension of these mixtures. The use of a single, constant binary interaction parameter somewhat reduces the magnitude of the deviations, but the model is still not very good with maximum deviations on the order of 5–13 mN·m−1. 1 3 110  Page 28 of 46 International Journal of Thermophysics (2023) 44:110 Table 5   Summary of results for aqueous mixtures Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Water/alcohol Heavy water/ethanol 84 40.53 13.18 27.65 15.06 5.14 12.25 0.353 Water/alcohol Heavy water/methanol 64 23.30 9.19 14.99 7.22 2.85 5.58 0.184 Water/alcohol Water/ethanol 615 32.34 11.24 25.27 15.23 5.07 12.90 0.304 Water/alcohol Water/methanol 401 18.62 7.14 16.73 5.48 2.04 5.42 0.164 Water/amine Water/DEA 212 4.93 2.67 6.74 1.84 1.03 5.79 0.037 Water/amine Water/MEA 273 5.41 3.05 7.10 2.30 1.32 4.13 0.041 Water/glycol Water/ethylene glycol 427 4.91 2.77 7.18 2.03 1.11 4.40 0.041 Water/ketone Water/acetone 403 55.44 18.90 40.51 14.90 5.33 12.96 0.433 1 3 International Journal of Thermophysics (2023) 44:110 Page 29 of 46  110 Without interaction parameters, all organic/aqueous mixtures investigated here show a common deviation pattern, where the deviations have an asymmetric shape with respect to composition, with a very rapid change as one nears the pure water end [8]. Water also has a very high surface tension (~ 70 mM·m−1 at 313 K) compared to other fluids. Figure  6, showing the percentage deviations of the acetone/water mixture as a function of composition, illustrates this pattern. The temperatures of the data covered 273 K to 343 K, the details for each data set are given in Table 2. One can see that although the use of an interaction parameter can somewhat reduce Fig. 5   Summary of results for aqueous mixtures Fig. 5   Summary of results for aqueous mixtures Without interaction parameters, all organic/aqueous mixtures investigated here show a common deviation pattern, where the deviations have an asymmetric shape with respect to composition, with a very rapid change as one nears the pure water end [8]. 4.3  Mixtures with Water Water also has a very high surface tension (~ 70 mM·m−1 at 313 K) compared to other fluids. Figure  6, showing the percentage deviations of the acetone/water mixture as a function of composition, illustrates this pattern. The temperatures of the data covered 273 K to 343 K, the details for each data set are given in Table 2. One can see that although the use of an interaction parameter can somewhat reduce Without interaction parameters, all organic/aqueous mixtures investigated here show a common deviation pattern, where the deviations have an asymmetric shape with respect to composition, with a very rapid change as one nears the pure water end [8]. Water also has a very high surface tension (~ 70 mM·m−1 at 313 K) compared to other fluids. Figure  6, showing the percentage deviations of the acetone/water mixture as a function of composition, illustrates this pattern. The temperatures of the data covered 273 K to 343 K, the details for each data set are given in Table 2. One can see that although the use of an interaction parameter can somewhat reduce 1 3 International Journal of Thermophysics (2023) 44:110 110  Page 30 of 46 Fig. 6   Relative deviations as a function of composition of water for acetone/water mixture Fig. 6   Relative deviations as a function of composition of water for acetone/water mixture the size of the deviations, it cannot properly reproduce the composition behavior. A small amount of the organic can greatly change the surface tension, and the parachor model does not have the ability to model this composition behavior. It is possible that a more complex, composition and temperature dependent interaction parameter could capture this behavior, but it is beyond the scope of this work. 4.4  Mixtures with Aromatics Table 6 summarizes the results for mixtures with aromatics, and Fig. 7 displays these results graphically. With a fitted binary interaction parameter all mixtures show an AAPD below 5 % except for the mixture toluene/octane that has an AAPD of 5 %. Without interaction parameters some of the points exceed 10 % deviation. However, these points occur at relatively high temperatures (380 K to 400 K) where the magnitude of the deviation is not excessively large (AAD of less than 0.82 mN·m−1) but the percentage deviations are larger due to the smaller value of the surface tension at higher temperatures. 4.4  Mixtures with Aromatics Other systems with deviations of approximately 10 % without interaction parameters are o-xylene/acetone, and 1 3 International Journal of Thermophysics (2023) 44:110 Page 31 of 46  110 Table 6   Summary of results for aromatic mixtures Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Aromatic/aromatic Benzene/o-xylene 8 1.33 0.38 0.52 0.32 0.09 0.15 0.008 Aromatic/aromatic m-Xylene/benzene 5 2.80 0.82 2.33 1.80 0.54 2.33 0.010 Aromatic/aromatic Toluene/benzene 27 1.05 0.28 0.99 1.30 0.34 0.76 0.005 Aromatic/br-alkane Benzene/isooctane 9 5.39 1.13 1.81 0.48 0.10 0.35 0.041 Aromatic/ether Benzene/diethyl ether 4 2.48 0.52 0.90 0.42 0.09 0.15 0.020 Aromatic/halocb Benzene/chlorobenzene 23 1.22 0.36 1.04 1.06 0.31 0.73 0.008 Aromatic/halocb Benzene/dichloroethane 13 3.85 1.05 1.74 2.09 0.57 1.74 0.021 Aromatic/halocb m-Xylene/chlorobenzene 18 0.62 0.18 0.61 0.62 0.18 0.63 0.001 Aromatic/halocb o-Xylene/chlorobenzene 18 0.73 0.22 0.42 0.23 0.07 0.15 0.005 Aromatic/halocb p-Xylene/chlorobenzene 18 0.80 0.24 0.67 0.87 0.26 0.53 0.004 Aromatic/halocb Toluene/chlorobenzene 6 3.35 0.97 1.16 0.59 0.17 0.28 0.021 Aromatic/ketone Benzene/acetone 33 0.94 0.24 0.77 0.85 0.21 0.77 0.003 Aromatic/ketone m-Xylene/acetone 9 2.14 0.56 1.02 0.76 0.20 0.74 − 0.013 Aromatic/ketone o-Xylene/acetone 8 8.78 2.39 3.16 1.06 0.29 0.62 − 0.062 Aromatic/ketone p-Xylene/acetone 9 1.36 0.35 0.91 0.85 0.22 0.75 − 0.008 Aromatic/ketone Toluene/acetone 110 1.10 0.27 0.83 0.84 0.20 0.71 0.007 Aromatic/n-alkane Benzene/dodecane 23 6.71 1.65 3.15 0.95 0.24 0.64 0.060 Aromatic/n-alkane Benzene/heptane 47 1.57 0.35 1.16 1.02 0.22 0.87 0.012 Aromatic/n-alkane Benzene/hexadecane 44 1.08 0.28 0.69 1.01 0.26 0.55 0.005 Aromatic/n-alkane Benzene/hexane 31 1.86 0.41 1.08 1.20 0.26 0.73 0.015 Aromatic/n-alkane Benzene/nonane 44 1.52 0.35 0.77 0.57 0.14 0.34 0.012 Aromatic/n-alkane Benzene/pentane 7 7.62 1.61 2.33 2.04 0.44 0.81 0.051 Aromatic/n-alkane Ethylbenzene/hexadecane 9 3.63 1.01 1.58 0.45 0.12 0.27 0.026 3 110  Page 32 of 46 International Journal of Thermophysics (2023) 44:110 Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Aromatic/n-alkane m-Xylene/heptane 11 2.31 0.54 0.89 0.13 0.03 0.11 0.019 Aromatic/n-alkane m-Xylene/hexane 29 3.00 0.68 1.30 0.87 0.19 0.35 0.024 Aromatic/n-alkane m-Xylene/octane 11 2.33 0.57 0.98 0.16 0.04 0.07 0.020 Aromatic/n-alkane m-Xylene/pentane 20 1.46 0.32 0.84 0.91 0.20 0.36 0.012 Aromatic/n-alkane o-Xylene/decane 11 5.26 1.33 1.86 0.81 0.21 0.58 0.039 Aromatic/n-alkane o-Xylene/nonane 11 4.59 1.14 1.68 0.92 0.23 0.52 0.034 Aromatic/n-alkane o-Xylene/octane 11 4.83 1.17 1.73 1.09 0.27 0.84 0.037 Aromatic/n-alkane p-Xylene/decane 22 4.68 1.12 1.51 0.67 0.17 0.49 0.031 Aromatic/n-alkane p-Xylene/hexane 16 3.42 0.76 1.13 0.51 0.11 0.21 0.024 Aromatic/n-alkane p-Xylene/octane 12 3.90 0.88 1.19 0.83 0.19 0.53 0.027 Aromatic/n-alkane p-Xylene/pentane 7 3.30 0.68 0.89 0.97 0.20 0.51 0.019 Aromatic/n-alkane Toluene/heptane 34 2.88 0.62 1.28 0.55 0.12 0.32 0.024 Aromatic/n-alkane Toluene/hexadecane 52 1.80 0.47 1.06 0.84 0.22 0.82 0.013 Aromatic/n-alkane Toluene/nonane 44 2.37 0.55 0.99 0.34 0.08 0.29 0.019 Aromatic/n-alkane Toluene/octane 17 6.06 0.82 1.73 5.03 0.77 1.15 0.027 Aromatic/n-alkane Toluene/pentane 8 8.31 1.72 2.24 0.91 0.18 0.30 0.050 Aromatic/naphthene Benzene/cyclohexane 96 0.53 0.13 0.37 0.50 0.13 0.41 0.001 Aromatic/naphthene Benzene/cyclopentane 9 1.63 0.40 0.54 0.22 0.06 0.14 0.011 Aromatic/naphthene Ethylbenzene/cyclohexane 28 1.56 0.40 0.82 0.50 0.13 0.24 0.013 Aromatic/naphthene m-Xylene/cyclohexane 28 1.38 0.35 0.70 0.36 0.09 0.31 0.011 Aromatic/naphthene o-Xylene/cyclohexane 28 1.31 0.34 0.76 0.45 0.11 0.26 0.010 Aromatic/naphthene p-Xylene/cyclohexane 28 1.13 0.29 0.56 0.31 0.08 0.23 0.009 Aromatic/naphthene Toluene/cyclohexane 11 4.40 1.12 1.55 0.11 0.03 0.07 0.031 International Journal of Thermophysics (2023) 44:110 Page 33 of 46  110 1 3 Table 6   (continued) Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Aromatic/naphthene Toluene/cyclopentane 10 0.20 0.05 0.07 0.07 0.02 0.03 − 0.001 Aromatic/other p-Xylene/dimethyl carbonate 10 2.39 0.62 1.09 0.72 0.19 0.42 − 0.019 1 3 110  Page 34 of 46 International Journal of Thermophysics (2023) 44:110 Fig. 4.4  Mixtures with Aromatics 7   Summary of results for mixtures with aromatics Fig. 7   Summary of results for mixtures with aromatics some points in benzene/dodecane, toluene/pentane, and m-xylene/benzene. With interactions parameters the AADP in these systems, except m-xylene/benzene, can be reduced to 1 %. The m-xylene/benzene point with near 10 % deviation (for both fitted and non-fitted cases) is due to a pure fluid point for m-xylene (that we believe is flawed) from the 1929 data set of Hammick and Andrew [56]. In summary, when a fitted binary interaction parameter is used, the aromatic/alkane and aromatic/napthene mixtures have an AAPD of no greater than 1 %, however the deviations are a function of composition. With the use of a binary interac- tion parameter these mixtures can generally be represented to within 3 % over the entire composition range. 4.4  Mixtures with Aromatics 1 3 International Journal of Thermophysics (2023) 44:110 Page 35 of 46  110 1 Table 7   Summary of results for halocarbon mixtures Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Halocb/halocb R1123/R1234yf 39 4.37 0.32 1.11 4.43 0.31 1.09 0.002 Halocb/halocb R125/R134a 21 1.13 0.07 0.25 0.99 0.06 0.18 0.004 Halocb/halocb R125/R143a 38 2.07 0.09 0.28 1.65 0.05 0.16 0.008 Halocb/halocb R125/R152a 75 3.24 0.25 0.68 1.66 0.11 0.31 0.020 Halocb/halocb R125/R32 262 1.87 0.07 0.38 1.81 0.05 0.50 0.004 Halocb/halocb R134a/R1234yf 23 8.05 0.19 0.37 4.88 0.09 0.22 − 0.025 Halocb/halocb R134a/R1234ze(E) 9 2.71 0.10 0.25 2.43 0.04 0.06 0.012 Halocb/halocb R143a/R134a 126 1.73 0.11 0.69 1.96 0.12 0.61 0.002 Halocb/halocb R143a/R227ea 241 3.57 0.17 0.31 1.89 0.08 0.21 − 0.013 Halocb/halocb R152a/R134a 21 1.50 0.15 0.38 1.06 0.12 0.33 − 0.006 Halocb/halocb R22/R115 1 29.91 2.39 2.39 0.00 0.00 0.00 − 0.196 Halocb/halocb R32/R1123 37 4.24 0.27 0.56 2.29 0.14 0.41 − 0.021 Halocb/halocb R32/R1234yf 60 7.65 0.23 0.47 6.24 0.18 0.43 − 0.017 Halocb/halocb R32/R1234ze(E) 52 4.14 0.28 0.97 3.07 0.15 0.41 0.026 Halocb/halocb R32/R134a 317 1.08 0.07 0.47 1.11 0.07 0.47 0.001 Halocb/halocb R32/R227ea 412 3.90 0.19 0.43 2.58 0.12 0.36 − 0.012 Halocb/ketone Chlorobenzene/acetone 1 6.36 1.69 1.69 0.00 0.00 0.00 − 0.036 Halocb/n-alkane Chlorobenzene/pentane 7 3.04 0.63 0.91 1.20 0.27 0.42 0.017 Halocb/n-alkane R152a/propane 51 10.61 0.87 1.09 3.54 0.25 0.60 − 0.050 Halocb/n-alkane R32/propane 99 2.60 0.16 0.51 2.53 0.15 0.45 − 0.010 Halocb/n-alkane RC318/butane 24 5.89 0.88 1.68 2.27 0.34 0.79 0.044 Halocb/naphthene Chlorobenzene/cyclohexane 18 0.89 0.24 0.64 0.49 0.13 0.54 − 0.005 3 International Journal of Thermophysics (2023) 44:110 110  Page 36 of 46 4.5  Mixtures with Halocarbons Table 7 summarizes the results for mixtures with halocarbons, and Fig. 8 dis- plays these results graphically. Included are mixtures containing some of the new low-GWP fluids such as R1234yf and R1234ze(E) in addition to HFC’s such as R32, R134a, R143a, R152a, and R125, and mixtures of polar halocar- bons with nonpolar alkanes such as propane and butane. Without using an inter- action parameter almost all results are within 10 % the AAPD’s are generally Fig. 8   Summary of results for halocarbon mixtures Fig. 8   Summary of results for halocarbon mixtures 4.5  Mixtures with Halocarbons Table 7 summarizes the results for mixtures with halocarbons, and Fig. 8 dis- plays these results graphically. Included are mixtures containing some of the new low-GWP fluids such as R1234yf and R1234ze(E) in addition to HFC’s such as R32, R134a, R143a, R152a, and R125, and mixtures of polar halocar- bons with nonpolar alkanes such as propane and butane. Without using an inter- action parameter, almost all results are within 10 %, the AAPD’s are generally less than 5 %. Exceptions are visible in Fig. 8; the single point for R22/R115 has 1 3 1 3 International Journal of Thermophysics (2023) 44:110 Page 37 of 46  110 1 Table 8   Summary of results for miscellaneous mixtures a 14 points omitted from statistics due to REFPROP calculation problems b 3 points omitted from statistics due to REFPROP calculation problems c 15 points omitted from statistics due to REFPROP calculation problems Mixture class Fluids Npts δij = 0 Fitted results AAPD (%) AAD (mN·m−1) max AD (mN·m−1) AAPD (%) AAD (mN·m−1) max AD (mN·m−1) δij Cryogen/cryogen Carbon monoxide/nitrogen 10 1.28 0.10 0.18 0.21 0.02 0.04 0.012 Cryogen/cryogen Helium/argon 33a 13.08 0.25 0.69 13.08 0.25 0.69 0.000 Cryogen/cryogen Hydrogen/argon 21 6.42 0.44 0.96 2.92 0.15 0.54 − 0.678 Cryogen/cryogen Hydrogen/deuterium 67 4.98 0.13 0.30 2.65 0.07 0.19 − 0.033 Cryogen/cryogen Krypton/argon 100b 4.92 0.24 1.35 4.92 0.24 1.35 0.000 Cryogen/cryogen Neon/argon 27 7.82 0.22 1.47 8.13 0.23 1.46 0.048 Cryogen/cryogen Nitrogen/argon 40 1.96 0.21 0.50 1.15 0.13 0.41 0.012 Cryogen/cryogen Nitrogen/helium 38c 4.94 0.16 1.67 4.94 0.16 1.67 0.000 Cryogen/cryogen Nitrogen/oxygen 183 5.41 0.68 2.41 3.31 0.33 1.26 0.055 Cryogen/cryogen Oxygen/argon 64 0.48 0.07 0.19 0.48 0.07 0.19 0.001 Siloxane/siloxane D4/MD2M 3 3.26 0.60 0.66 0.43 0.08 0.12 − 0.019 Siloxane/siloxane D4/MD4M 2 7.35 1.40 1.43 0.28 0.05 0.06 − 0.047 Siloxane/siloxane MD3M/D5 1 4.56 0.86 0.86 0.00 0.00 0.00 − 0.024 Siloxane/siloxane MD4M/D5 3 6.55 1.25 1.39 0.02 0.00 0.01 − 0.039 3 International Journal of Thermophysics (2023) 44:110 110  Page 38 of 46 Fig. 9   Summary of results for mixtures with miscellaneous compounds Fig. 9   Summary of results for mixtures with miscellaneous compounds very large deviations; it is unclear why this mixture should deviate from the oth- ers. The mixture of R152a/propane also has deviations slightly greater than 10 % without an interaction parameter. 4.5  Mixtures with Halocarbons It is unclear why R152a/propane should show this magnitude of deviation (AAPD 10.6 %), as a similar polar/nonpolar mixture of R32/propane displays smaller deviations (AAPD 2.6 %) without the use of an interaction parameter. The mixtures of halocarbons with other halocarbons with- out an interaction parameter have AAD of about 0.3 mN·m−1, while the mix- tures of polar halocarbons with nonpolar alkanes have a higher AAD of up to 0.9 3 International Journal of Thermophysics (2023) 44:110 Page 39 of 46  1 110 mN·m−1. The use of an interaction parameter improves the results, providing an AAD less than 0.35 mN·m−1 for both types of mixtures. 4.6  Mixtures with Miscellaneous Compounds Table 8 summarizes the results for mixtures with miscellaneous compounds, and Fig. 9 displays these results graphically. The mixtures are either of cryogens with other cryogens, or siloxanes with siloxanes. All mixtures without interaction parameters except helium/argon show an AAPD of less than 10 %. As shown in Table 2, the helium/argon mixture data were obtained only for extremely dilute solutions of helium less than about a helium mole fraction of 0.01. Without more data over a larger composition range, it is difficult to assess the performance of the parachor model for the helium/argon system. In addition, there were conver- gence failures in REFPROP for the systems helium/argon, krypton/argon, and nitrogen/helium; points without convergence were not included in the statistics and binary interaction parameters were not determined for these systems. There also was an extremely limited composition range for neon/argon, hydrogen/ argon, and nitrogen/helium so we cannot fully assess these systems either. The data for siloxane mixtures are very limited in the number of points, so it also is premature to assess these systems. For the cryogen/cryogen mixtures where there are a wide range of data, the parachor model appears to represent the data to within 10 % without interaction parameters, with AAPD’s of less than 5 %. 5  Conclusions Acknowledgements  We thank Dr. Allan Harvey for helpful discussions. Author contributions  All authors participated in the writing and review of the manuscript. AML deve oped the python code used to perform the analysis and generate figures. VD provided the data. Funding  Open access funding provided by NTNU Norwegian University of Science and Technology (incl St. Olavs Hospital - Trondheim University Hospital). This work was partially funded by the National Institute of Standards and Technology. Additional support was provided by the NCCS Centre, performed under the Norwegian research programme Centres for Environment-friendly Energy Research (FME), funded by industry partners and the Research Council of Norway (257579). Conflict of interest  The authors have no conflicts to declare. Open Access  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Com- mons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ ses/​by/4.​0/. 5  Conclusions We compiled a database for the surface tension of binary mixtures by extracting data from the NIST TDE database [34]. It contains a wide variety of fluids, cov- ering the chemical classes water, alcohols, amines, ketones, linear and branched alkanes, naphthenes, aromatics, refrigerants, and cryogens. The data set includes 65 pure fluids and 154 binary pairs with a total of 8205 points. We used this data- base to test the performance of a parachor model for mixtures, in both a predic- tive mode (no mixture data used) and with a single, constant binary interaction parameter found by fitting the mixture data. The parachor model is not new and variants of it have been used for many years, but a comprehensive summary of its performance on a wide variety of mixtures has not been available until now. The data are available in the supporting information to enable model comparisons for future research on binary mixtures with new models. In general, the parachor model in a predictive mode without fitted interaction parameters can predict the surface tension of binary mixtures of non-polar fluids such as linear and branched alkanes, linear and branched alkanes with naphthenes, aromatics with aromatics, aromatics with naphthenes, and mixtures of linear alkanes of similar sizes with an AAPD of about 3 % or less. For mixtures of linear alkanes of differing sizes, as the size difference increases it is necessary to use a fitted binary interaction 1 3 3 10  Page 40 of 46 International Journal of Thermophysics (2023) 44:110 110 parameter to reduce deviations. Similarly, in a predictive mode the model has large deviations for mixtures of n-alkanes with ­CO2, and an interaction parameter should be used. Mixtures of methanol and ethanol did not require an interaction parameter. Polar mixtures of halocarbons with other halocarbons and also polar/ nonpolar mixtures of alkanes with halocarbons could be modeled with an AAD of less than 0.35 mN·m−1 with the use of a binary interaction parameter for each pair of fluids. Future work on developing a predictive scheme for binary interac- tion parameters for classes of mixtures would make the parachor model more use- ful. Finally, the parachor model even with a fitted binary interaction parameter is not suitable for mixtures of water with organic compounds. Supplementary Information  The online version contains supplementary material available at https://​doi.​ org/​10.​1007/​s10765-​023-​03216-z. Acknowledgements  We thank Dr. Allan Harvey for helpful discussions. 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Analytical Investigation of the Factors Affecting the Supplier-Induced Demand in Healthcare: A Case Study of CT Scanning Department in Iran
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Analytical Investigation of the Factors Affecting the Supplier-Induced Demand in Healthcare: A Case Study of CT Scanning Department in Iran Samira Motaghi  Ehsan Farhadi  (  e_farhadi@modares.ac.ir ) Hamid Rajabian Research Article Keywords: Induced demand, healthcare provider organizations (HPOs), CT scanning, the Kolmogorov- Smirnov test, Iran Posted Date: October 30th, 2023 DOI: https://doi.org/10.21203/rs.3.rs-3488738/v1 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Additional Declarations: No competing interests reported. Additional Declarations: No competing interests reported. Page 1/20 Page 1/20 Page 1/20 Abstract The aim of this study is to investigate the factors affecting the supplier-induced demand in health care with the help of an analytical-survey approach and using a questionnaire tool, and to analyze the role of medical technology centers, such as centers equipped with a CT scanning department, in development of this type of demand. The statistical population of the present research consisted of the patients referring to this department, out of whom 80 people were selected as the research sample using the simple random sampling method. After checking the normality of the data distribution through the Kolmogorov- Smirnov test, three research hypotheses were developed, all of which were confirmed by analyzing them using the Pearson correlation parametric test. The results of the data analysis indicated that the low patient information, high physician information, and high costs of healthcare service provider institutions have a positive effect on the supplier-induced demand in healthcare (especially in the departments with therapeutic technologies such as CT scanning). In addition, according to the results, the variable of high costs of healthcare provider organizations plays a more significant role in development of supplier- induced demand for healthcare providers, compared to the other two variables. 1. Introduction This situation becomes increasingly worse when a significant portion of health costs in healthcare systems are paid out-of-pocket (OOP) by most people (De Jaegher and Jegers, 2000); because apart from the fact that wrong or irrelevant diagnosis makes the patient face more side effects and leads to waste of time, economic problems, and a lot of cost for him/her and his/her family, it causes additional costs for the government and reduces the efficiency of national resources (Bickerdyke et al., 2002). In this regard, the need to pay attention to the supplier-induced demand in healthcare and the factors affecting it, in all levels and departments of the healthcare system (including the CT scanning department), is of great importance and calls policymakers and researchers for discussing and examining this issue. 1. Introduction The healthcare sector throughout the world is developing increasingly, an issue that has made the behavior of this sector very similar to an economic market. In this regard, healthcare service providers, such as physicians, and patients have accepted their role as service providers and service receivers (customers), respectively. Therefore, healthcare economists seek to identify the relationship between the healthcare supply and demand and evaluate the differences between them in the healthcare sector and other economic sectors. In this regard, the important point is the relationship and mutual trust between the healthcare service providers and the patient (in addition to their economic relationship), which, due to the patient's incomplete information about his/her illness, makes him/her a debtor to the supplier, and due to his/her lack of access to information (incomplete information) and the patients' low literacy easily affects his/her demand function for healthcare resources (Calcott, 1999). This issue takes place in both developed and developing countries due to the exclusiveness of physicians’ and other healthcare providers’ knowledge, as well as the price-inelasticity of patients' demand (Bridge and Jones, 2007). However, in developing countries, it occurs more frequently due to the growth of resources providing healthcare to patients and the more restricted promotion of technology compared to developed countries (Talati and Pappas, 2006), as in these countries (developing countries), due to the smaller number of providers, the existing providers are the only available options for patients, and in such a situation, development of induced demand, which imposes financial burden on patients or affiliated organizations, is not avoidable and brings about a lot of economic justification for providers (Carlsen and Grytten, 2000). Page 2/20 Page 2/20 What stands out as the difference between the healthcare market and other markets is that the healthcare provider first evaluates patients’ problems and needs and then recognizes the type and amount of care needed for them; and this is the factor that intensifies the supplier-induced demand, and while leading the patient to absolute poverty (spending a percentage of his/her income needed in other sectors on his/her treatment), it is identified as the source of creating an inappropriate healthcare situation. 2. Theoretical Foundations (Supplier-Induced Demand) In this regard, the expansion of private hospitals and private physicians working in these hospitals has led to an increase in the unnecessary admission of patients who can be treated easily on an outpatient basis, but instead of being treated at home, they are hospitalized for a very long time. This somehow leads to an increase in induced demand from other health care providers (Grytten and Sorensen, 2001). However, this type of demand creation is among the most inappropriate methods of creating induced demand, because in this method (patient hospitalization for a long time), the patient not only faces an unfavorable financial situation (especially patients without coverage insurance), but he/she is also exposed to an inappropriate health environment in an unwanted way, which in turn causes many other diseases in the future and puts the patient in an inappropriate cycle of poverty and poor health (Grytten, 1992). Another perspective related to the creation of supplier-induced demand also refers to the supplier’s behavioral perspectives because the physician-patient relationship in the healthcare system, in addition to being subject to the non-identical information of the physician and the patient, is also subject to the physician’s judgments due to uncertainty. Moreover, since physicians are more informed than patients, it is this type of physician’s behavior and ethics in dealing with the patient that determines the type and amount of induced demand. Another decisive factor in the creation of induced demand by physicians is the monopoly of physicians. This issue is especially noticeable in developing and sometimes poor countries that have a limited number of physicians compared to developed countries, as the healthcare markets in these countries are always affected by suppliers (physicians) (Richardson and Peacock, 2006). Therefore, based on the discussed topics, it can be said that in some cases, the healthcare service provider, including physicians, and in some cases, patients, cause supplier-induced demand. Considering the patient as the factor affecting induced-demand is due to the fact that the patient accepts the physician's prescription and any treatment because of the specialized aspect of health services and his/her concern for the disease consequences, which is due to his/her lack of knowledge about his/her disease and physical conditions. 2. Theoretical Foundations (Supplier-Induced Demand) In general, the standard model used in the healthcare economics literature to investigate the agency relationship between healthcare providers and the patient and the effect of information asymmetry on the behavior of the supply side, i.e. the occurrence of supply side bias, is known as induced demand. In other words, the induced demand is a demand in addition to the patient's treatment needs, which is imposed on the patient by the healthcare deliberately (to earn more money) or undeliberately (due to lack of knowledge, experience, and skills), causing heavy expenses for him/her. For this reason, addressing this issue can be useful in order to reduce violations caused by the superficiality of healthcare service applicants, to reduce the tricks used by some healthcare providers to generate more income, and prevent unnecessary prescriptions (Carlsen and Grytten, 2000). The lack of agreement among physicians in diagnosing the disease type and the treatment type is one of the main reasons for the changes in treatment type used by different physicians, which involves many cases from multiple visits (in the form of face-to-face meetings) to the use of the state-of-art medical devices and outstanding treatment technologies. In addition, in addition to the mentioned factor (professional uncertainty in diagnosing the treatment type that varies from physician to physician), other various factors can play a potential role in development of induced demand, e.g., payment systems, physician density, competitive market, and the patient's ability to pay (Wennberg, Barnes and Zubkoff, 1982). The induced demand created by other suppliers can be seen in prolonging the period of timely treatment by the physician, as many physicians spend a very long time to treat a simple disease that could be treated in a very short time. In this regard, some physicians also put forward false justifications for prolonging the treatment period and even suggest treatments that are not needed. However, this type of Page 3/20 Page 3/20 induced demand has been diminished due to patients’ higher relative awareness about their health status. Another approach for development of induced demand is the creation of demand by hospitals (as one of the healthcare providing organizations (HPOs)). 2. Theoretical Foundations (Supplier-Induced Demand) Now, if this little information is combined with the insufficient knowledge and skill of the healthcare service provider, it will lead to unnecessary tests and drugs and induced contractions, the most important side effects of which include the loss of time, depression caused by treatment, and confusion for patients (Keyvanara et al., 2013). However, considering the healthcare service provider, especially the physician, as a factor affecting induced demand can be regarded as a result of the physician's large amount of information and the increase in the number of physicians compared to that of the patients, and consequently, the decrease in Page 4/20 Page 4/20 Page 4/20 their income share (Pourreza, 2004). On this basis and considering the topics presented, several studies have been conducted in this direction, some of which we present below: Sekimoto et al. (2015) studied the demand induced by applicants for chronic disease care in Japan, with the aim of investigating the existence of induced demand in the treatment of chronic diseases by analyzing the patients’ data. They hypothesize that clinic and hospital physicians in the high competitive areas (high physician density) recommend seeking advice earlier than those in the lower competition areas (low physician density). Then, using multilevel stochastic models, they examine the patients’ data and analyze the administrative claims in order to estimate the effects of physician density on encounter frequency and medical costs. In the data analysis, the average duration of drug use was considered as a proxy for the physician’s encounter frequency. Their findings indicated that the patient encounter frequency is significantly correlated with the clinic physician density, but there is no close correlation with the hospital physician density. Also, the increased physician density significantly depends on the increased clinic and hospital medical costs. In general, the results of their study showed that there is an induced demand in Japan. Sabatini Dwyer and Liu (2013) studied the effect of consumer health information on the demand for health services in order to empirically examine whether health information consumers use non-medical information sources as a substitute or supplement for health services (i.e., visits to physicians and emergency rooms (ER)). A measure of patient trust in physicians as a proxy for potential nonconforming heterogeneity can help consumers seek information and use physician services. 2. Theoretical Foundations (Supplier-Induced Demand) Considering the increased medical expenses for the elderly as a social problem in Japan, one of the strongest arguments to explain this increase is the physician-induced demand. They used the cost function method in order to investigate the hypothesis of physician-induced demand. In this method, the health improvement resulting from the medical treatment is adjusted in the model, and indirect use of medical services can be measured. In addition, it is possible to alternate between hospital services and outpatient care. In this model, a change in the proportion of physicians and patient populations can lead to a change in the proportion of inpatient services and outpatient care, ultimately resulting in an increase in medical expenses. According to their findings, when the number of physicians in outpatient services increases, the use of outpatient services increases according to their statistical significance. In this case, there is also an alternative between hospital services and outpatient services. In addition, the demand for hospitalization or outpatient services has a positive and significant relationship with the payment price. In this case, there is also an alternative between hospital services and outpatient services. Moreover, there is a significant positive relationship between the demand for hospitalization or outpatient services and the payment price. Dranove and Wehner (1994) made an attempt to study the physician-induced demand for delivery using the TSLS method, which is a controversial technique in the field of testing hypotheses related to physician-induced demand (including two stages of least squares regression (LSR) analysis of cross- sectional data on the physician supply and employment). They examined the strength of the TSLS by applying it where there is only a negligible amount of demand induction for deliveries, and found evidence of the delivery motivation by questioning the validity of the TSLS approach. Their findings suggested two unlikely factors. In the first factor, regression has not been identified, and in the second factor, the regression does not sufficiently show borderline paths. Panahi et al. (2015) studies the induction effect of the number of physicians and hospital beds on health expenditure in Iran in order to investigate the presence of physician-induced demand in Iran's provinces using the panel data of the provinces in the period of 2000–2009. The results of the research model estimation indicated that the change in the number of physicians has a significant positive impact on the amount of health expenditures in the provinces. 2. Theoretical Foundations (Supplier-Induced Demand) After modification, sample selection, and adverse non-compliance control, the results were in agreement with the literature that paying attention to the consumer health information increases the likelihood of physician visits as well as the average number of visits. However, consumers with less health information make more visits to physicians and ERs than better informed consumers, which indicates that information can improve market efficiency. Woo Lee (2012) made an attempt to study asymmetric information and the demand for private health insurance in Korea in order examine the relationship between self-assessed health status (predicted as health risk) and demand for private health insurance using the longitudinal study data. Contrary to theoretical predictions, their results indicated that buying insurance can improve health. Their research evidence showed that this phenomenon is likely to be due to the screening by the insurers in the private insurance market in Korea. Grytten et al. (2010) studied the impact of income and supplier-induced demand based on the evidence from primary care physicians in Norway. In their study, they investigated the relationship between the physician non-operating income and the provision of basic services by them. They argue that in the presence of induction, physicians with unsatisfactory low incomes work in municipalities where competition for patients is high and compensate for patient shortages by creating requirements. This model is compatible with the institutional setting of the Norwegian primary care physician, while there is Page 5/20 Page 5/20 a fixed fee schedule. Their analyses were performed on a data set from all the primary care physicians in Norway, considering each item of treatment cost. a fixed fee schedule. Their analyses were performed on a data set from all the primary care physicians in Norway, considering each item of treatment cost. The data related to the practicing output were merged with the information about the non-practicing income from the tax forms of physicians and their spouses, the results of which indicated that in the municipalities with a high density, physicians’ non-operating income does not influence the number of advices per physician or the number of treatment items per advise. Overall, the results are interpreted as evidence against the induced demand hypothesis. In an empirical study in Japan, Izumida et al. (1999) investigated physician-induced demand (cost function method for elderly medical expenses). 2. Theoretical Foundations (Supplier-Induced Demand) Therefore, the presence of induced demand in the health sector, which is known as Roemer's law, was confirmed in the provinces. However, in terms of the density Page 6/20 of hospital beds, it was concluded that there is no supplier-induced demand, and an inverse relationship between these two variables and health expenditures was observed. Keyvanara et al. (2013) investigated the challenges resulting from induced demand for healthcare services, with the aim of identifying the challenges of induced demand using the experts’ experiences in Isfahan University of Medical Sciences in Iran. Their methodology was qualitative, and semi-structured interview was used to collect the data. Based on the thematic analysis conducted by them, 41 sub- themes and 3 main themes were extracted, with each having some sub-themes. The three main themes included: the challenges of insurance organizations, health system challenges, and patient challenges. Their results presented the challenges caused by induced demand, the most obvious of which included those mentioned above, i.e., the challenges of insurance organizations, health system challenges, and patient challenges. These findings can help the policy makers of the health sector to design appropriate strategies to address the challenges by considering them. Abdoli and Varahrami (2010) investigated the role of asymmetric information in induced demand in medical services. In order to compare the induced demand between formally- and informally-employed physicians, they prepared 300 questionnaires that was completed by 300 physicians living in Tehran, out of which 70 people were excluded from the study due to the fact that they were both employed by the government and had their own clinic. The variables of the “time of each visit to the physician and “the average number of tests prescribed by the physician for each patient” were considered as dependent variables, and the variables of “gender”, patient’s age”, “type of degree”, “experience”, “physician’s preference of income over leisure”, and “providing special services on their behalf” were considered as explanatory variables. According to their research findings, although the average number of tests prescribed by the physician and the time of each visit to him/her are affected by the patient’s gender and age, the variables of preference of income over leisure, experience, and providing special services played an effective in increasing the number of prescribed tests and the time of each visit to the physician, especially in the case of informally-employed physicians. 2. Theoretical Foundations (Supplier-Induced Demand) Moreover, the research findings indicated that the induced demand for the use of medical and therapeutic services by general physicians is more, and the patients are more motivated to use all kinds of health and treatment services from informally- employed general physicians, compared to formally-employed ones. Accordingly, the adoption of standards and laws to monitor the performance of physicians who have private clinics can significantly reduce the unnecessary treatment expenses spent by patients. 3.1.1. Questionnaire Validity In this study, the content validity method was used to determine the questionnaire validity, as it is common to use this method in studies where the respondents must understand the influencing factors and answer the questionnaire questions according to their perception of these variables. Given that the research tool was a questionnaire, subjects such as appropriate appearance, legible typing, number of questions, how to write and use appropriate words, accurate translation, grammatical points according to the culture, and grammatical structure were considered in this study. Finally, for face validity, the questionnaires were presented to several expert professors in the field of health economics and relevant doctors, and their opinions on them were asked and applied, and after taking the corrective measures, the questionnaires were approved. 3. Research Methodology As an applied research in terms of purpose and a survey study in terms of nature, the current study was carried out using the questionnaire approach in the statistical year 2022. In addition, in order to more closely examine the third part of the questionnaire (i.e., high costs of medical centers), a number (N=15) of physicians, personnel, and owners of medical centers and professors of Tehran University of Medical Sciences were interviewed, who confirmed the final results of this section. Page 7/20 Page 7/20 The research statistical population (in the section of ordinary people) consisted of all people referring to the CT scanning department in Tehran city, with their number being 100 people. The statistical sample of this department was determined based on Morgan's sampling table and 80 people were estimated to be selected by the use of the simple random sampling method. A questionnaire was used as the tool for the data collection. It was a researcher-made questionnaire containing 15 questions with closed answers, which includes two parts: the first part containing demographic questions (the first part of the questionnaire) related to the respondents’ general characteristics, e.g., gender, marital status, age; and the second part containing component-based attitudinal questions. According to the statistical sample, 80 questionnaires were distributed. However, in the initial review of the questionnaires, it was found that 70 people answered the questionnaire correctly and completely, and their data were used in the research analysis. A ranking scale was used to rank the research data. In this approach, the respondent is asked to indicate his/her agreement or disagreement with each item based on a spectrum. This scale makes it possible to determine the respondent’s sensitivity, reasoning, and belief. A 5-point Likert scale was used in the questionnaire, with the values of the scale factors ranging from completely disagree (1) to completely agree (5). 3.1.2. Questionnaire Reliability Reliability refers to the feature that if the measurement tool is given to the groups of people in the same conditions several times in a short period of time, the results will be close to each other. To measure the reliability, we used an index called “reliability coefficient”, and its size usually varies in the interval [0,1]. A reliability coefficient of 0 indicates no reliability and a reliability coefficient of 1 indicates complete reliability (Khaki, 2000). Resource: research findings The coefficient derived indicates the reliability of the questionnaire. The coefficient derived indicates the reliability of the questionnaire. Page 8/20 The researcher can ask questionnaire questions to a few people using a preliminary research. If people in the same conditions give the same answers to the questions questionnaire, it can be said that the questionnaire questions have a good reliability (Sarmad et al., 2007). In this study, Cronbach's alpha coefficient was used to check the reliability of the measurement tool (the spectra). This method is used to calculate the internal consistency of the measurement tool that measures different characteristics. To calculate the Cronbach's alpha coefficient, first, the variance of the scores of each subset of the questions and the total variance must be calculated. Then, using Cronbach's alpha coefficient formula, the alpha coefficient values are calculated. The Cronbach's alpha values derived and the number of questions of each index and the entire questionnaire are presented in Table 2. Table 1. Cronbach's alpha values and the number of questions of each index and the entire questionnaire. Index Number of questions Cronbach’s alpha coefficient  Physician-induced demand Patient’s low information  5 0.816 Physician’s high information  5 0.708 High costs of HPOs 5 0.719 Entire questionnaire  15 0.748 Resource: research findings 3.3. Data Analysis Method The research method used in this study is survey-descriptive, and it is of applied type in terms of goal. In this research, descriptive and inferential statistics were used to analyze the information extracted from the questionnaire. In the descriptive part, the subjects’ demographic characteristics, including gender, marital status, and age, are determined through frequency and percentage tables, as well as the mean and standard deviation; and in the inferential part, the data normality is obtained through the use of the Kolmogorov-Smirnov test. Then, the hypotheses will be analyzed using the Pearson correlation parametric test through the SPSS statistical analysis software. 3.2. Conceptual Model of Research The conceptual model of this research was proposed by applying theoretical foundations and based on the research model used in Sabatini Dwyer and Liu (2014) and the results of Keyvanara et al. (2013) and (2013). In this model, the factors affecting the physician-induced demand are considered as the independent variables and the physician-induced demand is also considered as the dependent variable. According to the relationships between the variables of the research conceptual model, the following three hypotheses can generally be proposed: According to the relationships between the variables of the research conceptual model, the following three hypotheses can generally be proposed: The first hypothesis. Patient’s low information is positively correlated with physician-induced demand. The first hypothesis. Patient’s low information is positively correlated with physician-induced demand. The second hypothesis. Physician’s high information is positively correlated with physician-induced demand. The second hypothesis. Physician’s high information is positively correlated with physician-induced demand. The third hypothesis. High costs of healthcare provider organizations (HPOs) is positively correlated with physician-induced demand. The third hypothesis. High costs of healthcare provider organizations (HPOs) is positively correlated with physician-induced demand. Page 9/20 Page 9/20 3.4.1. Research Descriptive Findings The subjects’ gender status is presented in Table 2 and draw in Figure 1, according which 57.1% of the subjects were men and 42.9% were women. Table 2. Subjects' gender status Table 2. Subjects' gender status Table 2. Subjects' gender status Gender  Frequency Percentage  Cumulative frequency Male  40 57.1 57.1 Female 30 42.9 100 Total 70 100 100 esource: Research findings. The subjects’ marital status is presented in Table 3 and draw in Figure 2, as it can be seen that 20% of the subjects are single and 80% married. The subjects’ marital status is presented in Table 3 and draw in Figure 2, as it can be seen that 20% of the subjects are single and 80% married. Table 3. Subjects' marital status. Marital status Frequency  Percentage Cumulative frequency Single 14 20 20 Married 56 80 100 Total 70 100 100 Resource: Research findings. Resource: Research findings. Table 4 and Figure 3 present the subjects’ condition in terms of age by gender, according to which the age of men (with an average of 41.08 years) is greater than the age of women (with an average of 38.8 years). Table 4 and Figure 3 present the subjects’ condition in terms of age by gender, according to which the age of men (with an average of 41.08 years) is greater than the age of women (with an average of 38.8 years) Page 10/20 Table 4. Subjects’ age by gender status. Table 4. Subjects’ age by gender status. Gender  Number  Mean  Standard Deviation (SD) Standard error age Male  40 41.09 5.82 0.92 Female  30 38.8 4.37 0.79 Resource: Research findings. Resource: Research findings. Table 5 lists the mean scores of the subjects in the research main variables, i.e., patient’s low information, physician’s high information, and high costs of HPOs. As can be seen, the mean scores derived are higher than the average score, i.e., 3, and on the other hand, the mean scores derived for men and women are almost identical. Table 5. The mean scores of the subjects’ responses in terms of the variables of patient’s low information, physician’s high information, and high costs of HPOs, by gender. Table 5. The mean scores of the subjects’ responses in terms of the variables of patient’s low information, physician’s high information, and high costs of HPOs, by gender. Gender  Number  Mean  Standard Deviation (SD) Standard error Patient’s low information Male  40 3.52 0.6 0.09 Female  30 3.48 0.51 0.09 Physician’s high information Male  40 4.15 0.40 0.06 Female  30 4.16 0.51 0.09 High costs of HPOs Male  40 3.76 0.76 0.12 Female  30 3.74 0.82 0.15 Table 5. The mean scores of the subjects’ responses in terms of the variables of patient’s low information, physician’s high information, and high costs of HPOs, by gender. Resource: Research findings. 3.4.2. Research Inferential Findings Before analyzing each of the hypotheses, the Kolmogorov-Smirnov test was used to measure the data normality, and the results are listed in Table 6. Before analyzing each of the hypotheses, the Kolmogorov-Smirnov test was used to measure the data normality, and the results are listed in Table 6. Table 6. Results of Kolmogorov-Smirnov test to measure the data normality. Table 6. Results of Kolmogorov-Smirnov test to measure the data normality. Page 11/20 Index Patient’s low information Physician’s high information High costs of HPOs Number 70 70 70 Kolmogorov Smirnov's z- statistic 0.885 1.265 0.846 Significance level 0.413 0.081 0.472 Resource: Research findings. As can be seen in Table 6, a significance level greater than 0.05 has been derived for all the variables, indicating that according to the z-statistic, each of the variables of patient’s low information, physician’s high information, and high costs of HPOs are statistically significant are in a normal. Therefore, parametric tests can be used in the analysis of each hypothesis. 3.4.2.1. Analysis of Research Hypotheses A) Analysis of the first hypothesis Patient’s low information is positively correlated with physician-induced demand. In order to investigate the relationship between the patient's lack of information and the physician- induced demand, Pearson's correlation test was used, the results of which are listed in Tables 7 and 8. Table 7. Mean and standard deviation of the variables of patient’s low information and physician-induced demand in the subjects. Table 7. Mean and standard deviation of the variables of patient’s low information and physician-induced demand in the subjects. Mean  SD Number  Physician-induced demand 3.50 0.56 70 Patient’s low information 3.63 1.2 70 Resource: Research findings. Table 8. Pearson's correlation coefficient between the variables of patient's low information and physician-induced demand. Table 8. Pearson's correlation coefficient between the variables of patient's low information and physician-induced demand. Patient’s low information Physician-induced demand Pearson correlation 0.350 Significance level 0.003 Number 70 Resource: Research findings. Page 13/20 C) Analysis of the third research hypothesis High costs of healthcare provider organizations (HPOs) is positively correlated with physician-induced demand. High costs of healthcare provider organizations (HPOs) is positively correlated with physician-induced demand. Pearson correlation test was used to investigate the relationship between the high costs of HPOs and the physician-induced demand, the results of which are listed un Tables 11 and 12. Table 11. Mean and standard deviation of the variables of high costs of HPOs and the physician-induced demand in the subjects. Mean  SD Number Physician-induced demand 3.50 0.56 70 High costs of HPOs 3.47 1.17 70 esource: Research findings. Resource: Research findings. Table 12. Pearson's correlation coefficient between the variables of high costs of HPOs and physician- induced demand. Table 12. Pearson's correlation coefficient between the variables of high costs of HPOs and physician- induced demand. High costs of HPOs Physician-induced demand Pearson correlation 0.463 Significance level 0.000 Number 70 Resource: Research findings. High costs of HPOs Physician-induced demand Pearson correlation 0.463 Significance level 0.000 Number 70 Resource: Research findings. Resource: Research findings. As can be seen in Table 12, the Pearson correlation coefficient between the variables of high costs of HPOs and physician-induced demand is equal to r = 0.463, provided that P<0.01. Therefore, it can be said that the correlation between these two variables is significant with a confidence level of 99%. Therefore, according to the positive correlation coefficient, it can be concluded that as the costs of HPOs increases, the physician-induced demand increases, and vice versa. Therefore, the hypothesis H1 is confirmed and the hypothesis H0 is rejected, and the third hypothesis of the research is confirmed as well. Resource: Research findings. Resource: Research findings. As can be seen in Table 8, the Pearson correlation coefficient between the variables of physician-induced demand and patient's low information was obtained as r = 0.350, provided that P<0.01. Therefore, it can be said that the correlation between these two variables is significant with a confidence level of 99%. As can be seen in Table 8, the Pearson correlation coefficient between the variables of physician-induced demand and patient's low information was obtained as r = 0.350, provided that P<0.01. Therefore, it can be said that the correlation between these two variables is significant with a confidence level of 99%. Therefore, considering the positive correlation coefficient, it can be concluded that patient’s low information leads to an increase in the physician-induced demand and vice versa. Therefore, hypothesis H1 is confirmed and hypothesis H0 is rejected, and the first hypothesis of the research is confirmed. B) Analysis of the second research hypothesis Physician’s high information is positively correlated with physician-induced demand. Pearson correlation test is used to investigate the relationship between physician’s high information and physician-induced demand, the results of which are presented in Tables 9 and 10. Table 9. Mean and standard deviation of the variables of physician’s high information and physician- induced demand in the subjects. Table 9. Mean and standard deviation of the variables of physician’s high information and physician- induced demand in the subjects. Mean  SD Number  Physician-induced demand 3.50 0.56 70 Physician’s high information 3.63 1.2 70 Resource: Research findings. Table 10. Pearson's correlation coefficient between physician’s high information and physician-induced demand. Table 10. Pearson's correlation coefficient between physician’s high information and physician-induced demand. Physician’s high information Physician-induced demand Pearson correlation 0.465 Significance level 0.000 Number 70 Resource: Research findings. Physician’s high information Physician-induced demand Pearson correlation 0.465 Significance level 0.000 Number 70 Resource: Research findings. Resource: Research findings. Resource: Research findings. As can be seen in Table 10, Pearson's correlation coefficient between the variables of physician's high information and physician-induced demand is r 0.465, provided that P<0.01. Therefore, it can be said that the correlation between these two variables is significant with a confidence level of 99%. Therefore, according to the positive correlation coefficient, it can be concluded that as the physician's information increases, the physician-induced demand increases, and vice versa. Therefore, hypothesis H1 is confirmed and hypothesis H0 is rejected, and the second hypothesis of the research is confirmed. 4. Conclusions and Suggestions The standard model used in the healthcare economics literature to investigate the agency relationship between healthcare providers and the patient and the effect of information asymmetry on the behavior of the supply side, i.e. the occurrence of supply side bias, is known as induced demand. In other words, the induced demand is a demand in addition to the patient's treatment needs, which is imposed on the Page 14/20 patient by the healthcare deliberately (to earn more money) or undeliberately (due to lack of knowledge, experience, and skills), causing heavy expenses for him/her. For this reason, addressing this issue can be useful in order to reduce violations caused by the superficiality of healthcare service applicants, to reduce the tricks used by some healthcare providers to generate more income, and prevent unnecessary prescriptions. In developed countries, growing technology and various treatment methods are quickly integrated and used by physicians, while in developing countries such as Iran, this occurs at a much lower speed and with a limited number of physicians, which encourage physicians to create induced demand. Accordingly, determination of the factors affecting the induced demand is very effective and requires a lot of discussion and investigation; this made the researchers of the current study to investigate this issue in general (a task that was proposed in the previous research only for one of the indicators affecting the induced demand) and the following results were obtained: The indicators of patient’s low information, physician’s high information, and high costs of HPOs have a positive effect on the supplier-induced demand in healthcare services, or especially suppliers of treatment technologies such as CT scan. Therefore, as the patient’s information decreases, the physician’s information and the costs of HPOs increase, leading to an increase the supplier-induced demand, and the existence of induced demand is confirmed. In addition, the variable of high costs of HPOs (r = 0.463) plays a more significant role in increasing the supplier-induced demand than the other two variables do. In general, the results obtained in this research (factors affecting the induced demand of health care providers) can be considered to be aligned with the results of Khorasani et al. (2013), Abdulli and Varahrami (2010), Varahrami (2009) and Sekimoto et al. (2015). 4. Conclusions and Suggestions On this basis and considering the results of this study, it is suggested to increase the society’s awareness with the aim of controlling the induced demand, to monitor the financial incentives of the HPOs with the help of appropriate control policies, and to keep track of physicians’ performance. Also, paying attention to patients’ dignity and needs, increasing information, increasing patients’ information about treatment and medicine, and passing laws and standards related to physicians’ performance by the medical system organization can also play a significant role in reducing the induced demand. Acknowledgements Not applicable Funding None. Availability of data and materials The statistical population of the present research consisted of the patients referring to CT Scan department, out of whom 80 people were selected as the research sample using the simple random sampling method. Competing interests None. Authors’ contributions SM participated in the study design, collected the data, performed the statistical analysis and interpretation of data. EF participated in the study design, helped in the interpretation of data and helped Page 15/20 to draft the manuscript. HR helped to collect the data and draft the manuscript All authors reviewed and approved the final manuscript. to draft the manuscript. HR helped to collect the data and draft the manuscript All authors reviewed and approved the final manuscript. Ethics approval and consent to participate The manuscript does not involve human participants. Not applicable. Consent for publication Not Applicable References 1. Panahi H., Salmani B., Nasibparast S. (2015). “Investigating the induced effect of the number of physicians and hospital beds on health expenditure in Iran”, Quarterly journal of applied theories of economics, 2(2), 25-42. 1. Panahi H., Salmani B., Nasibparast S. (2015). “Investigating the induced effect of the number of physicians and hospital beds on health expenditure in Iran”, Quarterly journal of applied theories of economics, 2(2), 25-42. 2. Pourreza, A. (2003), Translation of “Health economics for developing countries”, Written by Witter, S. et al., First edition. 3. Khorasani, E., Kivanara, M., Karimi, S., Jafarian Jozi, M. (2013). “Understanding the role of patients in induced demand from the perspective of experts: a qualitative study”, Journal of Qualitative Research in Health Sciences, 2(4), 336-345. 4. Khaki, G. (2000). “Research methodology in management”, Tehran: Scientific and Research Publishing Center of Azad University. 5. Khani, M, (2012). “Examining the physician-induced demand: a case study of caesarean section in Iran, Master's thesis, Faculty of Management and Economics, Sharif University of Technology. 6. Sarmad, Z., Bazargan, A., Hijazi, A. (2007). “Research methods in behavioral sciences”. Tehran: Agah Publishing Institute. 7. Senjari, A. (2009). “Research methods in management”. First Edition. Tehran: Abed Publications. Senjari, A. (2009). “Research methods in management”. First Edition. Tehra Page 16/20 Page 16/20 8. Kivanara, M., Karimi, S., Khorasani, E., Jafarian Jozi, M. (2014). “Do healthcare provider organizations play a role in the induced demand phenomenon? A qualitative study?”, Journal of Faculty of Paramedicine, Tehran University of Medical Sciences, 8(4), 280-293. 9. Kivanara, M., Karimi, S., Khorasani, E., Jafarian Jozi, M. (2014). “Challenges arising from induced demand for health services: A qualitative study”. Health Information Management, 10(4): 538-548. 10. Kivanara, M., Karimi, S., Khorasani, E., Jafarian Jozi, M. (2013). “The opinion of health system experts about the macro factors affecting inducted demand: A qualitative study”. Hakim Research Journal, 16(4), 317-328. 11. Andersen LB, Serritzlew S. (2007). Type of Services and Supplier-Induced Demand for Primary Physicians in Denmark. Kobenhavn: Department of Political Science and Government. 12. Bickerdyke I, Dolamore R, Monday I, Preston R. (2002). Supplier-Induced Demand for Medical Services. Canberra: Productivity Commission Staff Working Paper. 13. Bridges JF, Jones C. (2007). Patient-based health technology assessment: a vision of the future. Int J Technol Assess Health Care; 23(1):30-35. 14. Dranove, David., Wehner, Paul. (1994). Physician-induced demand for childbirths, Journal of Health Economics, 13, 61-73. 15. Grytten, Jostein., Carlsen, Fredrik., Skau, Irene. (2010). References The income effect and supplier induced demand. Evidence from primary physician services in Norway, Applied Economics, 3, 11, 1455-1467. 16. Izumida, Nobuyuki., Urushi, Hiroo., Nakanishi, Satoshi. (1999). An Empirical Study of the Physician- Induced Demand Hypothesis: The Cost Function Approach to Medical Expenditure of the Elderly in Japan, Review of Population and Social Policy, No. 8,11-25. 17. Palesh M, Tishelman C, Fredrikson S, Jamshidi H, Tomson G, Emami A. (2010). We noticed that suddenly the country has become full of MRI. Policy makers’ views on diffusion and use of health technologies in Iran. Health Res Policy Syst; 8:9. 18. Sabatini Dwyer, Debra., Liu, Hong. (2013). The impact of consumer health information on the demand for health services, The Quarterly Review of Economics and Finance,53,1-11. 19. Sekimoto, Miho., MPH., Ii, Masako. (2015). Supplier Induced Demand for Chronic Disease Care in Japan: Multilevel Analysis of the Association between Physician Density and Physician-Patient Encounter Frequency, Value in Health Regional, Issues 6c, 103-110. 20. Woo Lee, Yong. (2012). Asymmetric information and the demand for private health insurance in Korea, Economics Letters, 116, 284–287. 20. Woo Lee, Yong. (2012). Asymmetric information and the demand for private health insurance in Korea, Economics Letters, 116, 284–287. Figures Figures Page 17/20 Figure 1 Conceptual model of research. Resource: research findings. Figure 1 Conceptual model of research. Resource: research findings. Figure 2 Page 18/20 Figure 1. Subjects' gender status. Figure 3 Figure 2. Subjects' marital status. Figure 3 Figure 2. Subjects' marital status. Figure 2. Subjects' marital status. Page 19/20 Figure 4 Figure 3. Subjects’ age by gender status. Page 20/20
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Blood Plasma TGF- β1 Concentration in Sporadic Dilatative Pathology of Ascending Aorta: More Questions than Answers
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Blood Plasma TGF- β1 Concentration in Sporadic Dilatative Pathology of Ascending Aorta: More Questions than Answers Ramune Sepetiene1*, Vaiva Patamsyte1, Giedrius Zukovas2, Giedre Jariene1, Zita Stanioniene1, Rimantas Benetis1,2, Vaiva Lesauskaite1 1 Institute of Cardiology of the Medical Academy, Lithuanian University of Health Sciences, Sukileliu 17, Kaunas, Lithuania, 2 Department of Cardiac, Thoracic and Vascular Surgery, Lithuanian University of Health Sciences, Eiveniu 2, Kaunas, Lithuania * sepetiene@yahoo.co.uk * sepetiene@yahoo.co.uk Data Availability Statement: All data are included within the manuscript. Data Availability Statement: All data are included within the manuscript. Data Availability Statement: All data are included within the manuscript. Funding: Funding was provided by the Research Council of Lithuania for National Research Programme “Chronic Noncommunicable Diseases” (Agreement No LIG 05/2012). Competing Interests: The authors have declared that no competing interests exist Abstract Transforming growth factor β1 (TGF- β1) is a cytokine that participates in a broad range of cellular regulatory processes and is associated with various diseases including aortic aneu- rysm. Increased TGF- β1 levels are associated with Marfan syndrome (MFS) caused by FBN1 mutations and subsequent defects in signaling system. We studied TGF- β1 levels in 62 patients with sporadic, non syndromic, dilatative pathology of ascending aorta (DPAA) and in reference group subjects (n = 212). An initial screening of 212 reference individuals identified TGF- β1 gender discrepancies and age-dependent cytokine increase in women. Patients with DPAA had increased levels of TGF- β1 in comparison to reference group sub- jects (median 7.7 ng/ml, range 2.1–25.3, and median 6.2 ng/ml, range 1.0–33.1, respective- ly). There is a significant association between TGF-β1 concentration and DPAA (OR 1.084, CI 1.027–1.144, p = 0.004) but the mechanisms of cause and effect have not been estab- lished yet. Slightly increased TGF-β1 concentrations in patients with sporadic DPAA in com- parison to the reference subjects show a potential use of TGF-β1 as a biomarker for the disease. However, cytokine dependence on age, gender, and other unknown factors among individuals with no cardiovascular complains reduces its specificity for DPAA. We would also like to raise awareness regarding the choice of methods when measuring TGF- β1 levels with an emphasis on preanalytical phase and the choice of sample. RESEARCH ARTICLE OPEN ACCESS Citation: Sepetiene R, Patamsyte V, Zukovas G, Jariene G, Stanioniene Z, Benetis R, et al. (2015) Blood Plasma TGF- β1 Concentration in Sporadic Dilatative Pathology of Ascending Aorta: More Questions than Answers. PLoS ONE 10(6): e0129353. doi:10.1371/journal.pone.0129353 Academic Editor: Hiromi Yanagisawa, UT- Southwestern Med Ctr, UNITED STATES Received: January 6, 2015 Accepted: May 7, 2015 Published: June 23, 2015 Copyright: © 2015 Sepetiene et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Citation: Sepetiene R, Patamsyte V, Zukovas G, Jariene G, Stanioniene Z, Benetis R, et al. (2015) Blood Plasma TGF- β1 Concentration in Sporadic Dilatative Pathology of Ascending Aorta: More Questions than Answers. PLoS ONE 10(6): e0129353. doi:10.1371/journal.pone.0129353 Academic Editor: Hiromi Yanagisawa, UT- Southwestern Med Ctr, UNITED STATES Received: January 6, 2015 Accepted: May 7, 2015 Published: June 23, 2015 Copyright: © 2015 Sepetiene et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: © 2015 Sepetiene et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Study subjects The study included 62 patients (median age 59 years, range 27–79) operated at the Department of Cardiac, Thoracic and Vascular Surgery of the Lithuanian University of Health Science (LUHS) in 2013–2014 years due to (a) ascending aortic aneurysm (AAA) (n = 35), (b) post-ste- notic dilatation (PSD) of the ascending aorta due to aortic valve stenosis (n = 21), and (c) Stan- ford A dissection (SAD), acute event (n = 6). Clinical characteristics of study subjects are presented in Table 1. PSD group featured 19 individuals (90%) with bicuspid aortic valve, one individual (5%) with a pseudobicuspid valve and the remaining one (5%) with a tricuspid aortic valve. The diagnosis was confirmed by transthoracic echocardiography before the surgery and/ or by direct inspection during surgical repair. Clinical information on concomitant or intercur- rent diseases was assessed by reviewing each patient’s medical history. Only 11% of the patients had no other apart from DPAA. Most commonly reported concomitant or intercurrent dis- eases are presented in Table 1. Histopathological investigation was carried out on all aortic specimens obtained during surgery. Exclusion criteria were phenotypic features of Marfan syn- dromes, aortitis and ulcerating atherosclerosis of the ascending aorta. A reference group was recruited from a randomised cluster sampling of local population (n = 212). One cluster consisted of students and staff volunteers from LUHS (n = 72, median age 49 years, range 23–67) and the second cluster consisted of volunteers (n = 140, median age 65 years, range 41–87) appointed to their physician in Dainavos outpatient’s clinic (Kaunas). Table 1. Concomitant or intercurrent diseases in patients with dilatative pathology of ascending aorta (DPAA) and in Reference group subjects. omitant or intercurrent diseases in patients with dilatative pathology of ascending aorta (DPAA) and in Refe ses in patients with dilatative pathology of ascending aorta (DPAA) and in Reference group subjects. Table 1. Concomitant or intercurrent diseases in patients with dilatative pathology of ascending aorta (D Table 1. Concomitant or intercurrent diseases in patients with dilatative pathology of ascending aorta (DPAA) and in Reference group subjects. Introduction Marfan syndrome (MFS) is caused by mutations in the fibrillin-1 encoding gene FBN1. It has been discovered that fibrillin-1 regulates the bioavailability of transforming growth factor –β1 (TGF-β1) [1]. The latter is a member of TGF- β pluripotent cytokine family involved in tissue morphogenesis and homeostasis [2]. Moreover, an altered TGF-β signaling contributes signifi- cantly to the pathology of MFS [1]. In humans, circulating total TGF- β1 concentrations are el- evated in patients with MFS in comparison to control individuals; in addition, correlation Competing Interests: The authors have declared that no competing interests exist. PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 1 / 7 TGF- β1 in Dilatative Pathology of Ascending Aorta between circulating TGF-β1 levels and aortic root diameters in MFS mutant Fbn1(C1039G/+) and wild-type mice is observed [3]. Recent studies demonstrate that Smad-independent TGF-β signaling has an essential function in aneurysm morphogenesis in MFS mice [4]. Hillebrand et al. (2014) demonstrated that TGF-β1 increase was observed not only in MFS patients, but also in other genetic aortic syndromes [5]. Considering the role of FBN1 polymor- phisms for sporadic thoracic aneurysm and dissection [6,7] we analysed TGF-β1 concentra- tions in blood plasma from patients with sporadic dilatative pathology of ascending aorta and reference group subjects. TGFß1 quantitative detection Blood samples from DPAA patients were obtained before the surgery and our reference group gave blood at the time of arrival. Blood was collected using 3ml Venosafe blood collection tubes containing 5.9 mg K2EDTA (Terumo Europe, Belgium). Plasma was obtained within 2 hours by spinning for 15 min at 2500 rpm, aliquoted and stored frozen at -20°C. Plasma sam- ples were tested in duplicate using eBioscience Platinum (Bender Med Systems GmbH, Aus- tria) human TGF-β1 ELISA kit based on standard sandwich enzyme-linked immune-sorbent assay technology according to manufacturers’ instructions. Absorbance was measured using Stat-fax 4200 microplate reader using 450 nm as a primary wave length. Manufacturers indi- cated cross reactivity with TGF-β2 and TGF-β3 was less than 0.01%. Statistical analysis Non-parametric Kruskal-Wallis test was used for statistical analysis. Spearman's rank order correlation was used to evaluate the effects of age and gender on TGF-β1 levels. The association of TGF- β1 concentration with DPAA was assessed using logistic regression model adjusted for gender and age. Statistical significance was set at p = 0.05. Study subjects Concomitant or intercurrent diseases DPAA (n = 62), n (%) Reference group (n = 212), n (%) SAD n = 6 PSD n = 21 AAA n = 35 Age (years) 54 (46–59) 60 (27–75) 59 (30–78) 62 (23–87) Gender M = 4 (66.7%) M = 15 (71.4%) M = 30 (85.7%) M = 105 (49.5%) F = 2 (33.3%) F = 6 (28.6%) F = 5 (14.3%) F = 107 (50.5%) Coronary artery disease 2 (33.3%)* 11 (52.4%)* 14 (40.0%)* 1 (0.4%) Hypertension 4 (66.7%)* 14 (66.7%)* 30 (85.7%)* 71 (31.3%) Atrial fibrillation 2 (33.3%)* 2 (9.5%)* 6 (17.1%)* - Diabetes mellitus - 1 (4.8%)* - 1 (0.4%) Urinary system pathology - - 4 (11.4%)* 2 (0.9%) Gastrointestinal and biliary system pathology 1 (16.7%)* 3 (14.3%)* 9 (25.7%)* 7 (3.1%) Locomotion system pathology - - - 6 (2.6%) Respiratory system pathology 1 (16.7%)* - 1 (2.9%)* 2 (0.9%) *percentage is calculated for each subgroup cases SAD—Stanford A dissection; PSD—Post Stenotic Dilatation; AAA—Ascending Aortic Aneurysm doi:10.1371/journal.pone.0129353.t001 PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 2 / 7 TGF- β1 in Dilatative Pathology of Ascending Aorta All volunteers completed questionnairs on the state of their health. Overall majority (63.9%) had no complains about their health state. Most commonly reported diseases are presented in Table 1. Neither of the included subjects reported having cancer or autoimmune diseases, asso- ciated with increased TGF-β1 level.[8] Ethical approval was obtained from the Ethics Committee of the Lithuanian Health Science University (No: BE-2-12) and all subjects provided written informed consent for participation in the study. PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 Results The reference group (n = 212) consisted of 105 males and 107 females (Table 1). Overall distri- bution of TGF-β1 values is shown in Fig 1. The lowest TGF-β1 concentration was 1.0 ng/ml and the highest was 33 ng/ml. Coefficient variation of results did not exceed the 4% detection limit of human TGF-β1 determined to be on average 8.6 ng/ml by six independent assays (Human TGF-β1 platinum ELISA product information and manual). Investigation of the ref- erence group indicated higher TGF-β1 concentration (p = 0.017) in males (median 7.27 ng/ml, range 1.00–33.12) compared to females (median 5.38 ng/ml, range 1.10–21.20) (Table 2). TGF- β1 level showed a tendency to increase with age in women (R = 0.338, p<0.001) but was steady in men (R = 0.105, p = 0.288) throughout lifetime. These results indicate that age and gender can be confounding effects when comparing TGF-β1 levels between the study groups. Patients with Stanford A dissection had slightly higher TGF-β1 concentration, but there were no significant differences in TGF-β1 concentration between patients with various pheno- types of DPAA or between each phenotype and the reference group subjects. Overall, patients with DPAA had significantly higher TGF-β1 concentration than the reference group (Table 3). Differences in TGF-β1 values between DPAA males (median 7.60 ng/ml) and the reference male population (median 7.27 ng/ml) were not statistically significant (p = 0.135) whereas con- centration between females in DPAA (median 8.80 ng/ml) and the reference group (median 5.38 ng/ml) were confidently higher (p = 0.004). Finally, we analyzed association between TGF-β1 concentration and DPAA which resulted in odds ratio (OR) 1.084 (95% confidence in- terval 1.027–1.144, p = 0.004). 3 / 7 PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 TGF- β1 in Dilatative Pathology of Ascending Aorta Fig 1. TGF-β1 concentration in the reference group according to the gender and age. Fig 1. TGF-β1 concentration in the reference group according to the gender and age. Fig 1. TGF-β1 concentration in the reference group according to the gender and age. Fig 1. TGF-β1 concentration in the reference group according to the gender and age. doi:10.1371/journal.pone.0129353.g001 doi:10.1371/journal.pone.0129353.g001 PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 TGF- β1 in Dilatative Pathology of Ascending Aorta variuos phenotypes of dilatative pathology of ascending thoracic and reference group subjects. Table 3. TGF-β1 concentration in patients with variuos phenotypes of dilatative pathology of ascending thoracic and reference group subjects. TGF-β1 Stanford A dissection, n = 6 Post stenotic dilatation, n = 21 Aneurysm n = 35 Total n = 62 Reference group, n = 212 Median range) ng/ml 10.1 (6.58–17.6) 7.7 (2.1–22.0) 7.8 (2.3–25.3) 7.7 (2.1–25.3)* 6.2 (1.0–33.1) *p = 0,010 versus Reference group doi:10 1371/journal pone 0129353 t003 ration in patients with variuos phenotypes of dilatative pathology of ascending thoracic and reference grou concentrations were reported in studies where blood serum was used. This phenomenon could be attributed to the presence of platelets which contain β-granules rich in TGF-β1 [12]. TGF- β1 concentration in serum accounts for both, the amount of cytokine in the systemic circula- tion and the amount released from platelet α-granules during clotting process [13]. TGF-β1 concentration detected in serum should be referred critically due to the strong positive correla- tion between platelet count and the serum concentration of TGF-β1 [14]. TGF-β1 variation among studies (Table 4) illustrates the importance of the blood sample used for testing and should always be taken into account when comparing results from different studies. concentrations were reported in studies where blood serum was used. This phenomenon could be attributed to the presence of platelets which contain β-granules rich in TGF-β1 [12]. TGF- β1 concentration in serum accounts for both, the amount of cytokine in the systemic circula- tion and the amount released from platelet α-granules during clotting process [13]. TGF-β1 concentration detected in serum should be referred critically due to the strong positive correla- tion between platelet count and the serum concentration of TGF-β1 [14]. TGF-β1 variation among studies (Table 4) illustrates the importance of the blood sample used for testing and should always be taken into account when comparing results from different studies. Our estimation of circulating TGF-β1 levels can be compared with the results reported by Matt and colleagues [3] since both studies used human blood plasma to obtain measurements. We obtained higher TGF-β1 values in the reference group compared to the latter study which could be attributed to the selection of the study subjects. Our reference group was three times larger and over a third of participants reported their health complains (Table 1). Discussion and Conclusions Recent studies draw attention to the role of TGF-β1 signaling system for aortic dilatation in MFS [3] or other genetic aortic syndromes [5]. We analyzed blood plasma TGF-β1 concentra- tion in patients with sporadic dilatative pathology of ascending aorta and in the reference group subjects. For the first time we reported irregularity of TGF-β1 concentration in blood plasma caused by age and gender in subjects from the reference group. TGF-β1 concentration in males did not change with age and was significantly higher in comparison to females, while TGF-β1 concentration in females showed a significant increase due to older age. The latter phe- nomenon might be attributed to TGF-β1 signaling system activation by follicle-stimulating hormone (FSH) [9, 10]. It is well known that levels of FSH in females increase at perimen- opausal age and decline only in the eighth/ninth decade [11]. FSH regulates post-menopausal endometrial atrophy by blocking TGF-β1 receptor II and blocking Smad2/3 activation path- way. FSH inhibitory action could compromise the ability of TGF-β1 to enter a cell and lead to an accumulation of TGF-β1 in blood plasma [9]. We gathered information on TGF-β1 concentrations in Marfan syndrome patients with DPAA and controls from previous studies and summarized it in Table 4. Higher TGF-β1 Table 2. Age and gender distribution among DPAA and Reference groups. Group Male Female Age (yrs) median (range) DPAA (N = 62) 49 13 59 (27–79) Reference (N = 212) 105 107 62 (23–87) DPAA—Dilatative pathology of ascending aorta doi:10.1371/journal.pone.0129353.t002 Table 2. Age and gender distribution among DPAA and Reference groups. PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 4 / 7 Some individ- uals with extremely high TGF-β1 values were not excluded from further analysis in order to evaluate TGF-β1 specificity in a real-life situation. This could partially explain why the cytokine values in our reference group were higher than the ones reported by Matt et al. [3]. Studies using both human blood plasma and serum indicate increased TGF-β1 values in Marfan patients with DPAA [3, 5, 14, 15]. We show that non-marfanoid patients with DPAA also have elevated plasma levels of TGF-β1 compared to the reference group. Patients with Stanford A dissection have particularly high TGF-β1 concentrations in comparison to patients with other phenotypes of DPATA. Such an increase could be caused by the liberation of TGF- β1 into the plasma from activated platelets during acute aortic rupture. Thus, we conclude that platelet activation might have an impact on the TGF-β1 concentration in blood plasma. Standard methodical steps are used when measuring TGF-β1 concentration including acid activation and neutralisation with subsequent incubation and washing application to obtain Table 4. Data on TGF-β1 concentration in patients with DPATA and controls. Marfan Syndrome Control group Plasma/ Serum Assay/kit Reference 43.78 ng/ml in dissection group 25.7 ng/ml Serum R&D Systems, Minneapolis, USA Agg et al., 2014 [12] 31.64 ng/ml in annuloaortic ectasia group 15 ng/ml in MFS without cardiovascular therapy 2.5 ng/ml Plasma R&D Systems, Minneapolis, USA Matt et al., 2009 [3] 44.4 ng/ml Without genetic aortic syndrome 32 ng/ml Serum R&D Systems, Minneapolis, USA Hillerbrand et al., 2014 [5] 109 pg/ml 54 pg/ml Plasma (?) Bio-Rad, Richmond, Canada Franken et al., 2013 [13] 1.31 ng/ml 1.17 ng/ml Plasma Mesco Scale Discovery, Gaithesburg, MD, USA Ogawa et al., 2012 [14] doi:10.1371/journal.pone.0129353.t004 Table 4. Data on TGF-β1 concentration in patients with DPATA and controls. PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 5 / 7 TGF- β1 in Dilatative Pathology of Ascending Aorta active TGF-β1. Unfortunately, none of the commercially available tests have been evaluated by standardised method comparison methodology [16]. To avoid misevaluation of cytokine levels strict preanalytical procedures are recommended: (i) special venipuncture without a tourniquet [17] and (ii) detection of markers for platelet degranulation (e.g. platelet factor 4) simulta- neously with TGF-β1 [12, 18] in order to reduce errors in preanalytical phase. The choice of ex- perimental design could explain the discrepancies among the results reported in the Marfan studies (Table 4). Acknowledgments Financial support for the study was provided by the Research Council of Lithuania for National Research Programme “Chronic Noncommunicable Diseases” (Agreement No LIG 05/2012) Financial support for the study was provided by the Research Council of Lithuania for National inancial support for the study was provided by the Research Council of Lithuania for National esearch Programme “Chronic Noncommunicable Diseases” (Agreement No LIG 05/2012). Research Programme “Chronic Noncommunicable Diseases” (Agreement No LIG 05/2012). Our study limitation is the fact that we did not carry out simultaneous mea- surements of markers for platelet degranulation so the effect of platelet activation on TGF-β1 concentration in blood plasma was not controlled analytically. Secondly, patients with DPAA had high prevalence (89%) of concomitant or intercurrent diseases which also might have an impact on higher levels of TGF-β1. We reported a significant association between TGF-β1 concentration and DPAA but the mechanisms of cause and effect have not been established yet. Slightly increased TGF-β1 con- centration in patients with sporadic DPAA in comparison to the reference subjects requires further investigation to establish its role in sporadic DPAA pathogenesis. We would also like to raise awareness regarding the choice of methods when measuring TGF-β1 levels with an em- phasis on preanalytical phase and the choice of sample. Author Contributions Conceived and designed the experiments: RS VP GJ VL. Performed the experiments: RS VP. Analyzed the data: RS VP ZS VL. Contributed reagents/materials/analysis tools: RS VP GZ GJ ZS RB VL. Wrote the paper: RS VP VL. Conceived and designed the experiments: RS VP GJ VL. Performed the experiments: RS VP. Analyzed the data: RS VP ZS VL. Contributed reagents/materials/analysis tools: RS VP GZ GJ ZS RB VL. Wrote the paper: RS VP VL. PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 References 1. Chaudhry SS, Cain SA, Morgan A, Dallas SL, Shuttleworth CA, et al. (2007) Fibrillin-1 regulates the bio- availability of TGFbeta1. J Cell Biol 176: 355–367. PMID: 17242066 2. Barrett PM., Topol EJ (2012) The fibrillin-1 gene: unlocking new therapeutic pathways in cardiovascular disease. Heart 99: 83–90. doi: 10.1136/heartjnl-2012-301840 PMID: 22942299 3. Matt P, Schoenhoff F, Habashi J, Holm T, Van Erp C, et al. (2009) Circulating transforming growth fac- tor-β in Marfan syndrome. Circulation 120: 526–532. doi: 10.1161/CIRCULATIONAHA.108.841981 PMID: 19635970 4. Holm TM, Habashi JP, Doyle JJ, Bedja D, Chen Y, et al. (2011) Noncanonical TGFβ signaling contrib- utes to aortic aneurysm progression in Marfan syndrome mice. Science 332: 358–361. doi: 10.1126/ science.1192149 PMID: 21493862 5. Hillebrand M, Millot N, Sheikhzadeh S, Rybczynski M, Gerth S, et al. (2014)Total serum transforming growth factor-β1 is elevated in the entire spectrum of genetic aortic syndromes. Clin Cardiol 37 (11): 672–9. doi: 10.1002/clc.22320 PMID: 25113270 6. LeMaire SA, McDonald ML, Guo DC, Russell L, Miller CC 3rd, et al. (2011) Genome-wide association study identifies a susceptibility locus for thoracic aortic aneurysms and dissections spanning FBN1 at 15q21.1. Nat Genet 43:996–1000. doi: 10.1038/ng.934 PMID: 21909107 7. Lesauskaite V, Sepetiene R, Jariene G, Patamsyte V, Zukovas G et al. (2014) FBN1 polymorphisms in patients with the dilatative pathology of the ascending thoracic. urJ Cardiothorac Surg, in press. 8. Bierie B, Moses HL (2010) "Transforming growth factor beta (TGF-β) and inflammation in cancer." Cy- tokine & growth factor reviews 21.1: 49–59 9. Zhang D, Li J, Xu G, Zhang R, Zhou C, et al. (2014) Follicle-stimulating hormone promotes age-related endometrial atrophy through cross-talk with transforming growth factor beta signal transduction path- way. Aging Cell. Available: http://onlinelibrary.wiley.com/doi/10.1111/acel.12278/full. Accessed 2014 Dec 16. 6 / 7 PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 TGF- β1 in Dilatative Pathology of Ascending Aorta 10. Gueripel X, Benahmed M, Gougeon A (2003) Sequential gonadotropin treatment of immature mice leads to amplification of transforming growth factor beta action, via upregulation of receptor-type 1, Smad 2 and 4, and downregulation of Smad 6. Biol Reprod 70:640–648. PMID: 14585817 11. Vaninetti S, Baccarelli A, Romoli R, Fanelli M, Faglia G et al. (2000) Effect of aging on serum gonadotro- pin levels in healthy subjects and patients with nonfunctioning pituitary adenomas. Eur J Endocrinol 142:144–149. PMID: 10664522 12. PLOS ONE | DOI:10.1371/journal.pone.0129353 June 23, 2015 References Assoian RK, Sporn MB (1986) Type beta transforming growth factor in human platelets: release during platelet degranulation and action on vascular smooth muscle cells. J Cell Biol 102: 1217–1223. PMID: 3457014 13. Meyer A, Wang W, Qu J, Croft L, Degen JL, et al. (2012). Platelet TGF-β1 contributions to plasma TGF- β1, cardiac fibrosis, and systolic dysfunction in a mouse model of pressure overload. Blood, 119(4): 1064–1074. doi: 10.1182/blood-2011-09-377648 PMID: 22134166 14. Agg B, Benke K, Szilveszter B, Polos M, Daroczi L, et al. (2014) Possible extracardiac predictors of aor- tic dissection in Marfan syndrome. BMC Cardiovasc Disord 14: 47. Available: http://www. biomedcentral.com/1471-2261/14/47. Accessed 2014 Dec 16. doi: 10.1186/1471-2261-14-47 PMID: 24720641 15. Franken R, den Hartog AW, de Waard V, Engele L, Radonic T, et al. (2013) Circulating transforming growth factor-β as a prognostic biomarker in Marfan syndrome. Int J Cardiol 168: 2 16. Kropf J, Schurek JO, Wollner A, Gressener AM (1997) Immunological measurement of transforming growth factor-beta 1 (TGF-beta1) in blood; assay development and comparison. Clin Chem 43: 1965– 1974. 441–2446. PMID: 9342020 17. Ludlam CA, Moore S, Bolton AE, Pepper DA, Cash JD (1975) The release of a human platelet specific protein measured by a radioimmunoassay. Thromb Res 6: 543–548. PMID: 1154329 18. Ogawa N, Imai Y, Nishimura H, Kato M, Takeda N, et al. (2013) Circulating Transforming Growth Factor β-1 Level in Japanese Patients With Marfan Syndrome. Int Heart J 54: 23–26. PMID: 23428920 7 / 7
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Demand Response From the Control of Aggregated Inverter Air Conditioners
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Received June 3, 2019, accepted June 23, 2019, date of publication June 28, 2019, date of current version July 18, 2019. Received June 3, 2019, accepted June 23, 2019, date of publication June 28, 2019, date of current version July 18, 2019. Digital Object Identifier 10.1109/ACCESS.2019.2925659 Digital Object Identifier 10.1109/ACCESS.2019.2925659 The associate editor coordinating the review of this manuscript and approving it for publication was Shantha Jayasinghe. his work is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://creativecommons.org/licenses/by/3.0/ YANBO CHE 1, (Member, IEEE), JIANXIONG YANG1, YUE ZHOU 2, (Member, IEEE), YUANCHENG ZHAO 1, WEI HE3, AND JIANZHONG WU 2, (Member, IEEE) 1Key Laboratory of Smart Grid of Ministry of Education, Tianjin University, Tianjin 300072, China 2School of Engineering, Cardiff University, Cardiff CF24 3AA, U.K. 3State Grid Jiangxi Electric Power Research Institute, Nanchang 330096, China Corresponding author: Yue Zhou (zhouy68@cardiff.ac.uk) Corresponding author: Yue Zhou (zhouy68@cardiff.ac.uk) This work was supported in part by the State Grid Corporation of China (SGCC) Program, Research on Extensive Application and Benefit Evaluation of Typical Power Substitution Technology Considering Power Quality Influence, under Grant 52182018000H, and in part by the Research Councils UK’s (RCUK’s) Energy Programme ‘Joint UK-India Clean Energy Centre (JUICE)’ under Grant EP/P003605/1. ABSTRACT Inverter air conditioners (ACs) account for a large proportion of air conditioning loads in many countries and, thus, contribute significantly to the peak loads in these areas, especially in summer. On the other hand, as an important category of thermostatically controlled load with thermal energy storage capability, inverter ACs also have the potential to provide considerable flexibility for electric power systems that are faced with increasing challenges posed by high penetration of renewable power generation. This paper focuses on the demand response from the control of the aggregated inverter ACs for load reduction. A virtual energy storage system (VESS) model that encapsulates the room with an inverter AC was established based on the electric model of an inverter AC and the thermodynamic model of a room. Based on the VESS model, a virtual state of charge (VSOC) priority-based load reduction control method with temperature holding and linear recovery strategies was proposed. The VSOC priority based control was designed to decrease the negative impact of load reduction on customers’ thermal comfort from the perspective of the whole AC population. The temperature holding strategy was designed to reduce the electric power of an AC while ensuring that the indoor temperature is always below the allowable limit. The linear recover strategy was proposed to reduce the load rebound after load reduction. Four cases were studied regarding the operation and load reduction of the 100 inverter ACs, and the simulation results verified the models established and the effectiveness and advantages of the proposed load reduction control method. INDEX TERMS Inverter air conditioner, demand response, load reduction, virtual energy storage system. VOLUME 7, 2019 This work is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://creativecommons. I. INTRODUCTION important, and there have been a huge number of research activities and industrial practices on demand response across the world [1]. Within the wide range of flexible loads, thermostatically controlled loads (TCLs) are important flexible resources due to their large electric power consump- tion and thermal energy storage capability. Within certain ranges, the power consumption of TCLs can be shifted, reduced or reshaped without compromising customers’ ther- mal comfort. Therefore, there have been abundant studies made on utilizing TCLs to provide multiple types of demand response services, including load following [2], frequency response [3], operating reserves [4], renewable generation following [5], voltage stability improvement [6], etc. With the global consensus on preventing global warming and boosting sustainable development, there is a rapidly increasing penetration of renewable power generation in elec- tric power systems. The intermittency and randomness of renewable energy, such as wind and solar energy, make it even more difficult and costly for power systems to maintain the balance between supply and demand. Furthermore, the associated decreasing share of conventional generators, such as thermal and hydro generating units, reduces the flexibility at the supply side of power systems, making the situation even more critical. Against this background, to utilize the flexibility at the demand side of power systems becomes increasingly Air conditioning loads are one of the major components of TCLs, which account for a large proportion of total and peak loads in many areas especially in summer, such as the south of China, California in the U.S., etc. As a result, The associate editor coordinating the review of this manuscript and approving it for publication was Shantha Jayasinghe. 88163 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs extensive studies have been conducted regarding the demand response from both residential (such as those in [7]–[9]) and commercial (as reviewed in [10]) air conditioning loads. detection errors analyzed [24]. Viriyautsahakul et al proposed to control inverter ACs to provide reactive power support for power systems [25]. Yao et al proposed market based autonomous control for inverter ACs to provide ancillary services, such as frequency regulation and microgrid tie- line power smoothing [26]. The proposed control method is of good generalizability and protects the customers’ privacy well. Customers’ comfort is also able to be guaranteed fairly. II. MODELLING METHODOLOGY In this section, the models involved in this paper are presented, including the electric model of an inverter AC, the thermodynamic model of the room, and the VESS model that encapsulates the room with an inverter AC. Furthermore, the third category of studies tried to control inverter ACs to provide ancillary services for power systems. Kim et al established a dynamic model of a variable speed heat pump (VSHP) responding to the frequency regulation signals, and small signal analysis was conducted to verify that direct load control could be generally applied to VSHPs [22]. Kim et al further conducted experimental studies to explore this research topic [23]. Hui et al proposed centralized and decentralized control methods for inverter ACs to provide primary frequency control services, with the signal delays and I. INTRODUCTION Wang et al proposed a distributed consensus control method for controlling inverter ACs for renewable energy integra- tion, where the impact of communication failure could be significantly reduced [27]. Cheng et al used inverter ACs to establish virtual synchronous generators to improve the inertia of power systems [28]. Most existing studies regarding the demand response from air conditioners (ACs) focus on single speed ACs. However, in recent years, the number of inverter ACs keeps growing, accounting for a significant share of total ACs installed in many areas and countries. For example, in the residential sector of China, the percentage of inverter ACs in total num- ber of ACs has reached about 40% [11]. This percentage is even higher in developed countries such as Japan, the U.S. and some European countries [12]. Compared to single speed ACs, the compressor of an inverter AC is able to operate at variable speeds, and thus inverter ACs have some advantages including 1) higher comfort level because the indoor temper- ature is maintained within a narrow band around the set point, 2) lower power consumption when thermostatically operating around the set point [13], and 3) better performance during startup, grid voltage variation and locked-rotor periods [13]. Most existing studies regarding the demand response from air conditioners (ACs) focus on single speed ACs. However, in recent years, the number of inverter ACs keeps growing, accounting for a significant share of total ACs installed in many areas and countries. For example, in the residential sector of China, the percentage of inverter ACs in total num- ber of ACs has reached about 40% [11]. This percentage is even higher in developed countries such as Japan, the U.S. and some European countries [12]. Compared to single speed ACs, the compressor of an inverter AC is able to operate at variable speeds, and thus inverter ACs have some advantages including 1) higher comfort level because the indoor temper- ature is maintained within a narrow band around the set point, 2) lower power consumption when thermostatically operating around the set point [13], and 3) better performance during startup, grid voltage variation and locked-rotor periods [13]. In this context, some preliminary research has been conducted regarding the demand response from inverter ACs, which could be further classified into three categories. The first category of studies are to explore the load reduction from inverter ACs. I. INTRODUCTION In [15], the maximum duration of load reduction was considered. Considering the load reduction strategy proposed in [15], power system network planning problems were addressed in [17] and [18]. The paper is organized as follows. Section II presents the models involved in this work, including the electric model of an inverter AC, the thermodynamic model of the room, and the VESS model that encapsulates the room with an inverter AC. Section III presents the VSOC priority based load reduction control method with temperature holding and linear recovery strategies. Section IV presents the case studies. Finally, Section V concludes the paper. The second category of studies were made to control inverter ACs to arbitrage in electricity markets. Song et al modeled inverter ACs as a thermal battery to be compatible with power system dispatch models, and a hierarchical con- trol framework was proposed to handle the heterogeneity of ACs, protect customers’ privacy and reduce the com- putational burden [19]. Hu et al established models for inverter ACs and room thermal dynamics, and proposed temperature set point and frequency control methods for arbitraging in day-ahead and real-time electricity markets respectively [20], [21]. I. INTRODUCTION Ninagawa et al established neural net- work models based on practical operational data of inverter ACs for simulating their load reduction response [14]. The practical communication environment was also emulated. Yang et al. [15] and Huang et al. [16] both focused on load reduction strategies of aggregated ACs. In [16], thermal com- fort of customers was considered through a model embedded with predicted mean vote (PMV) and predicted percentage of dissatisfied (PPD). In [15], the maximum duration of load reduction was considered. Considering the load reduction strategy proposed in [15], power system network planning problems were addressed in [17] and [18]. The work of this paper lies in the first category of studies as described above, focusing on the load reduction from the control of aggregated inverter ACs. However, compared to the existing studies, such as [14]–[18], this paper has the following contributions. Similar to that in [19], this paper models the space with inverter ACs as virtual energy storage systems (VESSs), but based on this model, this paper further proposes to control the ACs according to the descending order of virtual state of charge (VSOC) of VESSs. Moreover, an innovative ‘temperature holding’ strategy is proposed to conduct the load reduction for each inverter AC to guarantee that the indoor temperature will not deviate beyond the pre- agreed upper limit. Furthermore, this paper proposes a linear recovery strategy to reduce the load rebound after load reduc- tion, which has not been considered in the existing studies regarding load reduction from inverter ACs. Besides, this paper pays special attention to the load reduction for the peak caused by the turning ON of large numbers of inverter ACs within a short period of time. In this context, some preliminary research has been conducted regarding the demand response from inverter ACs, which could be further classified into three categories. The first category of studies are to explore the load reduction from inverter ACs. Ninagawa et al established neural net- work models based on practical operational data of inverter ACs for simulating their load reduction response [14]. The practical communication environment was also emulated. Yang et al. [15] and Huang et al. [16] both focused on load reduction strategies of aggregated ACs. In [16], thermal com- fort of customers was considered through a model embedded with predicted mean vote (PMV) and predicted percentage of dissatisfied (PPD). B. THERMODYNAMIC MODEL OF A ROOM The first order equivalent thermal parameters (ETP) model [7] is adopted in this paper to simulate the thermody- namics of the space installed with inverter ACs. The model is expressed as For an inverter AC which is turned ON, the relationship between the operating frequency and the difference between the indoor temperature and the set point is illustrated in Fig. 1 [29]. C · dTin dt = Tout −Tin R −Q (5) (5) where Tin(◦C) and Tout(◦C) represent the indoor and outdoor temperature; t is the variable representing the time; R(◦C/kW) and C(kWh/◦C) are the equivalent thermal resistance and thermal capacity respectively. The relationship shown in Fig. 1 can be expressed as f =    fmin 1T < u fmax −fmin u −v · 1T + (u −2v)fmax −vfmin u −v fmax 1T > v (1) The differential equation (5) is discretized as the difference equation as follows: (1) Tin(t+1)=Tout(t)−QR−[Tout(t)−Tin(t)−QR] · e−1t/(RC) where f (Hz) represents the operating frequency of the inverter AC; fmin(Hz) and fmax(Hz) are the minimum and maximum operating frequency of the inverter AC; 1T(◦C) is the difference between the indoor temperature and the set point; u(◦C) and v(◦C) are the knee points as illustrated in Fig. 1. (6) (6) where 1t(h) is the length of a time step. where 1t(h) is the length of a time step. A. THE ELECTRIC MODEL OF AN INVERTER AC For a conventional single speed AC, hysteresis control with two thresholds is adopted to control the ON/OFF status of the compressor to maintain the indoor temperature within the thresholds. The compressor periodically turns ON/OFF when the indoor temperature hits the upper/lower temperature thresholds. 88164 VOLUME 7, 2019 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs FIGURE 1. The relationship between the operating frequency and the difference between the indoor temperature and the set point for an inverter AC [29]. FIGURE 2. The model of the room with an inverter AC. FIGURE 1. The relationship between the operating frequency and the difference between the indoor temperature and the set point for an inverter AC [29]. By contrast, for an inverter AC, the operating frequency of its compressor can be adjusted continuously, based on the difference between the indoor temperature and the tem- perature set point. Therefore, when the indoor temperature is far from the set point, the inverter AC will operate at high frequency to cool the space quickly. When the indoor temperature is close to the set point, the inverter AC will operate at low frequency to maintain the indoor temperature closely around the set point. In this way, inverter ACs can provide higher level of thermal comfort and consume lower level of electricity during the temperature maintaining stage compared with single speed ACs [13]. FIGURE 2. The model of the room with an inverter AC. From (4), it is seen that the COP of an inverter AC is not a constant but varies with its operating frequency, which is different from that of a single speed AC. C. VESS MODEL ENCAPSULATING THE ROOM WITH AN INVERTER AC Based on the electric model and thermodynamic model pre- sented in the previous sub-sections (Sections II-A and II-B), the room with an inverter AC can be described by combining (1)-(6), which is illustrated in Fig. 2. The cooling and electric power of the inverter AC can be simplified as linear functions of the operating frequency, which are expressed as [19] Q = a · f + b, (2) P = c · f + d, (3) (2) (3) In order to conduct load reduction with minimum impact on customers’ thermal comfort, which will be detailed in Section III, the rooms with inverter ACs are modeled as VESSs. First of all, analogous to the SOC of batteries, the VSOC of the VESS is defined as where Q(kW) and P(kW) represent the cooling and electric power of the inverter AC respectively. a(kW/Hz), b(kW), c(kW/Hz) and d(kW) are constant coefficients. VSOC = T max in −Tin T max in −T setpoint in (7) (7) By taking (2) divided by (3), the coefficient of performance (COP) of the inverter AC is expressed as COP = a · f + b c · f + d . (4) where T max in (◦C) is the pre-agreed maximum indoor temperature during load reduction. Equation (7) is able to where T max in (◦C) is the pre-agreed maximum indoor temperature during load reduction. Equation (7) is able to (4) VOLUME 7, 2019 VOLUME 7, 2019 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs indicate the cooling energy stored in the room. When the indoor temperature Tin equals to the set point T setpoint in , the VSOC equals to 1 according (7), indicating that the room stores maximum level of cooling energy considering that normally the indoor temperature will not be lower than the set point. When the Tin equals to the maximum indoor temperature T max in , the VSOC equals to 0, indicating that the cooling energy stored reaches the lowest allowed level. Therefore, normally the value of VSOC will range within [0, 1]. When Tin exceeds T max in , the VSOC will be negative values, indicating that the VESS has been over-discharged, i.e. the customers’ thermal comfort has been violated. thermal comfort. C. VSOC PRIORITY BASED CONTROL In order to meet the load reduction target, a subset of inverter ACs need to be selected to be controlled with the tempera- ture holding strategy. The inverter ACs to be controlled are selected following the VSOC priority principle to minimize the impact of load reduction on customers’ thermal comfort (which will be assessed and verified in Case 4 in Section IV). Specifically, the inverter ACs are selected to be controlled following the descending order of their VSOC until the load reduction target is satisfied. Note that if the VSOC is negative, the corresponding AC will not be controlled, because neg- ative VSOC means that the indoor temperature has already exceeded the maximum limit (see Section II-C) and the tem- perature needs to be further decreased to satisfy customers’ thermal comfort. After the contracts are made, the power utility will directly control customers’ inverter ACs in a centralized manner to conduct load reduction, based on some measurements taken from the customers. The specific control method used is presented in the following sub-sections. III. CONTROL METHODOLOGY In this section, a VSOC priority based control method with temperature holding and linear recover strategies is presented for control aggregated inverter ACs for load reduction. 1P = c · (foriginal −fLR) + d. (10) (10) where foriginal is the operating frequency of the inverter AC if no load reduction control is imposed, which can be calculated by (1). C. VESS MODEL ENCAPSULATING THE ROOM WITH AN INVERTER AC From the angle of load reduction, the new fixed operating frequency instructed stops the indoor tem- perature from further decreasing, which thus results in less electric power consumption compared to that of the inherent control logic of the inverter AC. From the angle of customers’ thermal comfort, the new fixed operating frequency is able to maintain the indoor temperature unchanged, so will not make the indoor temperature beyond the maximum limit agreed, as long as the indoor temperature is below the maximum limit before load reduction. Specifically, the operating frequency of the AC to be controlled by the temperature holding strategy is calculated as follows. Firstly, as the indoor temperature is to be maintained unchanged, the target cooling power during load reduction should be The charging/discharging of the VESS depends on relationship between the cooling power of the inverter AC and the stand-by heat gain of the room due to the higher outdoor temperature, as described in the right side of (5). When the cooling power is larger than the stand-by heat gain, the indoor temperature is decreasing according to (5), so that the VESS is charging to increase the VSOC according to (7). On the other hand, if the cooling power is lower than the stand- by heat gain, the indoor temperature is increasing according to (5), so that the VESS is discharging to decrease the VSOC according to (7). Q = Tout −Tin R , (8) (8) which is derived by setting dTin as 0 in (5). Then the target operating frequency of the inverter AC during load reduction, fLR(Hz), can be calculated by substituting (8) into (2), being fLR = Tout −Tin −R · b R · a . (9) (9) With the fLR imposed on the inverter AC, the electric load reduction of this AC, 1P(kW), can be calculated by With the fLR imposed on the inverter AC, the electric load reduction of this AC, 1P(kW), can be calculated by III. CONTROL METHODOLOGY A. LOAD REDUCTION SCHEME In this paper, it is considered that power utilities contract with customers with inverter ACs to conduct load reduction during peak times of power systems, especially for those caused by simultaneous start-up of inverter ACs in summer. The magnitude and time duration of load reduction will be agreed in the contract. Moreover, the maximum indoor temperature during the load reduction will be agreed as well. D. LINEAR RECOVERY STRATEGY A sudden end of load reduction may result in severe load rebound, which may create a new peak for the power sys- tem. Therefore, a linear recovery strategy is proposed for tackling this issue. Specifically, within a pre-agreed length of recovery period after load reduction, the load reduction target is designed to diminish gradually, rather than to be set as 0 immediately. The load reduction target within the recovery period is expressed as Precovery reduction(t) =  1 − t τrecovery  · Preduction ∀t ∈[0, τrecovery]. (12) (12) where Precovery reduction(t)(kW) is the load reduction target at the time point t(h) in the recovery period, and τrecovery(h) is the length of the recovery period. IV. CASE STUDIES In this section, several case studies are presented to verify the effectiveness of the proposed load reduction control method for inverter ACs. After the load reduction ends, the load recovery process starts, where the load reduction target diminishes gradually until the end of the recovery period. Finally, the whole load reduction and recovery process ends. E. THE OVERALL FLOW CHART The proposed VSOC priority based load reduction control method with temperature holding and linear recovery strate- gies is summarized as the flow chart shown in Fig. 3. The flow chart is mainly composed of three parts: load reduction setting, load recovery setting and control of inverter ACs. Once the load reduction is needed, the load reduction target and period are set. Then the inverter ACs are con- trolled using the proposed temperature holding strategy in the descending order of VSOC. If the required amount of load reduction has been reached, or no more inverter ACs with eligible VSOC level can be controlled, the control in a time step finishes. This control procedure repeats for each time step until the load reduction period ends. FIGURE 3. The overall flow chart of the proposed load reduction method. B. TEMPERATURE HOLDING STRATEGY The temperature holding strategy is to control each inverter AC selected for conducting load reduction. As presented in Section II-A, after an inverter AC is turned ON, the compres- sor of the AC will operate at variable frequencies to decrease the indoor temperature to the set point continuously. With the temperature holding strategy proposed in this paper, during the load reduction, the power utility will override the inherent control of the inverter AC, and instruct the inverter AC to operate at a fixed frequency which maintains the current indoor temperature unchanged. Mathematically, the VSOC priority based control can be expressed as min J∗⊆J X j∈J∗ VSOCj s.t. Pbaseline − X j∈J∗ PCtrl j − X j∈J−J∗ PNonCtrl j ≥Preduction VSOCj ∈(0, 1], ∀j ∈J∗ (11) min J∗⊆J X j∈J∗ VSOCj s.t. Pbaseline − X j∈J∗ PCtrl j − X j∈J−J∗ PNonCtrl j ≥Preduction VSOCj ∈(0, 1], ∀j ∈J∗ (11) VOLUME 7, 2019 This strategy is adopted because it is able to reduce the electric load of the AC without endangering customers’ (11) VOLUME 7, 2019 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs 3. The overall flow chart of the proposed load reduction where J∗is the set of all the selected inverter ACs to be controlled; J is the set of all the ACs contracted with the power utility; j is the index of the AC; Pbaseline(kW) is the baseline load of the population of the ACs for measuring the load reduction, and it equals to the aggregated electric power of the AC population just before the load reduction period starts; PCtrl j (kW) and PNonCtrl j (kW) represent the elec- tric power of the AC under control and not under control respectively; Preduction(kW) is the load reduction target. The objective function of (11) guarantees that the inverter ACs with highest VSOC are selected to be controlled. The first constraint in (11) ensures that the load reduction target is satisfied, while the second constraint ensures that only ACs with the indoor temperature below the maximum limit are controlled. Note that although (11) is formulated as an optimization problem, it is not solved through standard opti- mization solvers, but achieved through a serious of steps as summarized in the flow chart which will be presented later in Section III-E. A. CASE DESIGN The load reduction of a population of 100 inverter ACs was simulated and studied. The required amount of load reduction VOLUME 7, 2019 88167 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs FIGURE 4. The aggregated electric power of the inverter AC population without load reduction (Case 1). FIGURE 4. The aggregated electric power of the inverter AC population without load reduction (Case 1). TABLE 1. Parameters of the inverter ACs and rooms. TABLE 1. Parameters of the inverter ACs and rooms. TABLE 1. Parameters of the inverter ACs and rooms. FIGURE 4. The aggregated electric power of the inverter AC population without load reduction (Case 1). FIGURE 5. The indoor temperature of the rooms without load reduction (Case 1). was assumed to be 30 kW, and the load reduction period was assumed to be 1 hour, starting from the 20th minute and ending at the 80th minute. Before the load reduction period, the 100 inverter ACs were assumed to be turned ON in batches within a short period of time (within 20 minutes), which created a peak and triggered the load reduction. After the load reduction period, a recovery period of 40 minutes was considered. The parameter settings of the inverter ACs and the associated rooms are listed in Table 1. FIGURE 5. The indoor temperature of the rooms without load reduction (Case 1). With the above setting, totally 4 cases were studied, which are summarized as follows: • Case 1: a case which shows the evolvement of electric power consumption and indoor temperature of the inverter ACs without enforcing any load reduction, to test the AC and room models used in this paper and act as a reference case. with the turning ON of the ACs in batches within 20 minutes. After reaching the peak, the aggregated electric power grad- ually decreased to a stable level of about 80 kW, with the indoor temperature of the associated rooms gradually reduced towards the set points as shown in Fig. 5. It is calculated that the peak load of the AC population is about 62.5% higher than the stable load, which highlights the importance of conducting load reduction. • Case 2: a case with the proposed load reduction method enforced, to verify its effectiveness. A. CASE DESIGN • Case 3: a case with the proposed load reduction method enforced without executing any recovery strategy, to ver- ify the validity of the proposed linear recovery strategy. Figs. 6 and 7 show the electric power and indoor temperature of a selected inverter AC and the associated room. From Fig. 6, it is seen that the inverter AC was turned ON at the first minute of the simulation, with a high initial electric power consumption close to 1.5 kW. Then the electric power decreased gradually to a stable level of about 0.85 kW. Observing Fig. 7, it is seen that the change of the indoor temperature has the similar trend as that of the electric power shown in Fig.6, verifying that the electric power of an inverter AC is proportional to the difference between the indoor temperature and the set point, as presented in Section II-A. • Case 4: a case where the proposed load reduction method was enforced with the ACs controlled in a random order instead of the descending order of VSOC, to verify the benefits of the VSOC priority based approach proposed. The sensitivity of the magnitude of the load reduction target was also examined in this case. B. CASE 1: REFERENCE CASE In this case, the inverter ACs were turned ON in batches within 20 minutes but no load reduction was enforced. The simulation results are shown in Figs. 4-7. In Fig. 7, it is also worth noting that the final stable indoor temperature is slightly larger than the set point. In some other studies, the final stable indoor temperature will fluctuate around the set point, such as that in [12], [15] and [26]. In Fig. 4, it is seen that the aggregated electric power of the AC population quickly increased to a peak over 130 kW, 88168 VOLUME 7, 2019 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs FIGURE 6. The electric power of one inverter AC without load reduction (Case 1). FIGURE 7. The indoor temperature of one room without load reduction (Case 1). FIGURE 8. The aggregated electric power of the inverter AC population with load reduction (Case 2). FIGURE 9. The indoor temperature of the rooms with load reduction (Case 2). FIGURE 8. The aggregated electric power of the inverter AC population with load reduction (Case 2). FIGURE 8. The aggregated electric power of the inverter AC population with load reduction (Case 2). FIGURE 6. The electric power of one inverter AC without load reduction (Case 1). FIGURE 7. The indoor temperature of one room without load reduction (Case 1). FIGURE 9. The indoor temperature of the rooms with load reduction (Case 2). FIGURE 7. The indoor temperature of one room without load reduction (Case 1). FIGURE 9. The indoor temperature of the rooms with load reduction (Case 2). This is because a linear function, as used in [19], is used to describe the relationship between the operating frequency and electric power of the inverter AC in this paper [see (3) in Section II-A], but in [12], [15] and [26], a more accurate non-linear function is used. Although a more simplified func- tion is used in this paper, it is sufficient to demonstrate and verify the performance of the load reduction method proposed. After all, the focus of this paper is not the detailed modeling of inverter ACs. Figs. 10 and 11 show the electric power and indoor temperature of a selected inverter AC and the associated room. From Fig. 11, it is seen that the indoor temperature kept unchanged during the load reduction. C. CASE 2: LOAD REDUCTION CASE From Fig. 9 where the indoor temperature of all the inverter ACs is illustrated, it is seen that the indoor temperature of some rooms still decreased in a staircase-like way during the load reduction period. This is because the load reduction was conducted following a VSOC priority principle. For some ACs, at the beginning they might be controlled for load reduction, but after some time, some other ACs which had higher VSOC might take their place so that they were no longer controlled and re-started to cool the rooms normally. In this case, the load reduction described in the case design (see Section IV-A) was enforced for the AC population. The results are shown in Figs. 8-11. Fig. 8 shows that the load reduction was activated soon after the peak load was detected, and lasted for 1 hour till the 80th minute. It is seen that the aggregated power of the AC population was controlled around 80 kW during the load reduction, reducing 30 kW load compared to the time point when the load reduction was activated. After the load reduction period ended, there was a mild load rebound for about 40 minutes. Then the aggregated power gradually converged to a stable value. Fig. 8 verified that the proposed load reduction method is able to achieve the intended target. B. CASE 1: REFERENCE CASE This verified that during the load reduction, the operating frequency of the inverter AC was reduced to a value which stopped the indoor temperature from further decreasing, as described in the tem- perature holding strategy (see Section III-B). As a result, the electric power of the inverter AC was reduced accordingly during the load reduction, as shown in Fig. 10. D. CASE 3: ASSESSMENT OF THE LOAD RECOVERY STRATEGY In this case, the load reduction without any recovery strategy enforced was conducted to demonstrate the effectiveness of 88169 88169 VOLUME 7, 2019 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs FIGURE 10. The electric power of one inverter AC with load reduction (Case 2). FIGURE 11. The indoor temperature of one room with load reduction (Case 2). the proposed linear recovery strategy. The results are shown in Fig. 12. Comparing Fig. 12 with Fig. 8, it is seen that without any recovery strategy, there would be a much steeper load rebound than that with the linear recovery strategy. With- FIGURE 12. The aggregated electric power of the inverter AC population with load reduction but without any recovery strategy (Case 3). TABLE 2. Comparison of the proposed load reduction method with the reference method with random selection. In Table 2, the load reduction methods, both the proposed and reference ones, are evaluated by two indexes, ‘Reduction Error’ and ‘Temperature Deviation’. The Reduction Error is defined as the average relative error between the actual l d d ti d th t t d l d d ti th h t FIGURE 12. The aggregated electric power of the inverter AC population with load reduction but without any recovery strategy (Case 3). FIGURE 12. The aggregated electric power of the inverter AC population with load reduction but without any recovery strategy (Case 3). FIGURE 10. The electric power of one inverter AC with load reduction (Case 2). FIGURE 12. The aggregated electric power of the inverter AC population with load reduction but without any recovery strategy (Case 3). FIGURE 10. The electric power of one inverter AC with load reduction (Case 2). TABLE 2. Comparison of the proposed load reduction method with the reference method with random selection. TABLE 2. Comparison of the proposed load reduction method with the reference method with random selection. TABLE 2. Comparison of the proposed load reduction method with the reference method with random selection. FIGURE 11. The indoor temperature of one room with load reduction (Case 2). FIGURE 11. The indoor temperature of one room with load reduction (Case 2). the proposed linear recovery strategy. The results are shown in Fig. 12. In Table 2, the load reduction methods, both the proposed and reference ones, are evaluated by two indexes, ‘Reduction Error’ and ‘Temperature Deviation’. D. CASE 3: ASSESSMENT OF THE LOAD RECOVERY STRATEGY The Reduction Error is defined as the average relative error between the actual load reduction and the targeted load reduction throughout the whole load reduction period, which quantifies the per- formance of a control method in terms of load reduction. The mathematical expression is as follows: Comparing Fig. 12 with Fig. 8, it is seen that without any recovery strategy, there would be a much steeper load rebound than that with the linear recovery strategy. With- out any recovery strategy, the maximum magnitude of load rebound was 105 kW, which was 21% higher than that with the proposed linear recovery strategy enforced (being 95 kW). This verified that the proposed linear recovery strategy is able to effectively reduce the negative impact of load rebound after load reduction. Reduction Error = P t∈T Pbaseline −P j∈J∗PCtrl j,t − P j∈J−J∗PNonCtrl j,t |T| · Preduction (13) [1] N. G. Paterakis, O. Erdinç, and J. P. S. Catalão, ‘‘An overview of demand response: Key-elements and international experience,’’ Renew. Sustain. Energy Rev., vol. 69, pp. 871–891, Mar. 2016. E. CASE 4: ASSESSMENT OF THE VSOC PRIORITY BASED CONTROL (13) |T| · Preduction where T represents the set of all the time steps across the load reduction period, and the meanings of other symbols have been explained below (11). In (13), the numerator represents the actual load reduction while the denominator represents the targeted load reduction. This case compares the performance of the proposed VSOC priority based control with a reference control of which the inverter ACs to be controlled are decided by random selection rather than by the descending order of VSOC. The other settings of the reference method, such as the temperature holding and linear recovery strategies, are all the same as those of the proposed load reduction method. The comparison results are presented in Table 2. The Temperature Deviation is defined as the standard deviation of the indoor temperature from the set points among all the rooms, which quantifies the average thermal comfort 88170 VOLUME 7, 2019 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs level of all the customers involved during the load reduction. The mathematical expression is as follows: conventional generators). The cost of temperature deviation for the power utility is that, if the temperature deviation is higher, the power utility may have to pay more remu- neration to customers for recruiting them to join the load reduction scheme. Therefore, for the results shown in Table 2, when the load reduction target was higher than 30 kW, detailed economic calculation would need to be conducted to decide to use the proposed method (with lower temper- ature deviation but higher reduction error) or the reference method (with higher temperature deviation but lower reduc- tion error), or even not to conduct any load reduction. When the load reduction target was no higher than 30 kW, although the proposed method was always preferable to the reference method, economic calculation would also need to be con- ducted to weigh the benefits and costs of conducting load reduction, and then to decide whether and how much load reduction should be conducted. Detailed economic assess- ment depends on the features of specific electricity markets, power systems and customers, and is somehow out of the scope of this paper. However, it is a valuable research topic for the future. Temperature Deviation = v u u u t P t∈T P j∈J  Tin,j,t −T setpoint in,j 2 |T| · |J| . E. CASE 4: ASSESSMENT OF THE VSOC PRIORITY BASED CONTROL (14) The larger the temperature deviation is, the worse the overall (14) The larger the temperature deviation is, the worse the overall thermal comfort level of the population will be. The larger the temperature deviation is, the worse the overall thermal comfort level of the population will be. From Table 2, it is seen that for both control methods, the reduction errors for the load reduction targets below 30 kW are all zero, but increase gradually with the targets over 30 kW. This shows that the load reduction capability of the AC population has an upper limit, being around 30 kW in this case, which is decided by the summation of the capability of each inverter AC of which the VSOC is between 0 and 1. Comparing the Temperature Deviations of the proposed and reference methods in Table 2, it is seen that the values of the proposed method are lower than those of the reference method, especially when the load reduction targets are within the AC population’s capability (i.e. when the load reduc- tion targets are below or equal to 30 kW). This is because the proposed VSOC priority based control will always con- trol the ACs of which the indoor temperature are closer to the set points, giving those with higher indoor temperature the opportunities to pull the indoor temperature back to the set points. By contrast, the reference method just randomly selects the ACs to be controlled, making the indoor temper- ature of some rooms far from the set points. As a result, the proposed VSOC priority based control is able to better take care of customers’ thermal comfort, as justified by the values of Temperature Deviations in Table 2. ACKNOWLEDGMENT Information on the data underpinning the results presented here, including how to access them, can be found in the Cardiff University data catalogue at http://doi.org/10.17035/ d.2019.0078671085. V. CONCLUSION A i l A virtual state of charge priority based control method with temperature holding and linear recovery strategies was proposed in this paper for conducting load reduction of aggregated inverter air conditioners. A virtual energy storage system model that encapsulates the room with an inverter AC was established, based on the electric model of an inverter AC and the thermodynamic model of a room, for designing, simulating and assessing the load reduction control method proposed. Simulation results verified the models established and the load reduction control method proposed. It was verified that the proposed control method was able to realize the tar- geted load reduction without violating the maximum indoor temperature limits. It was also verified that the proposed linear recovery strategy was able to effectively reduce the load rebound after the load reduction. The load rebound was reduced by 21% in the case study. Finally, compared with a reference method that randomly selected ACs for being controlled, the proposed VSOC priority based control was able to reduce the deviation of indoor temperature from the set points for the whole AC population, thus resulting in higher thermal comfort for customers. Comparing the proposed method with the reference method, it is seen from Table 2 that, when the load reduc- tion target was no higher than 30 kW, the proposed method could result in lower temperature deviations (and thus less compromise of customers’ thermal comfort) than those of the reference method, with the same reduction errors (all being zero). Therefore, in these scenarios, the proposed method was always preferable to the reference method. When the load reduction target was higher than 30 kW, the proposed method still resulted in lower temperature deviations than those of the reference method, but at the cost of higher reduction errors. However, in these scenarios, the temperature deviations of the proposed method were significantly lower than those of the reference method (being 9.6%, 7.7%, 5.8% and 4.8% lower at the load reduction target of 35 kW, 40 kW, 50 kW and 60 kW, respectively), whereas the reduction errors of the proposed method were just slightly higher than those of the reference method (being 2.8%, 1.4%, 0.5% and 0.4% higher at the load reduction target of 35 kW, 40 kW, 50 kW and 60 kW, respectively). REFERENCES In practice, the value of load reduction services for the power utility depends on the cost needed to purchase alter- native services if not using load reduction services (e.g. from VOLUME 7, 2019 88171 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs [2] Y. Zhou, C. Wang, J. Wu, J. Wang, M. Cheng, and G. Li, ‘‘Optimal scheduling of aggregated thermostatically controlled loads with renewable generation in the intraday electricity market,’’ Appl. 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Backhaus, ‘‘Frequency regulation from com- mercial building HVAC demand response,’’ Proc. IEEE, vol. 104, no. 4, pp. 745–757, Apr. 2016. YANBO CHE (M’16) was born in Shandong, China. He received the B.S. degree form Zhejiang University, Hangzhou, China, in 1993, and the M.S. and Ph.D. degrees from Tianjin University, Tianjin, China, in 1996 and 2002, respectively. Since 1996, he has been engaged in teaching and scientific research of power electronic technology and power systems. He is currently an Associate Professor with the School of Electrical and Infor- mation Engineering, Tianjin University. His cur- rent research interests include power systems, renewable energy resources, and micro-grids. YANBO CHE (M’16) was born in Shandong, China. He received the B.S. degree form Zhejiang University, Hangzhou, China, in 1993, and the M.S. and Ph.D. degrees from Tianjin University, Tianjin, China, in 1996 and 2002, respectively. 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YUE ZHOU (M’13) received the B.S., M.S., and Ph.D. degrees in electrical engineering from Tianjin University, Tianjin, China, in 2011, 2016, and 2016, respectively. He is currently a Post- doctoral Research Associate with the School of Engineering, Cardiff University, Cardiff, U.K. His research interests include demand response, peer- to-peer energy trading, and blockchain technology. [21] M. Hu, F. Xiao, J. B. Jørgensen, and S. Wang, ‘‘Frequency control of air conditioners in response to real-time dynamic electricity prices in smart grids,’’ Appl. Energy, vol. 242, no. 1, pp. 92–106, 2019. [22] Y.-J. Kim, L. K. Norford, and J. L. Kirtley, ‘‘Modeling and analysis of a variable speed heat pump for frequency regulation through direct load control,’’ IEEE Trans. Power Syst., vol. 30, no. 1, pp. 397–408, Jan. 2015. [23] Y.-J. Kim, E. Fuentes, and L. K. Norford, ‘‘Experimental study of grid frequency regulation ancillary service of a variable speed heat pump,’’ IEEE Trans. Power Syst., vol. 31, no. 4, pp. 3090–3099, Jul. 2016. 88172 VOLUME 7, 2019 Y. Che et al.: Demand Response From the Control of Aggregated Inverter ACs YUANCHENG ZHAO was born in Shandong, China. He received the B.S. degree from Hunan University, Changsha, China, in 2016, and the M.S. degree from Tianjin University, Tianjin, China, in 2019. His research interests include power electronics, demand response, and power quality. JIANXIONG YANG w JIANZHONG WU (M’04) received the B.S., M.S., and Ph.D. degrees in electrical engineering from Tianjin University, China, in 1999, 2002, and 2004, respectively. From 2004 to 2006, he held a postdoctoral posi- tion at Tianjin University. From 2006 to 2008, he was a Research Fellow with The University of Manchester, U.K. He joined Cardiff Univer- sity, U.K., as a Lecturer, in 2008, a Senior Lec- turer, in 2013, a Reader, in 2014, and a Professor, in 2015. He is currently a Professor of multi-vector energy systems and the Head of the Department of Electrical and Electronic Engineering, Cardiff University. He is also the Director of Applied Energy UNiLAB on Synergies Between Energy Networks. He is also a Co-Director of EPSRC Supergen Energy Networks Hub and the U.K. Energy Research Centre. His research interests include energy infrastructure and smart grid. He is also a Subject Editor of Applied Energy. WEI HE was born in Hubei, China. He received the B.S. degree from Wuhan University, Wuhan, China, in 2007, and the M.S. and Ph.D. degrees in electrical engineering from North China Elec- tric Power University, Hebei, China, in 2009 and 2013, respectively. He is currently a Senior Engi- neer with the State Grid Jiangxi Electric Power Research Institute, Nanchang, Jiangxi, China. His current research interests include power quality and smart grid. 88173 VOLUME 7, 2019
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A wide field-of-view low-resolution spectrometer at APEX: Instrument design and scientific forecast
Astronomy & astrophysics
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A wide field-of-view low-resolution spectrometer at APEX: Instrument design and scientific forecast The CONCERTO Collaboration: P. Ade1, M. Aravena2, E. Barria3,4, A. Beelen5, A. Benoit3,4, M. Béthermin5, J. Bounmy6,4, O. Bourrion6,4, G. Bres3,4, C. De Breuck7, M. Calvo3,4, Y. Cao5, A. Catalano6,4, F.-X. Désert8,4, C.A. Durán9, A. Fasano3,4, T. Fenouillet5, J. Garcia5, G. Garde3,4, J. Goupy3,4, C. Groppi10, C. Hoarau6,4, G. Lagache5, J.-C. Lambert5, J.-P. Leggeri3,4, F. Levy-Bertrand3,4, J. Macías-Pérez6,4, H. Mani10, J. Marpaud6,4, P. Mauskopf10, A. Monfardini3,4, G. Pisano1, N. Ponthieu8,4, L. Prieur5, S. Roni6, S. Roudier6, D. Tourres6,4, and C. Tucker1 1 Astronomy Instrumentation Group, University of Cardiff, The Parade CF24 3AA, UK 2 1 Astronomy Instrumentation Group, University of Cardiff, The Parade CF24 3AA, UK 2 2 Núcleo de Astronomía, Facultad de Ingeniería y Ciencias, Universidad Diego Portales, Av. Ejército 441, Santiago, C U i G bl Al CNRS G bl INP I i Né l 38000 G bl F 2 Núcleo de Astronomía, Facultad de Ingeniería y Ciencias, Universidad Diego Portales, 3 3 Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut Néel, 38000 Grenoble, France e-mail: monfardini@neel.cnrs.fr 4 Groupement d’Interet Scientifique KID, 38000 Grenoble and 38400 Saint Martin d’Hères, France 5 4 Groupement d’Interet Scientifique KID, 38000 Grenoble and 38400 Saint Martin d’Hères, France 5 5 Aix Marseille Université, CNRS, LAM (Laboratoire d’Astrophysique de Marseille), 13388 Marseille, Franc e-mail: guilaine.lagache@lam.fr g g 6 Univ. Grenoble Alpes, CNRS, LPSC/IN2P3, 38000 Grenoble, France 7 6 Univ. Grenoble Alpes, CNRS, LPSC/IN2P3, 38000 Grenoble, France 7 European Southern Observatory, Karl Schwarzschild Straße 2, 85748 Garching, Germany 7 European Southern Observatory, Karl Schwarzschild Straße 2, 85748 Garching, Germany 8 8 Univ. Grenoble Alpes, CNRS, IPAG, 38400 Saint Martin d’Hères, France 8 Univ. Grenoble Alpes, CNRS, IPAG, 38400 Saint Martin d’Hères, France 9 European Southern Observatory, Alonso de Cordova 3107, Vitacura, Santiago, Chile 10 S h l f E h d S E l i d D f Ph i A i S U i 9 European Southern Observatory, Alonso de Cordova 3107, Vitacura, Santiago, Chile 10 School of Earth and Space Exploration and Department of Physics, Arizona State Uni p y g 0 School of Earth and Space Exploration and Department of Physics, Arizona State University, Tempe, AZ 85287, US Received 20 May 2020 / Accepted 24 July 2020 ABSTRACT Context. Characterising the large-scale structure in the Universe from present times to the high redshift epoch of reionisation is essen- tial to constraining the cosmology, the history of star formation, and reionisation, to measuring the gas content of the Universe, and to obtaining a better understanding of the physical processes that drive galaxy formation and evolution. Using the integrated emission from unresolved galaxies or gas clouds, line intensity mapping (LIM) provides a new observational window to measure the larger properties of structures. This very promising technique motivates the community to plan for LIM experiments. Aims. We describe the development of a large field-of-view instrument, named CONCERTO (for CarbON CII line in post-rEionisation and ReionisaTiOn epoch), operating in the range 130–310 GHz from the APEX 12-m telescope (5100 m above sea level). CONCERTO is a low-resolution spectrometer based on the lumped element kinetic inductance detectors (LEKID) technology. Spectra are obtained using a fast Fourier transform spectrometer (FTS), coupled to a dilution cryostat with a base temperature of 0.1 K. Two two kilo-pixel arrays of LEKID are mounted inside the cryostat that also contains the cold optics and the front-end electronics. y y p Methods. We present, in detail, the technological choices leading to the instrumental concept, together with the design and fabrication of the instrument and preliminary laboratory tests on the detectors. We also give our best estimates for CONCERTO sensitivity and give predictions for two of the main scientific goals of CONCERTO, that is, a [CII]-intensity mapping survey and observations of galaxy clusters. g y Results. We provide a detailed description of the instrument design. Based on realistic comparisons with existing instruments devel- oped by our group (NIKA, NIKA2, and KISS), and on the laboratory characterisation of our detectors, we provide an estimate for CONCERTO sensitivity on the sky. Finally, we describe, in detail, two of the main scientific goals offered by CONCERTO at APEX. Key words. instrumentation: detectors – instrumentation: spectrographs – telescopes – cosmology: observations Open Access article, published by EDP Sciences, under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Astronomy & Astrophysics Astronomy & Astrophysics Astronomy & Astrophysics A&A 642, A60 (2020) https://doi.org/10.1051/0004-6361/202038456 c⃝The CONCERTO collaboration 2020 1. Introduction A pathfinder instrument, named KISS that is based on the same concept, has been built by our collabora- tion and deployed in November 2018, at the Teide Observatory (Fasano et al. 2020a). sky, the spectral dimension has to be added, without sacrificing the instantaneous field-of-view. The large field-of-view and the mapping speed are, actually, the main asset of single dish tele- scopes when compared to variable baseline interferometers, such as ALMA1 or NOEMA (Lefèvre et al. 2020). For this reason, we are developing a millimetre-wave low spectral resolution (R = ν/∆ν ≤300) spectrometer with an instantaneous field-of-view of 20 arcmin. In order to preserve the angular resolution at frequen- cies of around 300 GHz and assuming a 10-m class telescope, a focal-plane containing around 2000 spatial pixels is needed. Toachieve these figures, we adopt a room-temperature Martin- Puplett Interferometer (MpI) (Martin & Puplett 1970) coupled to a large field millimetre-wave LEKID camera. The instrument, named CONCERTO (for CarbON CII line in post-rEionisation and ReionisaTiOn epoch), has been designed to interface with the Atacama Pathfinder EXperiment (APEX) 12-m telescope (Güsten et al. 2006). A pathfinder instrument, named KISS that is based on the same concept, has been built by our collabora- tion and deployed in November 2018, at the Teide Observatory (Fasano et al. 2020a). Telescope primary mirror diameter [m] 12 Field-of-view diameter [arcmin] 20 Absolute spectral resolution [GHz] ≥1 Relative spectral resolution R [#] 1–300 Frequency range HF | LF [GHz] 195–310 | 130–270 Pixels on Sky HF | LF [#] 2152 | 2152 Angular resolution HF | LF [arcsec] 20–32 | 23–45 Average angular resolution HF | LF [arcsec] 26 | 34 Instrument geometrical throughput [sr m2] 2.5 × 10−3 Single Pixel geometrical throughput [sr m2] 1.16 × 10−6 Data rate [MBytes s−1] 128 Notes. For comparison, the NIKA2 instrument (6.5′ field-of-view, 30- metre telescope) geometrical throughput (A×Ω), characterising the camera collecting power, is 1.7×10−3 sr m2. Concerning the overall opti- cal transmission of CONCERTO compared to NIKA2, we refer the reader to Sect. 4.1. ( ) One important scientific driver that has motivated our devel- opments is the study of the [CII] emission line at high redshift. The [CII] line is among the brightest lines originating from star- forming galaxies and it is a reliable tracer of star formation on global scales. 1. Introduction With CONCERTO at APEX, we will map, in three dimensions, the fluctuations of the [CII] line intensity in the reionisation and post-reionisation epoch (z ≳5). This tech- nique, known as “intensity mapping”, will allow us to answer the questions of whether dusty star-formation contributes to early galaxy evolution, and whether [CII]-emitters play an important role in shaping cosmic reionisation. The dedicated [CII] survey will provide a (spatial-spectral) data cube in which intensity is mapped as a function of the sky position and frequency. The 3D fluctuations will then be studied in Fourier space with the power spectrum. The [CII] survey will also be sensitive to the CO intensity fluctuations arising from 0.3 < z < 2 galaxies, giving the spatial distribution and abundance of molecular gas over a broad range of cosmic time. The [CII] intensity mapping is also one of the main goals of CCAT-prime (Choi et al. 2020) and TIME (Crites et al. 2014), which are two experiments that are based on different technologies than CONCERTO: Gratings and TES bolometers are used for TIME, and KID and Fabry- Perot interferometers are used for CCAT-p. In addition to the main [CII] survey, we expect CONCERTO to bring a signifi- cant contribution in a number of areas, including the study of galaxy clusters (via the thermal and kinetic SZ effect), the obser- vation of local and intermediate-redshift galaxies, and the study of Galactic star-forming clouds. In this paper, we detail the main goals of the [CII] intensity mapping survey and galaxy cluster observations. To RTA & DISKS Fig. 1. Location of the CONCERTO sub-systems: the chassis and optics in the C-cabin, the Data AcQuisition computers (DAQ) in the middle container (“instrumentation container”), and the gas handling system and the pulse-tube compressor in the bottom container (“compressors room”). Real time analysis (RTA) computers and hard disks are not in the telescope tower. Fig. 1. Location of the CONCERTO sub-systems: the chassis and optics in the C-cabin, the Data AcQuisition computers (DAQ) in the middle container (“instrumentation container”), and the gas handling system and the pulse-tube compressor in the bottom container (“compressors room”). Real time analysis (RTA) computers and hard disks are not in the telescope tower. optics box. The “chassis” includes the camera (cryostat), the MpI interferometer, the readout, and control electronics. The “optics box” includes a number of mirrors and polarisers as well as a cold reference for the MpI. 1. Introduction In Table 1 we summarise the main instrument characteristics. The location of the CONCERTO sub- systems is shown in Fig. 1. In this section, we describe, in detail, the camera and its con- tent (Sect. 2.1), the MpI (Sect. 2.2), and the chassis and related electronics (Sect. 2.3). The room temperature optics, including the cold reference source, is presented in Sect. 2.4. Section 2.5 is devoted to a brief description of the CONCERTO hardware components, which are located elsewhere than in the telescope tower. Information about the installation at the telescope is found in Sect. 2.6. The paper is organised as follows. We present the instru- mental concept, design, and preliminary results in Sect. 2. The discussion pertains to KID detectors, cryogenics, and optics. In Sect. 3, we describe the first laboratory tests. In Sect. 4, we present the sensitivity estimates, while Sect. 5 is dedicated to the [CII] intensity mapping and SZ surveys. 1 https://almascience.eso.org 1. Introduction et al. 2018; Perotto et al. 2020). The particular type of KID used for NIKA2 are front-illuminated lumped element KID (LEKID; Doyle et al. 2010). They consist in inductor-capacitor (LC) superconducting planar resonators made by a long meandered inductor (wire), which is terminated at both ends by an inter- digitated capacitor. NIKA2 supersedes previous cameras based on transition edge sensors (referred to as TES bolometers) in the frequency range of 150–360 GHz, such as MAMBO2 at IRAM (Kreysa et al. 1998), LABOCA at APEX (Siringo et al. 2009), and SCUBA-2 at the JCMT (Holland et al. 2013). Modern imaging and polarimetry cameras, at millimetre and sub-millimetre wavelengths, are currently operating on large (e.g. D > 10 m) single-dish telescopes. The main goal of these instruments is to map, at relatively high angular resolution (e.g. 5–30 arcsec), large portions of the sky (e.g. several deg2) with a high sensitivity (e.g. RMSMAP ≲1 mJy). Polarised emissions are also measured with similar specifications. In this context, the dual-band NIKA2 camera represents the first kilo-pixel instrument operating at these wavelengths based on the kinetic inductance detectors (KID) technology (Adam In order to extend the capabilities of the existing instru- ments and to open new observational windows of the millimetre A60, page 1 of 13 A&A 642, A60 (2020) Table 1. Main characteristics of CONCERTO. sky, the spectral dimension has to be added, without sacrificing the instantaneous field-of-view. The large field-of-view and the mapping speed are, actually, the main asset of single dish tele- scopes when compared to variable baseline interferometers, such as ALMA1 or NOEMA (Lefèvre et al. 2020). For this reason, we are developing a millimetre-wave low spectral resolution (R = ν/∆ν ≤300) spectrometer with an instantaneous field-of-view of 20 arcmin. In order to preserve the angular resolution at frequen- cies of around 300 GHz and assuming a 10-m class telescope, a focal-plane containing around 2000 spatial pixels is needed. Toachieve these figures, we adopt a room-temperature Martin- Puplett Interferometer (MpI) (Martin & Puplett 1970) coupled to a large field millimetre-wave LEKID camera. The instrument, named CONCERTO (for CarbON CII line in post-rEionisation and ReionisaTiOn epoch), has been designed to interface with the Atacama Pathfinder EXperiment (APEX) 12-m telescope (Güsten et al. 2006). 2.1. The camera 2, are the image stop (IS) at a temperature of 4 K and the cold pupil (CP) at the base temperature of around 0.1 K. Three HDPE (High Density PolyEthilene) lenses are used in the camera: L1 (room temperature), L2 (4 K), and L3 (0.1 K). In order to analyse the polarised signal, the last polariser of the MpI (P3) is placed just in front of the LEKID arrays (FP) at the base temperature. P3 is a custom wire-grid polariser. It is realised on a 12 µm-thick Polyimide membrane, and with Copper wires with a pitch of 50 µm. A number of infrared (IR)-blocking (thermal) and metal- lic multi-mesh filters (Ade et al. 2006) are mounted at differ- ent stages. In particular, we have thermal filters on the warmest stages (room temperature to 50 K), low-pass multi-mesh filters at the intermediate temperatures (50 K–1 K), and band-defining fil- ters at the base temperature (i.e. just in front of each focal-plane array). A specially blackened baffle is installed at 4 K, between IS and L2, in order to suppress the stray light. chamber by soft ion milling. The superconducting film depo- sition, which is made of Aluminium with a thickness of 20 nm, is achieved by e-beam evaporation and under a residual cham- ber pressure of 5 × 10−8 mbars. The deposition rates is fixed at 0.1 nm s−1. The ultraviolet (UV) photo-lithography step is based on a positive resist and is followed by wet etching. The etch- ing is done using a standard aluminium etching solution based on phosphoric acid. The diced detectors arrays are packaged in custom holders and bonded, via 17 µm Aluminium wires, to the 50-Ohms micro-strip launchers. Those are then tin-soldered to the inner pin of the SMA3 feed-throughs. p g The front-end electronics stage is installed in the cryostat, at a temperature of 4 K. It is made of a series of twelve low- noise amplifiers (LNA) operating at the resonance frequencies4, that is, in the range of 1.5–2.5 GHz. A second stage of cryogenic amplification, made of twelve commercial LNA, has been added on the 50 K cryogenic stage to simplify the room-temperature electronics and reduce its power consumption. The connections between the cold electronics stages, the arrays, and the SMA vacuum feed-throughs plate (see Fig. 2), are ensured by commer- cial semi-rigid cryogenic coaxial cables. 2.1. The camera CONCERTO has been specifically designed to fit into the Cassegrain cabin (C-cabin) of the APEX telescope. It is com- posed of two main components: the so-called chassis and the The CONCERTO camera is based on a cryogenic-liquid-free custom dilution cryostat. The dilution insert and the pulse- tube orientation, in particular, have been specifically designed to allow the rotation of the cryostat axis following telescope A60, page 2 of 13 The CONCERTO collaboration: A wide field-of-view low-resolution spectrometer at APEX Polariser P3 Cold Pupil CP Lens L3 Focal-Plane LF Focal-Plane HF Fig. 3. Picture of the first “100 mK block” including the cold pupil, the L3 lens, the P3 polariser, and the two arrays (HF and LF) containing 2152 pixels each. The array holders are, in this case, realised in Alu- minium. A version of the block with Copper holders is also available. L1 285K L2 4K L3 0.1K P3 0.1K FP 0.1K IS 4K CP 0.1K Fig. 2. CONCERTO camera cross-section and 3D view (inset). The positions of the three HDPE lenses are shown (L1, L2, L3), together with the image stop (IS), the cold pupil (CP), the cold polariser (P3), and the two focal planes (FP). The diameter of L1 is around 250 mm. L1 285K L2 4K L3 0.1K P3 0.1K FP 0.1K IS 4K CP 0.1K L1 285K L2 4K L3 0.1K P3 0.1K FP 0.1K IS 4K CP 0.1K Cold Pupil CP Fig. 2. CONCERTO camera cross-section and 3D view (inset). The positions of the three HDPE lenses are shown (L1, L2, L3), together with the image stop (IS), the cold pupil (CP), the cold polariser (P3), and the two focal planes (FP). The diameter of L1 is around 250 mm. Focal-Plane LF Fig. 3. Picture of the first “100 mK block” including the cold pupil, the L3 lens, the P3 polariser, and the two arrays (HF and LF) containing 2152 pixels each. The array holders are, in this case, realised in Alu- minium. A version of the block with Copper holders is also available. movements. The cryostat is optimised for the range of telescope elevations (EL) comprised between 30 and 90 degrees. The best working point is achieved for EL = 60 degrees. The main camera optical features, shown in Fig. 3 SubMiniature version A. 4 http://thz.asu.edu/products.html 2.1. The camera In particular, we adopt NbTi superconducting coaxial cables for the portion connect- ing the output of the LEKID arrays to the input of the front-end amplifiers. Fixed attenuators are mounted on each input line at the 4 K stage. The overall electrical gain of each radio-frequency line to and from the room temperature electronics has been mea- sured and is about +25 dB. Since LEKID are sensitive to variations of magnetic fields, they have to be protected by a multi-stage B field screen. Four concentric high-permittivity alloy (i.e. mu-metal and cryogenics variations) cylinders are installed at 300 K, 50 K (double screen), and 4 K. An additional superconducting screen will be wrapped around the focal planes section. The focal plane arrays are microstrip-coupled LEKID simi- lar to those used for NIKA2 (Adam et al. 2018). Six feed-lines (i.e. excitation and readout lines) are needed to read out each of the 2152 pixel arrays. A total of twelve pairs of coaxial cables are thus running into the cryostat. The pixels design itself is derived from NIKA (Monfardini et al. 2011). The LEKID details have been optimised to meet the CONCERTO specifications. In par- ticular, the shape of the meander and its coupling quality fac- tor have been adjusted to the target range of frequencies and expected background. The coupling quality factor is designed to be Qc ≈∆f−3 dB/ f0 ≈2.5 × 104, where ∆f−3 dB is the typi- cal width of the resonance under dark conditions. The thickness of the dielectric substrate is calibrated in order to maximise the quantum efficiency, and it is in the range of 100–120 µm. 2 https://www.sil-tronix-st.com/en/ 2.2. The Martin-Puplett interferometer Two identical linear motors, which develop a force of ≥1000 N each, are acted on in counter-phase to null the total momentum. Fig. 4. Schematics of the MpI concept. Two options are shown for the reference source: (a) a de-focused image of the instantaneous field-of- view; and (b) a cold reference. The polariser P1 provides the needed polarised input to the MpI. P2 is the beam splitter defining the two arms, while P3, in the cryostat, dispatches the two projections of the polarised signal to the focal-plane arrays. The incoming beam is represented by a spectral distribution S(ν). include the camera itself, the MpI motors and moving mirror, and the electronics boards, along with a large number of modules devoted to monitoring and controlling the instrument. The chas- sis was designed and fabricated to match the constraints related to the limited space available in the C-cabin. It allows for the installation of multiple sub-systems of CONCERTO as a single element inside the APEX C-cabin. The chassis is pre-mounted in the laboratory and it can slide through the C-cabin door. mostly for laboratory characterisations, but also for narrow5 field-of-view observations from space in the past (Mather 1999; Griffin et al. 2010). The first examples of wide field instruments making use of an MpI to obtain spectral information are the stratospheric balloon OLIMPO (Schillaci et al. 2014) and the previously mentioned KISS ground-based spectro-photometer (Fasano et al. 2010b). y g Five microTCA6 racks mounted on the side of the chassis host the 12 advanced mezzanine cards (AMC) used to read out the two arrays. The cards have an architecture similar to those used for NIKA2 (Bourrion et al. 2012), but they have been improved to be able to generate up to 400 excitation tones span- ning 1 GHz in bandwidth. The data acquisition rate has been increased from less than 100 Hz to up to 4 kHz in order to prop- erly sample the interferograms generated by the MpI. The cali- bration strategy has been inherited from the NIKA and NIKA2 instruments (Calvo et al. 2014), but the continuous frequency modulation used there is no longer viable because of the high- sampling rate. As a consequence, in CONCERTO, the position and shape of each resonance circle, which is used to calibrate the data, is reconstructed by sampling three points around the resonance: f0, f0 + δ f, and f0 −δ f. 2.2. The Martin-Puplett interferometer The δ f is much smaller than the resonance width, and it is of the order of a few kHz. The calibration step is performed at the beginning of each interfero- gram, while the direction of motion of the MpI rooftop mirror is changing (Fasano et al. 2020a). In our opinion, this approach represents the best trade-offbetween optimal calibration and observing efficiency, that is, the fraction of time that is devoted to the science data stream. To achieve a spectral resolution better than 1 GHz, the maxi- mum range ∆lmax of the moving rooftop mirror has to be larger than 75 mm. In CONCERTO, the motors can move by up to 90 mm. The range ∆l spanned by the interferogram can be adjusted, on a scan-by-scan basis and depending on the science target, from zero to the maximum. The spectral resolution will then be ∆ν = c 4 × ∆l· The optical path difference is thus OPD = 2∆l. Leaving the rooftop mirror immobile at the zero-path difference position results in using CONCERTO as a broad- and dual-band large field-of-view imager. The optical path difference is thus OPD = 2∆l. Leaving the rooftop mirror immobile at the zero-path difference position results in using CONCERTO as a broad- and dual-band large field-of-view imager. g The distinctive feature of the CONCERTO (and KISS) MpI is the combination of the speed of movement of the rooftop mir- ror and its size and mass. In order to avoid atmospheric drifts during a single interferogram, the mechanical frequency of the motors is set to around 4 Hz, that is, eight full interferograms (and spectra) per second are produced by each of the pixels. The lateral size of the mirror that is to be moved exceeds 0.5 m for a mass exceeding 3 kg. In order to counterbalance the linear momentum associated with this moving mass, a second motor, with an equivalent mass, oscillates with an opposite instanta- neous velocity. With a maximum force around 1000 N, the accel- eration that can be imposed to the moving mass, including the motor piston, exceeds 100 m s−2. The theoretical curve that is commanded to the motor is a square wave (i.e. a constant speed for both directions and a maximum acceleration at the turn- backs).The real curve is of course smoothed out by the finite acceleration near the extremes. 2.2. The Martin-Puplett interferometer The MpI is a particular kind of Fourier transform spectrometer (FTS). It is capable of measuring the differential spectrum of a source, with respect to a given reference. The key elements are three polarisers (P1-beam divider, P2-splitter, and P3-analyser), two (one fixed and one variable) arms, and two (one fixed and one moving) rooftop mirrors (see Fig. 4). This technique is widely adopted in the millimetre and sub-millimetre domains, The fabrication process (Goupy et al. 2016) looks straight- forward when compared to competing detectors that have sim- ilar performances. The substrate, a 100-millimetre high-purity mono-crystalline silicon wafer2, is prepared in the deposition 2 https://www.sil-tronix-st.com/en/ A60, page 3 of 13 A&A 642, A60 (2020) a) b) Fig. 4. Schematics of the MpI concept. Two options are shown for the reference source: (a) a de-focused image of the instantaneous field-of- view; and (b) a cold reference. The polariser P1 provides the needed polarised input to the MpI. P2 is the beam splitter defining the two arms, while P3, in the cryostat, dispatches the two projections of the polarised signal to the focal-plane arrays. The incoming beam is represented by a t l di t ib ti S( ) COUNTER-BALANCE MOTOR MAIN MOTOR COUNTER-WEIGHT POSITION MPI MOVING ROOFTOP MIRROR Fig. 5. CONCERTO double-motors MpI. Two identical linear motors, which develop a force of ≥1000 N each, are acted on in counter-phase to null the total momentum. include the camera itself, the MpI motors and moving mirror, and the electronics boards, along with a large number of modules COUNTER-BALANCE MOTOR MAIN MOTOR COUNTER-WEIGHT POSITION MPI MOVING ROOFTOP MIRROR Fig. 5. CONCERTO double-motors MpI. Two identical linear motors, which develop a force of ≥1000 N each, are acted on in counter-phase to null the total momentum. a) b) Fig. 4. Schematics of the MpI concept. Two options are shown for the reference source: (a) a de-focused image of the instantaneous field-of- view; and (b) a cold reference. The polariser P1 provides the needed polarised input to the MpI. P2 is the beam splitter defining the two arms, while P3, in the cryostat, dispatches the two projections of the polarised signal to the focal-plane arrays. The incoming beam is represented by a spectral distribution S(ν). COUNTER-BALANCE MOTOR MAIN MOTOR b) a) b) a) MPI MOVING ROOFTOP MIRROR Fig. 5. CONCERTO double-motors MpI. 2.2. The Martin-Puplett interferometer We present a picture of the sys- tem that was built for CONCERTO in Fig. 5. The moving elements inside the chassis, in particular the MpI motors and the gas flowing in the pulse-tube head, gener- ate vibrations which could affect the detector performances. In order to suppress their propagation to the focal plane, the camera is fixed to the chassis only via a series of soft rubber pneumatic actuators, which strongly dampen the vibrations. Furthermore, the pressure inside the actuators (eight in total, with different orientations, as shown in Fig. 6) is constantly adjusted by a ded- icated software, so that the cryostat position and axis, which are monitored by means of linear position transducers, are kept con- stant independently of the telescope elevation. The cryostat posi- tion adjustment, requiring a few seconds to complete, is done automatically after each re-pointing and, upon request, between two subsequent observing blocks (scans). The position is, on the other hand, monitored in real time even during scans. 5 In this context, the field-of-view has to be expressed in the number of beams. The number of beams is around 2000 for CONCERTO and 300 for KISS, which can be compared to few tens, at most, for the previous instruments. 2.3. The chassis and electronics The chassis is a single, compact support structure to which many of the core components of CONCERTO are attached. These 6 https://en.wikipedia.org/wiki/MicroTCA 2.4. The cabin optics and the cold reference (optics box) A large number of mirrors (M5 to M11), the two polarisers P1 and P2, and the cold reference optics complete the optical chain. A remotely controllable three-position mirror is inserted in the optics chain in order to select the type of reference input for the MpI. The three options are as follows. the largest among the CONCERTO mirrors. The next mirror, M4, which is attached to C-cabin upper ring, reflects the beam towards the C-cabin floor and directly into the so-called optics box. A first virtual image is generated, by the combination M1- M2-M3-M4, before M5. This virtual image plane will be used for some of the CONCERTO qualification tests. – The first option is sky, which is a de-focused image of the full 20 arcmin instantaneous field-of-view. The distinctive advantage is that the atmospheric common-mode spectrum is optically subtracted, providing a differential measurement of the astrophysics source spectrum with respect to the atmosphere along the line-of-sight. This means that, when targeting a field populated by weak sources, and at the first order, we obtain a null interferogram. This configuration is ideally suited for a com- pact object, that is, one with an angular extension smaller than 20 arcmin. The “optics box” includes a large number of mirrors (M5 to M11), the two polarisers P1 and P2 (Fig. 4) and the part of the optics providing the cold reference for the MpI. It also includes the fixed rooftop mirror of the interferometer. A general 3D view is shown in Fig. 7. – The second option is an external cold black-body, which is a highly-emissive (ϵ ≥0.98) cold disk that is cooled down by an independent pulse-tube cryostat (TBB ≈8 K). This configura- tion is mostly adapted to extended emission observations, that is, when the spectral and photometric gradients extend, on average, more than 20 arcmin. The mirrors are held at the C-cabin temperature, which is regulated at 11 ◦C = 284 K. We expect an emissivity of the order of 1% per mirror, which is equivalent to an additional back- ground of about 3 K per surface, so not smaller than 30 K in total. The stability of the temperature in the cabin is ±1 K. This means that, for an emissivity of 1%, the effective background tempera- ture variation induced per mirror is around 10 mK. 2.4. The cabin optics and the cold reference (optics box) It is clear that the “walking” of the beam is well contained in the diffraction disk. lateral size of the MpI. In order to obtain a diffraction-limited combined beam for each position of the movable roof mirror (in the range of 0–90 mm), we imposed the criterion, for each field on the sky, producing a quasi-parallel beam inside the MpI. According to the geometrical throughput conservation rule, the field-to-field divergence is thus fixed by the diameter of the beam. For the 20 arcmin field-of-view, and considering a 12 m primary mirror, we obtained an overall beam diameter of about 420 mm inside the interferometer. A consequence of this method is that, in requiring that the combined beam does not “walk” in the focal plane (see Fig. 8), we must accept a jitter on the entrance pupil of the optical system, that is, the “active” portion of the primary mirror. This is, in the end, the main reason why we have decided to under-sample the size of the illuminated pri- mary mirror, to about 11 m. lateral size of the MpI. In order to obtain a diffraction-limited combined beam for each position of the movable roof mirror (in the range of 0–90 mm), we imposed the criterion, for each field on the sky, producing a quasi-parallel beam inside the MpI. According to the geometrical throughput conservation rule, the field-to-field divergence is thus fixed by the diameter of the beam. For the 20 arcmin field-of-view, and considering a 12 m primary mirror, we obtained an overall beam diameter of about 420 mm inside the interferometer. A consequence of this method is that, in requiring that the combined beam does not “walk” in the focal plane (see Fig. 8), we must accept a jitter on the entrance pupil of the optical system, that is, the “active” portion of the primary mirror. This is, in the end, the main reason why we have decided to under-sample the size of the illuminated pri- mary mirror, to about 11 m. Camera (refractive) Fig. 7. 3D view of the CONCERTO optics, evidencing the M3 mirror interfaced to the APEX sub-reflector (M2). M4 is attached to the ceiling of the C-cabin and represents the only reflective optics component, with M3 and the MpI rooftop moving mirror, outside of the optics box. 2.4. The cabin optics and the cold reference (optics box) The first CONCERTO element along the optical axis, after the telescope mirrors (M1 and M2), is the M3 foldable mir- ror mounted on the chassis. With a diameter of 900 mm, it is 5 In this context, the field-of-view has to be expressed in the number of beams. The number of beams is around 2000 for CONCERTO and 300 for KISS, which can be compared to few tens, at most, for the previous instruments. 6 https://en.wikipedia.org/wiki/MicroTCA A60, page 4 of 13 The CONCERTO collaboration: A wide field-of-view low-resolution spectrometer at APEX Fig. 8. Simulated focal plane image for the full, 20 arcmin, field-of- view. Each spot is shown for the two extreme positions of the roof mir- ror, i.e. green (0 mm) and blue (90 mm). The black circles represent the airy disks. It is clear that the “walking” of the beam is well contained in the diffraction disk. Fig. 6. Rotation of the camera (and chassis) following the telescope elevation (EL). The position of the eight soft rubber pneumatic actuators is shown. Two of them are dedicated to the pulse-tube head. For the six remaining actuators, we indicate (with black arrows) those that are in action for three representative elevation cases. Fig. 6. Rotation of the camera (and chassis) following the telescope elevation (EL). The position of the eight soft rubber pneumatic actuators is shown. Two of them are dedicated to the pulse-tube head. For the six remaining actuators, we indicate (with black arrows) those that are in action for three representative elevation cases. Optics Box Virtual Image X Y Z Camera (refractive) M4 M3 to M2 Optics Box Virtual Image X Y Z Camera (refractive) M4 M3 to M2 Fig. 7. 3D view of the CONCERTO optics, evidencing the M3 mirror interfaced to the APEX sub-reflector (M2). M4 is attached to the ceiling of the C-cabin and represents the only reflective optics component, with M3 and the MpI rooftop moving mirror, outside of the optics box. A large number of mirrors (M5 to M11), the two polarisers P1 and P2, and the cold reference optics complete the optical chain. Fig. 8. Simulated focal plane image for the full, 20 arcmin, field-of- view. Each spot is shown for the two extreme positions of the roof mir- ror, i.e. green (0 mm) and blue (90 mm). The black circles represent the airy disks. 2.5. CONCERTO hardware outside the C-cabin In addition to the elements described above and located in the C-cabin, CONCERTO is also made by modules elsewhere in the telescope tower and beyond, in particular, the commercial pulse- tube compressor (Cryomech CPA289C) and, more interestingly, the dilution cryostat gas handling system (GHS) and the Data AcQuisition (DAQ) and real time analysis (RTA) computers. The Atacama Pathfinder EXperiment (APEX) telescope is a modified prototype ALMA antenna with a primary mirror diam- eter of 12 m and a usable field-of-view of about 20 arcminutes. The location at around 5100 m a.s.l. on the Chajnantor plateau ensures optimal observing conditions (see Fig. 10). In particular, the fraction of time showing a precipitable water vapour (PWV) column that is lower than 2 mm is of the order of 70% or more. The GHS is composed of: (a) a series of pumps and com- pressors used to circulate the 3He-4He mixture and to provide compressed air to CONCERTO, and, (b) an electronic cabinet hosting a National Instrument CompactRIO7 real-time controller and multiple analogue and digital input-output modules. Ded- icated Labview-based software is loaded on the CompactRIO. The software continuously monitors the state of the cryostat and controls all of the pumps, compressors, valves, and actuators of the dilution circuit. It can perform many tasks automatically, such as pre-cooling the system or putting it in a safe mode if the security thresholds are exceeded. It also acts as a server-side programme for the client graphical user interface (GUI) that is used on remote computers. The GUI allows one to easily see the state of the system and control its components (Fig. 9). The structure of the Cassegrain cabin, and in general the telescope infrastructure, had been designed to host large field- of-view instrumentation. The primary mirror surface has been recently refurbished, and it achieves in some conditions a precision of the order of 10 µm RMS. To date, APEX is thus a state-of-the-art installation for millimetre and sub-millimetre astronomy. Since 2007, the telescope has hosted, in the same place that will be occupied by CONCERTO, the Large APEX BOlometer CAmera (LABOCA) operating at 360 GHz (Siringo et al. 2009). The CONCERTO optics box and chassis are slid separately through the C-cabin door and then fixed to the floor by a suf- ficient number of 12 mm metric screws. 2.4. The cabin optics and the cold reference (optics box) Considering roughly ten mirrors, this translates to a total effective background temperature variation of 0.1 K. The KID detectors, with a NET of the order of ≈mK· √s per pixel, are sensitive to this drift that will produce a correlated signal on all of the pixels. However, these instabilities are harmless since they are slower and smaller than the atmospheric fluctuations sitting on top. – The third option is cold cryostat, which is a de-focused image of the CONCERTO cryostat cold (inner) parts. In other words, CONCERTO “looks” into itself to find a cold auto- reference. Considering the number of optical elements (six mir- rors and three lenses) lying between the three-position mirror and the coldest stage of the cryostat, we expect an equivalent effective temperature of the order of 20 K. This is, in any case, lower than the loading of the sky plus the whole optics train between M1 and the focal plane, which is not lower than 50 K. We performed a trade-offbetween the requirements related to the image quality (and the interferometry efficiency) and the A60, page 5 of 13 A60 (2020) Fig. 10. Atmosphere transmission at APEX under 1 mm PWV (blue) and 2 mm PWV (orange) conditions. The CONCERTO bands for the HF and LF arrays are shown. A&A 642, A60 (2020) Fig. 9. GUI used to control the dilution refrigerator circuit. Fig. 9. GUI used to control the dilution refrigerator circuit. Fig. 9. GUI used to control the dilution refrigerator circuit. This innovative configuration will be investigated as a simpler alternative to the external cold black body. Fig. 10. Atmosphere transmission at APEX under 1 mm PWV (blue) and 2 mm PWV (orange) conditions. The CONCERTO bands for the HF and LF arrays are shown. We stress the fact that the external cold black-body, or its alternative “old cryostat”, are not used as spectral calibrators. They simply represent cold references, that is to say colder than the combined thermal emission of the atmosphere and the optical chain. In contrast to the “sky” reference case, the interferogram is not expected to be null at first order. In this case, we expect potential systematic effects to be minimised by the fact that both the reference and the dominant target (mostly the atmosphere in the common case of weak astrophysical sources) exhibit thermal black-body spectra. 2.4. The cabin optics and the cold reference (optics box) the environment and guarantee the flexibility required by the movement of the telescope. Inside the C-cabin, all of the con- nections are centralised on a dedicated panel located on the front side of the chassis, thus easing the procedures of plugging and unplugging. The DAQ system is located in the middle container and is connected to CONCERTO in the C-cabin, producing 128 MBytes per second, through five dedicated ethernet cables. The DAQ consists in two commercial computers with 48 GB of RAM and 24 cores each. The disk storage (432 TB) and the RTA systems are installed in the so-called servers room, located a few tens of metres away from the telescope tower. The RTA com- puter has 32 cores and 512 GB of RAM. The network connection between the DAQ and the disk storage or RTA is ensured by two 10 gigabit switches and underground cables. The best choice between the three references will depend on the particular science target, the observing conditions and the unknown systematic effects as of yet affecting this new kind of large field-of-view spectrophotometer. A crucial phase of the on- sky commissioning will be dedicated to investigating this item. We will report in further publications the results of this study, as well as a more detailed description of the CONCERTO MpI spectral reference system that is beyond the scope of the present paper. 7 https://en.wikipedia.org/wiki/CompactRIO 3. Detectors laboratory characterisation In this section, we describe the first tests performed on CON- CERTO detectors. Some of the electrical tests on the resonances occurred in the CONCERTO cryostat itself. On the other hand, the optical characterisation of the detectors has been achieved in the former NIKA2 test-bench. The so-called NIKA1.5 camera is an easily re-configurable optical dilution cryostat with a base temperature of 60 mK. It has been recently modified to host one CONCERTO array at a time. In particular, the optical filters can be easily replaced, and NIKA1.5 can be interfaced to a custom MpI for spectral characterisation, or alternatively to a sky simu- lator (described in detail in Monfardini et al. 2011) for sensitivity and beams’ geometry measurements. p The spectral response of two HF arrays, with slightly differ- ent substrate thicknesses, was measured. The results are reported in Fig. 14. The sensitivity was measured in terms of NET (noise equiva- lent temperature), with the NIKA1.5 optics system. The average NET per pixel of the CONCERTO arrays, in NIKA1.5, is around 2 mK √ Hz−1. This results in an NET of about 45 µK √ Hz−1 per array (polarisation), or 32 µK √ Hz−18 when combining both polarisations. Since the sensitivities per pixel are in accordance to what had been measured for the very similar NIKA2 detectors (Adam et al. 2018), we base our sensitivity estimate in Sect. 4 on NIKA2 values measured on-sky. We actually believe that the sensitivities measured on the maps on the sky for similar detec- tors are a more realistic prediction compared to somewhat ideal values estimated in laboratory. Since the twelve readout lines of the HF and LF arrays share a common local oscillator (LO, frequency reference for the read- out electronics), it is of vital importance to accommodate all of the blocks of resonances in a common ≤1 GHz band. This is nicely achieved, for example, in the case of the HF array shown in Fig. 12. The spread between blocks of resonances belonging to the same array, and between different arrays, is mainly due to inhomogeneities and uncertainties in the thickness of the Alu- minium film. The good imaging characteristics of the CONCERTO arrays are demonstrated by the Sky Simulator tests. An example is shown in Fig. 15. 2.5. CONCERTO hardware outside the C-cabin They have been acquired under dark conditions, in the CONCERTO cryostat, at T = 70 mK. 1·104 2·104 3·104 Coupling factor - QC Number of resonators 10 20 30 Fig. 13. Quality factors distribution for one representative block of resonances in the CONCERTO HF array. For this particular block Qc = 23k ± 12k, which is in line with all of the other blocks and with the designed Qc = 25k. These quality factors were measured in the CON- CERTO cryostat at T = 70 mK. 1·104 2·104 3·104 Coupling factor - QC Number of resonators 10 20 30 Fig. 11. Deformations of a wire sensor running between the floor and the top of the APEX Cassegrain cabin recorded for 48 h. The average absolute length of the wire is 2675.3 mm. Inset: picture of the wire sen- sor. standard APEX observations, is smaller than 0.2 mm and thus negligible for our purposes. The alignment of the mirrors in the optics box will be achieved in laboratory. The position of each mirror is adjusted with three micro-metric screws. No tuning will be possible at the telescope. The alignment of the optics box with respect to the chassis is ensured by the mechanical fixations. A set of spe- cific lasers will be mounted to achieve the internal alignments in laboratory. At the telescope, we will use these lasers to align the optics box with respect to M4, M4 with respect to M3, and M3 with respect to M2. The alignment procedures will represent a critical step in the installation. Fig. 13. Quality factors distribution for one representative block of resonances in the CONCERTO HF array. For this particular block Qc = 23k ± 12k, which is in line with all of the other blocks and with the designed Qc = 25k. These quality factors were measured in the CON- CERTO cryostat at T = 70 mK. is achieved without requiring complicated and risky additional technology steps, such as cross-the-line micro-bondings or sus- pended micro-bridges. Figure 13 shows an example of the statis- tics obtained for one readout line of the CONCERTO HF array. All of the lines, as well as the LF arrays tested so far, exhibit sim- ilar behaviours. The quality factor distribution does, as designed, peak around 25k. 8 We note that 32 µK √ Hz−1 is equivalent to 22.6 µK s1/2. 2.5. CONCERTO hardware outside the C-cabin Since the beam will bounce between the floor and the top of the cabin (M4), we mea- sured the deformations of the C-cabin itself under typical APEX observing conditions. This measurement was achieved using two linear wire sensors with a range of 3 m and a single measure- ment precision of 0.1 mm. As is shown in Fig. 11, the root mean square (RMS) of both sensors, over 48 hours of data taken during All of the pipes and cables that are needed to interconnect the elements of CONCERTO situated in different rooms (C-cabin, instrumentation, and compressors containers) are routed through flexible hoses. The hoses protect the CONCERTO cabling from A60, page 6 of 13 The CONCERTO collaboration: A wide field-of-view low-resolution spectrometer at APEX Fig. 11. Deformations of a wire sensor running between the floor and the top of the APEX Cassegrain cabin recorded for 48 h. The average absolute length of the wire is 2675.3 mm. Inset: picture of the wire sen- sor. standard APEX observations, is smaller than 0.2 mm and thus LO 1 GHz bandwidth Fig. 12. Frequency sweep (transmission of the feed-line between port 1 and 2, i.e. mod(S21)) of five blocks of resonances out of the base- line HF array. They have been acquired under dark conditions, in the CONCERTO cryostat, at T = 70 mK. Number of resonators 10 20 30 LO 1 GHz bandwidth Fig. 12. Frequency sweep (transmission of the feed-line between port 1 and 2, i.e. mod(S21)) of five blocks of resonances out of the base- line HF array. They have been acquired under dark conditions, in the CONCERTO cryostat, at T = 70 mK. 1·104 2·104 3·104 Coupling factor - QC Number of resonators 10 20 30 Fig. 13. Quality factors distribution for one representative block of resonances in the CONCERTO HF array. For this particular block Qc = 23k ± 12k, which is in line with all of the other blocks and with the designed Qc = 25k. These quality factors were measured in the CON- CERTO cryostat at T = 70 mK. Fig. 11. Deformations of a wire sensor running between the floor and the top of the APEX Cassegrain cabin recorded for 48 h. The average absolute length of the wire is 2675.3 mm. Inset: picture of the wire sen- sor. standard APEX observations, is smaller than 0.2 mm and thus negligible for our purposes. 2.5. CONCERTO hardware outside the C-cabin The alignment of the mirrors in the optics box will be achieved in laboratory. The position of each mirror is adjusted with three micro-metric screws. No tuning will be possible at the telescope. The alignment of the optics box with respect to the chassis is ensured by the mechanical fixations. A set of spe- cific lasers will be mounted to achieve the internal alignments in laboratory. At the telescope, we will use these lasers to align the optics box with respect to M4, M4 with respect to M3, and M3 with respect to M2. The alignment procedures will represent a critical step in the installation. LO 1 GHz bandwidth Fig. 12. Frequency sweep (transmission of the feed-line between port 1 and 2, i.e. mod(S21)) of five blocks of resonances out of the base- line HF array. They have been acquired under dark conditions, in the CONCERTO cryostat, at T = 70 mK. 1·104 2·104 3·104 Coupling factor - QC Number of resonators 10 20 30 Fig. 13. Quality factors distribution for one representative block of resonances in the CONCERTO HF array. For this particular block Qc = 23k ± 12k, which is in line with all of the other blocks and with the designed Qc = 25k. These quality factors were measured in the CON- CERTO cryostat at T = 70 mK. is achieved without requiring complicated and risky additional technology steps, such as cross-the-line micro-bondings or sus- LO 1 GHz bandwidth Fig. 12. Frequency sweep (transmission of the feed-line between port 1 and 2, i.e. mod(S21)) of five blocks of resonances out of the base- line HF array. They have been acquired under dark conditions, in the CONCERTO cryostat, at T = 70 mK. Fig. 11. Deformations of a wire sensor running between the floor and the top of the APEX Cassegrain cabin recorded for 48 h. The average absolute length of the wire is 2675.3 mm. Inset: picture of the wire sen- sor. Fig. 12. Frequency sweep (transmission of the feed-line between port 1 and 2, i.e. mod(S21)) of five blocks of resonances out of the base- line HF array. They have been acquired under dark conditions, in the CONCERTO cryostat, at T = 70 mK. Fig. 12. Frequency sweep (transmission of the feed-line between port 1 and 2, i.e. mod(S21)) of five blocks of resonances out of the base- line HF array. 3. Detectors laboratory characterisation A deeper geometrical characterisation of the thousands of beams is beyond the scope of this paper and will only be performed on the final arrays. Another important electrical parameter to be studied for large arrays of LEKID is the coupling quality factor Qc. The micro- strip configuration that has been chosen has the advantage of guaranteeing a relatively well-peaked distribution of Qc. This A60, page 7 of 13 A&A 642, A60 (2020) A60 (2020) TIME SINCE SCAN START (s) RESONANCE FREQUENCY SHIFT (kHz) 75 150 225 300 375 0 -1 -2 -3 Fig. 15. Sky simulator trace. A fake “planet” (point-like source) is cross- ing the field-of-view of the considered pixel. A raster scan with sub- scans at a fixed elevation is simulated. The “elevation” steps are 4 mm long each. This measurement was obtained using the NIKA1.5 cryostat at T = 120 mK and under a background temperature around 50 K. Fig. 14. Spectral response of two CONCERTO HF arrays (solid lines) and one NIKA2 260 GHz detector (dashed line). Red: HR Silicon sub- strate thickness of 110 ± 5 µm; blue: thickness of 100 ± 5 µm. Spectral responses were measured in the NIKA1.5 cryostat with low-pass filters defining an open band up to 300 GHz. TIME SINCE SCAN START (s) RESONANCE FREQUENCY SHIFT (kHz) 75 150 225 300 375 0 -1 -2 -3 Fig. 15. Sky simulator trace. A fake “planet” (point-like source) is cross- ing the field-of-view of the considered pixel. A raster scan with sub- scans at a fixed elevation is simulated. The “elevation” steps are 4 mm long each. This measurement was obtained using the NIKA1.5 cryostat at T = 120 mK and under a background temperature around 50 K Fig. 14. Spectral response of two CONCERTO HF arrays (solid lines) and one NIKA2 260 GHz detector (dashed line). Red: HR Silicon sub- strate thickness of 110 ± 5 µm; blue: thickness of 100 ± 5 µm. Spectral responses were measured in the NIKA1.5 cryostat with low-pass filters defining an open band up to 300 GHz. TIME SINCE SCAN START (s) RESONANCE FREQUENCY SHIFT (kHz) 75 150 225 300 375 0 -1 -2 -3 RESONANCE FREQUENCY SHIFT (kH Fig. 14. Spectral response of two CONCERTO HF arrays (solid lines) and one NIKA2 260 GHz detector (dashed line). 4.1. CONCERTO as an photometer: Dual-band sensitivity where 27.5 and 11 m are the IRAM and APEX telescopes effec- tive sizes, respectively, that is to say the portion of the primary mirrors that are optically conjugated to the cold pupils of the instruments (aperture stops). We first computed the sensitivity for CONCERTO as if it was a dual-band imager (LF and HF). For that, we relied on NIKA2 sensitivity measurements on the IRAM 30-m telescope. Aver- age NEFDs for NIKA2 (NEFDNIKA2) are equal to 9.8 and 36.1 mJy s1/2, at 150 and 260 GHz, respectively, for pwv = 2 and an elevation of 60 degrees (Perotto et al. 2020). These numbers already suffer from the transmission of the whole experiment. Then we assumed a frequency window of ∆ν = 115 GHz, making the assumption that the two arrays cover the frequency range of 195–310 GHz (HF) and 130–270 GHz (LF), with a notch filter removing 25 GHz of the low-frequency bandpass (around 183 GHz). Finally, we also had to take the decrease in transmission into account due to the increased optics complexity of CONCERTO compared to NIKA2 (in particular FTS optics will have some transmission loss and additional loading), which we estimate to be T = 0.8 for an unpolarised source. It is impor- tant to note that this is only an additional loss of transmission compared to NIKA2+P1 and not the overall transmission. y p We observe a large difference between the NIKA2 260 and 150 GHz channel performances. A combination of known effects explains the gap in sensitivity. Indeed, at 260 GHz, (i) the beam efficiency of the 30-m telescope is about 55%, (ii) the sensitivity is strongly affected (by 35%) by a known defect of the NIKA2 dichroïc, and (iii) the contribution of residual sky noise to the average NEFDs is important. Therefore, as a realistic starting point for CONCERTO, we assume that the sensitivity for the LF array equals that of NIKA2 at 150 GHz. For the HF array, we assume a sensitivity better than that of the NIKA2 260 GHz channel, thanks to a gain in beam efficiency at APEX (which is of the order of 80% at the CONCERTO wavelengths), the lack of dichroïc in CONCERTO, and better atmospheric conditions. 3. Detectors laboratory characterisation Red: HR Silicon sub- strate thickness of 110 ± 5 µm; blue: thickness of 100 ± 5 µm. Spectral responses were measured in the NIKA1.5 cryostat with low-pass filters defining an open band up to 300 GHz. Fig. 15. Sky simulator trace. A fake “planet” (point-like source) is cross- ing the field-of-view of the considered pixel. A raster scan with sub- scans at a fixed elevation is simulated. The “elevation” steps are 4 mm long each. This measurement was obtained using the NIKA1.5 cryostat at T = 120 mK and under a background temperature around 50 K. The typical response time of the LEKID used for CON- CERTO ranges between 30 µs and 100 µs, depending on the background. Even at the chosen sampling rate of 4 kHz, a cosmic-ray hit will thus represent a single-point glitch in the CONCERTO raw-time traces. The order of magnitude of the expected rate is 0.1 Hz per pixel. NEFDHF NIKA2 = 15 [10−20] mJy s1/2. (2) (2) The numbers in brackets give the uncertainties on our assump- tion. As it was the case for NIKA2, we make the hypothesis that no excess noise will appear in CONCERTO at APEX compared to CONCERTO in laboratory. Of course, this cannot be verified until installation. The numbers in brackets give the uncertainties on our assump- tion. As it was the case for NIKA2, we make the hypothesis that no excess noise will appear in CONCERTO at APEX compared to CONCERTO in laboratory. Of course, this cannot be verified until installation. 4. Sensitivity estimates Compared to NIKA2, for CONCERTO, we have to scale the sensitivities to match the APEX telescope size and add two polarisers in the optical path (P1 and P2, see Fig. 4). Sensitivity loss is only due to P1, by a factor between √ 2 (if photon noise dominates) and 2. To be conservative, we considered a factor of 2. Thus, for a single array of CONCERTO, the NEFD becomes: Due to the similarities between the NIKA2 and CONCERTO detectors, we used the NIKA2 sensitivity measured on sky and on the reduced maps as a base to estimate the sensitivity for CONCERTO. As already advocated, we think that this approach, coupled with our NET laboratory measurements, provides quite realistic predictions. NEFDLF,HF = NEFDLF,HF NIKA2 × 2 × 27.5 11 !2 (3) (3) 9 A voxel represents a value on a regular grid in three-dimensional space. 4.2. Sensitivity in spectroscopy For the spectroscopic mode, we consider a fix value for spectral resolution of δν = 1.5 GHz. The number of spectral elements in the frequency range is Nse = ∆ν/δν. The sensitivity per spectral element (in mJy s1/2) for a single spectrometer (we note that in our case, with an FTS, the number of pixel equals the number of spectrometers) is given by (9) where FOV is the field of view area (with a diameter of 20 arcmin). The numbers are given in Table 2. We note that we ignored the frequency overlap between the two arrays (and thus a gain of ∼ √ 2 on the sensitivity in the frequency overlap region). We considered NEFDLF DB for ν ≤150 GHz, NEFDHF DB for ν ≥260 GHz, and a linear interpolation between the two NEFDs for 150 < ν < 260 GHz. where FOV is the field of view area (with a diameter of 20 arcmin). The numbers are given in Table 2. We note that we ignored the frequency overlap between the two arrays (and 4.1. CONCERTO as an photometer: Dual-band sensitivity σarray = NEIFTS/ p NKIDS, (10) (10) where NKIDS is the number of pixels (KIDS) of each array; we use 1720 KIDS, which correspond to 80% of valid KIDS in each array. This would be the sensitivity of each voxel9 of large maps, assuming a RA-Dec (or AZ-EL) raster scan-like scanning strat- egy and also assuming that pixel sizes of the map are equal to beam sizes. Each voxel of the observed map would then be observed by each KIDS. We checked these numbers using a scanning strategy similar to NIKA2 raster scans, with three inter- ferograms per beam. 5. Low spectral-resolution spectroscopic surveys Thus we expect CONCERTO to bring a significant contribution in a number of areas, including the study of galaxy clusters (via the thermal and kinetic SZ effect), the follow-up of cosmological deep surveys, the observation of local and intermediate-redshift galaxies, and the study of Galac- tic star-forming clouds. In this section we provide a forecast on the expected signal-to-noise ratio (S/N) that can be obtained on the [CII]-emission power spectrum (Sect. 5.1). In addition, we give some predictions for observing the SZ signal of galaxy clus- ters (Sect. 5.2). with a FWHM that is determined by the Rayleigh criterion for a D = 11 m antenna (our illumination of the APEX 12 m antenna) at a given frequency, (which corresponds to a given redshift for the [CII] line), θbeam = 1.22λobs/D. (7) (7) θbeam = 1.22λobs/D. θbeam = 1.22λobs/D. We can then convert the sensitivity per spectral element from point-source (Eq. (5)) to diffuse emission (in MJy sr−1 s1/2) following NEIFTS = NEFDFTS × 10−9/Ωbeam. (8) (8) This is the noise equivalent intensity, on sky, per KIDS, per spec- tral bin (taken as δν = 1.5 GHz). We can finally compute the mapping speed MS (per spectral element) following, 4.1. CONCERTO as an photometer: Dual-band sensitivity The values are thus (for pwv=2 and an elevation of 60 degrees): p The sensitivity of CONCERTO as a dual-band photometer that is set when the optical path difference in the FTS is null is thus: NEFDLF,HF phot = NEFDLF,HF × s ∆νLF,HF NIKA2 ∆ν × 1 √ T . (4) NEFDLF,HF phot = NEFDLF,HF × s ∆νLF,HF NIKA2 ∆ν × 1 √ T . (4) (4) We have ∆νHF NIKA2 = 48 GHz and ∆νLH NIKA2 = 39.2 GHz (Perotto et al. 2020) and thus: NEFDLF NIKA2 = 10 [7.5−15] mJy s1/2 and (1) A60, page 8 of 13 he CONCERTO collaboration: A wide field-of-view low-resolution spectrometer at APEX The CONCERTO collaboration: A wide field-of-view low-resolution spectrometer at APEX p Table 2. Key parameters for CONCERTO instrument. ν [GHz] 131 156 211 238 272 302 Redshift of the [CII] line 13.5 11.2 8.0 7.0 6.0 5.3 Beam size [arcsec] 52.4 44.0 32.5 28.8 25.2 22.7 Beam solid angle [×10−8 sr] 7.30 5.15 2.81 2.21 1.70 1.37 Mapping speed [×10−3 deg2/(MJy sr−1)2 h−1] 42.8 [19.0–76.0] 19.8 [9.0–35.9] 3.4 [1.8–7.1] 1.7 [0.9–3.7] 0.8 [0.5–1.9] 0.5 [0.3–1.2] On sky map sensitivity σarray 2.1 [1.5–3.1] 3.0 [2.3–4.5] 7.3 [5.1–10.2] 10.4 [7.1–14.1] 14.8 [9.9–19.7] 18.2 [12.2–24.3] [(MJy sr−1) s1/2] Notes. Sensitivities and mapping speeds are given for one spectral element (with δν = 1.5 GHz), assuming 80% of valid KIDS, a precipitable water vapour of 2 mm, and an elevation of 60 degrees. Table 2. Key parameters for CONCERTO instrument. Notes. Sensitivities and mapping speeds are given for one spectral element (with δν = 1.5 GHz), assuming 80% of valid KIDS, a precipitable water vapour of 2 mm, and an elevation of 60 degrees. In Table 2, we also provide the sensitivity for the whole array, per spectral element, which is: NEFDLF phot = 81.6 [61.2–122.4] mJy s1/2 and NEFDHF phot = 135.4 [90.3–180.6] mJy s1/2. NEFDLF phot = 81.6 [61.2–122.4] mJy s1/2 and NEFDHF phot = 135.4 [90.3–180.6] mJy s1/2. We note that due to the FTS in front of the cryostat, CON- CERTO is a non-optimal instrument for imaging. However, the option of removing the first polariser for purely photomet- ric campaigns could be studied. In that case, the sensitivity is expected to be two times better for each individual array (as we took a factor 2 of penalty for P1). 5. Low spectral-resolution spectroscopic surveys CONCERTO will offer generic access to a large FoV and a low- frequency resolution spectroscopic instrument. This opening of 3D large-scale surveys is the next step after the broad-band pho- tometric experiments, either from the ground (e.g. LABOCA, SCUBA2, NIKA2) or from space (e.g. Herschel and Planck). NEFDFTS = NEFDphot × Nse. (5) (5) NEFDFTS = NEFDphot × Nse. The beam area is computed assuming a Gaussian beam, Ωbeam = 2π  θbeam 2 p 2 log 2  2 , (6 SCUBA2, NIKA2) or from space (e.g. Herschel and Planck). The first scientific aim of CONCERTO is to map, in three dimen- sions, the fluctuations of the [CII] line intensity in the reion- isation and post-reionisation epoch (z ≥5.3). This technique, known as intensity mapping, will measure the clustering of [CII] emissivity and allow for questions to be answered on how and when galaxies and quasars formed and on the history and topol- ogy of reionisation. Even if [CII] intensity mapping has been the basis of instrument definition, we extended the instrument capa- bilities to make CONCERTO a multi-purpose instrument (e.g. extending the frequency range down to 130 GHz for observa- tions of galaxies clusters). Thus we expect CONCERTO to bring a significant contribution in a number of areas, including the study of galaxy clusters (via the thermal and kinetic SZ effect), the follow-up of cosmological deep surveys, the observation of local and intermediate-redshift galaxies, and the study of Galac- tic star-forming clouds. In this section we provide a forecast on the expected signal-to-noise ratio (S/N) that can be obtained on the [CII]-emission power spectrum (Sect. 5.1). In addition, we give some predictions for observing the SZ signal of galaxy clus- ters (Sect. 5.2). (6) The first scientific aim of CONCERTO is to map, in three dimen- sions, the fluctuations of the [CII] line intensity in the reion- isation and post-reionisation epoch (z ≥5.3). This technique, known as intensity mapping, will measure the clustering of [CII] emissivity and allow for questions to be answered on how and when galaxies and quasars formed and on the history and topol- ogy of reionisation. Even if [CII] intensity mapping has been the basis of instrument definition, we extended the instrument capa- bilities to make CONCERTO a multi-purpose instrument (e.g. extending the frequency range down to 130 GHz for observa- tions of galaxies clusters). MS = FOV/NEI2 FTS, (9) MS = FOV/NEI2 FTS, (9) 5.1. [CII] intensity mapping with CONCERTO (2012) to link the intensity of emission lines to the galaxy infrared luminosity, they computed 3D emission line power spectra for all relevant lines, including [CII]. They computed the expected S/N of cross-power spectra between [CII] and other emission lines, which will constrain the mean amplitude of each signal and thereby help to gain insight into the mean properties of the ISM of high-z galaxies. It is important to note that in their paper, they use for CONCERTO a constant sensitivity for all redshifts of σarray = 155 mJy s1/2, while we have here σarray = [156, 206, 230, 250, 250] mJy s1/2 at z = [11.2, 8.0, 7.0, 6.0, 5.3]. We consider measurements spanning a redshift range of ∆z ∼0.6, which corresponds to a frequency range of Bν ∼ 20 GHz at z = 6.1 for the [CII] line. We note that Gong et al. (2012) give useful relations for computing Vs and Vvoxel for the [CII] line. Table 3 gives the numbers derived from the above compu- tations and Fig. 16 shows the predicted [CII] power spectrum with its error bars. Because these types of predictions are very uncertain, we assumed two extreme models, giving respectively low and high SFRD at z > 3 (see Fig. 3 of Lagache et al. 2018). Low SFRD is the pessimistic prediction as it corresponds to the lowest UV-driven SFRD; high SFRD is the optimistic prediction as it corresponds to the CIB-driven SFRD derived from the halo modelling of Planck CIB measurements (Planck Collaboration XXX 2014). emission lines to the galaxy infrared luminosity, they computed 3D emission line power spectra for all relevant lines, including [CII]. They computed the expected S/N of cross-power spectra between [CII] and other emission lines, which will constrain the mean amplitude of each signal and thereby help to gain insight into the mean properties of the ISM of high-z galaxies. It is important to note that in their paper, they use for CONCERTO a constant sensitivity for all redshifts of σarray = 155 mJy s1/2, while we have here σarray = [156, 206, 230, 250, 250] mJy s1/2 at z = [11.2, 8.0, 7.0, 6.0, 5.3]. 5.1. [CII] intensity mapping with CONCERTO 2019), providing an unbiased view of the dis- tribution of the gas that is difficult to assemble from targeted measurements of individual galaxies, and probing cosmologi- cal volumes, with maps on several-degree scale and large fre- quency (and thus redshift) coverage. Intensity mapping exploits the confusion-limited regime and measures the integrated light emission from all sources, including unresolved faint galaxies. (14) where ∆k is the Fourier bin size and Vs(z) is the survey volume, expressed as Vs(z) = χ(z)2yCIIBνA, (15) Vs(z) = χ(z)2yCIIBνA, (15) with Vs(z) = χ(z)2yCIIBνA, (15) with g g We will conduct with CONCERTO a major survey of about one square degree with 1200 h of APEX telescope time. The sur- vey will provide a data cube in which intensity is mapped as a function of sky position and redshift. Our main target is the [CII] line emission at z ≥5.3. But CONCERTO will also observe the CO intensity fluctuations arising from 0.3 < z < 2 galaxies, giv- ing the spatial distribution and abundance of molecular gas over a broad range of cosmic time. The 3D fluctuations will be stud- ied in Fourier space with the power spectrum. yCII(z) = λCII(1 + z)2/H(z), (16) (16) being the factor to convert the frequency intervals to the comov- ing distance at the wavelength λCII (rest frame wavelength of the [CII] line). In Eq. (15), Bν is the bandwidth considered for the measurement. The volume surveyed by each voxel (Vvoxel in Eq. (13)) is being the factor to convert the frequency intervals to the comov- ing distance at the wavelength λCII (rest frame wavelength of the [CII] line). In Eq. (15), Bν is the bandwidth considered for the measurement. The volume surveyed by each voxel (Vvoxel in Eq. (13)) is (17) Vvoxel = χ(z)2yCII(z)Ωbeamδν. (17) Vvoxel = χ(z)2yCII(z)Ωbeamδν. To compute the expected S/N on the [CII] power spectrum at high z, we used the [CII] model presented in Serra et al. (2016). Using measurements of the cosmic infrared background (CIB) angular power spectra from Herschel/SPIRE together with star formation rate density (SFRD) measurements, they constrain the galaxy FIR luminosity as a function of dark-matter halo mass at all relevant redshifts in the halo model framework. By using scal- ing relations from Spinoglio et al. 5.1. [CII] intensity mapping with CONCERTO The [CII] line is one of the brightest emission lines in the spec- tra of galaxies. It is an excellent coolant for neutral gas in thus a gain of ∼ √ 2 on the sensitivity in the frequency overlap region). We considered NEFDLF DB for ν ≤150 GHz, NEFDHF DB for ν ≥260 GHz, and a linear interpolation between the two NEFDs for 150 < ν < 260 GHz. A60, page 9 of 13 A&A 642, A60 (2020) Assuming a spherically averaged power spectrum measure- ment and a directionally independent on sky sensitivity, the vari- ance of the power spectrum is: photo-dominated regions and an extinction-free tracer of star for- mation at high z. Being redshifted into the sub-millimetre and millimetre atmospheric windows for z > 4.5, it has become one of the most popular lines at high z. Pointing on known objects, with, for example, ALMA, NOEMA, and APEX/FLASH, [CII] is now detected in a large number of galaxies at high z (>150 at z > 4.5, with a large contribution from the ALMA ALPINE survey, e.g. Bethermin et al. 2020). These types of observations are a tremendous step forward but we also need to look at the overall population, that is, observe large volume and unbiased surveys. First observations with ground-based interferometers, for example, with ALMA (‘ALMA Spectroscopic Survey in the Hubble Ultra Deep Field’ large programme – ASPECS, Walter et al. 2016) or JVLA (CO Luminosity Density at High Redshift survey – COLDz, Riechers et al. 2019) offer a three-dimensional view of the molecular gas content of galaxies. The covered areas are about 5–60 square arcmin. var[ ¯PCII(k)] = [PCII(k) + ¯PN CII(k)]2 Nm(k, z) , (12) (12) where Nm(k, z) is the number of modes that leads to the power spectrum measurement at each k and ¯PN CII(k) = Vvoxel σ2 voxel tvoxel , (13) (13) with Vvoxel the volume surveyed by each voxel. In the case of CONCERTO, each KIDS gets a spectrum, and considering one KID per beam, we have σvoxel = σarray. p , voxel array The number of modes at each k is given by p y The number of modes at each k is given by Nm(k, z) = 2π k2∆k Vs(z) (2π)3 , (14) q Intensity mapping complements these efforts beautifully (e.g Kovetz et al. 5.2. Observing galaxy clusters with CONCERTO 2014, 2015, 2016, 2017a; Ruppin et al. 2017, 2018). For the kSZ effect, which is also observed with, for example, NIKA2 (Adam et al. 2017b), a multi-wavelength spec- trometer such as CONCERTO would be a unique tool to separate the tSZ and kSZ as well as the different foreground components (CIB, CMB, and the Galactic emission) and to extract informa- tion about the cluster physics. Indeed, with sufficiently precise spectroscopy measurements (Birkinshaw 1999), we can measure the cluster mass (from the tSZ effect), proper motion along the line-of-sight (from the kSZ), and temperature (from the relativis- tic corrections to the tSZ). or observed with the ALMA ALPINE survey (Schaerer et al. 2020). Our power spectra are thus very likely to be underes- timated. In terms of point source sensitivities, our survey will reach 1σ = [14.4, 14.9, 19.7, 22.0, 23.9, 23.9] mJy, for a spectral element δν = 1.5 GHz, at ν = [131.0, 156.0, 211.0, 238.0, 272.0, 302] GHz, respectively. Finally, one major difficulty in inten- sity mapping surveys is the problem of foregrounds. For [CII], the main foregrounds will be the contamination from emission lines from lower redshifts, in particular emission from CO rota- tion transitions (e.g. Yue et al. 2015). Silva et al. (2015) and Breysse et al. (2015) show that this contamination can be par- tially removed by masking out the brightest pixels in the sur- vey or the low-redshift galaxies selected from other surveys. To that end, CONCERTO will highly benefit from the exten- sive visible-IR photometry and spectroscopy galaxy survey data that are available in the chosen field (i.e. the COSMOS field). In addition, one of the strengths of CONCERTO is in its wide frequency range: Several CO lines are simultaneously observed at the same redshift for all redshifts of z > 0.35. The cross- correlation between these lines will be a very powerful method Particularly, considering the angular resolution and the map- ping speed of CONCERTO, we expect to perform a precise esti- mate of the shape of the SZ spectrum for clusters of galaxies for redshifts between 0.2 and 0.8. As an illustration, we present in Fig. 17 a simulation of a typical cluster that could be observed with CONCERTO. In this simulation, the mass of the cluster is equal to 1015 M⊙and the cluster is located at a redshift of z = 0.4. 5.2. Observing galaxy clusters with CONCERTO Clusters of galaxies are the largest gravitationally bound objects in the Universe and, as such, they are key to understanding the hierarchical large scale structure (Kravtsov & Borgani 2012). The study of galaxy clusters and, in particular, their num- ber as a function of mass and redshift allows us to constrain cosmological parameters (Allen et al. 2011). In the frequency range covered by CONCERTO, a cluster of galaxies will be mainly detected via the thermal and kinetic Sunyaev-Zel’dovitch (SZ) effect (Sunyaev & Zel’dovich 1972; Sunyaev & Zeldovich 1980). The thermal SZ (tSZ) effect (Sunyaev & Zel’dovich 1972) refers to the interaction of the hot electrons in clusters with the CMB photons. It results in a distortion in the CMB spectrum at the position of the cluster. In the case of hot clusters, it will also be affected by relativistic corrections named rSZ (see Itoh & Nozawa 2004, for details on their computation). The kinetic SZ (kSZ) (Sunyaev & Zeldovich 1980) is a Doppler shift of the CMB photons induced by the proper motion of clusters of galax- ies along the line-of-sight. Fig. 16. Predicted [CII] power spectrum at z = 6. Three cases are shown, corresponding to three scenarios of SFRD at high z (see Lagache et al. 2018): high SFRD (dark blue), low SFRD (light blue), and the geo- metrical mean of the two (red). Only points with S/N > 1 are shown. S/Ns were computed considering A = 1.4 square degrees, tsurvey = 840 h, which corresponds to a total observation time of 1200 hours taking the overheads into account, and sensitivities as estimated in Sect. 4. The [CII] power spectra were derived from the modelling of CIB power spectra (Serra et al. 2016), using a conversion from SFR to [CII] that conservatively underestimates the [CII] luminosity by a factor of 6 at z = 5 compared to recent semi-analytical models (e.g. Lagache et al. 2018) or ALMA ALPINE measurements (Schaerer et al. 2020). Our estimates of [CII] power spectra are thus likely to be underestimated. The predicted [CII] power spectra from Yue & Ferrara 2019, using the local SFR-[CII] relation (black line) and Chung et al. 2020 (dashed black line) are also shown. Observations of the tSZ effect have been successfully per- formed at high angular resolution using continuum cameras based on KIDs, such as NIKA and NIKA2 at the IRAM 30-m telescope (Adam et al. 5.1. [CII] intensity mapping with CONCERTO Redshift z 5.5 6.2 7 8 S/N PCII mean SFRD 23 [14–44] 12 [6.9–24] 5.7 [3.1–12] 2.0 [1.0–4.1] S/N PCII low SFRD 4.5 [2.6–9.8] 1.9 [1.1–4.3] 0.78 [0.48–1.7] 0.23 [0.12–0.48] S/N PCII high SFRD 79 [57–112] 55 [36–87] 34 [21–60] 16 [8.5–29] Notes. PCII was computed for ∆z = 0.6 and given for k = [0.1, 1] h Mpc−1. See the caption of Fig. 16 for more details. Numbers in brackets reflect the range of sensitivities (as given in Table 2). Table 3. S/N on the [CII] power spectrum. Notes. PCII was computed for ∆z = 0.6 and given for k = [0.1, 1] h Mpc−1. See the caption of Fig. 16 for more details. Numbers in brackets reflect the range of sensitivities (as given in Table 2). Fig. 16. Predicted [CII] power spectrum at z = 6. Three cases are shown, corresponding to three scenarios of SFRD at high z (see Lagache et al. 2018): high SFRD (dark blue), low SFRD (light blue), and the geo- metrical mean of the two (red). Only points with S/N > 1 are shown. S/Ns were computed considering A = 1.4 square degrees, tsurvey = 840 h, which corresponds to a total observation time of 1200 hours taking the overheads into account, and sensitivities as estimated in Sect. 4. The [CII] power spectra were derived from the modelling of CIB power spectra (Serra et al. 2016), using a conversion from SFR to [CII] that conservatively underestimates the [CII] luminosity by a factor of 6 at z = 5 compared to recent semi-analytical models (e.g. Lagache et al. 2018) or ALMA ALPINE measurements (Schaerer et al. 2020). Our estimates of [CII] power spectra are thus likely to be underestimated. The predicted [CII] power spectra from Yue & Ferrara 2019, using the local SFR-[CII] relation (black line) and Chung et al. 2020 (dashed black line) are also shown. to remove the contamination. This will be specifically addressed for CONCERTO in a future paper. 5.1. [CII] intensity mapping with CONCERTO Covering an area of 1.4 square degrees, our survey will pro- vide the first measurements of the [CII] power spectrum up to z ∼7, considering the mean SFRD and average sensitivity esti- mate, and up to z ∼8 in the best case for the sensitivity esti- mate. We note that the low SFRD case is unlikely as it gives low shot-noise levels for the CIB, which are not compatible with the Planck and Herschel measurements nor with current SFRD measurements at high-z based on [CII] or far-infrared measure- ments. Moreover, on top of the exact level of the SFRD at high z, the relation used to convert SFR to [CII] luminosity is another capital ingredient of this type of model. Serra et al. (2016) used the relation from Spinoglio et al. (2012), which provides, for a given SFR, a [CII] luminosity that is six times lower than that obtained with the [CII]-SFR relations of Lagache et al. (2018) We followed Gong et al. (2012) to compute uncertainties on the power spectra. The observing time per map voxel, consider- ing one pixel equals one beam, is given by tvoxel = tsurvey ΩbeamNKIDS A , (11) tvoxel = tsurvey ΩbeamNKIDS A , (11) with A the survey area, tsurvey the on-sky survey time (i.e. 1200 × 0.7 = 840 h in our case, considering 30% of overheads), Ωbeam the solid angle of the beam (Table 2), and NKIDS, the number of pixels (we consider 80% of valid KIDS, thus NKIDS = 1720). A60, page 10 of 13 The CONCERTO collaboration: A wide field-of-view low-resolution spectrometer at APEX Table 3. S/N on the [CII] power spectrum. Redshift z 5.5 6.2 7 8 S/N PCII mean SFRD 23 [14–44] 12 [6.9–24] 5.7 [3.1–12] 2.0 [1.0–4.1] S/N PCII low SFRD 4.5 [2.6–9.8] 1.9 [1.1–4.3] 0.78 [0.48–1.7] 0.23 [0.12–0.48] S/N PCII high SFRD 79 [57–112] 55 [36–87] 34 [21–60] 16 [8.5–29] Notes. PCII was computed for ∆z = 0.6 and given for k = [0.1, 1] h Mpc−1. See the caption of Fig. 16 for more details. Numbers in brackets reflect the range of sensitivities (as given in Table 2). Table 3. S/N on the [CII] power spectrum. 5.2. Observing galaxy clusters with CONCERTO We assumed a universal pressure profile model from Arnaud et al. (2010) to compute the cluster’s Compton param- eter map. From left to right, we present the cluster’s SED as expected to be measured by CONCERTO at different radial dis- tances from the centre of the cluster. We considered six bands in frequency with typical bandwidths of 10–25 GHz. We explored both the sensitivity to the relativistic SZ effect (blue points), assuming a cluster temperature of 20 keV, and to the kinetic SZ (red points), assuming the cluster is moving towards the observer A60, page 11 of 13 A&A 642, A60 (2020) Fig. 17. Thermal (green), kinetic (orange), and relativistic (light blue) SZ effect for a simulated cluster at redshift z = 0.4, with a mass of 1015 M⊙ and a temperature of 20 keV, which is moving at 1000 km h−1 towards the observer. From left to right, we present the measured CONCERTO SEDs for tSZ+kSZ and rSZ+tSZ, including uncertainties (red and blue dots, respectively) for different radial bins with respect to the centre of the cluster (θ in arcmin) up to the cluster’s characteristic radius, θ500, which is the radial angular distance at which the mean cluster density is 500 times the critical density at the cluster redshift. Fig. 17. Thermal (green), kinetic (orange), and relativistic (light blue) SZ effect for a simulated cluster at redshift z = 0.4, with a mass of 1015 M⊙ and a temperature of 20 keV, which is moving at 1000 km h−1 towards the observer. From left to right, we present the measured CONCERTO SEDs for tSZ+kSZ and rSZ+tSZ, including uncertainties (red and blue dots, respectively) for different radial bins with respect to the centre of the cluster (θ in arcmin) up to the cluster’s characteristic radius, θ500, which is the radial angular distance at which the mean cluster density is 500 times the critical density at the cluster redshift. CONCERTO is currently in an advanced stage of fabrica- tion. The installation and technical commissioning at the APEX telescope is scheduled for the first semester of 2021. The com- missioning, scientific verification, and observations are foreseen by the end of 2022. CONCERTO is currently in an advanced stage of fabrica- tion. The installation and technical commissioning at the APEX telescope is scheduled for the first semester of 2021. The com- missioning, scientific verification, and observations are foreseen by the end of 2022. 5.2. Observing galaxy clusters with CONCERTO with a velocity of 1000 km h−1. Uncertainties were computed from the sensitivity estimates given in Sect. 4, assuming a map- ping area of 310 arcmin2 and a total integration time of 30 hours. In the Fig. 17, we also show the individual tSZ, kSZ, and rSZ effect contributions. We find that for reasonable observation times (tens of hours), CONCERTO would provide first spectral 2D mapping of the intracluster medium of high redshift clusters and should be able to measure cluster velocities via the kSZ effect. CONCERTO should also be able to detect the relativistic SZ effect and mea- sure the cluster temperature. A more detailed mapping of the cluster temperature would require observation times of about hundreds of hours. Acknowledgements. Besides the authors, the technicians and engineers more involved in the experimental setup development have been Maurice Grol- lier, Olivier Exshaw, Anne Gerardin, Gilles Pont, Guillaume Donnier-Valentin, Philippe Jeantet, Mathilde Heigeas, Christophe Vescovi, and Marc Marton. We acknowledge the crucial contributions of the whole Cryogenics and Electron- ics groups at Institut Néel and LPSC. The arrays described in this paper have been produced at the PTA Grenoble microfabrication facility. We warmly thank the support from the APEX stafffor their help in CONCERTO pre-installations and design. The flexible pipes, in particular, have been routed under the compe- tent coordination of Jorge Santana and Marcelo Navarro. We acknowledge sup- port from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (project CONCERTO, grant agreement No 788212) and from the Excellence Initiative of Aix-Marseille University-A*Midex, a French “Investissements d’Avenir” programme. GL warmly thanks Matt Bradford, Jamie Bock and Tzu-Ching Chang for insight- ful discussions on CONCERTO sensitivity computation and J.-G. Cuby for his help and support for the ERC proposal. We are grateful to our administrative staffin Grenoble and Marseille, in particular Patricia Poirier, Mathilde Berard, Lilia Todorov and Valérie Favre, and the Protisvalor team. We acknowledge the crucial help of the Institut Néel and MCBT Heads (Etienne Bustarret, Klaus Has- selbach, Thierry Fournier, Laurence Magaud) during the COVID-19 restriction period. 6. Conclusions We have presented the design of the CONCERTO instrument, a novel spectrometer that is set to be installed on the APEX tele- scope. CONCERTO is based on the development of new arrays in the millimetre using kinetic inductance detectors. It will con- tain two arrays of 2152 KIDS, mounted in a dilution cryostat that has a base temperature of 0.1 K. Spectra are obtained by a fast Martin-Puplett interferometer located in front of the cryo- stat. Frequency resolution can be up to δν = 1 GHz. The techno- logical choices leading to the final instrument design have been explained in detail. The characterisation of our current detectors is promising. Estimates of expected sensitivity are given, which are mostly based on the NIKA2 experience, that is, an instru- ment on sky that is subject to similar constraints as CONCERTO. The expected sensitivity, combined with the large field-of-view (20 arcmin diameter), will provide an unprecedented mapping speed for this kind of instrument. 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History and Applications of Dust Devil Studies
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Space Sci Rev (2016) 203:5–37 DOI 10.1007/s11214-016-0239-2 History and Applications of Dust Devil Studies Ralph D. Lorenz1 · Matthew R. Balme2 · Zhaolin Gu3 · Henrik Kahanpää4 · Martina Klose5,6 · Michael V. Kurgansky7 · Manish R. Patel2,8 · Dennis Reiss9 · Angelo Pio Rossi10 · Aymeric Spiga11 · Tetsuya Takemi12 · Wei Wei13 Ralph D. Lorenz1 · Matthew R. Balme2 · Zhaolin Gu3 · Henrik Kahanpää4 · Martina Klose5,6 · Michael V. Kurgansky7 · Manish R. Patel2,8 · Dennis Reiss9 · Angelo Pio Rossi10 · Aymeric Spiga11 · Tetsuya Takemi12 · Wei Wei13 Received: 12 September 2015 / Accepted: 2 February 2016 / Published online: 4 April 2016 © The Author(s) 2016. This article is published with open access at Springerlink.com Abstract Studies of dust devils, and their impact on society, are reviewed. Dust devils have been noted since antiquity, and have been documented in many countries, as well as on the planet Mars. As time-variable vortex entities, they have become a cultural motif. Three major stimuli of dust devil research are identified, nuclear testing, terrestrial climate stud- ies, and perhaps most significantly, Mars research. Dust devils present an occasional safety hazard to light structures and have caused several deaths. B R.D. Lorenz ralph.lorenz@jhuapl.edu 1 Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA 2 Open University, Walton Hall, Milton Keynes, MK7 6AA, UK 3 Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China 4 Finnish Meteorological Institute, 00101 Helsinki, Finland 5 Institute for Geophysics and Meteorology, University of Cologne, Pohligstr. 3, 50969 Cologne, Germany 6 Present address: USDA-ARS Jornada Experimental Range, Las Cruces, NM 88003, USA 7 A.M. Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Pyzhevsky 3, 119017 Moscow, Russia 8 Space Science and Technology Department, STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, UK 9 Institut für Planetologie, Westfälische Wilhelms-Universität, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany 10 Department of Physics and Earth Sciences, Jacobs University Bremen Campus Ring 1, 28759 Bremen, Germany 11 Laboratoire de Meteorologie Dynamique (LMD), 4 place Jussieu, 75252, Paris cedex 5, France 12 Disaster Prevention Research Institute, Kyoto University, Uji, Kyoto 611-0011, Japan 13 Wuhan University of Technology, Wuhan, Hubei 430063, China B R.D. Lorenz ralph.lorenz@jhuapl.edu 1 Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA 2 Open University, Walton Hall, Milton Keynes, MK7 6AA, UK 3 Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China 4 Finnish Meteorological Institute, 00101 Helsinki, Finland 5 Institute for Geophysics and Meteorology, University of Cologne, Pohligstr. Fig. 1 Image of a dust devil in Arizona, observed in a NASA field campaign. The large dust devil has a small ‘little brother’ to the right. Credit: NASA/U. of Michigan 1 Introduction “And so the hours dragged by until the sun stood dead above our heads, a huge white ball in the noon sky, beating, blazing down, and then it happened—suddenly, a whirlwind! Twisting a great duststorm up from the earth, a black plague of the heavens filling the plain, ripping the leaves off every tree in sight, choking the air and sky. We squinted hard and took our whipping from the gods.” Thus speaks a sentry in the play ‘Antigone’, written by Sophocles in Greece around 450 BCE (e.g. Bowker 2011), capturing a scene that many dust devil researchers two and a half millennia later will doubtless appreciate. Dust devils are therefore a phenomenon that has been documented for as long as there has been documentation of anything, and short of finding a prehistoric sketch of a dust devil on a cave wall, appears to be the first meteorological report in the West of this phenomenon. In the present paper, we review the history of dust devil research in various countries, and its motivations, and then the history of research on dust devils on Mars. We then survey the applications of dust devil research, and finally note the role of dust devils as a motif in culture. First, however, we offer some definitions and distinctions against other vortex structures, and note the designation of dust devils in different languages. Dust devils are dry convective vortices, rendered visible by lofted dust (Fig. 1). The definition offered by Oke et al. (2007a) is succinct: “A vortex rotating in either direction faster than its motion downwind. It must have a coherent columnar or cone shape extending in a vertical direction above the surface. It must carry dust to a height of at least 1 m and last for at least 10 s. It is distinct from a dust blow in that it maintains a fast rotating coherent structure with vertical extension and distinct from a small dust whirl in its size and duration.” Usually the instability is generated by strong solar heating, although cold air masses over warm ground may cause them. Vortices generated by purely mechanical forcing (that can for example also loft snow or leaves in conditions without strong heating) such as those caused by outflows from mesoscale convective systems (e.g. gustnados) are not usually considered to be dust devils, although this chapter will occasionally stray beyond the narrowest definition. History and Applications of Dust Devil Studies 3, 50969 Cologne, Germany 6 Present address: USDA-ARS Jornada Experimental Range, Las Cruces, NM 88003, USA 7 A.M. Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Pyzhevsky 3, 119017 Moscow, Russia 8 Space Science and Technology Department, STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, UK 9 Institut für Planetologie, Westfälische Wilhelms-Universität, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany 10 Department of Physics and Earth Sciences, Jacobs University Bremen Campus Ring 1, 28759 Bremen, Germany 11 Laboratoire de Meteorologie Dynamique (LMD), 4 place Jussieu, 75252, Paris cedex 5, France 12 Disaster Prevention Research Institute, Kyoto University, Uji, Kyoto 611-0011, Japan 13 Wuhan University of Technology, Wuhan, Hubei 430063, China R.D. Lorenz et al. 6 Italian Tornados, while of interest because of some dynamical vortex similarities (see e.g. the chapter by Kurgansky et al. in this volume) are quite distinct from dust devils in that their driving energy is from latent heat in moisture rather than sensible heat. Further, tornados are invariably associated with clouds, from which the vortex descends, whereas dust devils most usually occur in clear sky conditions and the visible structure grows upwards from the ground. Tornados and dust devils may have similar aspect ratios (height/diameter) but tornados are almost always much larger than dust devils, and are usually much more intense (in terms of core pressure drop and wind speed). Waterspouts are essentially tornado-like, in being usually associated with cloud, although they are often similar to dust devils in size. Hurricanes (and other cyclonic storms such as typhoons) have very much larger horizon- tal and vertical scales than dust devils, and rather smaller aspect ratios. The large horizontal scale leads to significant effects of planetary rotation (i.e. the Coriolis effect) which is negli- gible for dust devils. While associated with moist convection, hurricanes do have the feature that like dust devils, much of their energy is supplied at their base (and similar heat engine formalisms can be applied to the generation of mechanical energy in each), and there may be some analogies in the migration paths and vortex structure. 1 Introduction Where such outflows are cold (as is often the case in desert storms due to evaporative cooling), however, the distinction is less clear cut. Related phenomena include fire whirls associated with forest fires and the like, where flames may be collimated in narrow rotating columns. Fig. 1 Image of a dust devil in Arizona, observed in a NASA field campaign. The large dust devil has a small ‘little brother’ to the right. Credit: NASA/U. of Michigan 7 History and Applications of Dust Devil Studies Table 1 Terms for dust devils. Note that the Navajo word should not be used in casual conversation as it often has evil connotations in that culture. Note also some remarks in the Culture section at the end of this paper Location/language Name Etymology, Other remarks Australia Willy-willy Aboriginal/onomatopoeic? sometimes ‘Whirly-whirl’ Arabic Djinn Spirit, devil (qv the anglicized form ‘genie’) Japan Jin-sen-pu Dust whirlwind. Also tsumuji-kaze ‘whirlwind’ France Tourbillon de poussière Dust whirl Diable de poussière Dust devil Trombe de sable Sand trumpet (archaic) Germany Staubwirbel Dust whirl Kleintrombe Small trumpet Sandhose Sand hose Wirbelwind Whirlwind Staubteufel Dust devil (most common) Russia pyl’niy (peschaniy) vikhr’ Dust (sand) whirl pylny vihr China Dust whirl India Suntargalis or devva Devil wind Navajo Chiindii Spirit Spanish (inc. Americas) diablo de polvo Dust devil demonio de polvo Dust demon remolino de polvo Dust whirl burro (Donkey) Italian diavolo di sabbia (diavolo di polvere) Dust Devil (Sand Devil) 1.2 Scientific Significance of Dust Devil Studies It is the general impression of the authors that the public finds dust devils ‘interesting’, a qualitative endorsement of the utility of their study. However, the scientific level of interest can be at least crudely quantified. An informal bibliometric study, searching for refereed journal papers with “Dust devil” in the title in the Smithsonian Physics/Astronomy database found some 131 papers 1930–2015. It is recognized that this database will not capture all the literature (particularly that in languages other than English), but it can be considered representative. Figure 2 shows the cumulative number of papers versus time—it is seen that papers accu- mulate at the rate of about 1.5/yr until the early 21st century when there is an abrupt change in slope—essentially reflecting studies of dust devils on Mars as an ongoing enterprise—to ∼4/yr. There is also a flurry of activity in the late 1960s/early 1970s reflecting work in the USA (see later). The particular jump in 2006 largely reflects a special issue of the journal Geophysical Research Letters that published papers discussed at a workshop devoted to dust devils hosted in Flagstaff, Arizona by Ronald Greeley in August 2005. An inspection of the most-cited papers in this corpus (Table 2) attests to the importance of Mars discoveries, with half of the ‘top 10’ papers referring to Mars directly. 1.1 Dust Devil Terminology Table 1 summarizes the terms used for dust devils in different languages. Clearly some terms are simply descriptive of the phenomenon (‘dust whirl(wind)’), some are onomatopoeic, and R.D. Lorenz et al. 8 Fig. 2 The cumulative growth of the corpus of dust devil work in refereed journals in the ADS abstract database (http://adsabs. harvard.edu/). Note the slope change around 2003, and the jump circa 1970 some invoke the ephemeral/aethereal nature of them with reference to spirits or devils. It is of interest that the shape-inspired term ‘trombe’ appears in early French and German literature (sharing a root with the English ‘trombone’) but has largely fallen into disuse. some invoke the ephemeral/aethereal nature of them with reference to spirits or devils. It is of interest that the shape-inspired term ‘trombe’ appears in early French and German literature (sharing a root with the English ‘trombone’) but has largely fallen into disuse. some invoke the ephemeral/aethereal nature of them with reference to spirits or devils. It is of interest that the shape-inspired term ‘trombe’ appears in early French and German literature (sharing a root with the English ‘trombone’) but has largely fallen into disuse. 2.1 Overview 85 Dust Devil Vortices Seen by the Mars Pathfinder Camera 1983 Ryan & Lucich 79 Possible Dust Devils—Vortices on Mars 1960 Freier 71 The Electric Field of a Large Dust Devil 1970 Kaimal & Businger 71 Case Studies of a Convective Plume and a Dust Devil 1973 Sinclair 71 The Lower Structure of Dust Devils 2006 Balme & Greeley 67 Dust Devils on Earth and Mars 1969 Sinclair 61 General Characteristics of Dust Devils 2003 Greeley et al. 58 Martian Dust Devils: Laboratory Simulations Fig. 3 Map of reported dust devil studies or sightings (black stars, not all historical reports included) in reports cited in this paper—note the predominance around 30° latitude, where the downwelling branch of the Hadley circulation leads to generally dryer conditions. Grey stars denote undocumented sightings by the present authors (UAE and Ethiopia) and their correspondents (Svalbard, Botswana) In the 20th century, most scientific activity on dust devils was in the USA, a situation that broadly holds today. More recently, interest in dust devils has grown, in part due to environ- Table 2 The most widely-cited dust devil papers (Harvard-SAO Database Title Search ‘Dust Devil’) Year Authors Citations Title 1985 Thomas & Gierasch 120 Dust Devils on Mars 1998 Renno et al. 93 A Simple Thermodynamical Theory for Dust Devils 1999 Metzger et al. 85 Dust Devil Vortices Seen by the Mars Pathfinder Camera 1983 Ryan & Lucich 79 Possible Dust Devils—Vortices on Mars 1960 Freier 71 The Electric Field of a Large Dust Devil 1970 Kaimal & Businger 71 Case Studies of a Convective Plume and a Dust Devil 1973 Sinclair 71 The Lower Structure of Dust Devils 2006 Balme & Greeley 67 Dust Devils on Earth and Mars 1969 Sinclair 61 General Characteristics of Dust Devils 2003 Greeley et al. 58 Martian Dust Devils: Laboratory Simulations Fig. 3 Map of reported dust devil studies or sightings (black stars, not all historical reports included) in reports cited in this paper—note the predominance around 30° latitude, where the downwelling branch of the Hadley circulation leads to generally dryer conditions. Grey stars denote undocumented sightings by the present authors (UAE and Ethiopia) and their correspondents (Svalbard, Botswana) In the 20th century, most scientific activity on dust devils was in the USA, a situation that broadly holds today. More recently, interest in dust devils has grown, in part due to environ- mental concerns, in Japan and China. 2.1 Overview Dust devils are found (Fig. 3) in many parts of the world, although predominantly in desert regions. While dust devils have been reported from antiquity, their serious study began in the mid-19th century with the onset of global scientific exploration and growing commercial activity by the European powers: see the following sections on Britain, France and Germany. 9 9 History and Applications of Dust Devil Studies Table 2 The most widely-cited dust devil papers (Harvard-SAO Database Title Search ‘Dust Devil’) Year Authors Citations Title 1985 Thomas & Gierasch 120 Dust Devils on Mars 1998 Renno et al. 93 A Simple Thermodynamical Theory for Dust Devils 1999 Metzger et al. 85 Dust Devil Vortices Seen by the Mars Pathfinder Camera 1983 Ryan & Lucich 79 Possible Dust Devils—Vortices on Mars 1960 Freier 71 The Electric Field of a Large Dust Devil 1970 Kaimal & Businger 71 Case Studies of a Convective Plume and a Dust Devil 1973 Sinclair 71 The Lower Structure of Dust Devils 2006 Balme & Greeley 67 Dust Devils on Earth and Mars 1969 Sinclair 61 General Characteristics of Dust Devils 2003 Greeley et al. 58 Martian Dust Devils: Laboratory Simulations Fig. 3 Map of reported dust devil studies or sightings (black stars, not all historical reports included) in reports cited in this paper—note the predominance around 30° latitude, where the downwelling branch of the Hadley circulation leads to generally dryer conditions. Grey stars denote undocumented sightings by the present authors (UAE and Ethiopia) and their correspondents (Svalbard, Botswana) In the 20th century, most scientific activity on dust devils was in the USA, a situation that broadly holds today. More recently, interest in dust devils has grown, in part due to environ- mental concerns in Japan and China Table 2 The most widely-cited dust devil papers (Harvard-SAO Database Title Search ‘Dust Devil’) Year Authors Citations Title 1985 Thomas & Gierasch 120 Dust Devils on Mars 1998 Renno et al. 93 A Simple Thermodynamical Theory for Dust Devils 1999 Metzger et al. 2.2 Italy and the Roman Empire As our opening quotation suggests, the often dry and hot conditions around the Mediter- ranean Sea can yield dust. In military campaigns a cloud of dust kicked up by a marching or galloping army was often the earliest indication of its approach. Julius Caesar’s various chronicles make only scant mention of dust raised by the wind, but Lucan’s Pharsalia (an epic poetical account of the Roman Civil War, Lucanus, 65 C.E., 1926) has the following graphic account which offers a number of meteorological insights: “Libya has no mountains to oppose the rising wind and break its force, no cliffs to drive it back and scatter it, or to turn its hurricane to clear breezes; it does not fall upon forests and wear itself out by bending ancient oaks: all the land is level, and the wind travels freely and wreaks the fury of Aeolus all over the desert. There is no rain in the cloud of whirling dust which it drives furiously in circles; most of the land is lifted up by it and is suspended in the air, as the eddying motion is continuous. The needy Nasamonian sees his possessions flying in the wind and his dwelling blown to pieces; the Garamantian is laid bare, and his hut, beginning with the roof, is snatched away and flies aloft. Fire does not carry what it seizes to a greater height: as high as smoke may rise up and mar the face of day, so great is the dust that fills the air. And now, even fiercer than its wont, the wind attacked the Roman column; and the staggering men can find no footing on the sand, when even the spot they tread on is carried away. If Africa had a solid framework, so that the heavy weight of its cliffs might confine the South wind within hollow caverns, the wind would overset the whole world and wrench it from its foundations; but because the soil is easily driven about with its drifting sands, it remains stable by offering resistance at no point, and the lower stratum stands fast because the upper is dispersed. 2.1 Overview Dust devils would likely have remained a minor topic in meteorology, but for the Cold War. Specifically, nuclear weapons testing is typically conducted in desert areas for the obvious reason that these have low populations. Since dust devils might transport radioactive dust from these remote sites, some work on dust devils may have been sponsored by relevant agencies to assess this hazard (for example, Snow and McLelland’s work sponsored by the US Defense Nuclear Agency) (Snow and McClelland 1990). A second impetus to dust devil studies has been the exploration of Mars. While we review Mars dust devil work as an integrated whole in the next section, the impact of Mars explo- ration on dust devil research generally in different countries is noted here—work circa 1970 seems in part to have been associated with Mars and the US Viking program. The growing role of Europe in planetary exploration, with Mars Express, Beagle 2, and various proposed missions and involvements in NASA missions, has similarly stimulated dust devil research in other countries. In what follows we arrange the countries approximately by chronology of their first contributions to dust devil studies. Note that it is not the purpose of this paper to comprehensively review all publications on dust devils. Some representative references from various countries and on various topics are 10 R.D. Lorenz et al. identified only as a starting point. Other chapters in the present volume explore the literature more fully, and a useful overall review is Balme and Greeley (2006). identified only as a starting point. Other chapters in the present volume explore the literature more fully, and a useful overall review is Balme and Greeley (2006). 2.2 Italy and the Roman Empire Driving furiously, the blast snatched up the men’s helmets and shields and javelins, and rushed on, carrying them through the mighty void of heaven.” Clearly, this account may conflate dust/sand storms with dust devils, but it clearly notes the vortical motion characteristic of dust devils, and the fact that these strong motions are not associated with rainfall. Active saltation is described, and in addition to helmets and javelins being lofted, damage to structures is noted. Beyond these dramatic observations, some strikingly perceptive thoughts can be perceived—there is a hint that smoke plumes and dust reach the same height (both capped by the Planetary Boundary Layer, perhaps), and an argument that the low aerodynamic roughness of the African continent may enhance the ferocity of its winds. After Roman times, the most notable studies are those by Leonardo da Vinci on vortices in general. He suggests colliding winds generate vorticity, and observed the following (Ata- lay and Wamsley 2009), which could perhaps be a tornado or waterspout rather than a dust devil: “It often happens that, when one wind meets another at an obtuse angle, these two winds circle around together and twine themselves into the shape of a huge column; and having thus condensed, the air acquires wright. I once saw such winds, raging around together, produce a hollow in the sand of the seashore as deep as the height of a man, removing from it stones of considerable size, and carrying sand and seaweed through the air for the space of a mile and dropping them in the water, whirling them around and transforming them into a dense column, which formed dark thick clouds at its upper extremity.” In connection with waterspouts in Italy, it may be noted that the young British scientist Michael Faraday wrote an interesting account of them while traveling with Humphrey Davy History and Applications of Dust Devil Studies 11 Fig. 4 Dust devil depicted in Chinese ancient Poem thirteen centuries ago (drawn by Quanzong Zhang). Note that the dust column flares into a plume at the top, and occurs rather near sunset Fig. 4 Dust devil depicted in Chinese ancient Poem thirteen centuries ago (drawn by Quanzong Zhang). Note that the dust column flares into a plume at the top, and occurs rather near sunset Fig. 4 Dust devil depicted in Chinese ancient Poem thirteen centuries ago (drawn by Quanzong Zhang). in that country—his correspondence with Baddeley on dust devils is reported in that author’s 1860 book. As elsewhere, Mars exploration has stimulated terrestrial dust devil studies in Italy, and Rossi and Marinangeli (2004) reported the first observation of terrestrial counterparts to Martian dust devil tracks, in Niger. 2.2 Italy and the Roman Empire Note that the dust column flares into a plume at the top, and occurs rather near sunset in that country—his correspondence with Baddeley on dust devils is reported in that author’s 1860 book. 2.3 China In the year 737 C.E. (Kaiyuan 25th year, Tang Dynasty), the well-known ancient poet Wei Wang traveled to the frontier at the emperor’s order. He wrote the famous poem On Mission to the Frontier after viewing the spectacular scenery on the way. In the poem, the sentence “A plume of smoke rises up into the evening sky of the Great Desert, while the Yellow River dimmed as the setting sun goes down” depicted the view of vast boundless desert and endless river (as shown in Fig. 4). In fact, the “smokes” mentioned in the sentence may be interpreted as the dust and sand lofted in the swirling winds of a dust devil. China has extensive desert regions, especially in its north and west (see Fig. 5), and aeolian studies and efforts to mitigate the effects of sand dune migration on agricultural areas and infrastructure such as railway lines have become extensive, with research institutes devoted to aeolian studies. Sandstorms frequently occur in northern China (as many as 20 days a year in Mongolia), especially in Spring. In one recent example, in March in 2000, large sandstorms attacked Inner Mongolia and the Beijing district, with winds reaching force 8 or 9 (on the Beaufort scale, i.e. 17–24 m/s). Seven workers who worked in a two-floor building were blown down and two of them were killed. As for dust devils, specifically, before the 21st century, there were only cursory studies. Le (1983) compiled the diurnal variation of 193 dust devils that occurred in Taklimakan Desert from 1964 to 1970. According to the data of Lei et al. (2005), during 1971–2000, 594 dust devils occurred in Shaanxi Province. Dust devils in these two places had some common characteristics. They began appearing after 9 a.m., became frequent in 12:00–15:00 (local time) and then declined. Before 8 a.m. And after 18:00, no dust devils occurred. More recently, theoretical and simulation work has been pursued: e.g. Gu et al. (2006, 2010) simulated the formation process of dust devils with LES (Large Eddy Simulation) methods as a function of swirl ratio, and used an Euler-Lagrange approach to simulate the gas-solid two-phase flows of dust devils in the convective boundary layer. Gu et al. (2013) 12 R.D. Lorenz et al. Fig. 2.3 China 5 Spatial distribution and the occurrence days per year of sandstorms in China demonstrated a charging mechanism of sand particles with the adsorbed water on micro- porous surfaces of wind-blown sand, recognizing the mobility of water ions H+/OH−be- tween the contacting sand grains with a temperature difference. Much of this work was aggregated in a book on these topics (Gu 2010). Additionally, the Turpan desert in Western China was the site of the first in-situ examination of dust devil tracks on Earth (Reiss et al. 2011a, 2011b). Fig. 5 Spatial distribution and the occurrence days per year of sandstorms in China Fig. 5 Spatial distribution and the occurrence days per year of sandstorms in China demonstrated a charging mechanism of sand particles with the adsorbed water on micro- porous surfaces of wind-blown sand, recognizing the mobility of water ions H+/OH−be- tween the contacting sand grains with a temperature difference. Much of this work was aggregated in a book on these topics (Gu 2010). Additionally, the Turpan desert in Western China was the site of the first in-situ examination of dust devil tracks on Earth (Reiss et al. 2011a, 2011b). demonstrated a charging mechanism of sand particles with the adsorbed water on micro- porous surfaces of wind-blown sand, recognizing the mobility of water ions H+/OH−be- tween the contacting sand grains with a temperature difference. Much of this work was aggregated in a book on these topics (Gu 2010). Additionally, the Turpan desert in Western China was the site of the first in-situ examination of dust devil tracks on Earth (Reiss et al. 2011a, 2011b). 2.4 Britain and the British Empire He notes the striking similarity of the multiple co-rotating cores to the motion of dancing Dervishes (an analogy repeated by others), and hints at a possible origin of this religious dance from the motion of dust devils: makes the suggestion (erroneously) that electric forces are in fact the cause of the winds. This notion aside, the book usefully documents many visual observations of dust devils and storms in the vicinity of Lahore (now in modern Pakistan) including their ascent to more than 2000 ft, and the frequent presence of multiple cores. He notes the striking similarity of the multiple co-rotating cores to the motion of dancing Dervishes (an analogy repeated by others), and hints at a possible origin of this religious dance from the motion of dust devils: “This remarkable sight gives the idea of a fairy dance round a ring; and the motions are from all accounts, exactly imitated by the dancing Dervishes of Turkey; one of their holy exercises being to whirl round and round like a top; singly, or in company with several others, performing at the same time a gyration round in a circle, as if their dance originated in the very phenomenon now described.” He describes following on foot one dust devil for a mile, then being able to penetrate the centre and walk along inside it—he notes “The centre was perfectly calm, while round about, the winds were blowing in every direction”. A casual sentence in the book (p. 81), noting electrical activity associated with dust dev- ils observed with a gold-leaf electroscope and other means, makes the observation (13th October 1850) that a solution of starch and potassium iodide rapidly become discolored. Although the report does not offer any explanation or interpretation, it seems clear in retro- spect that this is evidence of atmospheric oxidants, and specifically ozone, and anticipates by almost 150 years the consideration of dust devil oxidants in atmospheric chemistry on Mars. It may be noted that ozone was only discovered in 1840 (and so it may have been a ‘hot topic’ at the time) and that the starch-iodide reaction was developed soon thereafter as a specific test. p Various reports appear in the scientific and popular media of the period, documenting dust devils and other storms in various parts of the empire, notably India and South Africa. 2.4 Britain and the British Empire While the cold and damp United Kingdom does not commonly have circumstances favor- able to dust devil formation, many territories formerly under British administration have desert areas that do. Most notably these include North Africa, the Middle East, and Aus- tralia. The dispersal of soldiers, officials and other professionals across the globe, together with a strengthening tradition of reporting observations, created the opportunity for careful studies of dust devils beginning in the mid-1800s. It is of note that in the same period, the same motivations prompted the Royal Navy to commission “A Manual of Scientific En- quiry; prepared for the use of Officers in Her Majesty’s Navy and Travellers in General”, edited by the astronomer John Herschel (and including a chapter on meteorology by him, and one on geology by Charles Darwin). The Meteorology chapter (Herschel 1851) instructs readers on the care and use of meteorological instruments, and the careful recording of their measurements. It gives particular guidance on observations of whirlwinds: ‘All circumstances from the first trace or prognostic to their final dissipation should be minutely noticed... At what distance is the whirling motion of the air perceptible? What are the indications of the barometer during their approach and recess? Do any and what electrical phenomena accompany them.’ p p y A century and a half later, this remains good advice for dust devil study, on any planet. Baddeley (1860), a surgeon in the Bengal Army, compiled an entire book, much of which is on the topic of dust devils—“Whirlwinds and Dust Storms of India: An Investigation into the Law of Wind and Revolving Storms at Sea”. This appears to be one of the first detailed investigations published on dust devils. The book struggles to develop a unified theory for vortical winds (such as cyclones as well as dust devils), and noting a number of electrical phenomena associated with dust devils History and Applications of Dust Devil Studies 13 makes the suggestion (erroneously) that electric forces are in fact the cause of the winds. This notion aside, the book usefully documents many visual observations of dust devils and storms in the vicinity of Lahore (now in modern Pakistan) including their ascent to more than 2000 ft, and the frequent presence of multiple cores. 2.5 Germany The interdisciplinary research of Alexander von Humboldt opened new avenues in many branches of the natural sciences. From one of Humboldt’s journeys to Southern America (Orinoco area), he offers what is likely one of the earliest ‘scientific’ reports on dust devils (von Humboldt 1849): “When under the vertical beam of the never-cloudy sun the charred grass layer has crumbled into dust, the hardened surface gapes open as if it would be shaken by strong quakes. When it is then touched by opposing air flows, whose quarrel balances through rotating movement, the plain allows a peculiar view. In the form of funnel shaped clouds with their tips sliding across the surface, sand rises vapor-like through the air-thin, elec- trically charged center of the whirl: similar to the rushing waterspouts that are feared by experienced skippers.” Other early reports about dust devils in German literature include observations in what is now Iraq by Schläfli (1870) who noted that small dust devils are frequent especially during summer. Early dust devil observations in Germany were also reported by Less (1891) and Budde (1883). The inventor of the photographic flash, Adolf Miethe (Miethe 1899) reported about ash devils (Aschehosen) in the Luneburg Heath in Lower Saxonia. These ash devils formed due to manmade peat fires; sometimes 20–50 per hour were observed with heights of 200–300 m. The author notes that the ash devils travel at speeds and in directions of the prevailing winds, and the formation ceased at wind speeds above ∼3.5 ms−1. p g p While better-known for his theory of continental drift, the meteorologist, polar explorer and geoscientist Alfred Wegener made an interesting report (Wegener 1914) of dust devils on a lava plain, Odà ¯dahraun, in Iceland, noting that he had previously only once seen a ∼20 m high dust devil on a hot summer day in Marburg, Germany. During their stay in Iceland in mid-June 1912, Wegener and his company saw 20–30 dust devils at a time on the wide plain with typical diameters of about 5–10 m and heights of more than 100 m. Wegener got the notion that dust devil height would be of the same order as the stratocumulus cloud base. In addition to dust devils, Wegener and his colleague frequently observed non-rotating convective plumes, which developed into dust devils and gave some insight into dust devil formation. 2.4 Britain and the British Empire In the Straits Times, “Dust devils in India, Observations Made of Curious Phenomena”, a report is made of observations of dust devils near Agra. Weather reports had predicted thunderstorms in the local area, which never manifested, and it was observed that “Numer- ous very large dust devils were forming during the middle of the day” instead. These dust devils were categorized to range in size from 20–100 m in diameter, in some cases exceeding 800 m in height. A curious observation was that of one dust devil that was noted to pause over a village for approximately 10 minutes, with no perceptible translational movement. Such stability and lack of movement is rare in dust devils and implies extremely quiescent ambient wind conditions, and though the reported static duration may potentially be some- what exaggerated, it represents a rare observation of a stable, non-moving dust devil. The journalist also reported observing varying rates of rotation and dust vertical flux (assumed to be from visual observation), along with irregular masses of dust being raised in the vicinity of the base of the dust devil, resembling a “dust curtain” extending some 50 m from the dust devil itself, which was attributed to a descending current from just outside the limit of the upwelling dust column. While not a meteorologist, it is worth noting William Rankine, a Scottish engineer who contributed significantly to the development of thermodynamics and its application to steam engine performance in the mid-late 1800s. Vortices figure prominently in his thinking, and his idealized model of a vortex (which like a temperature scale, and an engine cycle, bear his name) is often used in dust devil studies. Little further British work on dust devils is of note until an important contribution by Flower (1936), a meteorologist working in Egypt for the Air Ministry (it is tempting to speculate whether Flower ever met or worked with Ralph Bagnold, in the same part of the empire at the same time; Bagnold was a desert soldier and pioneer in aeolian studies, his 14 R.D. Lorenz et al. 1941 book ‘Physics of Blown Sand and Desert Dunes’ remains required reading today). Flower’s tabulations of dust devil diameters, heights, longevity etc. remain one of the most comprehensive visual datasets, and were recently used to develop analytic correlations of diameter and longevity (Lorenz 2013). 1941 book ‘Physics of Blown Sand and Desert Dunes’ remains required reading today). 2.4 Britain and the British Empire Flower’s tabulations of dust devil diameters, heights, longevity etc. remain one of the most comprehensive visual datasets, and were recently used to develop analytic correlations of diameter and longevity (Lorenz 2013). As evidenced above, the UK has a long tradition in meteorological research, but while dust-raising in general and its impact on climate has been a current research topic, dust devils in particular have not received much ‘mainstream’ interest. Only a few reports of dust devil vortices appear in British journals, often from other parts of the (former) empire (e.g. Libya and Cyprus, McGinnigle 1966, 1970). However, dust devil work in the 21st century at UK institutions was stimulated by the development of the Beagle 2 Mars lander, and the prospect of detecting dust devils in-situ on that mission. Some examples include a re-analysis of Viking data (Ringrose et al. 2003), consideration of the ‘Delta-P effect’ (Balme and Hagermann 2006), instrumentation trials and field measurements in Nevada (Mason et al. 2014), and analysis of Mars orbital imaging (Towner 2009). 2.5 Germany Wegener notes that the dark volcanic sand would effectively absorb the solar heat, driving the formation of convective vortices. This report may be one of the highest-latitude field reports of dust devils and is quite widely cited thereafter, notably in Geiger’s textbook 15 History and Applications of Dust Devil Studies ‘The Climate Near the Ground’ (1950). In this book, Geiger describes dust devils formed near Erlangen in southern Germany, where air flowing over a cliff edge induces vorticity causing devils on a heated chalky plain. Geiger notes an audible whistling of the devils, and goes on to summarize Flower’s (1936) observations. Letzmann (1939) aimed to facilitate a comprehensive investigation of dust devils by suggesting guidelines for the observations of atmospheric vortices, including dust devils. Among the focuses he suggests are shape, duration, track, atmospheric conditions, pressure changes and surface conditions, many of which are still used to characterize dust devils today. Lammert (1947) summarizes an intensive period of dust devil occurrence in advance of a thunderstorm on a summer day in northern central Germany (Salzderhelden, Lower Saxony). Few minutes before the thunderstorm began, numerous (50–60 in total, 4–7 at a time) dust devils with 3–5 m diameter and heights of hundreds of meters occurred and lifted “whistling and howling corkscrew-like” considerable amounts of sediment. According to eye-witness reports, the dust devils were superseded by a dust storm generated by the convective downdrafts associated with the thunderstorm. The event came to an end with the starting rain. Apart from natural dust devil occurrences in Germany (e.g. Koschmieder 1951), Mau- rer (1934) observed an interesting man-made dust devil. In May 1934, a group of about 30 young girls met on a sandy sports field in eastern Germany (Schwarza, Thuringia). As exercise, they were instructed to run in circles of about 15 m diameter. After four rounds, a dust devil began to form at the inside of the circle, grew to about 5 m height, left the field, and ceased quickly. Maurer emphasized the strong heating over sun exposed surfaces such as the sports field. Recent papers on dust devils by German scientists have included some work on Large Eddy Simulation (e.g. Raasch and Franke 2011), and field measurements of dust-lifting in the Morroccan desert (Ansmann et al. 2009). 2.5 Germany The development of the High-Resolution Stereo Camera (HRSC), and its arrival at the Red Planet in 2003 on Mars Express stimulated significant work on remote observation of Martian dust devils (e.g. Stanzel et al. 2008; Reiss et al. 2011b) as well as terrestrial dust devil tracks (e.g. Reiss et al. 2010, 2011b, 2013). 2.6 France The situation of historical dust devil reports in France is rather similar to Germany and the United Kingdom. Most of France itself is not prone to the formation of dust devils; convec- tive vortices might occur on very hot summer days, especially in Southern France, but dusty material to be carried within the vortices are rarely available to form proper dust devils. As with the United Kingdom, opportunities to report dust devils arose when France adminis- tered colonies in North Africa and Central Asia, and soldiers, merchants, and travellers used to report observations of desert environments they were exploring in the middle of the nine- teenth century. Other reports were based on observations in arid regions in America (e.g. Mexico, reports by M. Virlet d’Aoust) not under French administration. Dust devils were usually reported as either anecdotical features within a broader explo- ration report, or as an additional dusty example in the taxonomy of natural vortices (as in the book by Zurcher and Margoller (1876) ‘Trombes et Cyclones’, which cites Baddaley’s work). However, following the development of the French meteorological network in the late 1850s and 1860s, the interest for meteorological phenomena became more and more prominent amongst French scientists. Reports about dust devils started to be a matter of scientific interest, with questions arising about their properties and formation. 16 R.D. Lorenz et al. For instance, in a June 1883 report to the Comptes Rendus de l’Académie des Science, Colonel Prejevalski1 writes: “The various morphologies of dust devils are reminiscent of marine vortices: dust is transported upward, often in a spiraling motion”. This description of a dust devil within an exploration report written by a military traveler (likely in Central Asia—see Fig. 6) is typical of what was proposed at the time. However, it is notable that this report is not simply describing the occurrence of dust devils and their morphology: it pro- poses an analogy with another natural whirling phenomena, and describes the dust transport within the dust devil. This report led M. Faye, who authored several other discussions about dust devils in Comptes Rendus de l’Académie des Sciences and Annuaire du Bureau des Longitudes since 1877, to publish a report in the same journal to severely criticize Colonel Prejevalski’s observations. According to him, those “simply cannot be regarded as a scientific document worth being published in the Comptes Rendus”! M. 1Although mentioned here since the discussion is in the French literature, in fact Nikolai Przhevalsky (translit- erations of the Cyrillic vary) was a Russian geographer who explored Central and East Asia, which is pre- sumably where his familiarity with dust devils arose. A wild horse species in that region is named after him. Fig. 6 A French woodcut from the 19th century ‘Trombes de Sable dans la Steppe’, showing the threatening aspect of large dust devils, perhaps like those reported by Prejevalski 2.7 United States of America Although widespread familiarity with dust devils awaited the modern settlement of the desert Southwest, dust devils were recognized among the pantheon of rotating winds in William Ferrel’s2 discussion of cyclones and tornados (Ferrel 1881), where he describes ‘sand spouts’. That work is notable in recognizing that the centripetal acceleration of the sand and dust must be generated somehow, and he ascribes it to the radial drag of the in- rushing winds. Further, he suggests that since the drag on each particle varies as its diameter squared, while the required force varies as diameter cubed, ‘particles of sand of different sizes arrange themselves at different distances from the center’, an important insight. Although the Eastern part of the USA does not often encounter dust devils, having a more damp and temperate climate than the west, one of the earliest reports of dust devils was made there by Benjamin Franklin in Maryland (Franklin 1755). The report is remarkable not only in its observational detail, but also for Franklin’s experiment in modifying the devil. ‘It appeared in the form of a sugar-loaf, spinning on its point, moving up the hill towards us... its smaller part near the ground appeared no bigger than a common barrel, but widen- ing upwards, it seemed at 40 or 50 feet high, to be 20 or 30 feet in diameter.... I followed it, riding close by its side, and observed its licking up, in its progress, all the dust that was under its smaller part. As it is a common opinion that a shot, fired through a water-spout, will break it, I tried to break this little whirlwind, by striking my whip frequently through it, but without any effect.... Soon after, it quitted the road and took into the woods, growing every moment larger and stronger, raising, instead of dust, the old dry leaves with which the ground was thick covered, and making a great noise with them and the branches of the trees, bending some tall trees round in a circle swiftly and very surprisingly, though the progres- sive motion of the whirl was not so swift but that a man on foot might have kept pace with it; but the circular motion was amazingly rapid. 2.6 France Faye then explains that dust devils, similarly to tor- nados, find their swirling motion originating from regional-scale vorticity (thus comes from above the boundary layer rather than from the surface), and this motion when it finally gets down to the surface would cause dust lifting. He concludes that what Colonel Prejevalski reports about the apparent motion of dust within a dust devil is an illusion, one of the same kind that led sea men to conclude that marine vortices would pump water from the surface to the higher atmosphere. M. Faye might be right for marine tornados, but we now know he had a wrong interpretation about dust devils, while Colonel Prejevalski is completely in line with modern observations of those phenomena. This discussion in the French literature parallels analogous debates about cyclones and other weather systems in (at least) Britain and America in the 19th century. Recent dust devil research in France, like that in Germany, the UK and Italy, has been stimulated by climate studies and interest in dust-lifting in general, and by studies of the meteorology of Mars. The emphasis there has been on numerical simulation, e.g. Spiga and Forget (2009), although the French development of a seismometer instrument for the InSight Mars lander to be launched in 2016 may stimulate new observational studies. 1Although mentioned here since the discussion is in the French literature, in fact Nikolai Przhevalsky (translit- erations of the Cyrillic vary) was a Russian geographer who explored Central and East Asia, which is pre- sumably where his familiarity with dust devils arose. A wild horse species in that region is named after him. History and Applications of Dust Devil Studies 17 2The meridional circulation ‘Ferrel cell’ is named after this meteorologist. 2.7 United States of America By the leaves it was now filled with, I could plainly perceive that the current of air they were driven by, moved upwards in a spiral line; and when I saw the trunks and bodies of large trees invelop’d in the passing whirl, which continued intire after it had left them I no longer wondered that my whip had no effect on it in its smaller state. I accompanied it about three quarters of a mile, till some limbs of dead trees, broken off by the whirl, flying about and falling near me, made me more apprehensive of danger; and then I stopped, looking at the top of it as it went on, which was visible, by means of the leaves contained in it, for a very great height above the trees. Many of the leaves, as they got loose from the upper and widest part, were scattered in the wind; but so great was their height in the air, that they appeared no bigger than flies. My son, who was by this time come up with me, followed The whirlwind till it left the woods, and crossed an old tobacco-field, where, finding neither dust nor leaves to take up, it gradually became invisible below as it went away over that field. The course of the general wind then blowing was along with us as we travelled, and the progressive motion of the whirlwind was in a direction nearly opposite, though it did not keep a strait line, nor was its progressive motion uniform, it making little sallies on either hand as it went, proceeding sometimes faster and sometimes slower, and seeming sometimes for a few seconds almost stationary, then starting forward pretty fast again.’ In addition, the following observation by Thomas Jefferson, a farmer and careful recorder of meteorological phenomena as well as principal author of the Declaration of Indepen- dence, is of interest as being a likely description of dustless vortices (Jefferson 1787): 18 R.D. Lorenz et al. Going out into the open air, in the temperate, and in the warm months of the year, we often meet with bodies of warm air, which, passing by us in two or three seconds, do not afford time to the most sensible thermometer to seize their temperature. Judging from my feelings only, I think they approach the ordinary heat of the human body. 2.7 United States of America Some of them perhaps go a little beyond it. They are of about 20 or 30 feet diameter horizontally. Of their height we have no experience; but probably they are globular volumes wafted or rolled along with the wind. But whence taken, where found, or how generated? They are not to be ascribed to Volcanos, because we have none. They do not happen in the winter when the farmers kindle large fires in clearing up their grounds. They are not confined to the spring season, when we have fires which traverse whole counties, consuming the leaves which have fallen from the trees. And they are too frequent and general to be ascribed to accidental fires. I am persuaded their cause must be sought for in the atmosphere itself, to aid us in which I know but of these constant circumstances; a dry air; a temperature as warm at least as that of the spring or autumn; and a moderate current of wind. They are most frequent about sun-set; rare in the middle parts of the day; and I do not recollect having ever met with them in the morning. Dust devils occur in dry areas of the USA outside the Southwest, as in this observation of multiple vortices rotating around a common column in South Carolina (Anonymous 1902): “It consisted of four separate whirlwinds which followed each other to the left around the center of a circle 10 or 15 feet in diameter, like horses going around a horse power thrashing machine. The whole circle also seemed to be moving to the left and around the center of an enlarging coil. The motion was made apparent by dust taken up from the soil, and it could not well be seen above 10 or 15 feet from the ground. Sometimes one or more of the small whirls would rise so as not to be visible, but presently it would touch the soil again in its regular place in the procession. This beautiful and curious motion continued for five minutes or more over a spot only about 100 feet in diameter. It then advanced northward the four whirls enlarging their circle to about 75 yards and then vanishing.” Ives (1947) wrote a review of dust devils, recording his own observation of dust devils in the Bonneville salt flats in Utah, one lasting some seven hours and traveling 40 miles. 2.7 United States of America He also notes that dust devils can be started sometimes by driving a jeep across, or firing a shell into, the ‘lake’ in a mirage. Mirages require strongly superheated air, which is unstable to convection, so these anecdotes make sense. He speculates that activity of small animals might therefore trigger many dust devils—although this was obviously before the discovery of dust devils on Mars. He also summarizes some in-situ measurements of meteorological quantities, and noted reports that rabbits and hares can be lofted by dust devils, implying updrafts of 35 mph or more. He notes that such encounters were usually fatal to the animals involved, although he observed himself kangaroo rats falling from devils (and surviving). He then deduced (by dropping such rats from a tower and measuring their terminal velocity) the corresponding updraft velocities as 25 mph, recording memorably that the animal was “apparently unhurt, although usually very angry”. Wyett (1954) reported a dust devil encounter at the airport in St. George, Utah, wherein the pressure drop was recorded by a barograph (see Fig. 7). Several papers emerge in the 1950s and 1960s on electric fields in dust devils, as well as on analytic models of dust devil vortices and considerations of their energetics. There is not space for a full review here— the reader is referred to other papers in this volume, and to an earlier review by Balme and Greeley (2006). Many recognize the pivotal role of Peter C. Sinclair in dust devil research. Sinclair was a research student in the Atmospheric Sciences department at the University of Arizona in 19 History and Applications of Dust Devil Studies Fig. 7 Perhaps one of the first instrumental records of a dust devil encounter (arrowed), after Wyett (1954). The barograph scale is in inches of mercury—the 0.04 inch drop corresponds to ∼1.4 hPa Tucson, and generated some of the first usefully-robust statistics on dust devil occurrence and properties, as well as pioneering the active “chase and sample” methodology. A prelimi- nary report (Sinclair 1964) captures the highlights of his work, initially using a hand-carried mobile observing station (Fig. 8). Tucson, and generated some of the first usefully-robust statistics on dust devil occurrence and properties, as well as pioneering the active “chase and sample” methodology. A prelimi- nary report (Sinclair 1964) captures the highlights of his work, initially using a hand-carried mobile observing station (Fig. 8). Fig. 7 Perhaps one of the first instrumental records of a dust devil encounter (arrowed), after Wyett (1954). The barograph scale is in inches of mercury—the 0.04 inch drop corresponds to ∼1.4 hPa 2.7 United States of America Around the time of Sinclair’s early work, an important survey was conducted by Lam- beth (1966) of the Army Electronics Command at the White Sands Missile Range in New Mexico. This survey lasted May-September, using a linear array of six recording stations. When a human operator saw a dust devil, chart recorders were activated. Only 21 events were recorded in the five months of operation, a rather modest haul. Lambeth concludes with the suggestion that “dust devils can be measured in adequate numbers only by using mobile sensors”. Sinclair had by this time started to make many encounters using an impressive jeep- borne meteorology tower (Fig. 9), as well as measurements in a sailplane of the dust plumes atop dust devil. Sinclair’s papers (1965, 1969, 1973) and thesis are well worth reading even today, noting such challenges as the high-speed data acquisition required on a hot, dusty, bouncing jeep in the desert (a cine camera recorded film of instrument readings!). Sinclair also performed a couple of visual surveys from fixed stations, data still referred to today. It is of note that Sinclair’s work was funded by the Office of Naval Research (ONR), al- though it is not obvious whether this had any connection with nuclear testing, or was merely one of many areas of fundamental research supported by the US Defense Department. At this point space exploration and dust devil meteorology begin to intersect. J.A. Ryan, at the Missile and Space Systems Division of the Douglas Aircraft Corporation, speculated (Ryan 1964) that transient winds associated with ‘a cyclonic system (somewhat analogous to a terrestrial dust devil)’ might be responsible for the yellow clouds, presumed to be of dust, that had been seen telescopically on Mars. Later, Ryan and J. Carroll (then of the ‘Space Sciences Division’ of McDonnell-Douglas: the space program now allowed the progressively-consolidating aerospace industry to employ their own scientists, a situation that unfortunately is not widespread today) with NASA funding published several papers on field observations of dust devils in the Mojave desert in California, with a fixed meteo- rological station (e.g. Ryan and Carroll 1970). They appear to have been more lucky than 20 R.D. Lorenz et al. Fig. 8 Peter Sinclair with his portable measurement station with rather prominent anemometer and wind vane (from his Ph.D. thesis). 2.7 United States of America The box with electrical dial is a sensitive microbarometer designed by Sinclair Lambeth, observing 80 dust devils in just a few weeks, but they helped make their own luck by ‘grooming’ the surface around their mast to ensure dust availability. Lambeth, observing 80 dust devils in just a few weeks, but they helped make their own luck by ‘grooming’ the surface around their mast to ensure dust availability. After the early 1970s, dust devil research declined somewhat—a notable exception being Snow and McLelland’s survey at White Sands (New Mexico) in the late 1980s, funded by the Defense Nuclear Agency—until the resurge stimulated by Mars Pathfinder in the late 1990s (Metzger et al. 1999). Several field campaigns took place, in Eloy (between Phoenix and Tucson, Arizona) and at ElDorado Playa near Boulder City (just outside Las Vegas, Nevada), in many instances in order to trial instruments for the aborted Mars 2001 lander in a campaign called MATADOR (e.g. Tratt et al. 2003), for Beagle 2, the Mars Science Laboratory and other projects. Fig. 8 Peter Sinclair with his portable measurement station with rather prominent anemometer and wind vane (from his Ph.D. thesis). The box with electrical dial is a sensitive microbarometer designed by Sinclair 2.8 Australia (2007a, 2007b) conducted a field study of dust devils, the most extensive reported since Snow and McLelland. Beyond dust devils proper, it may be noted that Australia’s partly vegetated drylands (the “Bush”) are subject to periodic wildfires, and these often produce quite prominent fire devils. Also related are observations by Hess et al. (1988), who identified convection-driven updrafts that they proposed are similar to dust dev- ils, although they occurred over Port Phillip Bay in Victoria, Australia when cool air was advected over warm water. Recently, the signatures of dust devil vortices were identified in infrasound (i.e. high- pass-filtered pressure) signals at a Comprehensive Test Ban Treaty Organization (CTBTO) monitoring site at Wurramunga in Australia’s Northern Territory (Lorenz and Christie 2015). 2.8 Australia As a large, arid country, Australia sees frequent dust devil activity, and a local Aboriginal term is frequently adopted—“willy-willy”. Some notable researches have been stimulated there. The Australian Civil Aviation Authority (Bell 1969) noted that dust devils can present an appreciable hazard to light aircraft (which are an important means of transport and com- 21 History and Applications of Dust Devil Studies Fig. 9 Arizona desert west of Tucson, with Peter Sinclair’s mobile meteorology tower mounted on the sur- plus jeep he used to penetrate dust devils (from Sinclair’s Ph.D. thesis) Fig. 9 Arizona desert west of Tucson, with Peter Sinclair’s mobile meteorology tower mounted on the sur- plus jeep he used to penetrate dust devils (from Sinclair’s Ph.D. thesis) munication, given Australia’s large distances) and Spillane and Hess (1988) reviewed dry convective activity and its role in air accidents. Hess and Spillane (1990) reviewed the char- acteristics of dust devils in Australia, drawing on aviation reports, and noted that devils tend to ascend to a fraction (0.1 to 0.5) of the boundary layer height. They also suggested a con- dition of dust devil formation—h/L >50, where h is the boundary layer height and L the Obukhov length (this type of condition may have originated with Deardorff in the USA). More recently, Oke et al. (2007a, 2007b) conducted a field study of dust devils, the most extensive reported since Snow and McLelland. Beyond dust devils proper, it may be noted that Australia’s partly vegetated drylands (the “Bush”) are subject to periodic wildfires, and these often produce quite prominent fire devils. Also related are observations by Hess et al. (1988), who identified convection-driven updrafts that they proposed are similar to dust dev- ils, although they occurred over Port Phillip Bay in Victoria, Australia when cool air was advected over warm water. munication, given Australia’s large distances) and Spillane and Hess (1988) reviewed dry convective activity and its role in air accidents. Hess and Spillane (1990) reviewed the char- acteristics of dust devils in Australia, drawing on aviation reports, and noted that devils tend to ascend to a fraction (0.1 to 0.5) of the boundary layer height. They also suggested a con- dition of dust devil formation—h/L >50, where h is the boundary layer height and L the Obukhov length (this type of condition may have originated with Deardorff in the USA). More recently, Oke et al. 2.9 Japan Although there are no deserts or arid regions in the Japanese islands, dust devils are some- times reported on fine days especially in warm seasons. They commonly occur over sand- paved playgrounds in schools and in sports fields, because strong surface heating under fine-weather conditions generates intense thermals locally. An example was reported in Tachikawa and Deguchi (1987) who showed that a whirlwind blew away a tent over the playground in an elementary school during a sports festival at the school in October 1986. R.D. Lorenz et al. 22 Fig. 10 The locations of dust devil occurrence in Japan from 1961 to 2009, based on JMA database. (a) The locations over the Japanese island, and (b) those in the central part of Japan Fig. 10 The locations of dust devil occurrence in Japan from 1961 to 2009, based on JMA database. (a) The locations over the Japanese island, and (b) those in the central part of Japan The Japan Meteorological Agency (JMA) archives the information on tornados and other gust events that occur in Japan on the web (http://www.data.jma.go.jp/obd/stats/data/bosai/ tornado/index.html). Based on an inspection of this database for the present paper, it is found that there were 18 recorded occurrences of dust devils from 1961 to 2009 in Japan. Figure 10a exhibits the locations of dust devil occurrence in Japan during this time period. More frequent occurrence is seen in the central part of Japan. Figure 10b shows an enlarged map corresponding to a central part of Japan. Note that this JMA database is not compre- hensive, because the information is obtained by field investigations by JMA officials after the events. For example, the event reported by Tachikawa and Deguchi (1987) is not in- cluded in the JMA’s database. Although the JMA’s database does not provide full coverage for the dust-devil occurrence in Japan, the geographical features shown in Fig. 10 seem to be consistent with the notion that dust devils favorably occur in the inland regions in Japan. Since dust devils have typically a micro-scale (typically on the order of 1 m) with a very short lifetime (on the order of 10 seconds to a few minutes), direct meteorological observa- tions of such events are very rare. The impacts of dust devils in Japan are not significant; however, damages such as shown in Tachikawa and Deguchi (1987) are notable. 2.10 Russia, Canada, Argentina, Chile, Denmark and Other Countries In Russia dust (sand) devils regularly occur over its southern arid and semi-arid parts span- ning Kalmykia, Dagestan and Astrakhan regions (over the lowland north-west from the Kaspian Sea), and also over steppe territories in Voronezh and Rostov regions, and oth- ers. In particular, pilots flying over Kalmykia on light airplanes often observe high vertical dust columns associated with dust devils. Dust devils are observed in Kazakhstan, now an independent state, especially near the semi-dried Aral Sea. The observations by Przevalsky in the 1800s (reported in the ‘France’ section) were likely made in central Asia. Kennan (1886) describes ‘great whirling columns of sand, 100–150 ft in height swept slowly and majestically across the sun-scorched plain’ in the Kirgis steppes in Western Siberia. A dust devil was observed (Roland Neuber, AWI Potsdam, personal communication to MK) in Svalbard in the late spring after snow and ice melting and forming a clear spot of dry sandy land, over which the dust devil developed: at 78°N, this observation is more poleward than that of Wegener in Iceland, and we have recorded it in Fig. 2. In Chile dust devils occur in the north in the Atacama Desert and likely in the extreme south in Patagonia. In the Atacama Desert the dust devil activity was regularly reported by local people and also by travelers across the desert but the first regular field campaign to study dust devils was organized only in 2008–2009 (Kurgansky et al. 2011). A remarkable site was chosen near the settlement of Huara (about 50 km from the city of Iquique) with its unprecedented level of dust devil activity (up to more than 60 dust devils visible simultane- ously in a 360° panorama). A site near Huara is also famous for its petroglyphs, the largest in South America. Etymologically the naming Huara is usually attributed to the star (with the reference to aimara language), but by an alternative version, it might be related to the dust devil, which is so frequent there. The Huara dust-devil field campaign was the second one on the South America sub-continent (historically, the first dust-devil field study in the South America of which we are aware is by Metzger et al. (2010)). Recently, Lorenz and Radebaugh (2016) report observations of abundant dust devils at very high elevations (3600 m) in the Argentine Puna (a plateau somewhat southeast of, but higher than, the Atacama and Altiplano). 2.9 Japan There are sometimes newspaper reports typically in the warm season every year on the occurrence of damage due to gusty winds produced by dust devils. Recently remote-sensing techniques have become a powerful tool for measuring micro- scale vortices including dust devils in Japan. Inoue et al. (2011) successfully detected vor- tices such as tornados and mesocyclones, although not dust devils, during a winter storm event with the use of a low-level scanning X-band Doppler radar. Fujiwara et al. (2011, 2012) used a three-dimensional scanning Doppler lidar to detect dust-devil-like vortices that develop in the daytime under fair-weather convective conditions over an urban area. They revealed that invisible dust devils frequently occur from long-term observations. Doppler lidar was also used to detect an otherwise-invisible small-scale vortex over the sea i.e. a waterspout (Fujiwara and Fujiyoshi 2014). Ito and Niino (2014) applied a Particle Image Velocimetry (PIV) method to estimate the wind field in a dust devil which they encoun- tered in Arizona, USA. They estimated the maximum tangential wind in the dust devil as 16 ms−1. History and Applications of Dust Devil Studies 23 2.10 Russia, Canada, Argentina, Chile, Denmark and Other Countries 2.10 Russia, Canada, Argentina, Chile, Denmark and Other Countries The Campo Pedro Pomez site at which they measured several intense dust devils is the boundary between a plain of giant gravel rip- ples, and a field of yardangs carved in volcanic ash (ignimbrite)—a magnificent interplay of aeolian processes. Their report provides some circumstantial evidence that this site has quantitatively (2.5–10x) higher frequencies of dust devil occurrence than low-altitude sites like Eldorado. It may be noted, however, that over a century ago the Scottish astronomer Charles Piazzi-Smyth documented (Piazzi-Smyth 1858) several dust devil encounters, ‘be- ing peppered with little pebbles...almost blinded by dust’ at an elevation of about 3000 m in Tenerife, while exploring its volcanic mountains as possible sites for astronomical obser- vatories. The development of meteorological instrumentation, which is generally rather small and affordable, for Mars landers opened the way for some countries with modest budgets to con- tribute to dust devil studies: in particular, Finland, Denmark and Canada contributed pres- sure sensors, a wind indicator and a lidar respectively to the Phoenix mars lander mission, stimulating several papers. More recently Finland and Spain have contributed to the instru- mentation on the Curiosity rover, although so far rather few dust devils have been seen. One report of a dust devil in Canada exists, in sub-arctic Labrador at 65°N (Grant 1949). Finally, although we are unaware of detailed reports on dust devils in Peru and Niger, there have been studies of dust devil tracks in those countries (e.g. Rossi and Marinangeli 2004; Hesse 2012 and Reiss et al. 2013). Additionally, the authors of this paper have seen dust devils in Ethiopia and the United Arab Emirates, and have heard of them in Botswana. R.D. Lorenz et al. 24 Fig. 11 Viking Orbiter 2 image (ID 038B25) from September 1976 at 72 m/pixel showing several dust devils with their shadows, the illumination coming from the bottom of the image. The crater is about 19 km in diameter. Image center is Latitude 40.4°N Longitude 215.0°E. The solar elevation was about 45 degrees, so the shadow length indicates many plumes were several km high. Viking images including this one were studied by Thomas and Gierasch (1985). The regular-spaced black dots are reseau marks to correct for geometric distortion in the vidicon camera Fig. 12 Dust devil on Mars observed on the horizon by the Mars Pathfinder imager in 1997. Despite the modest image quality due to JPEG compression artifacts the detection of these features stimulated much modern dust devil research History and Applications of Dust Devil Studies History and Applications of Dust Devil Studies dust devils on the valley floor are clearly visible against the In fact, the images of lines of dust devils marching across the of dust devils in arid regions on Earth that it is sometimes hard observed. ments (see also Chap. 2 by Murphy et al. 2016, and Chap. 10 Fig. 13 Dust devils seen on Sol 543 (July 13, 2005) of the Spirit rover mission at Gusev crater. Improvements due to the experience of scientist operators, to the better cameras, and the higher bandwidth, lead to much higher quality images. These are just four frames of a movie sequence, showing the dust devils evolving and migrating from right to left. Note that the dust devils in the foreground have a faster angular motion and are seen only in two frames, while the distant tall devil is seen in all four Hills, and, in many images, dust devils on the valley floor are clearly visible against the background terrain beneath. In fact, the images of lines of dust devils marching across the valley are so similar to those of dust devils in arid regions on Earth that it is sometimes hard to tell which planet is being observed. Further in-situ measurements (see also Chap. 2 by Murphy et al. 2016, and Chap. 10 by Neakrase et al. 2016) and surface observations of dust devils were made by the 2008 Phoenix Mission (Ellehoj et al. 2010), showing that dust devils were active in the martian Fig. 13 Dust devils seen on Sol 543 (July 13, 2005) of the Spirit rover mission at Gusev crater. Improvements due to the experience of scientist operators, to the better cameras, and the higher bandwidth, lead to much higher quality images. These are just four frames of a movie sequence, showing the dust devils evolving and migrating from right to left. Note that the dust devils in the foreground have a faster angular motion and are seen only in two frames, while the distant tall devil is seen in all four Hills, and, in many images, dust devils on the valley floor are clearly visible against the background terrain beneath. In fact, the images of lines of dust devils marching across the valley are so similar to those of dust devils in arid regions on Earth that it is sometimes hard to tell which planet is being observed. 3 History of Dust Devil Studies—Mars The existence of dust devils on Mars was proposed well before any direct evidence for their presence was acquired, both Neubauer (1966) and Gierasch and Goody (1973) predicting that Mars’ arid surface, lack of cloud cover and large diurnal temperature variations should provide excellent opportunities for the presence of dust loaded convective vortices. Even be- fore those works, Ryan (1964) had made relevant speculation about the formation of ‘yellow clouds’. Indirect confirmation of these predictions came first from meteorology data sent back by the Viking 2 lander. In their analysis of the Viking 2 wind speed, wind direction and temperature data Ryan and Lucich (1983) showed that excursions in these parameters could be fit by models of convective vortices passing over or near the lander. More than a hundred such encounters were noted, although only a few were thought to be sufficiently intense that they could have lifted sediments and become visible dust devils. Visual confirmation of the presence of dust devils on Mars would await the results of analysis of images returned by the Viking Orbiter spacecraft, more than five years after the missions themselves had come to an end—Thomas and Gierasch (1985) finally presented observations (see Fig. 11) of columnar dust clouds on the martian surface that provided convincing evidence for the presence of dust devils on Mars. Observations of active martian dust devils were also made from the surface, first by the Mars Pathfinder mission (Metzger et al. 1999) and then in large numbers by the Mars Exploration Rover (MER) “Spirit” mission (Greeley et al. 2006, 2010). (Note that the Viking lander ‘camera’ was a facsimile imager which took many minutes to scan the scene, and so was not suitable for acquiring pictures of fast-moving objects like dust devils: famously the image of a tortoise in ground tests was smeared by its motion—e.g. Mutch 1978.) The Pathfinder images of dust devils (e.g. Fig. 12) are noisy and required significant processing to allow the dust-loaded vortices to be picked out against the dusty sky (note that unlike most subsequent Mars missions, Pathfinder data was transmitted directly to Earth, there being no relay orbiters yet in place, so the image bandwidth was somewhat more limited). The MER observations, however, were made from an elevated vantage point atop the Columbia History and Applications of Dust Devil Studies 25 History and Applications of Dust Devil Studies History and Applications of Dust Devil Studies Hills, and, in many images, dust devils on the valley floor are clearly visible against the background terrain beneath. In fact, the images of lines of dust devils marching across the valley are so similar to those of dust devils in arid regions on Earth that it is sometimes hard to tell which planet is being observed. Further in-situ measurements (see also Chap. 2 by Murphy et al. 2016, and Chap. 10 by Neakrase et al. 2016) and surface observations of dust devils were made by the 2008 Phoenix Mission (Ellehoj et al. 2010), showing that dust devils were active in the martian R.D. Lorenz et al. 26 Fig. 14 A dust devil on Mars, photographed by Mars Global Surveyor, climbing the wall of a crater. The long dark, slightly cycloidal streak is the track left by the dust devil, seen as a bright column at the top of the image. A short shadow extends from the base of the devil to the top-right. MSSS MGS image E16-01487 arctic. A disappointment for martian dust devil research, though, was that the 2004 MER missions were not equipped with in-situ meteorology instruments. Hence while Spirit ac- quired glorious images of dust devils (e.g. Fig. 13), no correlations with vortex wind speeds, pressure and temperature excursions, nor contextual weather data could be made. Although this was rectified for the 2012 (and ongoing at time of writing) Mars Science Laboratory ‘Curiosity’ Rover, its landing site—Gale Crater—does not appear to be an area with much dust devil activity—only a single visible devil has been reported after several years of ob- servations (Moores et al. 2015). One of the major differences between dust devil activity on Earth and Mars is that mar- tian dust devils often leave clear traces of their passage across the surfaces they move over— which is almost never the case on Earth—in the form of linear, curvilinear and even curlicue- shaped albedo markings. Dust devil tracks (see review Chapter by Reiss et al. 2016) were first recognized in Viking Orbiter images and interpreted to be ‘tornado’ tracks (Grant and Schultz 1987—their transient nature was recognized by comparison with Mariner 9 im- ages; they were not suggesting moist tornados of course, but rather “baroclinic wave pas- sage through an area of instability can trigger convective uplift and strong shear leading to tornadic-intensity vortex formation. History and Applications of Dust Devil Studies On Mars in the late summer, the occurrence of atmo- spheric instability, a deep convective layer, and onset of baroclinic wave passage represent a similar situation”). However, with the arrival of the Mars Global Surveyor mission, and with it the Mars Orbiter Camera (MOC) providing narrow-angle images of ∼2 m/pixel, it soon became clear that these dark (and occasionally bright) lineaments were formed by dust devils: one noted MOC image showing a dust devil ‘caught in the act’ of forming a track (Fig. 14; Edgett and Malin 2000). It was recently noted (Lorenz and Zimbelman 2014— see also chapter in this volume by Reiss et al.) that in fact dust devil tracks can be clearly seen—but were not recognized at the time—in Mariner 9 images of Proctor crater in the Hellespontus region of Mars, images in which dunes on Mars were first reported. It was assumed (J. Cutts, personal communication to RL) that these dark markings were simply fissures on the ground filled with dark material. The MOC dataset also provided the first opportunity to study dust devils as a popula- tion—the extensive coverage in time and space of both active dust devils and their tracks leading to several key conclusions, including (i) martian dust devils are, like on Earth, most active in spring and summer (e.g. Whelley and Greeley 2008), (ii) dust devils do not appear to trigger global dust storms on Mars (e.g., Balme et al. 2003a, 2003b) but do contribute to the persisting haziness of Mars’ atmosphere (Cantor et al. 2006), (iii) dust devils are more common in some parts of Mars than in others, especially in the Amazonis Planitia region (Cantor et al. 2006). Further discussion on orbital observations of dust devils at Mars is given in the Chapter by Fenton et al. (2016). 27 History and Applications of Dust Devil Studies In the last 15 years, martian dust devil data collection has focused on three areas: ob- servations of dust devils tracks from orbit, observations of active dust devils from orbit, and observations and measurements of dust devils from the surface. Recent advances include the first measurements from orbit of horizontal forward velocity of martian dust devils (tens of meters per second, based on multi-image acquisitions from the ESA Mars Express mission; Stanzel et al. 2008; Reiss et al. 2011b and from the NASA Mars Reconnaissance Orbiter mission; Reiss et al. 4 Applications and Relevance of Dust Devil Research The motivations for Mars and Earth dust devil research are several. Most obviously, ‘because they are there’—dust devils are one of the most dynamic observable features of the Martian environment. Their transient nature makes them ‘interesting’ objects to study and chase on Earth, an appeal which has motivated much unfunded casual research. In this section we list some other motivations and applications of dust devil studies History and Applications of Dust Devil Studies 2014) and, again from orbit, of wind speeds in martian dust devils, using comparison of the overlapping (but temporally slightly separated) RGB image strips in colour “HiRISE” images (wind speeds of 20–30 ms−1 were measured; Choi and Dundas 2011). ) As for in-situ measurements on landers, while wind speed data have been limited (see chapter by Murphy et al.) the detection of vortices—at least some of which are dust-laden— in the long time-series of pressure measurements from the Pathfinder (1997—Murphy and Nelli 2002) and Phoenix (2008—Ellehoj et al. 2010) landers allowed for the first time the systematic evaluation of the vortex population (Lorenz 2012) and its comparison with visual observations of dust devils (Lorenz and Reiss 2015). For many years—indeed since Ryan and Lucich (1983) and until only recently—the high-time resolution meteorological data needed to detect vortices was better at Mars than at Earth. Mars data have stimulated much numerical modeling work, applying LES methods (e.g. see Chap. 7 by Spiga et al. 2016) at high spatial resolutions. An outstanding question remains—much more so at Mars than Earth—how the dust is actually lifted, since (as recognized by Ryan 1964) the thin Mar- tian atmosphere requires very high wind speeds to overcome weight and cohesion of dust. Various solutions have been proposed, including ‘sandblasting’ by larger particles (Greeley 2002), and the ‘Delta-P’ (suction) effect (Balme and Greeley 2006). 4.1 Dust Devils as Dust Injectors into the Atmosphere Dust in the terrestrial and Martian atmospheres is important for several reasons (e.g. Knip- pertz and Stuut 2014; Read and Lewis 2004). Dust aerosols interact with radiation through scattering and absorption of shortwave radiation and through absorption and re-emission of longwave radiation. In the terrestrial atmosphere, dust particles act as ice and cloud conden- sation nuclei and can therefore influence cloud properties and precipitation. Moreover, the removal of dust from the soil, and its redeposition elsewhere, can be important in transport- ing toxins (see later), nutrients, minerals and carbon, thereby influencing continental and marine ecosystems as well as animals and humans. For example, Saharan dust is known to be an important nutrient source for the Amazon forest (e.g. Bristow et al. 2010). Not least, dust presents an air quality concern, thereby directly affecting human life. Although the importance of dust in the terrestrial and martian climates is evident, the contribution of dust devils to the Earth and Mars dust budgets is uncertain. On Earth, the first estimate by Koch and Renno (2005) was that dust devils may contribute by about 35 % 28 R.D. Lorenz et al. to the total dust burden. More recent estimates suggest a contribution of about a factor of 10 less (∼3.4 %, Jemmett-Smith et al. 2015). to the total dust burden. More recent estimates suggest a contribution of about a factor of 10 less (∼3.4 %, Jemmett-Smith et al. 2015). On Mars, a stronger focus has been on the contribution of dust devils to the dust cycle, leading to the development of dust devil parameterizations in Mars global climate models (e.g. Newman et al. 2002). While dust devils are no longer implicated in the formation of large-scale dust storms (and indeed their occurrence is anticorrelated, since dust-loading attenuates the convective instability that drives dust devils), dust lofting by dust devils is believed to be a significant contributor to Mars atmospheric dust loading. However, the need for model calibration against observed dust loadings, leads to uncertainties in the relative contributions of dust devils in comparison to other dust generating mechanisms. Dust devil occurrence frequencies and associated dust transport can be assessed through a variety of methods, including in situ observations, remote sensing, and modeling. Results based on the different perspectives are synthesized in Chap. 11 of this volume (Klose et al. 4.2 Formation of Dust Devil Tracks—The Martian Climate ‘Memory’ The martian atmosphere is rather thin, and responds quickly to changes in solar heating (e.g. Goody and Belton 1967). It is thus in fact comparatively easy to model, more so than the Earth. All else being equal, one Martian year should look very much like the next, since the atmosphere is too thin to convey much information over long periods. This is in sharp contrast to the Earth, where many multiannual cycles exist due to heat stored in the oceans, a prominent example being the Pacific Decadal Oscillation. Yet there are substantial interannual variations in Martian weather, notably in the occur- rence or not of large dust storms. It seems the distribution of dust on the surface may be a principal controlling factor, and it has been observed that large-scale albedo changes on the Martian surface (e.g. Geissler 2005—although see also Szwast et al. 2006) are often the re- sult of accumulated dust devil tracks (see Chapter by Reiss et al. 2016). Furthermore, these albedo changes are enough to cause variations in modeled temperatures and winds (Fenton et al. 2007). Thus, dust devils may be responsible for much of the variability in the Martian climate—they are a cause as well as an effect. 4.1 Dust Devils as Dust Injectors into the Atmosphere 2016) to provide a comprehensive picture on the role of dust devils in the terrestrial and martian climates, and the dust-lifting process is reviewed in Chap. 10 by Neakrase et al. (2016). 4.3 Atmospheric Electricity and Chemistry The generation of strong electric fields by dust devils on Earth is well-documented, and electric field measurements are planned at Mars—see the Chap. 11 by Harrison et al. (2016). A possible consequence of triboelectric charging on Mars, and the resulting corona dis- charge, is the generation of oxidizing chemicals, notably peroxides and ozone. These are important in that the nondetection of organic compounds by Viking (setting the stage for a sterile, dead world) may have been due to the presence of oxidants in the soil, and indeed the Phoenix lander discovered oxidizing perchlorates (e.g. Hecht et al. 2009). The associa- tion of the smell of ozone with electrical discharge is well-known, so this idea (Atreya et al. 2006) seems plausible. It is worth recalling Baddaley’s observations of century and a half ago, where evidence of ozone was noted (see earlier). History and Applications of Dust Devil Studies 29 Table 3 Dust devil and Tornado statistics compiled from US National Weather Service Hazards reports Dust devil death Dust devil injury Dust devil damage ($M) Tornado death Tornado injury Tornado damage ($M) 2001 1 40 743 637 2002 55 968 1 2003 1 3 0.1 54 1087 1281 2004 5 35 396 549 2005 38 537 503 2006 1 67 990 759 2007 81 659 1407 2008 1 14 0.06 126 1714 1865 2009 3 0.23 31 351 584 2010 0.06 45 699 1135 2011 8 0.03 553 5483 9492 2012 2 0.27 70 822 1649 Total 2 37 0.75 1195 14449 19862 Average 0.17 3.08 0.06 100 1204 1655 Table 3 Dust devil and Tornado statistics compiled from US National Weather Service Hazards reports 4.4 Dust Devil Hazard Dust devil vortex encounter frequencies in summer on Eldorado Playa in Nevada determined by a high-resolution pressure record in Lorenz and Lanagan (2014) are plotted as circles; NWS statistics of tornado mean swept area and intensity as defined in the text are plotted as diamonds. Weight loadings for various objects are noted by dashed lines Fig. 15 The cumulative frequency that a spot will encounter a vortex of a given intensity, defined by a pressure drop. Dust devil vortex encounter frequencies in summer on Eldorado Playa in Nevada determined by a high-resolution pressure record in Lorenz and Lanagan (2014) are plotted as circles; NWS statistics of tornado mean swept area and intensity as defined in the text are plotted as diamonds. Weight loadings for various objects are noted by dashed lines In addition to prompt injury, dust devils may adversely affect human health via injection of pathogens, toxins or irritants into the air (see Morman and Plumlee 2014). A particular concern in the USA is ‘Valley Fever’ wherein airborne fungal spores from the soil may be inhaled and lead to infection by Coccidioidomycosis, usually with minor symptoms but occasionally pneumonia, joint pain and fatige (e.g. Hector and Laniado-Laborin 2005). It may be noted that the dust at Eldorado Playa, near Boulder City, Nevada, USA—a popular field site for dust devil studies—has been documented (Buck et al. 2013) to contain large amounts of amphibolite, a carcinogenic natural asbestos. On Mars, in principle, dust devils might be associated with wind extremes that could be problematic for landers or rovers during their descent and landing phases. This is a partic- ular concern for parachute-borne vehicles, which would respond quickly to the wind shear associated with dust devil vortices. 4.4 Dust Devil Hazard Damage and discomfort due to dust devils has been noted since Greek and Roman times earlier in this paper. In the modern world, dust devils, and dry convection generally, can present a hazard to aviation. Typically this is due to sudden changes in wind speed and direction, although sometimes reduced visibility is a factor too. As discussed earlier, some studies in this direction were undertaken in Australia. Lorenz and Myers (2005) review US air accident reports, finding around 100 incidents in the NTSB Air Accident database 1995– 2005 pointing to dust devils as a contributing factor, and four fatal accidents. An informal survey of news media and the Internet reveals a number of reports of injury due to dust devils. Usually these are associated with lightweight structures—barns, tents, children’s bouncy castles and parachutes are often the mechanism by which a sudden wind can cause injury. In one instance, a vehicle in South Africa lost control on encountering a dust devil and an astronomer was killed. In another, a US airline pilot was out jogging, and apparently took shelter from a dust devil by a wooden barn, which collapsed, killing her. Table 3 summarizes injuries, deaths and damage from US National Weather Service (NWS) statistics. It is seen that the damage and casualties due to dust devils are between two and three orders of magnitude less than those associated with tornados. It is interesting that the area swept by tornados of a given pressure (the intensity on the Fujita scale of a tornado is associated with a speed range, which can be equated with a dynamic pressure, since these vertical systems are in roughly cyclostrophic balance) can be plotted (Fig. 15) on a diagram together with pressure drop encounter statistics from dust devil surveys. The weight loading of various structures (which can be equated with the dynamic pressure required to lift them) is also shown. Clearly, tornados are associated with much stronger pressures, but occur much more seldom. The death rate by dust devil (including parachuting and air accidents) is crudely ∼10 in ∼30 years, or adopting a mean population for the period of ∼300 million, about 0.001 death per year per million. 30 R.D. Lorenz et al. Fig. 15 The cumulative frequency that a spot will encounter a vortex of a given intensity, defined by a pressure drop. 4.5 Mars Solar Power and Planetary Protection There is a direct impact on the operation of spacecraft on the surface of Mars, in that dust progressively accumulates on up-facing surfaces, such as solar arrays. Indeed, the Pathfinder mission observed a steady 0.28 % per day decline in solar power due to dust deposition. This trend guided expectations that later missions (notably the Mars Exploration Rovers) might survive only ∼90 days. However, periodic sudden increases in solar power occurred due to ‘clearing events’ which swept the arrays clean. Lorenz and Reiss (2015) found that not only did these events seasonally coincide with the start of observed dust devils, but they occurred at a rate consistent with the vortex encounter rates measured by pressure drops on Pathfinder and Phoenix, extrapolated to a dust-lifting threshold intensity. Thus dust devils appear to significantly influence the capabilities of Mars surface assets. Sand and dust transport on vehicles on the surface of Mars also has a possibly surpris- ing relevance, in that stringent requirements (ultimately mandated by the UN Outer Space Treaty of 1967) on cleanliness and contamination control in order to comply with Plane- tary Protection policies. These ensure that bacteria or other contaminants are not introduced into Martian environments where they might flourish and disrupt efforts to detect extant or fossil life on Mars. The possibility exists that abrasive particles brought and/or removed by History and Applications of Dust Devil Studies 31 dust devils, might scour spacecraft surfaces on the upper part of the vehicle. Since these up- per surfaces might not normally be thought to have contact with the Martian ground, these transport processes may demand additional cleaning or bioassay during mission preparation. dust devils, might scour spacecraft surfaces on the upper part of the vehicle. Since these up- per surfaces might not normally be thought to have contact with the Martian ground, these transport processes may demand additional cleaning or bioassay during mission preparation. 4.6 Dust Devils as Dynamical Objects Like more general convective structures, such as the cells in Rayleigh-Benard convection, dust devils are interesting self-organized thermally-driven systems which deserve study as emergent entities. While they might be seen merely as parts of a convecting boundary layer, they can be usefully and accurately considered as discrete structures. The dynamical structure of dust devils is of interest from a purely fluid-mechanical stand- point, and many studies of analytic models, numerical models and laboratory-scale vortices have been made. There are furthermore useful analogies between dust devils and tornado and other vortices. A heat-engine formalism by Renno et al. (1998), analogous to similar thermodynamic studies of hurricanes, has been useful in reconciling the temperature perturbations seen in dust devils with the resultant pressure and velocity fields. Statistical studies of dust devil populations have found that their observed diameters and heights, observed pressure drops, and the widths of dust devil tracks, have highly-skewed distributions, that can be fit by power-laws or other functions (e.g. Lorenz 2011; Kurgansky 2006). There exists an association of power law statistics with self-organized criticality and other forced physical systems. Thus dust devils are of interest from a more general statisti- cal/physical standpoint. 5 Dust Devils in Culture This counterculture event is held on a playa which frequently sees dust devils (a web search will find many excellent videos and photos). This aerial image is notable in showing four dust devils apparently triggered by the updraft of the smoke plume from the burning icon. Note the vehicles for scale. Image by Duncan Rawlinson (duncan.co CC Attribution-NC license) space suit designs for Martian surface operation was made possible by the entertainment industry (Gaier et al. 2010), being tested with simulated dust devils during the production of a documentary ‘Storm Worlds’. A prominent counterculture festival ‘Burning Man’ is held annually on a remote playa in the Nevada desert, culminating in its eponymous bonfire. Dust devils are frequently encoun- tered at this location, with participants sometimes chasing them on bicycles or on foot. On some occasions, dust devils are actually triggered (see Fig. 16) by the smoke plume from the fire. Another cultural influence of dust devils is the film “Tornado” (2010) by the Belgian- born artist Francis Alys in Mexico, who possibly suggests the chaotic airflow in a dust devil as a metaphor for politics in that country. As reviewed by Rooney (2011), “the sight of his lean frame racing towards the twisters is at once ridiculous and hysterical—blithe qualities that quickly give way to gravitas as the artist physically enters the eye of the storm. In- side, chaos reigns and Alys, unprotected except for his handheld camera, is enveloped and pummeled by flying bits of sand, dust and dirt.” On a lighter note, ‘Dust Devil’ is the title of a US children’s book (and should not be confused with the aforementioned crime novel). Finally, towards the end of a popular chil- dren’s book (written in Swedish by Finnish author Tove Jansson and published in 1946) “Comet in Moominland”, the heroes are lifted in the air by a “cyclone”. The illustrations of the book reveal that this “cyclone” is only small in scale and there is no mention of rain. Also several other similar whirlwinds are seen in the illustration of the book. One of the characters, Snufkin, explains that they are caused by heating of the ground by the radiation of an approaching comet. Because of this formation mechanism, the whirlwind mentioned in “Comet in Moominland” should perhaps be classified as a gigantic dust devil instead of a cyclone or tornado. 5 Dust Devils in Culture The very name ‘dust devil’ suggests an association with the occult, shared with the Arabic term ‘djinn’, appealing to the notion that dust devils conjure themselves out of thin air. Because dust devils may have both clockwise and anticlockwise sense of rotation there was a belief among native people (Indians) that dust devils with one predefined sense of rotation correspond to a good genius and of opposite one to an evil spirit. Amazingly, both the native people in Chile, and the Navajo in the USA, about 10000 km distant from the Atacama Desert, have essentially the same belief in this respect. The occurrence of dust devils in India has a long history, and they are a regular phe- nomenon in arid regions such as those found in the Hyderabad-Karnatak region. Whilst they are accepted nowadays as commonplace atmospheric phenomenon, in rural Indian farming areas old superstitions relating to dust devils still persist; some farmers working in fields still fear dust devils and will hold their children and belongings flat on the ground until it passes. Like many evocative phrases, ‘dust devil’ has been appropriated by other fields of en- deavour. ‘Dust Devils’ is a common name for school sports teams in desert areas of the USA. ‘Dust Devil’ is the title of a thriller novel by Roger Smith, set in South Africa, and is also that of a violent 1992 horror movie set in Namibia, but aside from scenes at the real-world ghost town of Kolmanskop (notable for being overrun by sand dunes) has no meteorological significance. Dust storms on Mars are a common feature in science fiction movies set on that planet, and dust devils are seen prominently in the popular 2015 movie ‘The Martian’. It may be noted that scientific publication of tests of dust penetration into 32 R.D. Lorenz et al. Fig. 16 Aerial view of dust devils at the 2014 Burning Man festival in the USA. This counterculture event is held on a playa which frequently sees dust devils (a web search will find many excellent videos and photos). This aerial image is notable in showing four dust devils apparently triggered by the updraft of the smoke plume from the burning icon. Note the vehicles for scale. Image by Duncan Rawlinson (duncan.co CC Attribution-NC license) Fig. 16 Aerial view of dust devils at the 2014 Burning Man festival in the USA. 5 Dust Devils in Culture Comets are not traditionally associated with aeolian phenomena, but the discovery of ripples on the surface of a comet just prior to the workshop (Thomas et al. 2015) that stimulated this review paper reminds us that in science we must, as children do naturally, keep an open mind. History and Applications of Dust Devil Studies 33 6 Conclusions We have reviewed the history of dust devil research. Dust devils have been studied in a range of countries since the mid-19th century, initially somewhat informally in connection with other rotating wind systems. Instrumented studies of dust devils in their own right begin in earnest in the 1960s, perhaps in connection with nuclear weapons programs. Mars exploration emerged as a major stimulus of dust devil research, initially in the late 1960s, but again in the early 21st century. Dust devils present an occasional terrestrial hazard, roughly 2–3 orders of magnitude less severe than tornados. Their role in terrestrial dust-lifting is probably not dominant, but may be significant at Mars. Dust devils appear to be a significant factor in surface albedo changes on Mars, and the removal of dust from lander or rover solar panels by dust devils is an important issue in spacecraft power management and operations. Dust devils engage the public and have interesting properties, both in their individual dynamics and as a population, which are appealing topics of scientific investigation. Acknowledgements The work of R. 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Homeostatic regulation through GABA and acetylcholine muscarinic receptors of motor trigeminal neurons following sleep deprivation
Brain structure & function
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Homeostatic regulation through GABA and acetylcholine muscarinic receptors of motor trigeminal neurons following sleep deprivation Hanieh Toossi1 · Esther Del Cid‑Pellitero1 · Barbara E. Jones1 Received: 8 August 2016 / Accepted: 20 February 2017 / Published online: 15 March 2017 © The Author(s) 2017. This article is published with open access at Springerlink.com Abstract  Muscle tone is regulated across sleep-wake states, being maximal in waking, reduced in slow wave sleep (SWS) and absent in paradoxical or REM sleep (PS or REMS). Such changes in tone have been recorded in the masseter muscles and shown to correspond to changes in activity and polarization of the trigeminal motor 5 (Mo5) neurons. The muscle hypotonia and atonia during sleep depend in part on GABA acting upon both ­GABAA and ­GABAB receptors (Rs) and acetylcholine (ACh) act- ing upon muscarinic 2 (AChM2) Rs. Here, we examined whether Mo5 neurons undergo homeostatic regulation through changes in these inhibitory receptors following prolonged activity with enforced waking. By immunofluo- rescence, we assessed that the proportion of Mo5 neurons positively stained for ­GABAARs was significantly higher after sleep deprivation (SD, ~65%) than sleep control (SC, ~32%) and that the luminance of the ­GABAAR fluores- cence was significantly higher after SD than SC and sleep recovery (SR). Although, all Mo5 neurons were positively stained for ­GABABRs and AChM2Rs (100%) in all groups, the luminance of these receptors was significantly higher following SD as compared to SC and SR. We conclude that the density of ­GABAA, ­GABAB and AChM2 receptors increases on Mo5 neurons during SD. The increase in these receptors would be associated with increased inhibition in the presence of GABA and ACh and thus a homeostatic down-scaling in the excitability of the Mo5 neurons after prolonged waking and resulting increased susceptibility to muscle hypotonia or atonia along with sleep. prolonged waking and resulting increased susceptibility to muscle hypotonia or atonia along with sleep. Keywords  GABAA · GABAB · AChM2 · Mice · Muscle atonia · Waking Brain Struct Funct (2017) 222:3163–3178 DOI 10.1007/s00429-017-1392-4 Brain Struct Funct (2017) 222:3163–3178 DOI 10.1007/s00429-017-1392-4 ORIGINAL ARTICLE ORIGINAL ARTICLE * Barbara E. Jones barbara.jones@mcgill.ca 1 Department of Neurology and Neurosurgery, McGill University, Montreal Neurological Institute, 3801 University Street, Montreal, QC H3A 2B4, Canada Sleep deprivation and recovery experimental procedures A total number of 12 adult male mice (C57BL/6, 20-25g) were received from the supplier (Charles River) and housed individually under 12-h light : 12-h dark schedule (lights on from 7:00 to 19:00) at 22 °C ambient temperature and with unlimited access to food and water at all time. Ani- mals were maintained in their home cages for the duration of the experiment and recorded by video and telemetric electroencephalogram (EEG) using HomeCageScan soft- ware (HomeCageScan™ 3.0; Clever Systems) (del Cid- Pellitero, Plavski and Jones, unpublished results). For tel- emetric recording of the EEG, two electrodes were placed symmetrically over parietal cortex along with two for ref- erence over cerebellum and were connected by wires to a transmitter (F20-EET, Data Sciences International, DSI) implanted subcutaneously along the flank. Following sur- gery, the mice were allowed 1 week to recover. The sleep-waking cycle is known to be regulated in a homeostatic manner, since sleep deprivation (SD) with enforced waking leads to a subsequent decrease in wak- ing and increase in sleep, including both SWS and REMS (Borbely et al. 1984). The homeostatic drive is evident fol- lowing SD in both cortical activity, as an increase in slow wave activity, and peripheral muscle tone, as an increase in muscle atonia (Werth et al. 2002; Borbely and Achermann 1999; Tobler and Borbely 1986), which suggest homeo- static changes in central neurons, including motor neurons. g g The activity of individual neurons is also known to be regulated in a homeostatic manner, such that pro- longed increases in activity can lead to decreases in activity associated with decreases in excitability of the individual neurons (Turrigiano 1999). These cell autono- mous adjustments have been referred to as homeostatic synaptic scaling that is triggered and sensed by altered levels of neuronal discharge and/or membrane polariza- tion and is mediated by global changes in excitatory and/ or inhibitory receptors in individual neurons (Turrigi- ano et al. 1998; Kilman et al. 2002; Marty et al. 2004). In both in  vitro and in  vivo studies, prolonged activity has been shown to lead to increases in ­GABAA receptors that are associated with increases in post-synaptic inhibi- tory currents (Nusser et  al. 1998; Marty et  al. 2004). We thus hypothesized that prolonged activity of motor neurons during enforced waking with SD could lead to homeostatic increases in inhibitory receptors, including ­GABAA, ­GABAB and AChM2 receptors. Materials and methods All procedures were performed according to the guide- lines of the Canadian Council on Animal Care and approved by the animal care committee of McGill University. Introduction These results indicate that motor neurons in the brainstem, including the Mo5 neurons, are inhibited during sleep by both ionotropic glycine/GABA receptors and metabotropic ­GABAB and AChM2 receptors. control (SC) and sleep recovery (SR) conditions. The work has now been published in abstract form (Toossi et al. 2016a). Introduction Motor activity and muscle tone are regulated across the sleep-waking cycle. Muscle tone is maximal in alert wak- ing, reduced in slow wave sleep (SWS) and absent in para- doxical or REM sleep (PS or REMS) (Jouvet 1967; Chase 1983). During this cycle, motor neurons in the brainstem and spinal cord fire during waking, decrease their fir- ing during SWS and cease firing during REMS. Intracel- lular recordings showed that the motor trigeminal, 5th nerve (Mo5) neurons are slightly hyperpolarized during SWS and strongly hyperpolarized during REMS relative to active waking (Chandler et al. 1980; Chase et al. 1980), as are also motor neurons of the motor hypoglossal, 12th nerve (Mo12) and spinal cord (Morales and Chase 1978; Fung and Chase 2015). The post-synaptic inhibition of the Mo5 and motor spinal neurons was shown to be blocked by strychnine and thus dependent upon the inhibitory neu- rotransmitter, glycine and its postsynaptic receptors (Soja et  al. 1987; Chase et  al. 1989). Yet, studies also indi- cated that the atonia of the masseter muscles could not be fully blocked by antagonism of glycine receptors with strychnine alone but only by the additional antagonism of GABA receptors, and not solely of ­GABAARs with bicu- culline but only additionally of ­GABABRs with baclofen (Soja et al. 1987; Brooks and Peever 2008, 2012). It was also found that glycine and ­GABAA receptor antagonism increased tone during waking and SWS as well as REMS (01234 1 3 (0121 23456789) 3 3164 Brain Struct Funct (2017) 222:3163–3178 in both masseter and genioglossus muscles (Soja et  al. 1987; Brooks and Peever 2008; Morrison et al. 2003). In the genioglossus muscles, it was discovered that the mus- cle atonia during REMS could be selectively prevented by antagonism of acetylcholine (ACh) muscarinic (M) recep- tors using scopolamine or by blocking the inhibitory path- way through the G-protein coupled inwardly rectifying potassium channel (GIRK) to which the AChM2R is linked (Grace et al. 2013a, b). Given the demonstrated post-synap- tic inhibitory action of the AChM2R through GIRK chan- nels in motor neurons (Chevallier et al. 2006; Miles et al. 2007; Zhu et al. 2016), the demonstrated presence of ACh- M2Rs on Mo5 neurons (Hellstrom et al. 2003; Brischoux et al. 2008) and the established role of ACh in PS or REMS (Jones 1991), it would appear that such AChM2R-mediated inhibition could well occur during REMS. Immunohistochemistry For the image acquisition, the exposure time and contrast were set for each receptor series according to the param- eters which provided suitable images of the brightest to the dimmest fluorescence. These parameters were maintained for all sections and mice across all groups for each recep- tor series. In the Optical Fractionator Probe, a grid size of 200 × 200 μm2 and a counting frame of 120 × 120 μm2 were used in the image acquisition and assessment with mark- ing of positively labeled cells. Across the three sections, approximately 21 counting frames for Mo5 neurons were acquired and analyzed per series. Within these images, cell somata with visible nuclei located > 1  µm below the sur- face of the section were marked for counting, thus through 14 µm of the section. The motor neurons were identified in the FNS stained sections by their distinct morphology and thus referred to as MoFNS-positive (+). The average number of MoFNS + cells counted across series on one side was 32.86 ± 1.16 (mean ± SEM). For marking of cells positively stained for receptors, the immunostaining for the ­GABAA, ­GABAB and AChM2 receptors on the membrane or over the cytoplasm of the MoFNS + somata was assessed by moving through the z stack of 0.5 μm thick optical sec- tions of each MoFNS + cell soma. Estimated total num- bers of double-labeled cells were computed for each series ­(GABAAR-FNS, ­GABABR-FNS, and AChM2R-FNS) and expressed as % of MoFNS + cell population per series through the Mo5 nucleus. Luminance measurements of the receptor immunofluo- All the receptor antibodies employed were produced and characterized years ago and have since been in use over many years (as cited herewith). For the ­GABAAR, the antibody against the β2-3-chain was employed because it stains the most prevalent types of ­GABAA het- erodimeric receptors on neurons in the brain and stains clusters of the ­GABAAR on the plasma membrane, which are associated with functional inhibitory post-synaptic currents (IPSCs) (Fritschy and Mohler 1995; Wan et al. 1997; Nusser et  al. 1998). For the ­GABABR, the anti- body against the R1 subunit was employed because it also stains vast populations of neurons in the brain and is visible over cytoplasmic organelles and the plasma mem- brane, where it forms together with the R2 subunit the heteromeric functional receptor (Margeta-Mitrovic et al. 1999; Filippov et al. 2000; Straessle et al. 2003). Sleep deprivation and recovery experimental procedures We investigated this possibility by quantitative assessment of the recep- tors in immunofluorescent-stained sections from brains of mice following enforced waking with SD compared to those following normal or enhanced sleep with sleep The three experimental groups were composed of: (1) sleep control (SC) mice allowed to sleep undisturbed for 2  h from ~14:00 to ~16:00 (~ZT 7–9) (n = 3), (2) sleep deprived mice (SD) maintained awake for 2  h (n = 3) or 4 h (n = 3) from ~12:00 to ~16:00 (~ZT 5–9) and (3) sleep recovery (SR) mice allowed to sleep for 2 h from ~14:00 to ~16:00 (~ZT 7–9) after being maintained awake for 4 h prior to euthanasia (n = 3). The mice were maintained awake by gentle stimulation with a soft paintbrush of the whiskers each time the mouse appeared to be prepar- ing to sleep. Mice were immediately anaesthetized after the experimental period at ~16:00 (~ZT 9) with sodium pentobarbital (Euthanyl, 100 mg ⁄ kg; Bimeda-MTC) and perfused transcardially with 30 ml of cold saline followed by 200 ml of 3% paraformaldehyde solution. Brains were removed, post-fixed in 3% paraformaldehyde for 1 h at 4°C, then placed in 30% sucrose solution at 4 °C for 2 days, fro- zen to −50 °C and stored at −80 °C. Sleep and waking were scored by behavior and EEG using HomeCageScan software. 1 3 3 Brain Struct Funct (2017) 222:3163–3178 3165 Immunohistochemistry Brains were cut and processed for fluorescent staining in batches of 2–4 that included mice from SC, SD and/or SR groups of the same experimental session or period. Coronal sections were cut through the brainstem on a freezing microtome at a 20  µm thickness and collected in 5 adjacent series, such that sections were separated by 100 µm intervals in each series. Free floating sections were rinsed in 0.1 M trizma saline buffer (pH 7.4), then incubated in 6% normal donkey serum buffer for 30 min and subsequently incubated overnight at room tempera- ture in a buffer containing 1% normal donkey serum with one of the primary antibodies. The following anti- bodies were employed: mouse anti-GABAAR β2-3-chain (clone BD17, 1:100, Millipore (Chemicon), CAT# MAB 341, RRID: AB_2109419), guinea pig anti-GABABR1 (1:2500, Millipore (Chemicon), CAT# AB1531, RRID: AB_2314472) or rabbit anti-AChM2R (1:600, Sigma, CAT# M9558, RRID: AB_260727). Subsequently, sec- tions were incubated at room temperature for 2  h in Cyanine-conjugated (Cy3) secondary antibodies from donkey (Jackson ImmunoResearch Laboratories): Cy3- conjugated anti-mouse (1:1000, CAT# 715-165-150, RRID: AB_2340813), Cy3-conjugated anti-guinea pig (1:1000, CAT# 706-165-148, RRID: AB_2340460) or Cy3-conjugated anti-rabbit (1:1000, CAT# 711-165- 152, RRID: AB_2307443). Sections were subsequently stained with green fluorescent Nissl stain (FNS) (1:2000, CAT # N-21,480, Molecular Probes) for 20 min. Finally, sections were rinsed, mounted and coverslipped with glycerol (Fisher). Stained sections were viewed using a Leica DMLB micro- scope equipped with x/y/z motorized stage, a digital cam- era (Orca-R2, C10600-10B, Hamamatsu photonics K.K) and fluorescence filters for excitation and emission of Cy2 and Cy3 dyes. Images were acquired and analyzed using the Optical Fractionator Probe of StereoInvestiga- tor (MicroBrightField, MBF), which allows unbiased, sys- tematic random sampling of a region of interest for cell number estimation or measurement of specific parameters, including luminance. Given application of systematic ran- dom sampling for examining and marking cells at high magnification and the subsequent measurement of fluo- rescence intensity of the receptor staining in the marked receptor + cells employed here, double blind procedures were not applied in this process. In each series, three sec- tions (at 100  µm intervals) were taken through the Mo5 nucleus. In each section, a contour was traced around the Mo5 nucleus under a 5× objective. Multi-channel image stacks with 0.5 μm thickness of optical sections were then acquired under a 40× objective through the mounted his- tological section of approximately 15  µm thickness. Immunohistochemistry For the AChM2R, the antibody employed was shown to be highly specific and to stain most prominently the surface mem- branes of all cholinergic as well as diverse noncholiner- gic neurons in the brain (Levey et al. 1991). Luminance measurements of the receptor immunofluo- rescence were performed in the marked double-labeled cells, comprising 5–10 cells per animal for ­GABAAR+ 1 3 3166 Brain Struct Funct (2017) 222:3163–3178 and 10 cells per animal for ­GABABR+ and AChM2R+. The images had been acquired with the 8-bit setting of the digital camera, which thus provides converted gray scale images of the fluorescence with arbitrary units of 0–256 for luminance measures. Image acquisition was made as rapidly as possible for each cell so as to avoid bleach- ing of the fluorescence. As it was previously described in (Toossi et al. 2016b), two approaches were used to meas- ure the intensity of receptor immunofluorescence over the membrane vs. that over the cytoplasm plus membrane of the soma. A rectangular box sized at 1.5 × 0.3 μm2 was placed over the plasma membrane for luminance measure- ment of the membrane fluorescence and another box over the nucleus for luminance measurement and subsequent subtraction of the background fluorescence in each cell. A donut-shaped contour was drawn around the perikaryon to include the cytoplasm and plasma membrane for luminance measurement of the cytoplasm plus membrane and another spherical contour drawn around the nucleus for measure- ment and subtraction of background fluorescence in each cell. of the ­GABAAR immunofluorescence, which was quite dim in the SC brains, the brightness and contrast were enhanced uniformly across the three images of the three mice for bet- ter visibility of the receptor immunostaining in the image plate. Sleep‑wake states across groups Whereas mice are normally awake a small percentage of the time during the day, as evident in the SC (n = 3) group, the mice in the SD group (n = 6) were maintained awake ~ 100% of the time according to behavioral and EEG criteria during the 2 h prior to termination at 16:00 ­(F(2 ,9) = 1381, p < 0.001; n = 12) (Fig. 1A). During this time, the SD mice engaged in walking, rearing, eating and grooming behaviors, which were all significantly increased relative to the SC mice, or remained still while awake with eyes open. Mice in the SC group were awake ~ 24% of the time (23.79 ± 1.02%, Mean ± SEM) and mice in the SR group ~ 6% of the time (5.67 ± 2.63%, n = 3), which was significantly less than in the SC group (post hoc paired comparison, p < 0.001). Being undisturbed, the mice in the SC group, thus slept ~ 76% of the time and mice in the SR group, which were allowed 2  h recovery sleep after 4 h SD, slept ~ 94% of the time, indicating a homeostatic response to SD. The major proportion of time for the SC and SR groups was spent in NREMS (66.93 ± 1.71, and 82.29 ± 4.07%, respectively), and a minor proportion in REMS (9.28 ± 0.89 and 12.03 ± 0.87%, respectively). Both NREM and REMS were significantly increased during SR relative to SC. Cell counts and luminance measurements were ana- lyzed across experimental groups for each receptor series ­(GABAA, ­GABAB or AChM2R) using one-way analysis of variance (ANOVA) followed by post-hoc paired compari- sons with Fisher’s LSD using SYSTAT (SYSTAT Software Inc., version13). In an initial analysis, the proportion of ­GABAAR+/MoFNS + neurons was found to differ signifi- cantly across the original 4 groups ­(F(3,8) = 4.27, p = 0.045), however to not differ significantly between the SD2 and SD4 groups (post-hoc paired comparisons, p = 0.387), for which reason they were subsequently combined into one SD group for subsequent analysis and presentation of results. In addition, the proportion of ­GABABR+ and AChM2R + of the MoFNS + neurons was 100% in all groups. GABAARs on Mo5 neurons after SD and SR For higher resolution, images were also acquired using an LSM 710 confocal laser scanning microscope equipped with Ar 488-nm and He–Ne 543-nm lasers for excitation and emission of Cy2 and Cy3 dyes. Images were acquired under 63× oil objectives with a 1.0 airy unit pinhole size for each channel and 0.5 μm thick optical section. Immunostaining for the ­GABAAR was examined on the Mo5 neurons, which were positively (+) stained for Nissl substance with FNS and morphologically identified as motor neurons (MoFNS+) in brains of mice from SC, SD and SR groups (Fig. 2A–C). As evident in the fluorescent microscopic images examined for determining ­GABAAR positive (+) immunostaining and measuring its intensity (Fig. 2A–C) and in confocal microscopic images examined for its localization with higher resolution (Fig. 3A–C), the ­GABAAR immunostaining was located over the plasma membrane of the soma and dendrites of the MoFNS + neu- rons. As evident in these images, the immunofluorescent staining varied in intensity among neurons and mice yet appeared to be consistently most intense in neurons of the SD mice. Image plates were prepared and composed using Adobe Creative Suite (CS4, Adobe System) from fluores- cent microscopic images which were used for quantitative measurements and from confocal images which were used for qualitative assessment with higher resolution of the receptor immunostaining. In all cases as stated above, the parameters of acquisition including exposure time and con- trast, were set at the beginning for each receptor series and maintained the same across sections, mice and groups. In no case were brightness or contrast adjusted on individual images. However, for the fluorescent microscopic images 3 3 3167 Brain Struct Funct (2017) 222:3163–3178 Fig. 1   Sleep-wake states and GABA and AChM2 receptors in Mo5 neurons across groups. A The percentage of time spent in wake during the 2 h preceding termination differed significantly across groups, being higher in SD as compared to SC and SR and lower in SR as compared to SC. B The % of MoFNS + neurons which were positively immunostained for the ­GABAAR (+) differed sig- nificantly between groups, being greater in SD as compared to SC (B1). The luminance of the ­GABAAR immunofluorescence on ­GABAAR+/MoFNS + neu- rons differed significantly, being higher in SD as compared to SC and SR (B2). C All Mo5 neurons were positively immu- nostained for the ­GABABR in all groups (C1). GABAARs on Mo5 neurons after SD and SR Images of single optical sections show several large motor neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the ­GABAAR (red, A2, B2, C2) within the Mo5 nucleus of each mouse. Through the one optical section shown, ­GABAAR immunofluorescence is visible over the plasma membrane of one Mo5 neuron (arrowhead) which is magnified on the right (~3×, A3, B3, C3) for each mouse. In the SC mouse (MST23), the ­GABAAR immunofluorescence is very dim, whereas in the SD mouse (MST20), it is very bright and in the SR mouse (MST22), less bright than in the SD mouse. For measurement of the ­GABAAR fluores- cence intensity, a small rectangular box was placed over the plasma membrane and for that of the background fluorescence of the same cell, another over the nucleus to be subtracted from that of the plasma membrane (A3, B3, C3, see Methods). Scale bars 20  μm. Optical image thickness: 0.5 μm Fig. 2   Fluorescent microscopic images of ­GABAARs in Mo5 neu- rons across groups. Images of single optical sections show several large motor neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the ­GABAAR (red, A2, B2, C2) within the Mo5 nucleus of each mouse. Through the one optical section shown, ­GABAAR immunofluorescence is visible over the plasma membrane of one Mo5 neuron (arrowhead) which is magnified on the right (~3×, A3, B3, C3) for each mouse. In the SC mouse (MST23), the ­GABAAR immunofluorescence is very dim, whereas in the SD mouse (MST20), it is very bright and in the SR mouse (MST22), less bright than in the SD mouse. For measurement of the ­GABAAR fluores- cence intensity, a small rectangular box was placed over the plasma membrane and for that of the background fluorescence of the same cell, another over the nucleus to be subtracted from that of the plasma membrane (A3, B3, C3, see Methods). Scale bars 20  μm. Optical image thickness: 0.5 μm ­GABAAR immunostaining on the plasma membrane of ­GABAAR+/MoFNS + neurons was also significantly dif- ferent between groups ­(F(2,110) = 10.9, p < 0.001; n = 23–60 as compared to the SC group (32.34 ± 7.38%, post hoc paired comparison p = 0.008) and in a trend as compared to the SR group (47.38 ± 3.27%, p = 0.096). As meas- ured in the same fluorescent microscopic image stacks (Fig. GABAARs on Mo5 neurons after SD and SR The lumi- nance of the ­GABABR in the MoFNS + neurons differed significantly and was higher in SD as compared to SC and SR (C2). D All the Mo5 neurons were positively immunostained for the AChM2R in all groups (D1). The luminance of the AChM2R on MoFNS + neurons differed significantly, being higher following SD as com- pared to SC and SR (D2). Note that the changes in GABARs and AChM2Rs on Mo5 neurons parallel the % Wake across groups. Bars represent Mean ± SEM for each group, *indicates significant difference of SD relative to SC, †indicates significant difference of SD relative to SR, §indicates signifi- cant difference of SR relative to SC (p < 0.05), according to post hoc paired comparisons follow- ing one-way ANOVA 1 he fluorescent microscopic image ons (Fig. 2A–C), a proportion of appeared to be positively immu- AAR over the plasma membrane in all mice (Fig. 1B1). The proportion of ­GABAAR+/ MoFNS + neurons, however, differed significantly between groups ­(F(2,9) = 6.1, p = 0.021; n = 3–6 mice per group) and was significantly greater in the SD group (65.34 ± 6.57%) f ed ared R of re r g- eing o he nce u- eing mu- n in R s ed ps ons ote t f nce tes nifi- e to ost ow- As determined in the fluorescent microscopic image stacks of optical sections (Fig. 2A–C), a proportion of the MoFNS + neurons appeared to be positively immu- nostained for the ­GABAAR over the plasma membrane As determined in the fluorescent microscopic image stacks of optical sections (Fig. 2A–C), a proportion of the MoFNS + neurons appeared to be positively immu- nostained for the ­GABAAR over the plasma membrane in all mice (Fig. 1B1). The proportion of ­GABAAR+/ MoFNS + neurons, however, differed significantly between groups ­(F(2,9) = 6.1, p = 0.021; n = 3–6 mice per group) and was significantly greater in the SD group (65.34 ± 6.57%) 1 3 3168 Brain Struct Funct (2017) 222:3163–3178 as compared to the SC group (32.34 ± 7.38%, post hoc paired comparison p = 0.008) and in a trend as compared ­GABAAR immunostaining on the plasma membrane of ­GABAAR+/MoFNS + neurons was also significantly dif- Fig. 2   Fluorescent microscopic images of ­GABAARs in Mo5 neu- rons across groups. GABAARs on Mo5 neurons after SD and SR 2A–C), the average luminance measures of the 1 3 Brain Struct Funct (2017) 222:3163–3178 3169 Fig. 3   Confocal microscopic images of ­GABAARs in Mo5 neurons across groups. Images of single optical sections show large Mo5 neurons stained for Nissl with FNS (green, A1, B1, C1) and immu- nostained for the ­GABAAR (red, indicated by arrowheads) in single (A2, B2, C2) and merged images (A3, B3, C3). The ­GABAAR immu- nofluorescence is evident over the plasma membrane, as very dim in the SC mouse (MST24), as very bright in the SD mouse (MST2), and as less bright in the SR mouse (MST11) than in the SD mouse. In all cases, the immunostaining is relatively continuous though with nonuniform intensity along the plasma membrane of the soma and proximal dendrites of the Mo5 neurons. Note that particularly in the SD mouse, the ­GABAAR immunostaining is prominent on the mem- brane of large dendrites cut in cross section. Scale bar 20 μm. Optical image thickness: 0.5 μm Fig. 3   Confocal microscopic images of ­GABAARs in Mo5 neurons across groups. Images of single optical sections show large Mo5 neurons stained for Nissl with FNS (green, A1, B1, C1) and immu- nostained for the ­GABAAR (red, indicated by arrowheads) in single (A2, B2, C2) and merged images (A3, B3, C3). The ­GABAAR immu- nofluorescence is evident over the plasma membrane, as very dim in the SC mouse (MST24), as very bright in the SD mouse (MST2), and as less bright in the SR mouse (MST11) than in the SD mouse. In all cases, the immunostaining is relatively continuous though with nonuniform intensity along the plasma membrane of the soma and proximal dendrites of the Mo5 neurons. Note that particularly in the SD mouse, the ­GABAAR immunostaining is prominent on the mem- brane of large dendrites cut in cross section. Scale bar 20 μm. Optical image thickness: 0.5 μm cells per condition, Fig. 1B2) and was significantly higher in SD (45.63 ± 2.61) as compared to SC (36.26 ± 2.53, post hoc paired comparison, p = 0.023) and SR groups (28.67 ± 1.84, p < 0.001). GABABRs on Mo5 neurons after SD and SR cells per condition, Fig. 1B2) and was significantly higher in SD (45.63 ± 2.61) as compared to SC (36.26 ± 2.53, post hoc paired comparison, p = 0.023) and SR groups (28.67 ± 1.84, p < 0.001). Immunostaining for the ­GABABR was examined on the Mo5FNS + neurons in brains from mice of the SC, SD and SR groups (Fig. 4A–C). As evident in the fluorescent microscopic images and in the higher resolution confocal 1 3170 Brain Struct Funct (2017) 222:3163–3178 Fig. 4   Fluorescent microscopic images of ­GABABRs in Mo5 neu- rons across groups. Images of single optical sections show several large Mo5 neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the ­GABABR (red, A2, B2, C2) within the Mo5 nucleus of each mouse. Through the one optical section shown, ­GABABR immunofluorescence is clearly visible over the cytoplasm of all Mo5 neurons of which one representative one is magnified for each mouse (A3, B3, C3, indicated by arrowheads). In the SC mouse (MST21), the ­GABABR immunofluorescence is moderately bright, whereas in the SD mouse (MST20), it is very bright, and in the SR mouse (MST8), it is also moderately bright and similar to that in the SC mouse. For measurement of the intensity of the ­GABABR immu- nofluorescence, a donut-shaped contour was traced around the peri- karyon to include all the cytoplasm and plasma membrane, and for that of the background fluorescence for subtraction, a spherical con- tour to contain the nucleus of each cell (A3, B3, C3, see Methods). Scale bars 20 μm. Optical image thickness: 0.5 μm Fig. 4   Fluorescent microscopic images of ­GABABRs in Mo5 neu- rons across groups. Images of single optical sections show several large Mo5 neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the ­GABABR (red, A2, B2, C2) within the Mo5 nucleus of each mouse. Through the one optical section shown, ­GABABR immunofluorescence is clearly visible over the cytoplasm of all Mo5 neurons of which one representative one is magnified for each mouse (A3, B3, C3, indicated by arrowheads). In the SC mouse (MST21), the ­GABABR immunofluorescence is moderately bright, whereas in the SD mouse (MST20), it is very bright, and in the SR mouse (MST8), it is also moderately bright and similar to that in the SC mouse. GABABRs on Mo5 neurons after SD and SR For measurement of the intensity of the ­GABABR immu- nofluorescence, a donut-shaped contour was traced around the peri- karyon to include all the cytoplasm and plasma membrane, and for that of the background fluorescence for subtraction, a spherical con- tour to contain the nucleus of each cell (A3, B3, C3, see Methods). Scale bars 20 μm. Optical image thickness: 0.5 μm cytoplasm extending from the nucleus out to the periph- ery and in some cases near the plasma membrane of the soma and proximal dendrites. The specific association microscopic images of the same material (Fig. 5A–C), ­GABABR immunostaining appeared over granules or vesicles of different sizes which were evident through the 1 3 3 3171 Brain Struct Funct (2017) 222:3163–3178 3171 Brain Struct Funct (2017) 222:3163 3178 l Fig. 5   Confocal microscopic images of ­GABABRs in Mo5 neurons across groups. Confocal images of fluorescent stained sections show Mo5 neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the ­GABABR (red, indicated by arrowheads) in single (A2, B2, C2) and merged images (A3, B3, C3). In the mice from all three groups, the ­GABABR immunofluorescence is visible as small to large granules or vesicles, which are distributed through the cytoplasm out to the plasma membrane of the Mo5 neurons. Differ- ing in density and intensity, these granules appear to be more dense and bright in the SD mouse (MST20), as compared to the SC mouse (MST21). In the SR mouse (MST11), they are lesser than in the SD mouse. Scale bars 20 μm. Optical image thickness: 0.5 μm Fig. 5   Confocal microscopic images of ­GABABRs in Mo5 neurons across groups. Confocal images of fluorescent stained sections show Mo5 neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the ­GABABR (red, indicated by arrowheads) in single (A2, B2, C2) and merged images (A3, B3, C3). In the mice from all three groups, the ­GABABR immunofluorescence is visible as small to large granules or vesicles, which are distributed through the cytoplasm out to the plasma membrane of the Mo5 neurons. Differ- ing in density and intensity, these granules appear to be more dense and bright in the SD mouse (MST20), as compared to the SC mouse (MST21). In the SR mouse (MST11), they are lesser than in the SD mouse. Scale bars 20 μm. AChM2Rs on Mo5 neurons after SD and SR Immunostaining for the AChM2R was examined on the MoFNS + neurons across the three groups of mice (Fig. 6A–C). As evident in the fluorescent microscopic images and in the higher resolution confocal microscopic images of the same material (Fig. 7A–C), the AChM2R immunostaining was observed over the plasma membrane of the soma and dendrites of the Mo5 neurons. It appeared to extend along the entire membrane of most cells though to vary in intensity, appearing most intense in the brains of the SD group of mice.l As determined in the fluorescent microscopic image stacks of optical sections (Fig. 6A–C), all MoFNS + neu- rons were judged to be positively immunostained for the AChM2R on the plasma membrane of the soma and proxi- mal dendrites (100%, n = 3 to 6 mice per group, Fig. 1D1). On the other hand, as measured in the same fluorescent microscopic image stacks (Fig. 6A–C), the luminance of the AChM2R immunofluorescence over the membrane of the AChM2R+/MoFNS + cells was significantly differ- ent between groups ­(F(2,117) = 16.34, p < 0.001; n = 30 to 60 cells per group, Fig. 1D2) and was significantly greater in the SD (96.41 ± 3.90) as compared to SC (58.71 ± 4.27, post hoc paired comparison p < 0.001) and SR groups (75.47 ± 6.56, p = 0.002). Pharmacological evidence indicates that the ­GABAAR together with the glycine receptor on motor neurons is implicated in the muscle hypotonia and atonia that respec- tively occur during SWS and REMS (Brooks and Peever 2012; Morrison et  al. 2003; Soja et  al. 1987). Indeed, mutant mice with deficient ­GABAA and glycine receptors present symptoms of incomplete muscle atonia and motor inhibition with aberrant twitches and movements during SWS and REMS that resemble the symptoms of REMS behavior disorder in humans (Brooks and Peever 2011). Hypertonic mutant mice were also shown to harbor defi- cient ­GABAARs in the CNS and on motor neurons, such as to suggest that dysregulation of ­GABAAR homeostasis can cause hypertonia in multiple clinical disorders (Gil- bert et al. 2006). Here, we present evidence that ­GABAARs are normally homeostatically regulated on motor neurons according to activity and state. GABABRs on Mo5 neurons after SD and SR immunofluorescence in the perikarya of the ­GABABR+/ MoFNS + somata was significantly different between groups ­(F(2,117) = 9.35, p < 0.001; n = 30 to 60 cells per group) (Fig. 1C2) being significantly higher in the SD (46.97 ± 2.11) as compared to the SC (32.26 ± 2.99, post hoc paired comparison p < 0.001) and SR groups (36.45 ± 3.07, p = 0.005). immunofluorescence in the perikarya of the ­GABABR+/ MoFNS + somata was significantly different between groups ­(F(2,117) = 9.35, p < 0.001; n = 30 to 60 cells per group) (Fig. 1C2) being significantly higher in the SD (46.97 ± 2.11) as compared to the SC (32.26 ± 2.99, post hoc paired comparison p < 0.001) and SR groups (36.45 ± 3.07, p = 0.005). Homeostatic regulation through ­GABABRs GABABRs were apparent through the cytoplasm of all Mo5 neurons; however the luminance of the ­GABABRs was higher in SD than in the SC and SR groups. Given a lack of resolution to distinguish receptor labeling over the plasma membrane, the increased immunostaining for the R1 subunit cannot be inferred to represent an increase in functional ­GABABRs but only an increased expression or trafficking of these receptors within intracellular organelles. Nonetheless, the increased expression during SD suggests a contribution of the ­GABABR to homeostatic down-scaling Discussion The present results indicate that ­GABAA, ­GABAB and AChM2 receptors increase in Mo5 neurons with enforced waking during the day when mice normally sleep the majority of the time. The results suggest that the Mo5 neu- rons undergo homeostatic down-scaling in their excitability through increases in inhibitory receptors following pro- longed activity during SD. GABABRs on Mo5 neurons after SD and SR Optical image thickness: 0.5 μm As determined in the fluorescent microscopic image stacks of optical sections (Fig. 4A–C), all MoFNS + neu- rons were judged to be positively immunostained for the ­GABABR through their cytoplasm in all groups (100%, n = 3–6 mice per group, Fig. 1C1). On the other hand, as measured in the same fluorescent microscopic image stacks (Fig. 4A–C), the luminance of the ­GABABR of these granules with the plasma membrane, however, could not be adequately resolved to be distinguished from the granules distributed through the cytoplasm. The den- sity and intensity of the granular immunostaining through the cytoplasm however appeared to vary across neurons and mice and to be consistently greatest in the SD group of mice. 1 3172 Brain Struct Funct (2017) 222:3163–3178 ­GABAARs following enforced waking and presumed pro- longed activity during SD. These increases following SD are similar to those seen on orexin neurons, which are also active during waking and silent during sleep. They are opposite to decreases in ­GABAARs seen on MCH neurons, which are silent during waking and active during sleep (Toossi et al. 2016b). The increases in ­GABAARs follow- ing SD are also similar to the increases in ­GABAARs seen in vitro and in vivo on cortical neurons pharmacologically or electrophysiologically stimulated to fire continuously at high rates (Marty et al. 2004; Nusser et al. 1998). More- over, increases in the density of the ­GABAARs in these experiments were shown to be associated with increases in inhibitory postsynaptic currents (IPSCs). The increased clusters of the ­GABAAR on the membrane seen here thus likely correspond to increases in functional receptors. Reciprocally, pharmacologically induced cessation of fir- ing in vitro led to a decrease of ­GABAARs on the mem- brane associated with a decrease in miniature IPSCs (Marty et al. 2004; Kilman et al. 2002). Similarly here, the density of ­GABAARs was reduced to return to SC levels following SR, when the Mo5 neurons would be mostly silent during increased SWS and REMS. immunofluorescence in the perikarya of the ­GABABR+/ MoFNS + somata was significantly different between groups ­(F(2,117) = 9.35, p < 0.001; n = 30 to 60 cells per group) (Fig. 1C2) being significantly higher in the SD (46.97 ± 2.11) as compared to the SC (32.26 ± 2.99, post hoc paired comparison p < 0.001) and SR groups (36.45 ± 3.07, p = 0.005). Homeostatic regulation through ­GABAARs In immunofluorescent stained sections, ­GABAARs were apparent on the plasma membrane in a proportion of the Mo5 neurons, which was much higher in the SD group than in the SC group, and for which the luminance or den- sity was also higher, indicating increases in membrane 3 3173 Brain Struct Funct (2017) 222:3163–3178 ( ) Fig. 6   Fluorescent microscopic images of AChM2Rs in Mo5 neu- rons across groups. Images of single optical sections show sev- eral motor neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the AChM2R (red, A2, B2, C2) within the Mo5 nucleus of each mouse. Through one optical section, AChM2R immunofluorescence is noticeably visible on the membrane of all Mo5 neurons, of which one is magnified for each mouse (A3, B3, C3, indicated by filled arrowheads). In the SC mouse (MST21), the AChM2R immunofluorescence is relatively dim, whereas in the SD mouse (MST2), it is very bright, and in the SR mouse (MST22), it is less bright than in the SD mouse. For measurement of the intensity of the AChM2Rs immunofluorescence, a small rectangular box was placed over the plasma membrane and for that of the fluorescence background for subtraction, another over the nucleus of each cell (A3, B3, C3, see Methods). Scale bars 20 μm. Optical image thickness: 0.5 μm Fig. 6   Fluorescent microscopic images of AChM2Rs in Mo5 neu- rons across groups. Images of single optical sections show sev- eral motor neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the AChM2R (red A2 B2 C2) within the AChM2R immunofluorescence is relatively dim, whereas in the SD mouse (MST2), it is very bright, and in the SR mouse (MST22), it is less bright than in the SD mouse. For measurement of the intensity of the AChM2Rs immunofluorescence a small rectangular box was Fig. 6   Fluorescent microscopic images of AChM2Rs in Mo5 neu- rons across groups. Images of single optical sections show sev- eral motor neurons stained for Nissl with FNS (green, A1, B1, C1) and immunostained for the AChM2R (red, A2, B2, C2) within the Mo5 nucleus of each mouse. Through one optical section, AChM2R immunofluorescence is noticeably visible on the membrane of all Mo5 neurons, of which one is magnified for each mouse (A3, B3, C3, indicated by filled arrowheads). Homeostatic regulation through ­GABAARs In the SC mouse (MST21), the AChM2R immunofluorescence is relatively dim, whereas in the SD mouse (MST2), it is very bright, and in the SR mouse (MST22), it is less bright than in the SD mouse. For measurement of the intensity of the AChM2Rs immunofluorescence, a small rectangular box was placed over the plasma membrane and for that of the fluorescence background for subtraction, another over the nucleus of each cell (A3, B3, C3, see Methods). Scale bars 20 μm. Optical image thickness: 0.5 μm Pharmacological evidence has shown that ­GABABRs in addition to the glycine and ­GABAA receptors are implicated in muscle hypotonia and atonia of sleep and that only with antagonism of all three receptors can com- plete muscle atonia be prevented (Brooks and Peever in the excitability of the motor neurons with enforced wak- ing. We recently found that SD induced a similar increase of ­GABABRs in orexin neurons which fire during waking, whereas it induced a decrease in ­GABABRs on MCH neu- rons, which are silent during waking (Toossi et al. 2016b). in the excitability of the motor neurons with enforced wak- ing. We recently found that SD induced a similar increase of ­GABABRs in orexin neurons which fire during waking, whereas it induced a decrease in ­GABABRs on MCH neu- rons, which are silent during waking (Toossi et al. 2016b). 1 3 3174 Brain Struct Funct (2017) 222:3163–3178 Fig. 7   Confocal microscopic images of AChM2Rs in Mo5 neurons across groups. Images of single optical sections show large Mo5 neurons stained for Nissl with FNS (green, A1, B1, C1) and immu- nostained for the AChM2R (red, indicated by arrowheads) in single (A2, B2, C2) and merged images (A3, B3, C3) for each mouse. The AChM2R immunofluorescence is evident over the plasma mem- brane in all three mice, though just barely visible in the SC mouse (MST21). In the SD mouse (MST2), the AChM2R staining is very bright and clearly visible along the full membrane of the soma and proximal dendrites. In the SD mouse, it is also prominent on the plasma membrane of the large dendrites which are cut in cross sec- tion. In the SR mouse (MST8), the staining is less bright than in the SD mouse. Scale bars 20 μm. Optical image thickness: 0.5 μm Fig. 7   Confocal microscopic images of AChM2Rs in Mo5 neurons across groups. Role of GABA in regulating muscle tone across sleep‑wake states markedly increased following SD, presumably due to pro- longed activity of the Mo5 neurons during enforced wak- ing, and then returned to SC levels following SR, presum- ably due to quiescence of the Mo5 neurons during sleep. These changes are interpreted as a homeostatic response to enhanced neuronal activity, which to our knowledge, have not previously been described for AChMRs. GABA and GABAergic neurons have been shown to play roles in sleep including SWS, PS or REMS and associated muscle hypotonia or atonia (Boissard et al. 2002; Holmes and Jones 1994; Maloney et al. 1999, 2000; Xi et al. 1999; Jones 1991; Weber et al. 2015; Krenzer et al. 2011). Jux- tacellular recording and labeling of neurons located in the region of the laterodorsal and sublaterodorsal tegmental nuclei (LDT and SubLDT) identified GABAergic neurons that fire at increasingly higher rates during SWS and PS relative to waking and in negative correlation with neck muscle tone (Boucetta et al. 2014). Motor neurons receive GABAergic and glycinergic input from local interneurons in the brainstem and spinal cord. They also receive such input from projecting neurons as was demonstrated in the Mo5 neurons as monosynaptic inhibitory input from neu- rons in the medullary reticular formation (Chase et  al. 1984), where both GABAergic and glycinergic neurons are located (Holmes et al. 1994; Jones et al. 1991; Rampon et al. 1996). They discharged at progressively higher rates during SWS and REM as compared to waking in a man- ner reciprocally related to the increasing inhibition of the Mo5 neurons during sleep (Chase et al. 1984) and thus in a manner similar to identified GABAergic neurons in the pons (Boucetta et  al. 2014). Such identified GABAergic pontine and presumed GABAergic (or glycinergic) medul- lary neurons could thus be responsible for the progressive inhibition of motor neurons during sleep, culminating in that during PS or REMS. Pharmacological evidence has indicated that ACh partic- ipates in the muscle atonia of REMS through M2 receptors on Mo12 neurons (Grace et al. 2013a). Acting upon GIRK channels, ACh inhibits spinal motor neurons through M2Rs (Chevallier et al. 2006; Miles et al. 2007), which have also been visualized here and in previous studies upon the post- synaptic membrane of Mo5 neurons opposite cholinergic terminals (Hellstrom et  al. 2003; Brischoux et  al. 2008). The Mo5 neurons could thus be homeostatically regu- lated following enforced waking by down-scaling through increases in inhibitory AChM2Rs. Homeostatic regulation through ­GABAARs Images of single optical sections show large Mo5 neurons stained for Nissl with FNS (green, A1, B1, C1) and immu- nostained for the AChM2R (red, indicated by arrowheads) in single (A2, B2, C2) and merged images (A3, B3, C3) for each mouse. The AChM2R immunofluorescence is evident over the plasma mem- brane in all three mice, though just barely visible in the SC mouse (MST21). In the SD mouse (MST2), the AChM2R staining is very bright and clearly visible along the full membrane of the soma and proximal dendrites. In the SD mouse, it is also prominent on the plasma membrane of the large dendrites which are cut in cross sec- tion. In the SR mouse (MST8), the staining is less bright than in the SD mouse. Scale bars 20 μm. Optical image thickness: 0.5 μm the ­GABABR results in a disrupted sleep-waking cycle (Vienne et al. 2010) and hyper locomotor activity along with seizures (Schuler et  al. 2001). The present results suggest that homeostatic regulation of the ­GABABR in motor neurons may be important in down-scaling their excitability during prolonged activity with SD. 2012). In vitro evidence has indicated that the ­GABABR is essential for homeostatic regulation of firing within hippocampal circuits (Vertkin et  al. 2015). Compensa- tory increases in ­GABABR immunostaining have been reported in dentate gyrus of mice in response to recur- rent seizures (Straessle et al. 2003). Genetic deletion of 1 3 3 3175 Brain Struct Funct (2017) 222:3163–3178 Role of GABA in regulating muscle tone across sleep‑wake states Such increases in these receptors would render the motor neurons more susceptible to inhibition by ACh and thus the muscles to atonia. Role of ACh in regulating muscle tone across sleep‑wake states ACh has long been known to play an important role in wak- ing and PS or REMS, including muscle atonia as evidenced by severe reduction or elimination of PS following lesions of the LDT/PPT cholinergic neurons (Webster and Jones 1988) and induction of PS or REMS by administration of cholinergic agonists into the pontine reticular formation, an effect which is dependent upon AChM2Rs (Baghdoyan and Lydic 1999; Velazquez-Moctezuma et al. 1989). ACh can apparently play this role in part through direct influence on motor neurons, which for the Mo5 and Mo12, have been shown to receive input from cholinergic neurons of the LDT and pedunculopontine tegmental (PPT) nuclei and of the medullary reticular formation (Jones 1990; Woolf and Butcher 1989; Rukhadze and Kubin 2007; Fort et al. 1990). Cholinergic neurons of LDT/PPT discharge during waking and PS and are silent during SWS (Boucetta et al. 2014). They could thus exert an inhibitory influence through AChM2Rs during PS, but also during waking. According to the pharmacological studies on Mo12 neurons, how- ever, antagonism of muscarinic receptors only affects the muscle atonia of REMS and not the level of muscle tone during waking or SWS (Grace et  al. 2013a), suggesting differences that might in part be due to the density of the AChM2Rs. Accordingly, the homeostatic increase in ACh- M2Rs on motor neurons following SD could contribute to the increased propensity in waking to cataplexy and paral- ysis following sleep deficits in patients having narcolepsy with cataplexy (Nishino and Mignot 1997). Indeed, the sleep cycle of these patients is greatly disrupted and often Here, the increase in both ­GABAA and ­GABAB recep- tors following prolonged waking would suggest that motor neurons would become progressively more responsive to GABA released during waking and sleep and accordingly more susceptible to inhibition and resulting muscle hypo- tonia and atonia with SD. Such homeostatic changes could underlie the increases in muscle atonia that occur during SWS following SD (Werth et al. 2002) and the increased propensity to cataplectic attacks and paralysis with sleep deficiency or disruption in patients having narcolepsy with cataplexy (Nishino and Mignot 1997). Moreover, daytime cataplectic attacks can be prevented in these patients by administration during the night of gamma hydroxybutyrate (GHB), a ­GABABR agonist, which allows consolidation of sleep during the night (Boscolo-Berto et al. 2012), pre- sumably associated as suggested here, with decreases of ­GABABRs to normal levels on motor neurons. Homeostatic regulation through AChM2Rs Although AChM2Rs were apparent on the plasma mem- brane of all Mo5 neurons, the luminance of the AChM2Rs 1 3 3176 Brain Struct Funct (2017) 222:3163–3178 mesopontine tegmentum and their potential role in sleep-wake state control. J Comp Neurol 510(6):607–630. doi:10.1002/ cne.21803 associated with insomnia during the night, which according to our results could result in increased AChM2, along with ­GABAA and ­GABAB, receptors on motor neurons during the day. Brooks PL, Peever JH (2008) Glycinergic and GABA(A)-mediated inhibition of somatic motoneurons does not mediate rapid eye movement sleep motor atonia. J Neurosci 28(14):3535–3545. doi:10.1523/JNEUROSCI.5023-07.2008 We conclude that Mo5 neurons are homeostatically reg- ulated across the sleep-waking cycle through changes in the inhibitory receptors for GABA and ACh. Their prolonged activity during enforced waking with SD results in homeo- static down-scaling through increases in ­GABAA, ­GABAB and AChM2Rs and their subsequent quiescence with SR in restorative up-scaling to return the neurons to normal sta- ble levels of excitability and activity. The increases in these inhibitory receptors following SD would render the motor neurons more responsive and thus susceptible to inhibition by GABA and ACh, which would also render the muscles more susceptible to hypotonia or atonia, as can occur with sleep deficits and particularly in association with sleep dis- orders, such as narcolepsy with cataplexy. 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J Neurophysiol 44(2):349–358 Acknowledgements  We thank Lynda Mainville for her technical assistance and Anton Plavski for his participation in the experiments. The research was supported by a research grant (to B.E.J.) from the Canadian Institutes of Health Research (CIHR MOP-130502). Homeostatic regulation through AChM2Rs Chase MH, Enomoto S, Hiraba K, Katoh M, Nakamura Y, Sahara Y, Taira M (1984) Role of medullary reticular neurons in the inhibi- tion of trigeminal motoneurons during active sleep. Exp Neurol 84(2):364–373 Open Access  This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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Biomass production, carbon stock and sequestration potential of prominent agroforestry systems in north-western Himalaya, India
Frontiers in forests and global change
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OPEN ACCESS OPEN ACCESS EDITED BY Donald Mlambo, National University of Science and Technology, Zimbabwe REVIEWED BY Gopal Shukla, Uttar Banga Krishi Viswavidyalaya, India Bhupendra Singh, VCSG Uttarakhand University, India *CORRESPONDENCE Nazir A. Pala nazirpaul@gmail.com RECEIVED 23 March 2023 ACCEPTED 30 August 2023 PUBLISHED 14 November 2023 CITATION Saleem I, Mugloo JA, Pala NA, Bhat GM, Masoodi TH, Mughal AH, Baba AA and Mehraj B (2023) Biomass production, carbon stock and sequestration potential of prominent agroforestry systems in north-western Himalaya, India. Front. For. Glob. Change 6:1192382. doi: 10 3389/ffgc 2023 1192382 EDITED BY Donald Mlambo, National University of Science and Technology, Zimbabwe REVIEWED BY Gopal Shukla, Uttar Banga Krishi Viswavidyalaya, India Bhupendra Singh, VCSG Uttarakhand University, India Ishrat Saleem 1, J. A. Mugloo 2, Nazir A. Pala 1*, G. M. Bhat 1, T. H. Masoodi 3, A. H. Mughal 3, Afshan A. Baba 4 and Basira Mehraj 5 1 Division of Silviculture and Agroforestry, Faculty of Forestry SKUAST-K, Malangpora, Jammu and Kashmir, India, 2 KVK, Directorate of Research, Malangpora, Jammu and Kashmir, India, 3 Directorate of Research, Malangpora, Jammu and Kashmir, India, 4 Division of FPU, Malangpora, Jammu and Kashmir, India, 5 Division of NRM-SKUAST-Kashmir, Srinagar, Jammu and Kashmir, India Agroforestry is an age-old practise of integrating farming with practises, preferably on the same unit of land on sustainable basis. There is tremendous scope for Agroforestry because India has achieved self-sufficiency in food production. Now its attention is becoming more focused on the ecological problems and shortage of fuel, fodder and other outputs as well as unemployment. So, agroforestry land use systems offer a better option by serving as carbon sinks and contributing in attaining food safety, subsistence income, and habitat amelioration. The current study was conducted in this context in the south Kashmir area of India with the objective of recognising the capability of various agroforestry systems for biomass estimation and carbon sequestration assessment for mitigating climate variation. The present study entitled “Biomass production, carbon stock and sequestration potential of prominent agroforestry systems in North-western Himalaya, India” was carried out, during 2018–2019. The study site is located between 33° 72’N and 75° 14’E at an altitude ranging from 2,900 to 5,900  M (amsl). Multistage random sampling technique was used for selection of sampled tehsils, blocks, villages and farmers in Anantnag district. frontiersin.org Frontiers in Forests and Global Change TYPE  Original Research PUBLISHED  14 November 2023 DOI  10.3389/ffgc.2023.1192382 TYPE  Original Research PUBLISHED  14 November 2023 DOI  10.3389/ffgc.2023.1192382 TYPE  Original Research PUBLISHED  14 November 2023 DOI  10.3389/ffgc.2023.1192382 1. Introduction The soil and plant biomass that make up the large terrestrial carbon pool have the ability to take in and store atmospheric carbon through photosynthesis (Kaul et al., 2010). Agroforestry is the deliberate coexistence of woody vegetation with agricultural crops, grasses, or farm animals on the same plot of land to benefit the environment, the economy, and society (Rapidel et al., 2015; Armengot et al., 2020). Agroforestry systems have different structural and functional compositions depending upon the temperature, elevation, soil structure, and rainfall pattern (Rajput et  al., 2017; Chisanga et al., 2018; Singh et al., 2019; Birhane et al., 2020; Salve and Bhardwaj, 2020; Nath et al., 2022; Sharma et al., 2022). Given the significance of this activity, India developed a national agroforestry plan in 2014 to promote the full spread of agroforestry practises. The Green India Mission has also noticed agroforestry interferences. The promise of agroforestry to mitigate climate and assist farmers in adapting to its effects is a key driving force behind India’s agroforestry programme. The Green India Mission has also noticed agroforestry interferences. The potential of agroforestry to slow climate change and help farmers adapt to its impacts is a major impetus behind India’s agroforestry plan. As evidenced by the multiple-purpose trees (such as fodder, fruit, fuelwood, and timber trees) purposefully retained on farm bunds (Semere, 2019; Chavan et al., 2020), agroforestry has been practised historically for as long as anyone can remember. It also plays a significant role in preserving sustainability in farming systems (Chandra and Singh, 2018). Agroforestry has been identified as having the greatest potential for carbon sequestration among all the land uses that were the subject of the Land-Use, Land-Use Change, and Forestry (LULUCF) report’s research (Nair and Garrity, 2012). Agroforestry is receiving increased attention in global initiatives like Reducing Emissions from Deforestation and Forest Degradation (REDD) because of its implication in improving and regulating climate variability (Jose and Bardhan, 2012). It is well known that forestry can improve carbon sinks and lower CO2 emissions, thus playing a crucial role in carbon cycling and aids in mitigating climate change (Besar et al., 2020; Sarkar et al., 2021). However, the dynamics of nutrients (carbon and nitrogen) in the terrestrial environment were affected by rapid increases in urbanisation and anthropogenic activity (deforestation, land use change, biodiversity loss, and forest degradation; Dhyani et al., 2021; Mey and Gore, 2021; Kumar et al., 2022). 1. Introduction non-forested environments like agricultural land, have a important impact on process. Productivity in plantation is higher (3.2 Mg ha/1 year) than productivity of natural forest (1.1 Mg ha/1 year), so it can benefit from better silvicultural techniques than a wild forest (Lal and Singh, 2000). Additionally, resource management through agroforestry may offer a natural way to synchronise the implementation of adaptation and mitigation measures with the satisfaction of forest-based needs (Komal et al., 2022). Agroforestry has been acknowledged as a GHG mitigation strategy under the Kyoto Protocol because it is an integrated approach (Birhane et  al., 2020; Das et  al., 2020; Sarkar et  al., 2021). This recognition is based on carbon capture and utilisation efficiency leading to greater carbon sequestration (Das et al., 2020; Semere et al., 2022). In the modern era of global warming, interconnected climate indicators provide a comprehensive view of climate change and the rising threats to the Sustainable Development Goals (SDGs) affecting environmental, social, and economic systems. Carbon dioxide (CO2) is the principal greenhouse gas (GHG) produced as a result of anthropogenic activity and the cumulative impact of humans during the past, along with industrialisation (Malhi et al., 2021; Zandalinas et al., 2021). The well-known “greenhouse effect” is the link between CO2 and global warming that leads to climate change (Anderson et al., 2016). According to the WMO (2021), the amount of CO2 concentration in the earth’s atmosphere is around 413.20 0.2 ppm, and 55% of it is absorbed by oceans and land vegetation. Since the middle of the 20th century, anthropogenic landscape activity has been a significant contributor to climate change, which accelerated in 2020 and 2021 despite a 5.6% decrease in fossil fuel CO2 emissions as a result of COVID-19 pandemic restrictions (WMO, 2021). Climate change and the rise in land-use conflicts necessitate the creation of sustainable land-use systems that balance agricultural production with the provisioning of several ecological services. According to global estimates, land use interventions help reduce emissions by roughly 30% through the process of carbon sequestration and are crucial for achieving the carbon reduction goal set by the COP-25 summit (Aynekulu et al., 2020). According to Mangalassery et al. (2014), carbon capture has been considered as a way to help minimise the rising CO2 accumulation in the environment. OPEN ACCESS The results of the current study could have a big impact on how alternative agroforestry systems and tree combinations are chosen for efficient carbon budget management in delicate Himalayan ecosystems. OPEN ACCESS The first stage was the random sampling of six tehsils namely Anantnag, Shangus, Kokernag, Dooru, Sallar, and Larnu and blocks per tehsil namely, viz.; Anantnag, Shangus, Sagam, Shahabad, Pahalgam and Larnu. Then four villages within each block like Anantnag (Ruhoo, Dialgam, Wanihama and Donipawa), Shangus (Shangus, Nowgam, Kutheir and Andoora), Sagam (Hiller, Khalhar, Sagam and Bidder), Shahabad (Larkipora, Shankerpora, Nathipora and Bragam), Pahalgam (Yanner, Charigam, Movra and Wahdan) and Larnu (Leesu, Dandipora, Bidhard and Larnu). Ten farmers within each village were selected, thus making a total of 240 farmers, which accounts 25% sampling intensity. Four agroforestry systems including horti-agriculture, agrisilviculture, (boundary planting), agri-horti-silviculture and horti-silvipasture were chosen for the study as the experimental configuration. Maximum biomass was found in horti-silvipastoral contributing 66.55  t  ha−1 followed by agri-horti-silviculture as 50.18  t ha−1, horti-agriculture as 36.22 t  ha−1 and agri-silviculture as 34.87 t ha−1. The maximum mean biomass of fruit trees (30.54  t  ha−1), forest trees (25.19 t ha−1), grass (7.18 t  ha−1) during the first cut and 3.64  t  ha−1 during the second cut, was calculated in horti-silvipasture system. The overall biomass output of diverse agroforestry systems goes along with the sequence: horti-silvipasture  > agri- horti-silviculture  > horti-agriculture  >  boundary plantation, respectively. As a result, estimates of carbon stocks and carbon sequestration for all systems showed the same trend as values for biomass since they are both directly related to the capacity for biomass generation of various plant components. By providing for rural livelihoods and serving as an efficient carbon sink through carbon Front. For. Glob. Change 6:1192382. doi: 10.3389/ffgc.2023.1192382 Front. For. Glob. Change 6:1192382. doi: 10.3389/ffgc.2023.1192382 COPYRIGHT © 2023 Saleem, Mugloo, Pala, Bhat, Masoodi, Mughal, Baba and Mehraj. This is an open- access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Frontiers in Forests and Global Change Frontiers in Forests and Global Change 01 Saleem et al. 10.3389/ffgc.2023.1192382 10.3389/ffgc.2023.1192382 sequestration, these agroforestry systems in the Himalayas can significantly increase total production and productivity. Frontiers in Forests and Global Change frontiersin.org Himalaya, climate, landuse, energy, greenhouse KEYWORDS Himalaya, climate, landuse, energy, greenhouse 2.1. Study site The study area is situated in the southern region of Kashmir covering Anantnag district of Jammu and Kashmir, India. The district is 33 miles (53 km) away from Srinagar (the capital city), and is situated between 33o 20′ and 34o15’ N latitude and 74o30’ and 75o35’ E longitude. There is a mild climate in Anantnag (Koppen climate classification). As per Koppen climate classification, district Anantnag is having a mild climate compared to other regions of Kashmir valley Geographical factors like the Karakoram range to its east and the Pir Panjal range to its south greatly influence its climate. A typical description of the climate is that it is cool in the spring and the autumn season, warm in the summer, and frigid in the winter. The region has a temperate climate, with substantial winter snowfall occurring in the higher elevations. The entire southern sector of the study area, which borders the Jammu province tehsils of Reasi, Banihal, and Kishtwar, as well as the eastern sector, which borders the Ladakh division tehsil of Kargil. Pulwama district borders its northern and western sides, and Kulgam district is located on its western side. Anantnag has the most streams (Nallas) in Kashmir valley including Sandran, Brengi, Arpath, and Lidder,. Lidder, which emerges from Sheshnag Lake and irrigates the largest territory in the district, is the most significant of these. The Anantnag district has a wide intermountain valley and is hilly and mountainous in the north-east and south-west. Productivity is vulnerable in higher ranges and fertile in central regions because soil is poor in steep locations and rich in plain areas. Hapludalf is the name given to the medium- to fine-textured soils that have grown on Karewa tops and upland locations. Clay loam soils, which are dark brown in colour, are typical in plains. For different agroforestry systems at different sites, one 20 m × 20 m quadrant was laid for measuring tree biomass and three 1 m × 1 m quadrant were laid within 20 m × 20 m quadrant for measuring crop biomass thus making a total of 240 quadrats for trees and 720 quadrats for crops. During survey across the field, in horti-agriculture system, a total number of 555 trees/ha in combination C1(Apple + radish-kale), 555 trees/ha in combination C2(Apple + kale-chilli), 555 trees/ha in combination C3(Apple + kale-beans) and 80 trees/ha in combination C4(Walnut + oats-maize) were recorded. 1. Introduction A total of 240 households were selected for the field study from the sample villages with a 25% sampling intensity using a basic random sampling technique. Household heads/eldest members were the respondents interviewed during survey programme. agroforestry systems in the region. Keeping this in view, the present investigation was carried out with the objective of quantifying the biomass, carbon stock and carbon sequestration potential of different agroforestry systems in district Anantnag of Kashmir division. The study might be helpful in giving information to decision-framers and agriculturists for efficient and long-term carbon balancing and climate variability mitigation in the temperate region of the Kashmir Himalayan ecosystem. 3.1. Biomass production The study calculated both above- ground and below-ground biomass in trees and crops in all agroforestry systems. The above- ground biomass of several plant components, including stems, branches, leaves, and roots, was estimated. Biomass of forest trees, fruit trees and agricultural crops were calculated separately as below: Frontiers in Forests and Global Change 2.1. Study site In agri-silviculture system (boundary plantation), a total of 138 trees /ha in combination C1(Poplar + salix + oats-paddy) and 160 trees /ha in combination C2(Poplar + mustard-paddy) were documented (Table 1). Also, in agri-horti-silviculture system, a total number of 336 trees/ha (156 fruit trees and 180 forest trees), 380 trees/ha (180 fruit trees and 200 forest trees) and 444 trees/ha (204 fruit trees and 240 forest trees) were recorded in combination C1(Poplar + apple + kale- beans), C2(Poplar + apple + kale-chilli) and C3(Poplar + apple + turnip-kale) respectively. Similarly, in horti-silvipasture system, a total of 753 trees/ha (625 fruit trees and 128 forest trees) and 756 trees/ha (625 fruit trees and 131 forest trees) were recorded in combination C1(Apple + poplar + grasses) and C2(Apple + poplar + salix + grasses) respectively (Table 1). All the above-mentioned trees (forest and fruit trees) and crops were further evaluated for biomass, carbon stock and carbon sequestration potential. In district Anantnag land use land cover category, there is a total of 341 ha dense built-up, 337 ha mixed built-up, 2,176 ha agriculture, 480 ha plantation, 118 ha water bodies, 60 ha wastelands, 196 ha sparse forests and 95 ha dense forests forming a total of 3,803 ha land (Malik, 2012). Nowadays, agroforestry is considered as the primary route to success for farmers and rural residents in the region, thereby generating work and income, ensuring the security of food and nutrition, satisfying other fundamental human requirements and protecting farmers from the effects of climate change (Figure 1). 1. Introduction However, it is impossible to ignore the role that trees outside forests (TOFs) play in enhancing human well-being and offering ecosystem services. In addition to supplying the needs for timber, industry, and livelihoods in both agricultural and human-dominated landscapes, the TOFs will successfully and effectively enable carbon dioxide (CO2) emissions to be offset by the forest ecosystems (Chauhan et al., 2020). Since they constitute one of the major C pools that contribute to global carbon (C) cycling, tree-based land use systems, particularly those in Current study focused on the accurate estimation of carbon stock in the prominent agroforestry systems in the eco-sensitive Himalayan region in order to understand the carbon sequestration potential of 02 frontiersin.org Saleem et al. 10.3389/ffgc.2023.1192382 prevalent in selected representative areas was carried. Six tehsils, namely Anantnag, Shangus, Kokernag, Dooru, Sallar, and Larnu, were chosen out of a total of twelve. The blocks were chosen using a multistage stratified random selection procedure viz.; Anantnag, Shangus, Sagam, Shahabad, Pahalgam and Larnu. Then four villages within each block like Anantnag (Ruhoo, Dialgam, Wanihama and Donipawa), Shangus (Shangus, Nowgam, Kutheir and Andoora), Sagam (Hiller, Khalhar, Sagam and Bidder), Shahabad (Larkipora, Shankerpora, Nathipora and Bragam), Pahalgam (Yanner, Charigam, Movra and Wahdan) and Larnu (Leesu, Dandipora, Bidhard and Larnu). Ten farmers within each village were selected, thus making a total of 240 farmers to document the land use pattern of district Anantnag. A total of 240 households were selected for the field study from the sample villages with a 25% sampling intensity using a basic random sampling technique. Household heads/eldest members were the respondents interviewed during survey programme. prevalent in selected representative areas was carried. Six tehsils, namely Anantnag, Shangus, Kokernag, Dooru, Sallar, and Larnu, were chosen out of a total of twelve. The blocks were chosen using a multistage stratified random selection procedure viz.; Anantnag, Shangus, Sagam, Shahabad, Pahalgam and Larnu. Then four villages within each block like Anantnag (Ruhoo, Dialgam, Wanihama and Donipawa), Shangus (Shangus, Nowgam, Kutheir and Andoora), Sagam (Hiller, Khalhar, Sagam and Bidder), Shahabad (Larkipora, Shankerpora, Nathipora and Bragam), Pahalgam (Yanner, Charigam, Movra and Wahdan) and Larnu (Leesu, Dandipora, Bidhard and Larnu). Ten farmers within each village were selected, thus making a total of 240 farmers to document the land use pattern of district Anantnag. frontiersin.org Frontiers in Forests and Global Change 3.1.1. Forest tree The current research was performed in year 2018–2019 in district Anantnag of Kashmir division. For conducting this study regarding different land use patterns, field survey of all the agroforestry systems Forstem biomass with a diameter tape and a Ravi’s multimeter, the diameter of trees at breast height (dbh) that fell in the 03 Saleem et al. 10.3389/ffgc.2023.1192382 20 m quadrat were measured In order to get the volume using Belowground biomass was measured by using a factor of 0 25 GURE 1 Map of sampled villages of district Anantnag, Kashmir. FIGURE 1 Map of sampled villages of district Anantnag, Kashmir. FIGURE 1 Map of sampled villages of district Anantnag, Kashmir. Belowground biomass was measured by using a factor of 0.25 for forest trees (Schulze, 1983). Thus, biomass of stem wood = specific gravity × volume. For branch biomass on each sample tree, the aggregate number of branches were calculated regardless of size. Belowground biomass was measured by using a factor of 0.25 for forest trees (Schulze, 1983). Thus, biomass of stem wood = specific gravity × volume. For branch biomass on each sample tree, the aggregate number of branches were calculated regardless of size. 20 × 20 m quadrat were measured. In order to get the volume using the Pressler (1854) and Bitterlich (1984) formula, the form factor was computed using the Spiegel relascope. Specific gravity was calculated by using formula proposed by Smith (1954). 04 frontiersin.org Saleem et al. 10.3389/ffgc.2023.1192382 10.3389/ffgc.2023.1192382 10.3389/ffgc.2023.1192382 TABLE 1  Inventory of tree-crop combinations in prominent agroforestry systems in study area. Agroforestry systems Tree crop combinations Tree and crop components Fruit trees Forest trees Avg. ht. (m) (Mean  ±  S.E) Collar dia. (cm) (Mean  ±  S.E) Total no. of trees ha−1 Avg. ht. (m) (Mean ± S.E) dbh (cm) (Mean ± S.E) Total no. 3.1.1. Forest tree of trees ha−1 Horti-agriculture C1 Apple + radish-kale 4.98 ± 0.46 54.5 ± 2.88 555 – – – C2 Apple + kale-chilli 4.73 ± 0.41 42.33 ± 2.27 555 – – – C3 Apple + kale-beans 4.925 ± 0.41 45.5 ± 3.16 555 – – – C4 Walnut + oats-maize 6.85 ± 0.17 50.5 ± 3.0 80 – – – Agri-silviculture (boundary plantation) C1 Poplar + salix + oats-paddy – – – 17.66 ± 1.08 7.5 ± 0.74 55.25 ± 1.24 (Poplar) 50.11 ± 1.50 (Salix) 108 + 30 (Poplar + Salix) C2 Poplar + mustard-paddy – – – 17.92 ± 1.33 55.27 ± 0.79 160 Agri-horti-silviculture (homegardens) C1 Poplar + apple + kale-beans 4.0 ± 0.34 32.5 ± 2.82 156 22.9 ± 1.09 54.5 ± 1.32 180 C2 Poplar + apple + kale-chilli 4.41 + 0.29 40.08 + 2.81 180 18.7 ± 1.61 59.22 ± 0.99 200 C3 Poplar + apple + turnip-kale 4.38 ± 0.27 37.63 ± 3.53 204 20.4 ± 0.98 53.1 ± 0.932 240 Horti-silvipasture C1 Apple + poplar + grasses 4.71 ± 0.34 39.07 ± 3.5 625 25.36 ± 1.76 58.5 ± 4.86 128 C2 Apple + poplar + salix + grasses 4.11 ± 0.22 31.56 ± 3.04 625 19.6 ± 3.11 8.92 ± 1.04 62.77 ± 3.3 56.5 ± 1.84 111 Poplar 20 Salix Based on the basal diameter, the branches were categorised into three groups: small, medium, and large. Each group’s two sampled branches weight was recorded individually. The formula given by Chidumaya (1990) was used to calculate the branch biomass in trees. Leaf biomass by dividing the sample tree’s branches into three groups based on basal diameter, small, medium, and large, the leaf biomass was calculated. Fresh weight of two sampled branches from each group was recorded separately. Immediately after being severed from the branch, the leaf biomass of each representative branch of the sample trees in each diameter class was counted in 20× 20 m quadrat. The leaf samples from two sampled branches of each group were put in individual bags and oven-dried at 65°C for 72 h, or until the consistent weight is obtained (Chapman, 1964). 3.1.2. Fruit tree For stem biomass it was calculated by means of the regression equation, prescribed by Brown et al. (1989) and the formula is given as: Y = exp. {−2.4090 + 0.9522 ln (D2HS)}, where, Y = Biomass/tree (kg), D = Tree collar diameter, H = Height of tree (cm), S = Density of wood (g cm-3). Canopy biomass Canopy biomass was estimated by multiplying crown volume by specific gravity. Crown volume was estimated by using formula given by Avery and Burkhart (2002) {Crown volume = (db2L)/12, where, db = Crown base diameter (m), L = Length of crown}. For the purpose of calculating specific gravity, Smith’s (1954) maximum moisture method was applied. Fruit samples weighing 1 kg were sun dried followed by oven dried at 60°C until their weight remained constant. Belowground biomass was determined by using formula given by Singh (2010). Then total biomass was computed by summing up of the total above-ground biomass and belowground biomass of the fruit trees. frontiersin.org 3.1.3. Crop biomass Crop (rabi and kharif) and grass biomass were measured by means of (1 × 1) m quadrates. At the time of harvest, the total biomass was determined by uprooting, which was then evaluated to calculate green/fresh weight. The samples were put in individual bags and dried in an oven at 65°C for 72 h, or until the weight remained consistent (Chapman, 1964). Estimation of carbon. The calculation of carbon stock was determined by multiplying total biomass by a conversion factor that represents the average carbon content in biomass. The default value of 0.45 for the conversion of biomass to carbon was used (Woomer, 1999). Therefore, the total carbon stock (C) present in the calculated total biomass was equal to C = 0.45 × Biomass (total). The mitigation potential of the system was worked out by calculating equivalent carbon dioxide (eCO2) as per formula: CO2e = C × 3.67. 5. Discussion The horti-silvi-pasture system recorded maximum aboveground tree biomass (43.11 t/ha), belowground tree biomass (12.58 t/ha) and total tree biomass (55.73 t/ha) and was significantly greater than all other agroforestry systems. Also, lowest aboveground tree biomass (15.44 t ha −1), belowground tree biomass (3.84 t ha − 1) and total tree biomass (19.3 t ha −1) was recorded in agri-silviculture system (boundary plantation). In horti-silvi-pasture systems, the density of trees being high and greater average height and dbh values of individual trees will contribute to the higher values of total tree biomass and vice-versa (fewer trees per hectare in agri-silviculture). Also, aboveground biomass is a valuable resource in most land use regimes, so more biomass is allocated to aboveground components as it includes biomass from tree’s trunk, stump, branch, twig, and leaves, as opposed to the tree’s underground biomass, which only includes biomass from its fine and coarse roots. The number of woody plants in a specific agro-forestry system, as well as management strategies, play a vital impact in affecting biomass in a particular agro forestry system (Dar et al., 2019; Siarudin et al., 2021; Kumar et al., 2022). Agroforestry systems are complex and heterogeneous and, the more the heterogeneity, the more efficiently the carbon is sequestered compared to simpler systems (Rai et al., 2021; Tamang et al., 2021). However, the efficiency of Agroforestry systems as carbon sinks is governed by their size, natural site qualities, choice of species and management practises followed, i.e., carbon sequestered by an AFS depends on its structure and composition modified by environmental and socio-economic factors. Moreover, inter- and intra-specific variation in tree diameter, stand age, stand structure and diversity of the system also affect variation in biomass and its carbon (Bajigo et al., 2015; Panwar et al., 2022). Similarly, study conducted by Devagiri et al. (2020) in western Ghats region of peninsular India found that coffee agroforests resembled natural forest and mixed species plantations in terms of biomass production due to presence of tree diversity in this system. Also, study conducted by Panwar et al. (2022) reported that AGB was highest in block plantations (mean = 109.8 Mg ha − 1), followed by plantation crop systems (mean = 88.49 Mg ha − 1), with the lowest AGB observed in boundary plantations (mean = 17.14 Mg ha − 1). 5. Discussion BGB was highest in homegardens (mean = 34.68 Mg ha − 1), followed by block plantations (mean = 26.19 Mg ha − 1), and lowest in boundary plantations (mean = 2.67 Mg ha − 1). Since both carbon storage and carbon capture capability of all the systems are directly linked to the biomass production of the various plant components, so they both match their capacity for biomass production. Plant biomass can vary significantly in terms of carbon content in an intricate agroforestry system, and this variation affects production. Productivity is determined by a variety of elements, including age, kind of soil, crop type, growing habits, and management intensity. So, in our study, a similar trend was observed in values of carbon stock and carbon sequestration potential as that of above- mentioned total biomass estimations in agroforestry systems. Horti- silvipasture was having highest values for tree carbon stock (25.07 t ha−1) and tree carbon sequestration potential (92.04 t ha−1) and were significantly higher than all other systems. The agri-silvipasture (homegardens) however was found next to horti-silvipasture recording 38.82 t ha−1 and 64.33 t ha−1 as tree carbon stock and carbon sequestration potential respectively, while as significantly lowest tree carbon stock and sequestration potential as 8.68 t ha−1and 31.85 t ha−1, respectively, were recorded in agri-silviculture system (boundary plantation).Also, maximum total crop carbon stock and carbon sequestration potential was found in agri-silviculture (boundary plantation) as 7.98 t ha−1 and 25.65 t ha−1 respectively, which was significantly higher than all other agroforestry systems. The horti- agriculture system was found next to agri-silviculture (boundary plantation) recording 5.63 t ha−1and 20.62 t ha−1as total crop carbon stock and sequestration potential, while as lowest total crop carbon stock and sequestration potential (4.86 t ha−1 and 17.93 t ha−1 respectively) were recorded in horti-silvipasture system (Tables 3, 4). The overall comparison of agroforestry systems practised by the farmers of Anantnag district clearly shows that the horti-silvipastoral system outperforms the other agroforestry systems and are most productive in terms of total biomass accumulation (66 55tha−1) Current study also witnessed that agri-silviculture (boundary plantation) contributed maximum crop biomass as 15.54 t ha−1, which was significantly higher than all other agroforestry systems and minimum was recorded in horti-silvipasture system (10.82 t ha−1; Table 2). 3.2. Data analysis The data obtained were subjected to the statistical analysis as per procedure given by Gomez and Gomez (1984) using R-software and SAS statistical package. Also, one-way ANOVA was used for analyzing the data of different systems in the present study. 05 frontiersin.org 10.3389/ffgc.2023.1192382 Saleem et al. Walnut + oatsunder horti-agriculture Apple + beans under horti-agriculture Poplar + mustard under boundary plantation Poplar, salix and paddy under boundary plantation Poplar, apple, turnip and kale under homegardens Poplar + apple + kale + beans under homegardens Apple, poplar and grasses under horti-silvi-pasture Apple + poplar + salix + grasses under horti-silvi-pasture Apple + beans under horti-agriculture Walnut + oatsunder horti-agriculture Apple + beans under horti-agriculture Apple + beans under horti-agriculture Walnut + oatsunder horti-agriculture Poplar + mustard under boundary plantation Poplar + mustard under boundary plantation Poplar + mustard under boundary plantation Poplar, salix and paddy under boundary plantation Poplar, salix and paddy under boundary plantation Poplar + apple + kale + beans under homegardens Poplar, apple, turnip and kale under homegardens Poplar, apple, turnip and kale under homegardens Poplar + apple + kale + beans under homegardens Apple + poplar + salix + grasses under horti-silvi-pasture Apple + poplar + salix + grasses under horti-silvi-pasture Apple, poplar and grasses under horti-silvi-pasture 06 Frontiers in Forests and Global Change frontiersin.org Saleem et al. Saleem et al. 10.3389/ffgc.2023.1192382 frontiersin.org Frontiers in Forests and Global Change 4. Results horti-silvipastoral system was 37.83%, fruit trees as 45.86% and crop (rabi and kharif) contributed 16.29% in biomass, carbon stock and carbon sequestration potential. Agri-silviculture, on the other hand, was least productive in terms of total biomass (34.87 t ha−1), carbon stock (15.67 t ha−1) and CO2 sequestration potential (57.58 t ha−1). The contribution of forest trees in agri-silviculture system was 55.36% and crops contribute 44.61%. Among four different systems under study, the horti-silvi-pasture system recorded maximum aboveground tree biomass (43.11 t/ha), belowground tree biomass (12.58 t/ha) and total tree biomass (55.73 t/ ha) and was significantly greater than all other agroforestry systems. The agri-silvipasture (homegardens) however was found next to horti- silvipasture recording 30.80 t/ha, 8.16 t/ha and 32.76 t/ha as aboveground tree biomass, belowground tree biomass and total tree biomass respectively, while as significantly lowest aboveground tree biomass (15.44 t ha −1), belowground tree biomass (3.84 t ha − 1) and total tree biomass (19.3 t ha −1) were recorded in agri-silviculture system (boundary plantation). Also, maximum total crop biomass was found in agri-silviculture (boundary plantation) as 15.54 t ha−1, which was significantly higher than all other agroforestry systems. The horti- agriculture system was found next to agri-silviculture (boundary plantation) recording 12.52 t/ha as total crop biomass, while as lowest total crop biomass (10.82 t ha−1) was recorded in horti-silvipasture system. Total biomass production (tree+ crop component) followed a similar pattern as that seen in above and below ground tree biomass, with horti-silvi-pastoral system contributing maximum as 66.55 t ha−1 which was significantly higher than all other systems and was followed by agri-horti-silviculture as 50.18 t ha−1 and horti-agriculture as 36.22 t ha−1. Minimum value was recorded under agri-silviculture (boundary plantation) as 34.87 t ha−1 (Table 2). 5. Discussion Greater crop biomass observed in case of agri-silviculture system might be due to the consistent and enough solar incidence in open agricultural fields as a result of larger open photosynthetic area, and the absence of competition between The overall comparison of agroforestry systems practised by the farmers of Anantnag district clearly shows that the horti-silvipastoral system outperforms the other agroforestry systems and are most productive in terms of total biomass accumulation (66.55 t ha−1), carbon stock (29.94 t ha−1) and carbon dioxide sequestration potential of 104.4 t ha−1 (Tables 2–4). The involvement of forest trees in the 07 Saleem et al. 10.3389/ffgc.2023.1192382 TABLE 2  Aboveground, belowground and total biomass (t ha−1) production in prominent agroforestry systems. Agroforestry system Aboveground tree biomass Belowground tree biomass Total tree biomass Total crop biomass Total biomass Fruit tree Forest tree Total Fruit tree Forest tree Total Fruit tree Forest tree Total Rabi Kharif Total Horti-agriculture 17.8 – 17.8c 5.87 – 5.87c 23.7 – 23.7c 5.20 7.32 12.52b 36.22c Agri-silviculture (boundary plantation) – 15.44 15.44c – 3.84 3.84d – 19.3 19.3d 5.64 9.9 15.54a 34.87c Agri-horti- silviculture (homegardens) 5.95 24.85 30.80b 1.95 6.21 8.16b 7.91 24.85 32.76b 5.53 5.62 11.15c 50.18b Horti-silvipasture 22.96 20.15 43.11a 7.56 5.02 12.58a 30.54 25.19 55.73a 7.18 3.64 10.82c 66.55a C.D(p ≤ 0.05) 3.43 0.37 3.73 1.25 3.77 S.E± 1.03 0.10 1.05 0.35 1.07 L d b i i h d l d i i ifi i TABLE 3  Aboveground, belowground and total carbon stock (t ha−1) in prominent agroforestry systems. TABLE 3  Aboveground, belowground and total carbon stock (t ha−1) in prominent agroforestry systems. Agroforestry systems Aboveground tree carbon stock Belowground tree carbon stock Total tree carbon stock Total crop carbon stock Total carbon stock Fruit tree Forest tree Total Fruit tree Forest tree Total Fruit tree Forest tree Total Rabi Kharif Total Horti-agriculture 8.01 – 8.01c 2.64 – 2.64c 10.66 – 10.66c 2.33 3.29 5.63b 16.28c Agri-silviculture (boundary plantation) – 6.95 6.95d – 1.73 1.73d – 8.68 8.68d 2.54 5.44 7.98a 15.67c Agri-horti- silviculture (homegardens) 2.68 11.18 13.86b 0.88 2.79 3.67b 13.97 24.85 38.82a 2.49 2.53 5.02c 22.56b Horti-silvipasture 10.33 9.06 19.39a 3.40 2.26 5.66a 13.74 11.33 25.07b 3.23 1.63 4.86d 29.94a C.D(p ≤ 0.05) 0.49 0.16 1.68 0.56 1.7 S.E± 0.14 0.04 0.47 0.15 0.48 Letters used as subscript represents variance among the systems and same letters depict non significant variance among two systems. Frontiers in Forests and Global Change frontiersin.org 5. Discussion 08 frontiersin.org Saleem et al. 10.3389/ffgc.2023.1192382 10.3389/ffgc.2023.1192382 TABLE 4  Aboveground, belowground and total carbon sequestration (t ha−1) potential in prominent agroforestry systems. Agroforestry systems Aboveground tree carbon sequestration Belowground tree carbon sequestration Total tree carbon sequestration Total crop carbon sequestration Total carbon sequestration Fruit tree Forest tree Total Fruit tree Forest tree Total Fruit tree Forest tree Total Rabi Kharif Total Horti-agriculture 29.39 – 29.39c 9.68 – 9.68c 39.12 – 39.12c 8.55 12.07 20.62b 59.83c Agri-silviculture (boundary plantation) – 25.50 25.50d – 6.35 6.35d – 31.85 31.85c 9.32 16.33 25.65a 57.58c Agri-horti-silviculture (homegardens) 9.83 41.04 50.87b 3.23 10.24 13.47b 13.06 51.27 64.33b 9.14 9.28 18.42c 82.8b Horti-silvipasture 37.9 33.28 71.18a 12.5 8.32 20.82a 50.44 41.60 92.04a 11.9 6.03 17.93c 104.4a C.D(p ≤ 0.05) 1.813 0.61 6.17 2.06 6.24 S.E± 0.514 0.17 1.74 0.58 1.77 Letters used as subscript represents variance among the systems and same letters depict non significant variance among two systems. Similary, carbon stock and carbon sequestration values of different agroforestry systems follows same trend as in above mentioned biomass production being significantly more in horti-silvipasture followed by agri- horti-silviculture (homegardens) and horti-agriculture and minimum values in agri-silviculture (boundary plantation). The inclusion of forest trees in the agroforestry system, which results in continuous carbon locking in woody plants, and the natural accumulation of fallen leaf debris to soil, which assists in the build-up of carbon in soil beds and, consecutively, aids in considerable production of structure, may be the primary causes of the maximum carbon reserve in horti-silvipasture and agri-horti-silviculture (homegardens). However, most of the biomass in horti-agriculture and agri-silviculture (boundary planation) is taken yearly by harvesting, trimming, and felling. The ability to capture carbon dioxide rely on variety of characteristics, involving species type, genetic make-up, maturity, structure, functional components, and number. Tree plantations are a better option for reducing atmospheric carbon since they store more carbon, but due to population pressure and the rising demands for agricultural land, these plantations fail to extend. As a result, the agroforestry system appears to be  a better alternative for preserving biodiversity while still providing economic advantages to society. Nair et al. (2009) reported that the capacity for carbon capture in agroforestry land use systems is based on the woody element. Farmlands has greater capacity to sequester carbon with highest woody component than other land use systems (lesser woody components; Sureshbhai et al., 2017; Dar et al., 2019). 5. Discussion woody perennials and agricultural crops for moisture, light, nutrients, and space, among other factors. Minimum biomass of grass species in case of horti-silvipasture might be because trees and grasses compete for the same resources, such as sunlight, water, and nutrients. Our results are corroborated with Nandal and Singh (2001), Handa et al. (2004), Yadav (2010), and Chauhan et al. (2008) who found that increasing the distance between trees and crops, improved crop performance and production. Chavan et al. (2022) also, reported that the performance of sorghum and wheat crops is strongly influenced by the distance from tree lines and the age of the poplar trees and might be due to significant interaction between distance and aspect that was attributed to small differences in the intensity and duration of shadows cast by the boundary stands. Such study also observed a significant reduction of fodder biomass of sorghum and wheat yield was observed up to 9 m distant from the tree line. The reduction was 10–60% for the kharif season and 7.2–29.5% for rabi crops from the 2nd year to 8 years after planting, respectively. Similarly, Honfy et  al., 2023 investigated the tree planting pattern of black locust (Robinia pseudoacacia L.) when intercropped with triticale (x Triticosecale W.) and observed that more the trees planted on a hectare, the higher the volume of the stand, and the less yield of triticale. Studies carried out by various researchers observed that a significant yield reduction of more than 70% was observed near the tree base (0–3 m) and about a 10–35% reduction up to 9 m away from the tree (Yang et al., 2015). Total biomass (tree + crop component) followed a similar pattern as in above and below ground tree biomass, with horti-silvi-pastoral system contributing maximum as 66.55 t ha−1 which was significantly higher than all other agroforestry systems and was followed by agri- horti-silviculture as 50.18 t ha−1 and horti-agriculture as 36.22 t ha−1. Also, minimum total biomass was recorded under agri-silviculture as 34.87 t ha−1 (Table 2). This could be attributed to higher tree density and difference in management regimes; for example, in horti- silvipasture system, farmers retain native trees in large numbers to provide them fruit on a large scale and forest trees serve as live fence, thus overcomes fodder scarcity. 5. Discussion The ability of different agroforestry systems to store carbon varies greatly, and the amount of carbon stored is mostly influenced by the kind of agroforestry system utilised, its arrangement and role, as well as the surrounding environment and socioeconomic factors. Tree species and system management are two further elements that may influence carbon storage in agroforestry system (Nair et al., 2010). frontiersin.org Frontiers in Forests and Global Change References Anderson, T. R., Hawkins, E., and Jones, P. D. (2016). 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The present study recognised the capability of various agroforestry systems for biomass estimation and carbon sequestration potential for mitigating climate variation in north- western Himalayas. Agroforestry systems differed in terms of biomass output and carbon sequestration potential. As seen from the data, the horti-silvipasture system recorded maximum values for biomass and carbon sequestration potential, agri-silviculture system (boundary plantation) recorded minimum values. So, the study concluded that horti-silvipasture system outperforms the other agroforestry systems and are most productive in terms of carbon sequestration potential. Thus, adopting these agroforestry systems not only contributes to environmental stability by reducing carbon dioxide emissions, but it also increases farming income, so improving farmer livelihood. As a result, if the carbon trapped by these systems is traded to rich countries, there is a compelling financial incentive for farmers to use them thus, by development of suitable agroforestry systems in diverse agroclimatic zones, not only the area of greenery in the country be increased, but the proportion of greenhouse gases in the environment may also be  significantly reduced. Therefore, agroforestry will be  a workable method for reducing climate crises if it is encouraged for greater adoption by cultivators in the nation. 09 frontiersin.org Saleem et al. 10.3389/ffgc.2023.1192382 Author contributions IS and JAM framed the concept. IS, BM, and AA did the field work. IS, JAM, NAP, GMB, AHM, and THM did the analysis and drafted the manuscript. IS and NAP finalised the manuscript. All authors contributed to the article and approved the submitted version. All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. Data availability statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author. References Carbon sequestration in agroforestry and pasture systems in arid northwestern India. Curr. Sci. 107, 1290–1293. Chavan, S. B., Dhillon, R. S., Sirohi, C., Keerthika, A., Kumari, S., Bharadwaj, K. K., et al. (2022). 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Linear-algebraic bath transformation for simulating complex open quantum systems
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Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA Published Version doi:10.1088/1367-2630/16/12/123008 Published Version doi:10.1088/1367-2630/16/12/123008 Permanent link http://nrs.harvard.edu/urn-3:HUL.InstRepos:27692660 Citation Huh, Joonsuk, Sarah Mostame, Takatoshi Fujita, Man-Hong Yung, and Alán Aspuru-Guzik. 2014. “Linear-Algebraic Bath Transformation for Simulating Complex Open Quantum Systems.” New J. Phys. 16 (12) (December 2): 123008. doi:10.1088/1367-2630/16/12/123008. Joonsuk Huh1, Sarah Mostame1, Takatoshi Fujita1, Man-Hong Yung2 and Alán Aspuru-Guzik1 Joonsuk Huh1, Sarah Mostame1, Takatoshi Fujita1, Man-Hong Yung2 and Alán Aspuru-Guzik1 1 Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA 2 Center for Quantum Information, Institute for Interdisciplinary Information Sciences, Tsingh University, Beijing, 10084, Peopleʼs Republic of China E-mail: huh@fas.harvard.edu and aspuru@chemistry.harvard.edu Received 17 August 2014, revised 9 October 2014 Accepted for publication 27 October 2014 Published 2 December 2014 New Journal of Physics 16 (2014) 123008 doi:10.1088/1367-2630/16/12/123008 Joonsuk Huh1, Sarah Mostame1, Takatoshi Fujita1, Man-Hong Yung2 and Alán Aspuru-Guzik1 1 Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA 2 Center for Quantum Information, Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 10084, Peopleʼs Republic of China E-mail: huh@fas.harvard.edu and aspuru@chemistry.harvard.edu Joonsuk Huh , Sarah Mostame , Takatoshi Fujita , Man Hong Yung and Alán Aspuru-Guzik1 1 Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA 2 Center for Quantum Information, Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 10084, Peopleʼs Republic of China E-mail: huh@fas.harvard.edu and aspuru@chemistry.harvard.edu Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA 2 Center for Quantum Information, Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 10084, Peopleʼs Republic of China E-mail: huh@fas.harvard.edu and aspuru@chemistry.harvard.edu Received 17 August 2014, revised 9 October 2014 Accepted for publication 27 October 2014 Published 2 December 2014 Received 17 August 2014, revised 9 October 2014 Accepted for publication 27 October 2014 Published 2 December 2014 New Journal of Physics 16 (2014) 123008 doi:10.1088/1367-2630/16/12/123008 Share Your Story The Harvard community has made this article openly available. Please share how this access benefits you. Submit a story . Accessibility Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. 1. Introduction Problems associated with open quantum systems are of interest in various research fields [1]. In the theory of open quantum systems, the universe is partitioned into system and bath components. The system of interest is then coupled to the bath degrees of freedom (DOF) by means of an effective Hamiltonian. Solving the full quantum dynamics with currently known exact analytic or numerical methods is not feasible as the system and bath DOF increase. A simple but effective approach to model these vibrations is to treat them as a collection of non- interacting quantum harmonic oscillators bilinearly coupled to the system [1, 2]. The system- bath interaction is then characterized by a spectral density function (SDF) that represents the coupling strength in the frequency domain [1, 2]. The energy transfer in photosynthetic systems is an example of a complex open quantum system, where the pigments involved in the energy transfer interact with a richly structured set of molecular vibrations, and hence a very structured SDF [3]. The spin-boson model [1] is one of the simplest models for studying the dynamics of open quantum systems. In the most common representation, the spin-boson model is mathematically represented as a set of non-interacting oscillators coupled to the system. This can be graphically represented in a star configuration as shown in figure 1(A) [4, 5]. Generalized spin-boson models, such as the Hubbard-Holstein model, have been successfully employed to describe the energy transfer process in photosynthetic antenna complexes [6]. Some numerically-exact methods have been so far developed to solve these models; see, for example, reduced-density- matrix approaches, such as hierarchy equations of motion (HEOM) [7–9], stochastic approaches [10–14], multi-configuration time-dependent Hartree [15], numerical renormalization group [4, 5, 16–19], and path-integral approaches [20], amongst many others. However, the applicability of numerically exact methods is limited by the system size and the bath DOF. For example, the simulation of HEOM with current computers is limited to ≈40 sites of the system with only a single Drude–Lorentzian peak representing the bath [9, 21]. On the other hand, the renormalization group approach [16, 19, 22] could be used for relatively large systems. However, the system and bath size that can be handled is still far from that required for solving problems at biological scales. In this approach, then, the bath transformation from the non- interacting bath model (figure 1(A)) to the 1-D Wilson chain (figure 1(B)) [23–25] is necessary. Abstract In studying open quantum systems, the environment is often approximated as a collection of non-interacting harmonic oscillators, a configuration also known as the star-bath model. It is also well known that the star-bath can be transformed into a nearest-neighbor interacting chain of oscillators. The chain-bath model has been widely used in renormalization group approaches. The transformation can be obtained by recursion relations or orthogonal polynomials. Based on a simple linear algebraic approach, we propose a bath partition strategy to reduce the system-bath coupling strength. As a result, the non-interacting star-bath is transformed into a set of weakly coupled multiple parallel chains. The trans- formed bath model allows complex problems to be practically implemented on quantum simulators, and it can also be employed in various numerical simula- tions of open quantum dynamics. Keywords: open quantum system, quantum simulator, bath transformation, spin- boson model, energy transfer, superconducting qubit, chain bath model Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journ and DOI. New Journal of Physics 16 (2014) 123008 1367-2630/14/123008+16$33.00 New Journal of Physics 16 (2014) 123008 1367-2630/14/123008+16$33.00 © 2014 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft New J. Phys. 16 (2014) 123008 J Huh et al 1. Introduction The collective modes of the bath oscillators in the chain model have been used widely in various fields such as quantum molecular dynamics [26, 27], open quantum dynamics [28–32], quantum information [33] and nuclear physics [34, 35]. Quantum simulators defined as controlled quantum devices that can effectively reproduce the dynamics of any other quantum system [36–39] could become an attractive alternative for solving the dynamics of open quantum systems ‘directly’. Different platforms can be used for implementing quantum simulators, such as superconducting qubits [21, 33, 40–46], trapped ions [47–55], quantum optics [56–60], nuclear magnetic resonance [12, 61–64] or a system of electrons [65, 66]. The experimental implementation of quantum simulators of open quantum system dynamics, for example, using superconducting circuits [21, 41], poses challenges due to at least two of the main current constraints in the realizable circuits. First, the number of quantum bath oscillators, which are directly coupled to a system operator (qubit), is limited by the physical size of the superconducting loop that embodies the qubit. Hence, a star-model approach with many oscillators coupled to the qubit may pose fabrication challenges. A physical layout that 2 New J. Phys. 16 (2014) 123008 J Huh et al Figure 1. Top panels: Various harmonic oscillator bath models. The red spheres represent system operators and the couplings are shown as springs. The couplings of primary modes, which are directly coupled to the system, are indicated in red. The yellow and blue spheres represent bath oscillators. (A). Star-bath model: non-interacting quantum harmonic oscillators (yellow) are coupled to a system operator (red). (B). Chain-bath model: a system operator (red) is coupled to a single interacting bath oscillator chain (blue). (C). Multiple-chain-bath model: a system operator (red) is coupled to multiple interacting bath oscillator chains (blue). (D). Star-chain-bath model: a system operator (red) is coupled to multiple chains of bath operators (blue) and final bath oscillators are coupled to non-interacting bath oscillators (yellow). Down panels: The matrix representations (equation (6)) are shown for the corresponding top panel diagrams. The primary mode couplings to the system are given in red squares and other non-zero elements are shown in gray squares. The first column and row of each matrix correspond to the primary system-bath couplings. The diagonal elements, except the first one, are the frequencies of the bath oscillators. Figure 1. Top panels: Various harmonic oscillator bath models. 1. Introduction The red spheres represent system operators and the couplings are shown as springs. The couplings of primary modes, which are directly coupled to the system, are indicated in red. The yellow and blue spheres represent bath oscillators. (A). Star-bath model: non-interacting quantum harmonic oscillators (yellow) are coupled to a system operator (red). (B). Chain-bath model: a system operator (red) is coupled to a single interacting bath oscillator chain (blue). (C). Multiple-chain-bath model: a system operator (red) is coupled to multiple interacting bath oscillator chains (blue). (D). Star-chain-bath model: a system operator (red) is coupled to multiple chains of bath operators (blue) and final bath oscillators are coupled to non-interacting bath oscillators (yellow). Down panels: The matrix representations (equation (6)) are shown for the corresponding top panel diagrams. The primary mode couplings to the system are given in red squares and other non-zero elements are shown in gray squares. The first column and row of each matrix correspond to the primary system-bath couplings. The diagonal elements, except the first one, are the frequencies of the bath oscillators. involves fewer oscillators directly coupled to a qubit is more experimentally realizable [41]. In addition, the coupling strength of the qubit to the bath may be limited. In superconducting qubits, the system-bath coupling strength should not exceed a certain percentage of the frequency of the quantum oscillator [21]. involves fewer oscillators directly coupled to a qubit is more experimentally realizable [41]. In addition, the coupling strength of the qubit to the bath may be limited. In superconducting qubits, the system-bath coupling strength should not exceed a certain percentage of the frequency of the quantum oscillator [21]. In this work, we address the question of how the two afore-mentioned implementation issues can be resolved by a unitary bath transformation which introduces interaction terms among the transformed quantum oscillators. In chain-like bath models (figure 1(B)) [4, 5, 18, 22, 31–33, 67, 68], only one bath oscillator is directly coupled to the system. However, in some cases, one needs to couple more than a single chain to deal with the limitation of the oscillator-qubit coupling mentioned above. Here, we propose a partitioning strategy of the bath modes for multiple parallel chains to reduce primary mode coupling strengths and also the number of the modes directly coupled to the system operator. This is shown in figures 1(C) and (D), respectively. 1. Introduction We found that the coupling strength of the primary modes, which are directly coupled to the system, can be reduced as we increase the number of chains; at the same time, we can also shorten the lengths of each chain. In addition to the fabrication and implementation benefits for open quantum simulators using quantum hardware, these methods are also potentially applicable to simulations in classical computers. In this case, 3 New J. Phys. 16 (2014) 123008 J Huh et al J Huh et al perturbative methods may be employed to simulate these chain models with reduced system- bath coupling [31, 32]. perturbative methods may be employed to simulate these chain models with reduced system- bath coupling [31, 32]. A recurrence equation derived by Bulla et al [5] has been used in the renormalization group approaches to construct the 1-D Wilson chain (figure 1(B)). This recurrence relation, however, potentially shows numerical instabilities [5, 17, 69]. Recently, Chin et al [22] developed an exact mapping approach for a continuous SDF using orthogonal polynomials without discretizing the SDF. However, this approach may pose challenges applicable to arbitrary structured SDFs. In many applications of chemistry and biology, structured SDFs appear when atomistic details are involved in open quantum dynamics, as already mentioned in the introduction. Therefore, the SDFs may not be well approximated as simple analytic functions such as Ohmic spectral functions. In this paper, we test a generalized linear algebraic transformation approach for any given discrete SDFs, where a transformation on multiple parallel chains is involved, as shown in figure 1(C). With the multiple-chain–bath transformation described in the following sections, complex open quantum systems, such as photosynthetic antennae, can be studied practically via quantum simulators. In the next sections we present the model Hamiltonian and the linear algebraic bath transformation. As an example, a two-oscillator bath transformation is presented analytically. This example shares many features of our general scheme of bath partitioning. Numerical stability of the bath transformation methods is discussed in the result section and the results are compared with Bullaʼs transformation approach [5]. Then, we propose a way to partition the bath modes into multiple parallel chains to reduce the system-bath coupling strengths. We apply the proposed leaping partitioning (LP) strategy to a structured spectral density of the chlorosome [70, 71], as an example. The numerical result is compared with a ‘standard’ sequential partitioning (SP) scheme. 2.1. Linear algebraic bath transformation With a suitable choice of unitary transformation on the bath oscillators, one can turn a star-bath into a multiple-chain-bath. The multiple-chain-bath has a few primary bath oscillators and the remaining oscillators (secondary bath modes) are coupled to the primary bath modes in a chain as depicted in figure 1(C). A mixture of star and chain models is also possible as shown in figure 1(D). Burghardt et al [31, 32, 75] exploited the latter model to develop a perturbative truncated bath model, which approximates the terminal star-coupled yellow oscillators in figure 1(D) as Markovian baths. The bath transformation from the star model (equation (2)) to the 1-D Wilson chain (figure 1(B)) can be simply obtained by a unitary transformation of the matrix Γn that keeps the system operators unchanged. We introduce, here, an arbitrary unitary transformation ( = U U I n n † ) satisfying the following conditions: ⎛ ⎝ ⎜⎜ ⎞ ⎠ ⎟⎟ ∑ Γ + = ( ) b b H H L L ˆ ˆ ˆ ˆ ˜ ˆ ˆ , (5) n n n n n n SB B † † ⎛ ⎝ ⎜⎜ ⎞ ⎠ ⎟⎟ ⎛ ⎝ ⎜ ⎞ ⎠ ⎟ ⎛ ⎝⎜ ⎞ ⎠⎟ Γ κ κ Ω Γ = = U U ˜ 0 ˜ ˜ ˜ 1 0 0 1 0 0 , (6) n n n n n n n t t † t ⎛ ⎝ ⎜⎜ ⎞ ⎠ ⎟⎟ ∑ Γ + = ( ) b b H H L L ˆ ˆ ˆ ˆ ˜ ˆ ˆ , (5) n n n n n n SB B † † (5) ⎛ ⎝ ⎜⎜ ⎞ ⎠ ⎟⎟ ⎛ ⎝ ⎜ ⎞ ⎠ ⎟ ⎛ ⎝⎜ ⎞ ⎠⎟ Γ κ κ Ω Γ = = U U ˜ 0 ˜ ˜ ˜ 1 0 0 1 0 0 , (6) n n n n n n n t t † t (6) where = b a U ˆ ˆ n n n † . The first column of Un is κ κ − || || n n 2 1 and the remaining columns are constructed using the Gram–Schmidt process with random vectors (or unit vectors) [76]. As a result, Γ˜n is a dense symmetric matrix and κ κ = … ˜ (˜ , 0, , 0) n n;1 t is the new system-bath coupling strength vector. 2. Chain-bath transformation As mentioned in the Introduction, in the theory of open quantum systems, the system-bath Hamiltonian Hˆ is composed of three parts, namely, = + + H H H H ˆ ˆ ˆ ˆ , (1) S SB B = + + H H H H ˆ ˆ ˆ ˆ , (1) S SB B = + + H H H H ˆ ˆ ˆ ˆ , S SB B (1) where HˆS is the system Hamiltonian. The phonon bath HˆB is approximated as a set of non- interacting harmonic oscillators. The coupling term HˆSB between the system and bath is almost universally treated as a bilinear coupling. More precisely, we write + H H ˆ ˆ SB B in a compact form [72, 73] as follows, ⎛ ⎝ ⎜ ⎞ ⎠ ⎟ ∑ Γ + = ( ) a a H H L L ˆ ˆ ˆ ˆ ˆ ˆ , (2) n n n n n n SB B † † (2) ⎛ ⎝ ⎜ ⎞ ⎠ ⎟ Γ κ κ Ω = 0 , n n n n † ⎛ ⎝ ⎜ ⎞ ⎠ ⎟ Γ κ κ Ω = 0 , (3) n n n n † (3) (3) where each N-dimensional creation (annihilation) operator vector a a ˆ (ˆ ) n n † of oscillators for the site n are coupled to the operator =ǀ >< ǀ Lˆn n n that acts on the system. We note here that the bath transformation is independent of the system-bath coupling when the coupling is bilinear. where each N-dimensional creation (annihilation) operator vector a a ˆ (ˆ ) n n † of oscillators for the site n are coupled to the operator =ǀ >< ǀ Lˆn n n that acts on the system. We note here that the bath transformation is independent of the system-bath coupling when the coupling is bilinear. 4 New J. Phys. 16 (2014) 123008 J Huh et al Therefore the bath transformation can be applied to the spatially correlated noise as well, where the system coupling operator is = 〉〈 L n m ˆ | | nm , ≠ n m. Lower case bold and capital bold fonts are used for a column vector and a matrix, respectively. 2. Chain-bath transformation The bosonic operators satisfy a commutation relation, δ δ = a a [ˆ , ˆ ] n i m j nm ij ; ; † where = … a a a ˆ (ˆ , , ˆ ) n n n N ;1 ; t. Here Ωn is a diagonal matrix, which has the harmonic frequencies as the elements, i.e. Ω ω ω = … diag( , , ) n n n N ;1 ; . κn is the system-bath coupling strength vector. Accordingly, the SDF ω J ( ) n is defined [74] as, ∑ ω π κ δ ω ω = − J ( ) ( ). (4) n j n j n j ; 2 ; (4) In this work, the coupling strength vector κn, which is in general a complex vector, is chosen to be a positive real vector. That is, the vector elements are given by κ κ = ⩾ | | 0 n j n j ; ; 2 . The non- interacting bath in equation (2) is the star-bath model (figure 1(A)), where the independent harmonic oscillators are all coupled directly to the system. In this work, the coupling strength vector κn, which is in general a complex vector, is chosen to be a positive real vector. That is, the vector elements are given by κ κ = ⩾ | | 0 n j n j ; ; 2 . The non- interacting bath in equation (2) is the star-bath model (figure 1(A)), where the independent harmonic oscillators are all coupled directly to the system. 2.2. Multiple chain transformation In this subsection we explain the multiple parallel chain transformation that is depicted in figure 1(C). We introduce a unitary transformation, = U P U ˜ , n n n = U P U ˜ , ( n n n (7) that additionally rearranges (using a permutation matrix Pn) the non-interacting bath oscillators as multiple groups of several interacting oscillators, i.e. = b a U ˆ ˜ ˆ n n n † . The unitary transformation matrix Un is block diagonal and does not allow the interaction between oscillators from different groups (an example of the rearrangement is given in appendix B). We also define the following relations for the unitary transformation: Ω Ω κ κ = = U U U ˜ ˜ ˜ and ˜ ˜ . n n n n n n n † † Ω Ω κ κ = = U U U ˜ ˜ ˜ and ˜ ˜ . (8) n n n n n n n † † (8) The primary modes, which are directly coupled to the system operators, are defined as collective oscillator modes by choosing the first column of the lth subblock Un l( ) to be − g g || || n l n l ( ) 2 1 ( ). The normalized vector corresponds to the rearranged coupling strength vector of ⎛ ⎝ ⎜ ⎜ ⎜ ⎞ ⎠ ⎟ ⎟ ⎟ κ = = ⋮ g g g P , (9) n n n n n N † (1) ( ) eff (9) with Neff being the number of subblocks (or the number of group of oscillators). The chain-bath model can be obtained via tridiagonalization of the lth subblock with Neff being the number of subblocks (or the number of group of oscillators). The chain-bath model can be obtained via tridiagonalization of the lth subblock Ω Ξ = T T ˜ (10) n l l l l ( ) ( ) ( ) ( ) † Ω Ξ = T T ˜ (10) n l l l l ( ) ( ) ( ) ( ) † Ω Ξ = T T ˜ n l l l l ( ) ( ) ( ) ( ) † (10) with the application of the Hessenberg transform [76] via the Householder procedure. 2.2. Multiple chain transformation Ξ l( ) is a tridiagonal matrix that defines the frequencies (diagonal elements) of the transformed bath modes and coupling strengths (off-diagonal elements) between the oscillators in the chain model. T l( ) is a Hessenberg unitary transform matrix that makes no transformation to the primary bath mode such that the first column of the matrix is … (1, 0, , 0)t. The resulting transformed bath coupling vector κ T ˜ l n l ( ) ( ) of the lth subblock has only a single non-zero first element, which corresponds to the primary mode coupling strength. In appendix C, we provide a MATLAB [77] code for the GSH with the LP scheme. The alternative numerical transformation from the star-bath model to the chain-bath model can be obtained by Bullaʼs recursion method [4, 5]. The two methods will be compared numerically later. 2.1. Linear algebraic bath transformation (See appendix A for the details, and down panels of figure 1 for the structures of Γ˜n.) Now we have new sets of interacting harmonic oscillators while the system operators remain unchanged. The tridiagonalization of Γn in equation (2) for the Wilson chain (figure 1(B)) can be performed numerically by Householder or Lanczos procedures [76]. Alternatively, we use here tridiagonalization of Ω˜n with a Hessenberg reduction of a symmetric matrix [76]. We refer to the later transformation method as Gram–Schmidt–Hessenberg (GSH). The Hessenberg reduction of a symmetric matrix produces a tridiagonal matrix and then the numerical procedures for the reduction, such as Householder, Lanczos and Gauss transform, 5 New J. Phys. 16 (2014) 123008 J Huh et al can be applied. These numerical algorithms are standard numerical linear algebraic techniques, see e.g. [76]. can be applied. These numerical algorithms are standard numerical linear algebraic techniques, see e.g. [76]. 3.1. Numerical stability of the transformations As expected, Bullaʼs original method generates a curve that deviates significantly from the original one, especially around 1550–1600 cm−1. The EP improves the result but is still in disagreement with the original. The Lanczos curve seems to agree well with the original but the discrete data points do not match with the original data points in the frequency domain and it produces negative frequencies that are not shown in the figure. The GSH and Householder, on the other hand, can reproduce the original SDF with high accuracy. Both methods are based on the Householder procedure, which has an unconditional stability [79]. (green line). The GSH curve is shown as a red line and unfilled red circles. Householder and Lanczos transformations of Γn in equation (3) are plotted in brown and purple lines, respectively. As expected, Bullaʼs original method generates a curve that deviates significantly from the original one, especially around 1550–1600 cm−1. The EP improves the result but is still in disagreement with the original. The Lanczos curve seems to agree well with the original but the discrete data points do not match with the original data points in the frequency domain and it produces negative frequencies that are not shown in the figure. The GSH and Householder, on the other hand, can reproduce the original SDF with high accuracy. Both methods are based on the Householder procedure, which has an unconditional stability [79]. Figure 2(B) indicates the Huang–Rhys (HR) factors of secondary bath oscillators with nearest-neighbor couplings in a chain, that are obtained from different methods. The HR factor χj of a harmonic oscillator with frequency ω j is a normalized coupling strength given by κ ω χ = j j j. For the secondary modes, HR factors are defined with the frequencies of the oscillators and the coupling strengths with the nearest neighbors in the chain. As one compares the results from Bullaʼs method (green cross) and Bullaʼs method with EP (blue triangle), they are significantly different from each other. This shows that Bullaʼs recursion relation is numerically unstable. Comparing the Bullaʼs and GSH methods, one can see the Bullaʼs method (green cross) produces larger HR factors than the GSH method (red circle). The GSH bath transformation can produce oscillators with frequencies distributed on a narrower band. The reason for this difference is that the unitary transformation for the chain model is not unique. 3.1. Numerical stability of the transformations Bullaʼs method does not allow the secondary bath modes to have negative interactions, while the GSH has no such constraint. Since the unitary matrix for the GSH transform is constructed via orthogonalization of the random vectors, the signs of the interactions in a single chain can vary in each transformation, but their magnitudes are invariant. 3.1. Numerical stability of the transformations To test the numerical stability of the 1-D Wilson chain transformation methods, we perform back transformations from the chain-bath Hamiltonian to the star-bath Hamiltonian 6 New J. Phys. 16 (2014) 123008 J Huh et al Figure 2. Reconstructed spectral densities of the chlorosome from a chain-bath. (A). Reconstructed spectral densities of chlorosome from different numerical transforma- tions are compared with the original one. (B). Huang–Rhys (HR) factors of the secondary bath oscillators with nearest-neighbor couplings in a single chain model. Two different unitary mapping methods are compared. Red circles are calculated by the GSH transform. Green crosses and blue triangles are obtained from Bullaʼs method [5] with and without the extended precision (EP), respectively. Figure 2. Reconstructed spectral densities of the chlorosome from a chain-bath. (A). Reconstructed spectral densities of chlorosome from different numerical transforma- tions are compared with the original one. (B). Huang–Rhys (HR) factors of the secondary bath oscillators with nearest-neighbor couplings in a single chain model. Two different unitary mapping methods are compared. Red circles are calculated by the GSH transform. Green crosses and blue triangles are obtained from Bullaʼs method [5] with and without the extended precision (EP), respectively. (equation (2)) by a straightforward diagonalization of Ω˜n. The structured SDFs are reconstructed by the back transformation and then compared with the original SDF of the chlorosome, as an example system. The chlorosome is a giant light-harvesting antenna complex of green sulfur bacteria [78]. The excitation energy is transferred within the antenna via the fluctuating environment. Various models were developed to study the system from the open quantum dynamics perspective [6, 70, 71]. Here we use the SDF of the chlorosome that some of us [70] obtained via quantum mechanics/molecular mechanics calculations that contain 253 peaks corresponding to the quantum bath oscillators. In figure 2(A), only the peaks in 1300–1700 cm−1 are shown for clarity. The original SDF is plotted as a black line and filled black circles. Bullaʼs method (blue line) suffers from numerical instability as the iteration increases. Therefore, we also test extended precision (EP; 100 digits) with Bullaʼs method 7 New J. Phys. 16 (2014) 123008 J Huh et al (green line). The GSH curve is shown as a red line and unfilled red circles. Householder and Lanczos transformations of Γn in equation (3) are plotted in brown and purple lines, respectively. 3.2. Multiple-chain-bath model In this subsection, we apply the GSH transformation method to a couple of illustrative examples. First, to get some insights into the weakly coupled multiple chain model, we employ this method analytically to transform a bath with two oscillator modes. Then, we continue with a multidimensional example of a chlorosome. In the chain-bath model for two oscillators, the mixing of the two modes with frequencies ω ω ⩽ 1 2 leads to a HR factor for the primary mode χc: (11) χ χ = R , (11) c HR 1 = + + ω ω ( ) ( ) R f f 1 1 , (12) HR 2 3 2 2 2 1 χ χ = R , c HR 1 = + + ω ω ( ) ( ) R f f 1 1 , HR 2 3 2 2 2 1 = + + ω ω ( ) ( ) R f f 1 1 , (12) HR 2 3 2 2 2 1 (12) where κ κ = f 2 1 and χ κ ω = 1 1 2 1 2. In figure 3, the normalized HR factor RHR of equation (12) is plotted while varying the frequency ratio (ω ω 2 1) at fixed coupling strength ratios f, 0.5, 1 and 2. For fixed f, the values of RHR decrease as the frequency ratio increases. f determines the slopes of the curves. Larger f makes the curve decrease faster as ω ω 2 1 increases. When the oscillators have similar frequencies ω ω ≃1 2 1 , RHR is larger than 1, which makes the chain-bath couplings stronger than the star-bath model. However, as the frequency ratio increases RHR drops down and it can become arbitrarily small as the frequency difference increases. This gives a hint of 8 J Huh et al New J. Phys. 16 (2014) 123008 Figure 3. Normalized HR factor RHR for the example of bath with two oscillator modes. With selected fixed f values, the normalized HR factors are evaluated while varying the frequency ratio (ω ω 2 1). Figure 3. Normalized HR factor RHR for the example of bath with two oscillator modes. With selected fixed f values, the normalized HR factors are evaluated while varying the frequency ratio (ω ω 2 1). 3.2. Multiple-chain-bath model how to mix the oscillator modes and reduce the coupling strength of the primary modes by forming weakly coupled multiple chains. The oscillators, which have large frequency differences, should be mixed to make the weakly coupled multiple-chain-bath models. Next, we apply the GSH method to the example of chlorosome. The SP approach divides the bath oscillators into a sequence of groups of oscillators, as illustrated in figure 4(A) using a different color for each group. Figure 4(B) represents the LP scheme, where only the peaks below 500 cm−1 are shown for clarity. As indicated here, the oscillators are partitioned into six groups to use the LP scheme. In the LP scheme, the elements of the kth group are composed of + k N j eff -th (⩽N) modes, where Neff is the number of groups, j is an integer (⩾0) and N is the total number of oscillators. For example, when one has ten modes and three groups to partition, the SP approach groups modes of (1, 2, 3), (4, 5, 6) and (7, 8, 9, 10) as group 1, 2 and 3, respectively. On the other hand, the LP strategy makes the partition (1, 4, 7, 10), (2, 5, 8) and (3, 6, 9) for group 1, 2 and 3, respectively. In figure 5, the maximum HR factor and the corresponding coupling strength of the primary modes are plotted by varying the number of chains from one to six. The LP and SP schemes are used for this calculation. The maximum HR factor of the star-bath model is 0.0315. The single chain model has an even larger HR factor of the primary mode than the star-bath model for both partitioning schemes. The maximum HR factors from the SP scheme (blue cross) do not decrease as the number of chains increases. The figure shows, however, that the maximum HR factor (black circle) and the corresponding coupling strength (red triangle) decrease as the number of chains increases for the LP scheme. The maximum HR factor from the LP scheme with six chains is below 0.01, which corresponds to 10% of the corresponding harmonic frequency. Therefore six chains make the chain model suitable for implementation on quantum simulators, since a quantum simulator can have only a few parallel chains and, in 9 New J. Phys. 16 (2014) 123008 J Huh et al Figure 4. Partitioning schemes of the SDF. (A). 3.2. Multiple-chain-bath model The sequential partition of the spectral density of chlorosome is depicted. The group of oscillators is indicated with six different colors. (B). The leaping partition of the spectral density is depicted. The peaks in the spectral density of the chlorosome [70, 71] are partitioned into six groups. Only the peaks below 500 cm−1 are shown for clarity. Figure 4. Partitioning schemes of the SDF. (A). The sequential partition of the spectral density of chlorosome is depicted. The group of oscillators is indicated with six different colors. (B). The leaping partition of the spectral density is depicted. The peaks in the spectral density of the chlorosome [70, 71] are partitioned into six groups. Only the peaks below 500 cm−1 are shown for clarity. Figure 5. Maximum HR factor of primary modes of the chlorosome. The maximum HR factor (black circles) of primary modes and the corresponding coupling strengths (red triangles) are plotted as increasing the number of chains for the LP scheme. Blue crosses are used for the maximum HR factors from the SP strategy. Figure 5. Maximum HR factor of primary modes of the chlorosome. The maximum HR factor (black circles) of primary modes and the corresponding coupling strengths (red triangles) are plotted as increasing the number of chains for the LP scheme. Blue crosses are used for the maximum HR factors from the SP strategy. 10 J Huh et al New J. Phys. 16 (2014) 123008 Figure 6. The HR factor of each a chain of the chlorosome in different partition schemes. The bath oscillators of the chlorosome are transformed to a six chain-bath model with the two different grouping strategies. The SP (blue cross) and LP (black circle) strategies are compared. Lower HR factors lead to more feasible quantum simulator schemes. Figure 6. The HR factor of each a chain of the chlorosome in different partition schemes. The bath oscillators of the chlorosome are transformed to a six chain-bath model with the two different grouping strategies. The SP (blue cross) and LP (black circle) strategies are compared. Lower HR factors lead to more feasible quantum simulator schemes. addition, the primary mode HR factor is limited. In principle, the values can be reduced further as long as mixing modes is still possible. The LP and SP schemes are further compared in figure 6. This plot shows the HR factor of the primary modes of each chain. 3.2. Multiple-chain-bath model The results are indicated in blue crosses and black circles for the SP and LP schemes, respectively. As evidenced by the figure, the LP scheme gives all values below 0.01 while the SP strategy produces bigger values and the maximum value is more than four times larger than the LP values. Another important aspect of the LP scheme is that all of the primary HR factors have nearly similar values while the results of the SP scheme deviate greatly from each other. Appendix A. GSH algorithm We explain here in detail how to construct the unitary transform matrix Un of GSH transformation in equation (6) for Ω˜n. A MATLAB [77] script is given in appendix C. 1. Set the first column of Un to be the normalized coupling strength vector κ κ − || || n n 2 1 . n p g g n n 2 2. Assign random vectors to the remaining columns (from 2 to N). We use a normal distribution with the first column to be a mean vector for the random vectors. 2. Assign random vectors to the remaining columns (from 2 to N). We use a normal distribution with the first column to be a mean vector for the random vectors. 3. Perform the Gram–Schmidt orthogonalization to Un. 4. Compute Ω U U n n n † for Ω˜n. 4. Compute Ω U U n n n † for Ω˜n. 4. Conclusion and outlook In this paper we show that a multiple-chain-bath model, in combination with the leaping bath partitioning scheme, may lead to a practical implementation of quantum simulators for complex open quantum dynamics. We have shown that the multiple-chain-bath model can be employed for the realization of quantum simulators for open quantum systems or for numerical studies in classical computers. Furthermore, the LP scheme can reduce the primary mode coupling strength almost homogeneously for all parallel chains. The reason is that the mixing of oscillators with large frequency differences can result in small HR factors. The two-oscillator model was presented with an analytic expression for the chain transformation and provides a hint for the bath partitioning scheme, i.e. LP. We also tested the unitary transformation algorithm that exploits the GSH transformation, and compared the results with the values from Bullaʼs recursion method [5]. The GSH transformation can produce smaller HR factors of the 11 New J. Phys. 16 (2014) 123008 J Huh et al secondary bath modes with oscillators being in a narrower band. The numerical stability of Bullaʼs method was discussed and the GSH method was shown to be numerically stable. secondary bath modes with oscillators being in a narrower band. The numerical stability of Bullaʼs method was discussed and the GSH method was shown to be numerically stable. Our bath transformation method could be useful for the perturbative approaches as well, because of the resulting weak system-bath couplings. The effective spectral density can be obtained based on the chain-model transformation. It can also be used for the reduced density matrix methods [31, 32] for the simulation of non-Markovian dynamics. The effective bath approach with the parallel chain-bath model can also be useful for the HEOM method. The effective bath spectral density can reduce the number of Drude–Lorentzian peaks, then the HEOM method can handle larger systems [21]. Further work in this direction will be conducted. Acknowledgments We acknowledge Jarrod McClean, Florian Schroeder, Dr. Christoph Kreisbeck and Dr. Semion K Saikin for discussions. J H, T F and A A-G acknowledge support from the Center for Excitonics, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science and Office of Basic Energy Sciences under award DE-SC0001088. J H and S M and A A-G also acknowledge Defense Threat Reduction Agency grant HDTRA1-10-1-0046 and the Air Force Office of Scientific Research grant FA9550-12-1-0046. Further, A A-G is grateful for the support from Defense Advanced Research Projects Agency grant N66001-10-1- 4063, and the Corning Foundation for their generous support. M-H Y acknowledges the support from the National Basic Research Program of China Grant 2011CBA00300, 2011CBA00301, the National Natural Science Foundation of China Grant 61033001, 61361136003, and the Youth 1000-talent program. Appendix B. Example of permutation matrix Here we represent a permutation matrix P†, as an example. It permutes a vector of length 4 (v) to arrange odd and even elements sequentially, 12 New J. Phys. 16 (2014) 123008 J Huh et al ⎛ ⎝ ⎜ ⎜ ⎜ ⎞ ⎠ ⎟ ⎟ ⎟ ⎛ ⎝ ⎜ ⎜ ⎜ ⎞ ⎠ ⎟ ⎟ ⎟ ⎛ ⎝ ⎜ ⎜ ⎜ ⎞ ⎠ ⎟ ⎟ ⎟ = = v v v v v v v v v P 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 . (B.1) † 1 2 3 4 1 3 2 4 (B.1) Appendix C. LP scheme with GSH We provide here a MATLAB [77] script for the LP scheme with the GSH procedure. The script produces a single chain for a subblock, which is assigned by the user. Multiple chains can be obtained by using this script for each subblock. The details of the script can be found in the comments of the script, which are indicated with %. function [HRF,Dn,Xi]=LP(SDF,Sub,Neff) %-Inputs- p %SDF: Spectral density function = [frequency spectral-density] %Sub: Subblock of interest (starting index in the full SDF) %Neff: Number of subblocks (index step size for LP scheme) %SDF: Spectral density function = [frequency spectral-density] %SDF: Spectral density function = [frequency spectral-density %Sub: Subblock of interest (starting index in the full SDF) %Neff: Number of subblocks (index step size for LP scheme) %Sub: Subblock of interest (starting index in the full SDF) %Sub: Subblock of interest (starting index in the full SDF) %Neff: Number of subblocks (index step size for LP scheme) %Neff: Number of subblocks (index step size for LP scheme) %HRF: HR factor of the primary mode of the subblock %Dn: norm of the coupling vector (equivalent to the coupling strength of the primary mode) %Xi: Tridiagonal coupling bath coupling matrix % equation (10), OmegaTilde=T*Xi*T’, T*T’=I %Scale SDF with 1/pi SDF(:,2)=SDF(:,2)/pi; %dimension of the SDF dim=max(size(SDF)); %LP scheme for the subgroup SDF=spd(Sub:Neff:dim,:); %new dimension dim=max(size(SDF)); %t1: first column of U, U*U’=I t1=sqrt(SDF(:,2)); Dn=norm(t1); t1=t1/Dn; %Random vectors for the Gram-Schmidt orthogonalization %are assigned to columns from 2 to N. %Random vectors for the Gram-Schmidt orthogonalization %are assigned to columns from 2 to N. U0=randn(dim,dim-1); U0=randn(dim,dim-1); 13 J Huh et al New J. Phys. 16 (2014) 123008 U0=[t1 U0]; for k=2:dim U0(:,k)=U0(:,k)+t1; end %Gram-Schmidt orthogonalization, user should provide the GS routine. U=GS(U0); %OmegaTilde in equation 8 OmegaTilde=U’*diag(SDF(:,1))*U; %Hessenberg transformation [T,Xi]=hess(OmegaTilde); HRF=Dn2ˆ/Xi(1,1)2ˆ; d U0=[t1 U0]; for k=2:dim U0(:,k)=U0(:,k)+t1; end %Gram-Schmidt orthogonalization, user should provide the GS routine. %OmegaTilde in equation 8 %OmegaTilde in equation 8 OmegaTilde=U’*diag(SDF(:,1))*U; %Hessenberg transformation [T,Xi]=hess(OmegaTilde); HRF=Dn2ˆ/Xi(1,1)2ˆ; OmegaTilde=U’*diag(SDF(:,1))*U; %Hessenberg transformation [T,Xi]=hess(OmegaTilde); HRF=Dn2ˆ/Xi(1,1)2ˆ; end References [1] Breuer H P and Petruccione F 2006 The Theory of Open Quantum Systems (New York: Oxford University Press) [2] May V and Kühn O 2011 Charge and Energy Transfer Dynamics in Molecular Systems 3rd edn (Weinheim: Wiley-VCH) [3] van Amerongen H, Valkunas L and van Grondelle R 2000 Photosynthetic Excitons (Singapore: World Scientific) [4] Bulla R, Tong N H and Vojta M 2003 Phys. Rev. Lett. 91 170601 lla R, Tong N H and Vojta M 2003 Phys. Rev. Lett. 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English
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Spatiotemporal Interpolation Methods for the Application of Estimating Population Exposure to Fine Particulate Matter in the Contiguous U.S. and a Real-Time Web Application
International journal of environmental research and public health/International journal of environmental research and public health
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cc-by
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Lixin Li 1,*, Xiaolu Zhou 2, Marc Kalo 1 and Reinhard Piltner 3 Particle pollution, also known as particulate matter (PM), is composed of microscopic solids or liquid droplets that are so small that they can get deep into the lungs and cause serious health problems. Keywords: fine particulate matter (PM2.5); spatiotemporal interpolation; shape function; Inverse Distance Weighting (IDW); cross validation; population exposure; web application; visualization; real-time air pollution International Journal of Environmental Research and Public Health International Journal of Environmental Research and Public Health Spatiotemporal Interpolation Methods for the Application of Estimating Population Exposure to Fine Particulate Matter in the Contiguous U.S. and a Real-Time Web Application Lixin Li 1,*, Xiaolu Zhou 2, Marc Kalo 1 and Reinhard Piltner 3 Lixin Li 1,*, Xiaolu Zhou 2, Marc Kalo 1 and Reinhard Piltner 3 1 Department of Computer Sciences, Georgia Southern University, Statesboro, GA 30460, USA; marc.kalo@gmail.com 1 Department of Computer Sciences, Georgia Southern University, Statesboro, GA 30460, USA; marc.kalo@gmail.com g 2 Department of Geology and Geography, Georgia Southern University, Statesboro, GA 30460, USA; xzhou@georgiasouthern.edu 2 Department of Geology and Geography, Georgia Southern University, Statesboro, GA 30460, USA; xzhou@georgiasouthern.edu 3 Department of Mathematical Sciences, Georgia Southern University, Statesboro, GA 30460, USA; rpiltner@georgiasouthern.edu 3 Department of Mathematical Sciences, Georgia Southern University, Statesboro, GA 30460, USA; rpiltner@georgiasouthern.edu p g g * Correspondence: lli@georgiasouthern.edu; Tel.: +1-912-478-7646 Academic Editor: Kim Natasha Dirks Academic Editor: Kim Natasha Dirks Received: 28 March 2016; Accepted: 4 July 2016; Published: 25 July 2016 eceived: 28 March 2016; Accepted: 4 July 2016; Publish Abstract: Appropriate spatiotemporal interpolation is critical to the assessment of relationships between environmental exposures and health outcomes. A powerful assessment of human exposure to environmental agents would incorporate spatial and temporal dimensions simultaneously. This paper compares shape function (SF)-based and inverse distance weighting (IDW)-based spatiotemporal interpolation methods on a data set of PM2.5 data in the contiguous U.S. Particle pollution, also known as particulate matter (PM), is composed of microscopic solids or liquid droplets that are so small that they can get deep into the lungs and cause serious health problems. PM2.5 refers to particles with a mean aerodynamic diameter less than or equal to 2.5 micrometers. Based on the error statistics results of k-fold cross validation, the SF-based method performed better overall than the IDW-based method. The interpolation results generated by the SF-based method are combined with population data to estimate the population exposure to PM2.5 in the contiguous U.S. We investigated the seasonal variations, identified areas where annual and daily PM2.5 were above the standards, and calculated the population size in these areas. Finally, a web application is developed to interpolate and visualize in real time the spatiotemporal variation of ambient air pollution across the contiguous U.S. using air pollution data from the U.S. Environmental Protection Agency (EPA)’s AirNow program. Abstract: Appropriate spatiotemporal interpolation is critical to the assessment of relationships between environmental exposures and health outcomes. A powerful assessment of human exposure to environmental agents would incorporate spatial and temporal dimensions simultaneously. This paper compares shape function (SF)-based and inverse distance weighting (IDW)-based spatiotemporal interpolation methods on a data set of PM2.5 data in the contiguous U.S. 1. Introduction Particulate matter (PM) is the generic term for a broad class of chemically and physically diverse substances that exist as discrete particles (liquid droplets or solids) over a wide range of sizes [1]. Some particulates occur naturally, originating from volcanoes, dust storms, forest and grassland fires, living vegetation, and sea spray. Some other particulates are made from human activities, such as the burning of fossil fuels in vehicles, power plants, and various industrial processes [2]. The United States Environmental Protection Agency (EPA) first established national ambient air quality standards for PM in 1971. The published evidence supports an association between PM and an increased Int. J. Environ. Res. Public Health 2016, 13, 749; doi:10.3390/ijerph13080749 www.mdpi.com/journal/ijerph www.mdpi.com/journal/ijerph 2 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 Int. J. Environ. Res. Public Health 2016, 13, 749 risk of mortality. It has been shown that those with cardiovascular or respiratory conditions and the youth and elderly are the most susceptible to the adverse effects of PM. The pollutant class studied in this paper is specifically fine particulate matter, or PM2.5, which refers to particles with a mean aerodynamic diameter less than or equal to 2.5 micrometers. PM2.5 is considered one of the most unhealthy particulate air pollutants because it is more likely to be toxic and can be breathed more deeply into the lungs. PM2.5 has been associated with visibility reduction [3,4], acute stroke mortality [5], and daily mortality in many U.S. cities [6]. y y y y In order to find the association between air pollutants such as PM2.5 and health effects, researchers need to estimate pollutant concentrations in the continuous space-time domain. Since concentration values are typically measured only at discrete monitoring sites and at certain time instances, estimation of pollutant concentrations at unmeasured locations and times is needed. Implementing an appropriate interpolation method is critical to the assessment of relationships between air pollution exposure and health outcomes. p p Spatial interpolation has been well developed and widely used in Geographic Information Systems (GIS). It is used to estimate values at unknown locations based upon values that are spatially sampled. Traditional spatial interpolation models have been extensively investigated over the years. Popular spatial interpolation methods are Inverse Distance Weighting (IDW) [7,8], shape functions [9,10], radial basis functions [11], spline [12], natural neighbor [13], trend surfaces [14], Kriging [15], model-data fusion (sometimes called analysis) [16,17], and optimal interplation [18]. 1. Introduction IDW, shape functions, radial basis functions, splines, natural neighbor, and trend surfaces are deterministic methods. They provide no indication of the extent of possible errors. Their output is fully determined by the parameter values and the inputs. There are no strict assumptions about the variability or randomness of a feature. These methods are relatively simple to implement. On the other hand, Kriging, model-data fusion, and optimal interpolation are stochastic methods that possess some inherent randomness. The same set of parameter values and inputs will lead to an ensemble of different outputs. Stochastic methods provide probabilistic estimates. One of the advantages of stochastic methods is that they treat clusters more like single points and assign individual points within a cluster less weight than isolated data points, which helps to compensate for the effect of data clustering. In the field of atmospheric data analysis, model-data fusion and optimal interpolation methods are developed to include physics and chemistry of an air quality model in the interpolation mechanism and thus achieve better prediction and representation of air quality. Nowadays, modern sensors are able to monitor different variables (such as particulate matter, sulfur dioxide, and ozone) at an increasing temporal resolution, resulting in rich spatiotemporal data sets. This calls for appropriate theories and methods to deal with these data sets to gain a better understanding of the observed spatiotemporal processes. Traditionally, many GIS researchers treat space and time separately [19]. They simply reduce spatiotemporal interpolation problems to spatial interpolation problems by assuming that time can be incorporated by conducting a sequence of snapshots of spatial interpolations. Since the spatiotemporal interpolation considers the additional time attribute, it can provide more accurate predictions than pure spatial interpolation. However, adding the temporal domain implies that variability in space and time must be modeled, which is more complicated than modeling purely spatial or purely temporal variability. A review of some air pollution exposure assessment methods utilized in epidemiological studies and the use of GIS for resolving problems with spatiotemporal attributes can be found in [20]. Other work on spatiotemporal interpolation are presented in the literature [9,21–28]. The main challenge presented by the spatiotemporal interpolation relates to the spatiotemporal dependence structure, i.e., the relative importance of time with reference to space. A powerful assessment of human exposure to air pollution would incorporate spatial and temporal dimensions. 1. Introduction The temporal dimension of environmental exposure analysis is often ignored, underemphasized, or isolated from the spatial domain mainly due to the few efficient and effective tools to interpolate complex spatiotemporal datasets. The popular ArcGIS software (version 10.3, ESRI, Redlands, Int. J. Environ. Res. Public Health 2016, 13, 749 3 of 20 CA, USA) cannot handle spatiotemporal interpolation and is computationally inefficient with large datasets. This paper has three goals. First, it investigates and compares two different spatiotemporal interpolation methods for an actual set of PM2.5 data measured by U.S. EPA monitoring sites in the contiguous United States: shape function (SF)-based vs. Inverse Distance Weighting (IDW)-based methods using the so-called extension approach. The extension approach has been proposed in [9] to integrate space and time simultaneously by extending spatiotemporal interpolation problems into higher dimensional spatial interpolation problems. SF and IDW are originally deterministic spatial interpolation methods. Since they can be extended to higher dimensions, they are both suitable for the extension approach. Furthermore, IDW is one of the most commonly used interpolation methods [7,23,29–31] for GIS applications. Although SF was initially from engineering, it has shown great interpolation performance in various GIS application data such as real estate data [9] and air pollution data [23,24,32]. Second, after obtaining the comparison results of the SF-based and IDW-based spatiotemporal interpolation methods, we apply the better method to estimate population exposure to PM2.5 in the contiguous United States using interpolated daily PM2.5 concentration values at the centroids of census block groups. Third, we aim to develop a web application to interpolate and visualize in real time the spatiotemporal variation of ambient air pollution (including but not limited to PM2.5) across the contiguous U.S. using air pollution data from the U.S. EPA’s AirNow program. 2.1. Shape Function-Based Spatiotemporal Interpolation Using the Extension Approach Shape functions (SF) have been popular and utilized in engineering applications such as finite element algorithms [10,33]. Just like other traditional spatial interpolation methods used in GIS such as IDW [8] and Kriging [15], SF-based methods assume a stronger correlation among points that are closer than those farther apart. Therefore, SF-based methods can be spatial interpolation methods for GIS applications [9,25,34–38]. In addition, because the computational complexity of SF-based methods is linear, they can be efficient interpolation methods for large data sets. 2.1.1. General Formula of the SF-Based 3D Spatial Interpolation Method 2.1.1. General Formula of the SF-Based 3D Spatial Interpolation Method In order to apply SF-based interpolation methods, a mesh that divides the total domain into a finite number of simple sub-domains or elements should be generated. For a 3D spatial problem, a mesh composed of tetrahedral elements should be generated if one wants to use shape functions for tetrahedra to interpolate unknown values in the 3D (x, y, z) coordinate system. Considering the tetrahedral element in Figure 1, the SF-based interpolation result w at an unknown point (x, y, z) located inside the tetrahedron can be obtained by using the measurement values w1, w2, w3, and w4 at the four known locations, which serve as the corner vertices of the tetrahedron as in [9]: z)w1 + N2(x, y, z)w2 + N3(x, y, z)w3 + N4(x, y, z)w4 (1) (1) w(x, y, z) = N1(x, y, z)w1 + N2(x, y, z)w2 + N3(x, y, z)w3 + N4(x, y, z)w4 (1) where N1, N2, N3 and N4 are the following linear shape functions: N1(x, y, z) = V1 V , N2(x, y, z) = V2 V , N3(x, y, z) = V3 V , N4(x, y, z) = V4 V (2) (2) V1, V2, V3 and V4 are the volumes of the four sub-tetrahedra ww2w3w4, w1ww3w4, w1w2ww4, and w1w2w3w, respectively; and V is the volume of the bounding tetrahedron w1w2w3w4 as shown in Figure 1. 4 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 w1(x1,y1,z1) w3(x3,y3,z3) w4(x4,y4,z4) w(x,y,z) w2(x2,y2,z2) Figure 1. A tetrahedral element. Computing 3D shape functions by tetrahedral volume divisions. w1, w2, w3 and w4 are measured values, while the value w at the location (x, y, z) is unknown and needs to be interpolated. w1(x1,y1,z1) w1(x1,y1,z1) Figure 1. A tetrahedral element. Computing 3D shape functions by tetrahedral volume divisions. w1, w2, w3 and w4 are measured values, while the value w at the location (x, y, z) is unknown and needs to be interpolated. It can be seen from Figure 1 that V1 is the volume of the sub-tetrahedron with four corner vertices as the unknown point (x, y, z) and three known points 2–4. Suppose the unknown point moves closer to the known point 1. V1 is increasing, while V2, V3 and V4 are decreasing, which lead to the increment of N1 and decrement of N2, N3 and N4. 2.1.1. General Formula of the SF-Based 3D Spatial Interpolation Method In an extreme case, when the unknown point moves to the exact location 1, the weight of N1 becomes 1 and the other three weights N2, N3 and N4 become 0. Similar observations can be made that any of the other three known points 2–4 will contribute a heavier weight in interpolating the value at the unknown point when the unknown point gets closer to this particular known point. In finite element methods, shape functions of different orders (linear, quadratic, cubic, etc.) are used. In engineering, finite elements are used to approximate processes governed by differential equations such as deformations and stresses in a car. Whereas in engineering the nodal values at the corners of finite elements are all unknown and have to be computed from a large system of equations, in GIS applications, the nodal values at the element corner points come from measured data collections. The common point between finite element and GIS applications is that with nodal values the interpolation function can be evaluated for the complete domain. The size of the finite elements depends on the gradients and the changes in the function. For high gradients and oscillating functions, more elements of smaller size are needed. For the data interpolation, the situation is similar: if we expect high gradients and a lot of changes in a relatively small area, then we would ideally need a sufficiently high number of discrete data values to result automatically in a larger number of smaller elements. 2.1.2. Extension Approach of the SF-Based Spatiotemporal Interpolation Method Although spatial interpolation methods are well developed and widely adopted in various GIS applications [39–42] , the traditional spatial interpolation methods face many challenges when handling spatiotemporal data because of the addition of the time attribute of the data set. One of the major challenges is that traditional GIS researchers tend to treat space and time separately when interpolation needs to be conducted in the continuous space-time domain. The primary strategy identified from the literature is to reduce spatiotemporal interpolation problems to a sequence of snapshots of spatial interpolations [19]. However, integrating space and time simultaneously is anticipated to yield better interpolation results than treating them separately for certain typical GIS applications [43]. In order to integrate space and time simultaneously for a spatiotemporal interpolation, the extension approach has been proposed in [9] and reviewed in [37,38]. This approach treats time as another dimension in space, thereby extending the spatiotemporal interpolation problem into a higher-dimensional spatial interpolation problem. Applications using the extension approach can be found in [9,32,44,45]. To develop the extension approach for SF-based interpolation methods, Int. J. Environ. Res. Public Health 2016, 13, 749 5 of 20 we substitute the z variable in Equations (1) and (2) by ct, where t is the time variable and c is a factor of [spatial distance unit/time unit]. Equations (3) and (4) define our SF-based spatiotemporal interpolation method for 2D space and 1D time problems: we substitute the z variable in Equations (1) and (2) by ct, where t is the time variable and c is a factor of [spatial distance unit/time unit]. Equations (3) and (4) define our SF-based spatiotemporal interpolation method for 2D space and 1D time problems: w(x, y, ct) = N1(x, y, ct)w1 + N2(x, y, ct)w2 + N3(x, y, ct)w3 + N4(x, y, ct)w4 (3) (3) where N1, N2, N3 and N4 are the following linear shape functions: where N1, N2, N3 and N4 are the following linear shape functions: N1(x, y, ct) = V1 V , N2(x, y, ct) = V2 V , N3(x, y, ct) = V3 V , N4(x, y, ct) = V4 V (4) (4) Please note that there are some assumptions and resulting limitations for this approach. We assume that there are sufficient data measurements in space and time so that simple functions can be used to describe what is happening between two measurements. 2.1.2. Extension Approach of the SF-Based Spatiotemporal Interpolation Method If there would be a relatively large time interval or data are scarcely sampled in space, and the type of data under consideration have the potential of strong oscillations between the points in space and time, we would not be able to use a simple linear function to interpolate from one space-time point to the next point. Therefore, before using this simple spatiotemporal approach, we have to make sure that the process that we analyze cannot show strong oscillations, and that we have sufficient measurements in space and time. We are only using the method to evaluate for events that already happened. We are not trying to predict the future with this method. 2.2. IDW-Based Spatiotemporal Interpolation Using the Extension Approach Inverse Distance Weighting (IDW) is also known as Shepard’s method [7,8]. Similar to SF-based interpolation methods, IDW is based on Tobler’s First Law of Geography [46], which states: “Everything is related to everything else, but near things are more related than distant things”, page 236. IDW is generally considered a spatial interpolation method, but this paper applies IDW to spatiotemporal interpolation by using the extension approach and treating time as a third dimension [9,37]. 2.3.1. K-Fold Cross Validation Classic validation divides the full data set into two data sets: a training data set and a validation data set. The validation data set is used for estimating the performance of the interpolation method based on the training data set. The interpolation method with the smallest error is selected as the best method. However, a potential flaw is that we may miss some characteristics in the full data set and make an inaccurate estimate of our model’s interpolation ability. Thus, k-fold cross validation is used to avoid this limitation. In this framework, the full data set is randomly split into k equal-sized data sets, with one group as the validation set and the remaining k-1 groups together forming the training set. This is repeated k times. In practice, 10-fold (k = 10) cross-validation is accepted as providing a highly accurate estimate of a model’s prediction errors. For large data sets, this approach may be computationally expensive. Using 10-fold cross validation, the PM2.5 data set in our experiment is partitioned to ten nearly equally sized folds randomly. Ten iterations of training and validation are performed such that, within each iteration, a different fold of the data is held-out for validation while the remaining nine folds are used for learning. More specifically, within each iteration, the following two actions are taken: 1. The points in one fold (test data) of the PM2.5 data set are interpolated using the remaining nine folds (training data). Therefore, each point in the test data will have both the original PM2.5 concentration measurement and an interpolated PM2.5 concentration value. 1. The points in one fold (test data) of the PM2.5 data set are interpolated using the remaining nine folds (training data). Therefore, each point in the test data will have both the original PM2.5 concentration measurement and an interpolated PM2.5 concentration value. concentration measurement and an interpolated PM2.5 concentration value. 2. Error statistics are calculated to compare the original and interpolated PM2.5 values in the test data. p Error statistics are calculated to compare the original and interpolated PM2.5 values in the test data. 2.2.1. General Formula of the IDW-Based Spatial Interpolation Method According to [47], the general formula of the IDW-based interpolation method in 2D space is w(x, y) = N ∑ i=1 λiwi, λi = ( 1 di )p ∑N k=1( 1 dk )p (5) (5) where w(x, y) is the interpolated value at the unknown (or unsampled) location (x, y), N is the number of nearest known points surrounding (x, y), wi are the measurement values at the nearest known points of (xi, yi) (with 1 ≤i ≤N), λi are the weights assigned to wi, di are the Euclidean distances between each (xi, yi) and (x, y), and p is the exponent that influences the weighting of wi on w. 2.2.2. Extension Approach of the IDW-Based Spatiotemporal Interpolation Method The formula of the extension approach of IDW used in this paper is The formula of the extension approach of IDW used in this paper is w(x, y, ct) = N ∑ i=1 λiwi, λi = ( 1 di )p ∑N k=1( 1 dk )p (6) (6) where di = q (xi −x)2 + (yi −y)2 + c2(ti −t)2 (7) di = q (xi −x)2 + (yi −y)2 + c2(ti −t)2 (7) 6 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 and c is a factor defined as [spatial distance unit/time unit]. Compared with Equation (5), Equation (6) replaces w(x, y) with w(x, y, ct) and calculates the distance di using the 3D Euclidean distance between (xi, yi, cti) and (x, y, ct). 2.3. Cross Validation The first goal of this paper is to compare whether SF-based or IDW-based spatiotemporal interpolation using the extension approach is more accurate in interpolating an actual set of data of daily fine particulate matter PM2.5 in the contiguous United States. K-fold cross validation [48] is used in this paper for this purpose. 3. Experimental Data The data used in this study are daily PM2.5 concentrations measured in 2009 by U.S. EPA monitoring sites in the contiguous United States. 2.4. Linking PM2.5 to Census Population We collected population data at the census block group level. To map PM2.5 and population spatial distribution, we created choropleth maps based on the interpolated values as well as population data. Because PM2.5 may exhibit different spatial patterns in different seasons, we also investigated the seasonal variations. In order to associate the PM2.5 values with the national standard, the revised U.S. EPA National Ambient Air Quality Standards for PM2.5 in 2006 were adopted in this paper. We conducted spatial queries to identify areas where annual and daily PM2.5 are above the standard and calculated the population size in these areas. 2.3.2. Error Statistics The error statistics used in this paper are: MAE (Mean Absolute Error), MSE (Mean Squared Error), RMSE (Root Mean Squared Error) and MARE (Mean Absolute Relative Error). They are defined as follows: MAE = ∑N i=1 | Ii −Oi | N MSE = ∑N i=1(Ii −Oi)2 N (8) RMSE = s ∑N i=1(Ii −Oi)2 N MARE = ∑N i=1 |Ii−Oi| Oi N (8) where N is the number of observations, Ii is the interpolated value, and Oi is the original measurement value. For each iteration of 10-fold cross validation, we have the assumption that a different set of training data has true measurements. From the mathematical point of view, it is reasonable to calculate averages of 10 sets of error statistics. We use MAE, MSE, RMSE and MARE to denote the average error statistics results in this paper. where N is the number of observations, Ii is the interpolated value, and Oi is the original measurement value. For each iteration of 10-fold cross validation, we have the assumption that a different set of training data has true measurements. From the mathematical point of view, it is reasonable to calculate averages of 10 sets of error statistics. We use MAE, MSE, RMSE and MARE to denote the average error statistics results in this paper. In addition, we use an R2 error statistic, which is also known as the coefficient of determination. The regular R2 error statistic measures how close the data are to the fitted regression line, whereas the R2 . Res. Public Health 2016, 13, 749 7 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 7 of 20 in [49] measures how close the data are to the 1–1 line. In this paper, we use the R2 error statistic defined in [49]: R2 CV = max(0, 1 −RMSE2 MSEobs ) MSEobs = ∑N i=1(Oi −O)2 N (9) (9) where O is the mean of the original values. As for the other error statistics in Equation (8), the average of the ten R2 CV results needs to be calculated. We use R2 CV to denote the average R2 CV result in this paper. 3.1. PM2.5 Data Set with Measurements The data coverage contains locations of the monitoring sites, the daily concentration measurements of PM2.5, and the days of the measurements. We obtained a number of data sets from the U.S. EPA website [50] and reorganized them into a data set with the schema (id, x, y, [time], w), where x and y are the longitude and latitude coordinates of the monitoring sites, [time] is (year, month, day) when a PM2.5 measurement is taken, and w is the measured PM2.5 value. The reorganized data set has some entries with zero PM2.5 values, which means no measurements were available at a particular site and on a particular day. After all the zero entries are deleted, there are 146,125 daily measurements at 955 monitoring sites. The monitoring sites are illustrated as stars (∗) in Figure 2. Figure 2. U.S. Environmental Protection Agency (EPA) monitoring sites. These monitoring sites have PM2.5 (fine particulate matter) measurements across the contiguous United States in 2009. Figure 2. U.S. Environmental Protection Agency (EPA) monitoring sites. These monitoring sites have PM2.5 (fine particulate matter) measurements across the contiguous United States in 2009. Int. J. Environ. Res. Public Health 2016, 13, 749 8 of 20 4.1.1. Choice of Time Scale In order to decide on an appropriate time scale for the SF-based method using the extension approach, we tested four time scales as shown in Table 1. The factor c in the table is from Equations (3) and (4). Table 1. Four times scales tested for the PM2.5 (fine particulate matter) data set. Table 1. Four times scales tested for the PM2.5 (fine particulate matter) data set. Time Scale A Scale B Scale C Scale D (c = 1) (c = 1/10) (c = 1/5) (c = 1/15) 01/01/2009 1 0.1 0.2 0.067 01/02/2009 2 0.2 0.4 0.133 01/03/2009 3 0.3 0.6 0.2 01/04/2009 4 0.4 0.8 0.267 . . . . . . . . . . . . . . . 12/31/2009 365 36.5 73 24.333 A challenge of using the extension approach for spatiotemporal interpolation is the correlation between space and time, and which choice of the factor c is optimal for a particular data set. This is an open question and a research topic in GIS that has been rarely studied. In this paper, authors tested only four possible time scales in Table 1. More research is needed to address this challenge in the future. 4.1.2. Cross Validation and Error Statistics 3.2. Census Block Group Data Set to Interpolate In our experiment, we want to interpolate daily PM2.5 concentration values in 2009 at the centroids of all the 207,630 census block groups in the contiguous United States. Census block groups are statistical divisions of census tracts and are generally defined to contain between 600 and 3000 people. They are the smallest geographical unit for which the United States Census Bureau publishes sample data. Our experimental data set with locations to compute interpolation has the format of (id, x, y) with id as the identification number of a census block group and (x, y) as the longitude and latitude coordinates of the centroid of a census block group. Since PM2.5 concentration values at the centroid of each census block group and on each day in 2009 are not measured, there are 207,630 × 365 = 75,784,950 PM2.5 values to be interpolated. The motivation of interpolating at the small geographic level of the census block group is that we aim to link the interpolation results with the census block group population data in the same year for the second goal of this paper. As discussed in the Results section of the paper, we analyze population exposure to PM2.5 and estimate the U.S. population with unhealthy PM2.5 exposure. In future work, such estimates are important and we plan to link them to a variety of health outcomes to evaluate PM2.5’s adverse impact on human health. 4. Results 4.1. Cross Validation Results of the SF-Based Method 4.1.2. Cross Validation and Error Statistics Ten-fold cross validation was implemented to test the four time scales in Table 1. Since there are ten iterations in 10-fold cross validation and a different fold of the data is held-out for validation during each iteration, the average of ten error statistics has been calculated for each error statistic in Equation (8). q Table 2 shows the results for the average error statistics (MAE, MSE, RMSE, MARE, and R2 CV) using the SF-based extension method for the PM2.5 data set. All of these five measures of error 9 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 statistics are based on interpolated and original values, Ii and Oi in Equations (8) and (9), but they have different sensitivity to error patterns. The ideal situation is that MAE, MSE, RMSE, and MARE are lowest, while R2 CV is the highest for the same time scale choice. If not, we need to make a choice according to the characteristics of the five error measures. MSE, RMSE, and R2 CV are sensitive to individual outliers. MAE is less sensitive to outliers but could not reflect the relative prediction errors. MARE is less sensitive to outliers and also incorporates the predictive mean to measure the error from a model prediction. The same size of an error is not acceptable for a small predicted mean but could be acceptable for a large predicted mean. MARE is a better choice to evaluate overall model performance. However, if outliers are major concerns, RMSE or R2 CV would be better choices. Table 2. Error statistics for the PM2.5 data set using the shape function-based extension method and 10-fold cross validation before removing outliers. Table 2. Error statistics for the PM2.5 data set using the shape function-based extension method and 10-fold cross validation before removing outliers. Error Scale A Scale B Scale C Scale D Statistics (c = 1) (c = 1/10) (c = 1/5) (c = 1/15) MAE 3.1512 3.5576 3.2463 3.7307 MSE 85.8621 78.5322 78.4890 77.1072 RMSE 8.8832 8.6045 8.6067 8.5023 MARE 3.2162 0.4158 0.3745 0.4365 R2 CV 0.3079 0.3226 0.3138 0.3382 We produced a scattered plot to compare observed daily PM2.5 values with interpolated daily PM2.5 values across monitoring sites. Please see Figure 3. Descriptive statistics show that the original PM2.5 values contain 16 outliers with PM2.5 values above 250 µg/m3, which were much higher than the normal range. 4.1.2. Cross Validation and Error Statistics According to the National Ambient Air Quality Standards (NAAQS) established by the U.S. EPA under authority of the Clean Air Act, the 24 h standard for PM2.5 is met if the three-year average of the annual 98th percentile of values at designated monitoring sites in an area is less than or equal to 35 µg/m3 [51]. The PM2.5 values above 250 µg/m3 might be wrongly recorded or some short and extreme conditions happened. These conditions are not usual, so we removed these 16 outliers with PM2.5 values greater than 250 µg/m3 from the original 146,124 values. The new error statistics result after removing the outliers are recorded in Table 3. Figure 3. Scattered plots. Comparing observed daily PM2.5 values with interpolated daily PM2.5 values across monitoring sites across the contiguous United States in 2009. Figure 3. Scattered plots. Comparing observed daily PM2.5 values with interpolated daily PM2.5 values across monitoring sites across the contiguous United States in 2009. Int. J. Environ. Res. Public Health 2016, 13, 749 10 of 20 Table 3. Error statistics for the PM2.5 data set using the shape function-based extension method and 10-fold cross validation after removing outliers. Error Scale A Scale B Scale C Scale D Statistics (c = 1) (c = 1/10) (c = 1/5) (c = 1/15) MAE 3.0941 3.4976 3.1812 3.6751 MSE 42.2910 37.7745 35.6601 39.2077 RMSE 6.5032 6.1461 5.9716 6.2616 MARE 3.2135 0.4128 0.3708 0.4349 R2 CV 0.4817 0.5371 0.5630 0.5195 Compared with Table 2, Table 3 shows better error statistics for all measures. Scale C outperformed the other three scales on all error statistics, except for Scale A on MAE. However, Scale A performed significantly poorly on MARE, RMSE, R2 CV, and MSE. Thus, Scale C is selected as the best time scale for daily PM2.5 interpolation using the SF-based extension method. Compared with Table 2, Table 3 shows better error statistics for all measures. Scale C outperformed the other three scales on all error statistics, except for Scale A on MAE. However, Scale A performed significantly poorly on MARE, RMSE, R2 CV, and MSE. Thus, Scale C is selected as the best time scale for daily PM2.5 interpolation using the SF-based extension method. 4.2. Cross Validation Results of the IDW-Based Method 4.2. Cross Validation Results of the IDW-Based Method 4.2.1. Choice of Time Scale, Number of Neighbors, and Exponents In order to choose an appropriate time scale for the IDW-based method using the extension approach and compare it with the SF-based method, the same four times scales in Table 1 were tested for the IDW-based method. We evaluated 45 IDW methods with five choices for the number of nearest neighbors N (3, 4, 5, 6 and 7) and nine choices for the exponent p (1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5 and 5.0). 4.2.2. Cross Validation and Error Statistics Similar to evaluating the SF-based method, 10-fold cross validation was implemented to test the time scales, as well as the choices for the number of nearest neighbors N and the exponent p. The optimal average error statistics among the forty-five combinations of N and p are summarized in Table 4 for each chosen time scale, along with the values of N and p when the optimal averages were obtained. Based on Table 4, we choose Scale B as the best of the four time scales for the IDW-based method since it provides the lowest MARE, MSE, and RMSE, as well as the second highest R2 CV. Table 4. Error statistics for the PM2.5 data set using the IDW-based extension method and 10-fold cross validation. MAE (Mean Absolute Error), MSE (Mean Squared Error), RMSE (Root Mean Squared Error), MARE (Mean Absolute Relative Error) and R2 CV are the optimal averages of the error statistics. Error Scale A Scale B Scale C Scale D Statistics (c = 1) (c = 1/10) (c = 1/5) (c = 1/15) 3.1586 3.2856 3.1070 3.4207 MAE (N = 4, p = 1.0) (N = 3, p = 2.0) (N = 3, p = 2.0) (N = 5, p = 2.5) 75.3792 67.8379 68.0293 68.2309 MSE (N = 7, p = 1) (N = 7, p = 1.5) (N = 6, p = 1.0) (N = 7, p = 1.5) 8.3258 7.8888 7.8967 7.9143 RMSE (N = 7, p = 1.0) (N = 7, p = 1.5) (N = 7, p = 1.0) (N = 7, p = 1.5) 2.7005 0.3803 0.9717 0.3963 MARE (N = 7, p = 1.0) (N = 3, p = 5.0) (N = 3, p = 5.0) (N = 3, p = 2.5) 0.3789 0.4413 0.4416 0.4374 R2 CV (N = 7, p = 1.0) (N = 7, p = 1.0) (N = 7, p = 1.0) (N = 7, p = 1.0) The decision of what values of N and p to use in order to achieve the best IDW interpolations possibly depends on the error statistic deemed most important to optimize. It should be noted 11 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 that [31] also discussed the character of the exponent and suggested that the exponent should be deduced from the form of pollution encountered. 4.2.2. Cross Validation and Error Statistics For air pollution, [31] suggests that elementary reasoning shows that the exponent should be 2 or 3, but more sophisticated considerations could show that the exponent may vary between 1 and 3. For our study, the best exponent could depend on the specific outcome or measure we wanted to model. Hence, we experiment with different exponents p (1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5 and 5.0) in order to select the one with the best performance via error analysis. If it were only possible to run an interpolation for one choice of the number of nearest neighbors N and the exponent p (because of time constraints, lack of computational resources, etc.), then the configurations of (N = 7, p = 1.0) and (N = 3, p = 5.0) seem better than the other configurations that were tested. The configuration of (N = 7, p = 1.0) yields the second highest R2 CV among all time scales with a very close result to the highest R2 CV, whereas the configuration of (N = 3, p = 5.0) yields the least MARE among all time scales. In order to further investigate the difference between configurations of (N = 7, p = 1.0) and (N = 3, p = 5.0) under Scale B, we conducted a further experiment to compare just these two configurations. The comparison results are shown in the first two columns of Table 5. We consider the configuration of (N = 3, p = 5.0) better than (N = 7, p = 1.0) under Scale B because (N = 3, p = 5.0) yields a smaller MARE. Similar to the SF-based interpolation method, we removed the same outliers, recomputed the error statistics for the configuration of (N = 3, p = 5.0) under Scale B, and recorded them in the third column of Table 5. All of the error statistics improved after removing outliers. Table 5. Error statistics comparison of two configurations under Scale B using the IDW-based extension method and 10-fold cross validation. Table 5. Error statistics comparison of two configurations under Scale B using the IDW-based extension method and 10-fold cross validation. extension method and 10-fold cross validation. 4.2.2. Cross Validation and Error Statistics Error Statistics N = 7, p = 1.0 N = 3, p = 5.0 N = 3, p = 5.0 Scale B (c = 1/10) Scale B (c = 1/10) Scale B (c = 1/10) before Removing Outliers before Removing Outliers after Removing Outliers MAE 3.4519 3.3378 3.2765 MSE 68.0348 79.5497 37.5608 RMSE 7.8909 8.6320 6.1287 MARE 1.2594 0.3803 0.3773 R2 CV 0.4413 0.3359 0.5399 4.3. Comparison of SF-Based and IDW-Based Extension Methods 4.3. Comparison of SF-Based and IDW-Based Extension Methods The first goal of this paper is to compare the performance of the SF-based and IDW-based spatiotemporal interpolation methods in order to find the most suitable method for the PM2.5 data. It is evident from the error statistics, as shown in Tables 2 and 3 for the SF-based method and Tables 4 and 5 for the IDW-based method, that Scale C using the SF-based method is the best interpolation method among all the methods that we have tested for the PM2.5 data set. Both the SF-based and IDW-based methods see improvements in the accuracy of all error statistics, except MAE, when choosing a different time scale than Scale A, with significant improvement of MARE. The SF-based method outperforms the IDW-based method even in the IDW-based method’s best scenarios, i.e., the combinations of the number of nearest neighbors and exponents that minimize the relevant error statistics. Therefore, we choose the SF-based extension method using Scale C to interpolate the PM2.5 data set for population exposure analysis. In addition to accuracy comparison based on cross validation, the SF-based spatiotemporal interpolation method using the extension approach is computationally efficient because the algorithm is linear according to Equations (3) and (4). On the other hand, the IDW-based method is non-linear according to Equation (6). Therefore, the IDW-based spatiotemporal interpolation method is not as computationally efficient as the SF-based method. Int. J. Environ. Res. Public Health 2016, 13, 749 12 of 20 12 of 20 4.4. Population Exposure Analysis The second goal of this paper is to evaluate the population exposure to fine particulate matter PM2.5 in the contiguous United States. Annually updated population data are only available from the five-year American Community Survey at the census block group level. Therefore, we used census block groups in our analysis. The SF-based spatiotemporal interpolation using Scale C and the extension approach was implemented to compute a total of 75, 784, 950 (207, 630 × 365) PM2.5 values at the centroids of 207, 630 census block groups in the contiguous U.S. on each day in 2009. The interpolated census block group-level PM2.5 was then linked to 2009 census block group population data. To analyze the spatial relationship between the PM2.5 concentration and the population distribution at the census block group level, we first plot the population distribution in Figure 4a. Second, we plot the annual PM2.5 average values in Figure 4b. Several hotspots of high PM2.5 values, such as central south California, the Idaho–Montana border, and some regions in Pennsylvania, are distinctively shown in Figure 4b. Figure 4. Spatial relationship between the PM2.5 concentration and the population distribution across the contiguous United States in 2009. (a) population distribution; (b) annual average PM2.5. We used natural breaks to define the color ramps. A lighter color represents a smaller value, while a darker color represents a higher value. Figure 4. Spatial relationship between the PM2.5 concentration and the population distribution across the contiguous United States in 2009. (a) population distribution; (b) annual average PM2.5. We used natural breaks to define the color ramps. A lighter color represents a smaller value, while a darker color represents a higher value. 13 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 To investigate whether this pattern varies in different seasons, we break the annual average into seasonal averages. Because we used 2009 data, January, February, and December are combined as the winter season. Spring starts from March and ends in May. Summer starts from June and ends in August. The rest of the time is the fall season. Figure 5 shows the seasonal differences. We find that, in spring, the average PM2.5 values were high in the west and mountainous areas. The values substantially decreased in summer. In fall, the values increased in the southeast region. Some areas such as central south California had high PM2.5 values almost all year around. Figure 5. 4.4. Population Exposure Analysis Seasonal differences. The average PM2.5 in different seasons across the contiguous United States in 2009. In order to make the color scheme consistent in four seasons, we manually defined the classification scheme. The legend shows the class ranges. Figure 5. Seasonal differences. The average PM2.5 in different seasons across the contiguous United States in 2009. In order to make the color scheme consistent in four seasons, we manually defined the classification scheme. The legend shows the class ranges. In addition, we observe from Figure 5 that a region near the Idaho–Montana border shows higher PM2.5 values during spring and winter than during summer and fall of the year 2009. To verify this pattern, we used the PM2.5 Federal Reference Method (FRM)/Federal Equivalent Method (FEM) Mass (88101) daily data (arithmetic mean value) from AirNow to plot the PM2.5 values in 2009 at two monitoring stations in Idaho and Montana, as shown in Figure 6. The trends at these two stations are consistent with what we observed in Figure 5. The reason for this pattern remains unclear, despite efforts elucidate its cause. More investigation on the cause for high PM2.5 values in this region in 2009 is needed in the future. Finally, in order to associate the PM2.5 values with the national standard, the revised U.S. EPA National Ambient Air Quality Standards for PM2.5 in 2006 [51] were adopted in this paper: • 35 micrograms per cubic meter (35 µg/m3) for 24 h: • 15 micrograms per cubic meter (15 µg/m3) for the annual m W id if bl k h h l PM l We identify block groups that have annual PM2.5 values greater than 15 µg/m3. Int. J. Environ. Res. 4.4. Population Exposure Analysis                                                             0 10 20 30 Jan 2009 Apr 2009 Jul 2009 Oct 2009 Jan 2010 PM2.5 (µg/m3) PM2.5 at Station Shoshone, Idaho PM2.5 at Station Silver Bow, Montana PM2.5 at Station Shoshone, Idaho PM2.5 at Station Shoshone, Idaho Jul 2009                                                                                                                 0 10 20 30 40 50 Jan 2009 Apr 2009 Jul 2009 Oct 2009 Jan 2010 PM2.5 (µg/m3) PM2.5 at Station Silver Bow, Montana PM2.5 at Station Silver Bow, Montana Figure 6. Verification of a spatial pattern in a region near the Idaho–Montana border in 2009. Plots of PM2.5 measurements at two monitoring stations in Idaho and Montana using PM2.5 daily data from AirNow in 2009. Figure 7 shows the geographic distribution of such census block groups with the annual and/or 24 h exceeding the U.S. EPA National Ambient Air Quality PM2.5 standards. The results suggest: Figure 7 shows the geographic distribution of such census block groups with the annual and/or 24 h exceeding the U.S. EPA National Ambient Air Quality PM2.5 standards. The results suggest: • there is a population of 27, 809, 017 (27.8 million) residing in 18, 017 census block groups in the contiguous United States with an annual PM2.5 exceeding the national standard of 15 µg/m3; • more than one-third of the U.S. 4.4. Population Exposure Analysis Public Health 2016, 13, 749 14 of 20 14 of 20                                                             0 10 20 30 Jan 2009 Apr 2009 Jul 2009 Oct 2009 Jan 2010 PM2.5 (µg/m3) PM2.5 at Station Shoshone, Idaho                                                                                                                 0 10 20 30 40 50 Jan 2009 Apr 2009 Jul 2009 Oct 2009 Jan 2010 PM2.5 (µg/m3) PM2.5 at Station Silver Bow, Montana Figure 6. Verification of a spatial pattern in a region near the Idaho–Montana border in 2009. Plots of PM2.5 measurements at two monitoring stations in Idaho and Montana using PM2.5 daily data from AirNow in 2009. 4.5. Web Application The third goal of this paper is to develop a web application to interpolate and visualize in real time the spatiotemporal variation of ambient air pollution (including but not limited to PM2.5) across the contiguous U.S. The web application is based on the MEAN framework [52]. This framework relies on the MongoDB database [53] to store the application’s data, Express framework [54] to facilitate HTTP routing, AngularJS [55] to construct an MVC (Model View Controller) architecture to simplify building of responsive web pages, and NodeJS [56] to support the application. The use of MongoDB, Node.js, Express, and AngularJS provides a unified development approach. Each of the technologies is based on JavaScript which allows for more code reuse and less context switching for developers as they move between server side and client side application development. In addition, a REST (REpresentational State Transfer) [57] Application Program Interface (API) is utilized to handle requests from clients, including user sign up and authentication, requests for interpolated pollution data, and requests for triangulations of measurement sites. A REST call is used to initiate the downloading of pollution data from the AirNow [58] File Transfer Protocol (FTP) server and initiate the triangulation and interpolation of the data using the SF-based method. AirNow is a U.S. EPA program that provides real-time observed air quality information across the U.S., Canada, and Mexico. It receives real-time air quality observations from over 2,000 monitoring stations and collects forecasts for more than 300 cities. The AirNow program includes a web services API for accessing current and historical pollution data [59]. However, queries to this service are generally rate limited to 500 per hour. Therefore, the web application presented in this paper uses an alternative FTP server method to access the AirNow data. This web application uses an SF-based interpolation to compute and update any hour/parameter combination when data has not been updated. Using this method, the system can always include the data for the latest downloaded hour and may include data for previous hours if a time-based interpolation has been calculated. Triangulations are stored in the MongoDB database in a “triangles” collection. When a query is received, the web application can use a geospatial query supported by MongoDB to locate the containing triangle in the triangulation and interpolate the PM2.5 concentration. 4.4. Population Exposure Analysis population (115, 310, 354) residing in 80, 399 census block groups where PM2.5 exceeded 35 µg/m3 for at least one day in 2009. • there is a population of 27, 809, 017 (27.8 million) residing in 18, 017 census block groups in the contiguous United States with an annual PM2.5 exceeding the national standard of 15 µg/m3; • more than one-third of the U.S. population (115, 310, 354) residing in 80, 399 census block groups where PM2.5 exceeded 35 µg/m3 for at least one day in 2009. Figure 7. Geographic distribution of census block groups in the contiguous United States that exceeded the PM2.5 air quality standards in 2009. Figure 7. Geographic distribution of census block groups in the contiguous United States that exceeded the PM2.5 air quality standards in 2009. Figure 7. Geographic distribution of census block groups in the contiguous United States that exceeded the PM2.5 air quality standards in 2009. 15 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 15 of 20 4.5. Web Application In order to use the web application, the user needs to sign up by filling out a simple form or log in if they already have an account at the website [60]. After successful log in, the user will see the screen in Figure 8. The screen includes an options menu on the left and an embedded Google Maps application on the right. The Google Maps application is the main panel used for visualization of pollution data, developed using the Google Maps API. When the user changes visualization options in the options menu, such as selecting the pollution parameter type, date, time, or visualization rendering parameters, the data in the Google Maps application will be updated automatically and responsively rendered. Visualization of the pollution data is rendered on the client side by embedding a Google Maps application within the AngularJS application. Figure 9 shows the interpolated PM2.5 concentrations across the contiguous U.S. on 22 March, 2016 at 18:00 GMT. This web application allows a user to visualize six air pollution parameters: O3 (ppb), PM2.5 (µg/m3), PM10 (µg/m3), CO (ppm), SO2 (ppb), and NO2 (ppb). 16 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 16 of 20 Figure 8. Web application. Map overview screen after logging in. Figure 8. Web application. Map overview screen after logging in. Figure 9. Web application. Rendering of PM2.5 concentrations across the contiguous U.S. on 22 March 2016 at 18:00 GMT, including intensities at known measurement sites and the resultant triangulations used in the shape function (SF)-based interpolation method. Figure 9. Web application. Rendering of PM2.5 concentrations across the contiguous U.S. on 22 March 2016 at 18:00 GMT, including intensities at known measurement sites and the resultant triangulations used in the shape function (SF)-based interpolation method. 5. Discussion Due to the technological advances and the societal need for analysis of physical phenomena that continuously change in space and time, such as weather and air quality variables, etc., the collection 17 of 20 Int. J. Environ. Res. Public Health 2016, 13, 749 and processing of spatiotemporal data becomes more and more important. There are significant spatial and temporal dependencies among these data, which are usually ignored or underemphasized by a purely spatial interpolation approach. Investigating the additional temporal information has the potential to improve the interpolation result. Therefore, developing appropriate spatiotemporal interpolations is critical to estimate missing values at points from neighboring observations by looking deep into the spatial and temporal correlations. This study compares performance of the SF and IDW based spatiotemporal interpolation methods in order to find an interpolation method suitable for an actual set of daily PM2.5 values in the contiguous U.S. This paper also explored population exposure to PM2.5 in the contiguous U.S. by linking interpolated PM2.5 at the centroids of census block groups to census population. Finally, we implemented a web application to interpolate and visualize in real time the spatiotemporal variation of ambient air pollution (including but not limited to PM2.5) across the contiguous U.S. using air pollution data from the U.S. EPA’s AirNow program. There are some limitations and future work with our study: • This study is limited to investigating only four choices for time scales, five choices for the number of nearest neighbors, and nine choices for the exponents. In future work, we plan to apply machine learning methods to efficiently learn the best possible configurations in the model, using a lightning-fast cluster computing framework Apache Spark [61]. g g p g p p [ ] • The SF-based and IDW-based methods are deterministic methods. In this paper, we did not compare our methods with geostatistical interpolation methods such as Kriging, neural networks, and land use regression. In future work, we plan to develop multidimensional and stochastic spatiotemporal interpolation methods suitable for ambient air pollution data (NO2, O3, PM2.5, and PM10) by incorporating factors associated with the environmental exposure of interest, and then make comparisons with other commonly-applied geostatistical interpolation methods. • Finally, there is a limitation in the currently implemented SF-based algorithm with respect to missing data close to some boundaries of the contiguous United States. 5. Discussion For example, along the west coast in Oregon and Washington, there are monitoring stations relatively far away from the coastal border. Because of missing data, an unrealistic stripe next to the coast is visible in our map presentations of the interpolated results. In order to avoid this type of problem, we will need additional measurements along the coast, or use meshless interpolation methods such as IDW with a limited number of neighboring measurements in future work. Additionally, in future work, we plan to link interpolated air pollution concentration values to a variety of health outcomes to evaluate air pollution’s adverse impact on human health, as well as link the interpolated pollution values with individual GPS trajectory to better estimate personal-based air pollution exposure. 6. Conclusions In conclusion, this study has made three contributions to the ambient air pollution and spatiotemporal interpolation research community. First, using an actual set of daily PM2.5 values measured by U.S. EPA monitoring sites in the contiguous United States, the performance of the SF and IDW based spatiotemporal interpolation methods is compared in order to find an interpolation method suitable for the PM2.5 data. The SF-based interpolation method performed better overall than the IDW-based method for the daily PM2.5 data. Second, more than 75 million PM2.5 spatiotemporal interpolation results are calculated using the SF-based spatiotemporal method in the contiguous U.S. at the fine geographic level of census block groups. The interpolation results are linked to 2009 census block group population data so that the population with unhealthy PM2.5 exposure in the contiguous U.S is estimated. To map PM2.5 and Int. J. Environ. Res. Public Health 2016, 13, 749 18 of 20 population spatial distribution, we generated choropleth maps based on the interpolated values as well as the population data. Because PM2.5 may exhibit different spatial patterns in different seasons, we also investigated the seasonal variations. We conducted spatial queries to identify areas where annual and daily PM2.5 are above the standard and calculated the population size in these areas. Third, this study implemented a web application to interpolate and visualize in real time the spatiotemporal variation of ambient air pollution (including but not limited to PM2.5) across the contiguous U.S. using air pollution data from the U.S. EPA’s AirNow program. Acknowledgments: The authors of this paper would like to thank Xingyou Zhang for providing valuable input on population exposure analysis for this study. The authors would also like to thank Jason Franklin for his generous help on programming, generating IDW-related error statistics, and proofreading. Finally, the authors would like to thank Weitian Tong for giving his insight into error statistics and cross validation. 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This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). c⃝2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
https://openalex.org/W4289284150
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Gene therapy progress: hopes for Usher syndrome
HAL (Le Centre pour la Communication Scientifique Directe)
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To cite this version: Charlotte Calvet, Ghizlene Lahlou, Saaid Safieddine. Progrès de la thérapie génique : espoirs pour le syndrome d’Usher. Médecine/Sciences, 2018, 34 (10), pp.842 - 848. ￿10.1051/medsci/2018210￿. ￿hal-02365420￿ Distributed under a Creative Commons Attribution 4.0 International License HAL Id: hal-02365420 https://hal.science/hal-02365420v1 Submitted on 15 Nov 2019 La surdité, parfois associée à des troubles de l’équilibre, est le déficit sensoriel le plus fréquent chez l’homme. Il peut s’agir d’une surdité de transmission due à une atteinte de l’oreille externe ou moyenne, ou d’une surdité de perception (ou surdité neurosensorielle) due à un dys- fonctionnement de l’oreille interne ou des voies auditives centrales. L’atteinte de la cochlée, organe sensoriel de l’audition, et plus particulièrement des cellules senso- rielles auditives, représente la cause la plus fréquente de surdité d’origine génétique, et on estime qu’environ 80 % des cas de surdité congénitale sont d’origine génétique. 1 http://hereditaryhearingloss.org/. 2 http://www.abedia.com/wiley/. HAL Id: hal-02365420 https://hal.science/hal-02365420v1 Submitted on 15 Nov 2019 À ce jour, une centaine de gènes ont été identifiés comme responsables de surdité isolée, et plusieurs centaines ont été impliqués dans les sur- dités syndromiques (i.e., où la surdité est associée à d’autres anomalies en dehors du système auditif). Cependant, de nombreux gènes impliqués dans des formes rares de surdité restent à identifier1. Aucun traitement curatif des surdités neurosensorielles d’origine génétique n’existe à ce jour, soulignant ainsi le potentiel d’une approche de thérapie génique dans ce domaine. À ce jour, une centaine de gènes ont été identifiés comme responsables de surdité isolée, et plusieurs centaines ont été impliqués dans les sur- dités syndromiques (i.e., où la surdité est associée à d’autres anomalies en dehors du système auditif). Cependant, de nombreux gènes impliqués dans des formes rares de surdité restent à identifier1. Aucun traitement curatif des surdités neurosensorielles d’origine génétique n’existe à ce jour, soulignant ainsi le potentiel d’une approche de thérapie génique dans ce domaine. La thérapie génique consiste à introduire, à l’aide d’un vecteur, un gène correctif dans des cellules d’un patient ou à modifier directement le génome de ces cellules dans un but thérapeutique. Grâce à une meilleure connaissance de la génétique humaine et à la découverte de nouveaux vecteurs de transfert de gènes, une thérapie génique curative est désor- mais sérieusement envisageable pour diverses maladies. Plusieurs essais cliniques de thérapie génique sont actuellement en cours chez l’homme pour le traitement de maladies cardiovasculaires, métaboliques, neu- rodégénératives, ou cancéreuses2, mais un seul essai de phase I/II a été entrepris pour le traitement des surdités neurosensorielles acquises. La surdité, parfois associée à des troubles de l’équilibre, est le déficit sensoriel le plus fréquent chez l’homme. Il peut s’agir d’une surdité de transmission due à une atteinte de l’oreille externe ou moyenne, ou d’une surdité de perception (ou surdité neurosensorielle) due à un dys- fonctionnement de l’oreille interne ou des voies auditives centrales. L’atteinte de la cochlée, organe sensoriel de l’audition, et plus particulièrement des cellules senso- rielles auditives, représente la cause la plus fréquente de surdité d’origine génétique, et on estime qu’environ 80 % des cas de surdité congénitale sont d’origine génétique. L’approche de thérapie génique des surdités la plus activement étudiée est celle qui vise à remplacer le gène défectueux ou à augmenter son expression afin de rétablir un fonctionnement cochléaire et/ou vestibulaire normal. 1 http://hereditaryhearingloss.org/. 2 http://www.abedia.com/wiley/. HAL Id: hal-02365420 https://hal.science/hal-02365420v1 Submitted on 15 Nov 2019 L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. Distributed under a Creative Commons Attribution 4.0 International License médecine/sciences médecine/sciences médecine/sciences 2018 ; 34 : 842-8 médecine/sciences 2018 ; 34 : 842-8 Progrès de la thérapie génique Espoirs pour le syndrome d’Usher > La perte de l’audition et/ou de la fonction d’équi- libration est un problème de santé publique majeur. La surdité touche des millions de personnes dans le monde. Leur prise en charge actuelle repose sur une réhabilitation prothétique sans réelle thérapie curative. Après deux décennies de recherches qui ont permis de progresser dans la physiopathologie de différentes formes génétiques de surdité, des avancées majeures ont été obtenues grâce à des études précliniques utilisant la thérapie génique virale chez l’animal. Ce succès, largement dû à l’amélioration des vecteurs de transfert, pourrait à terme révolutionner la prise en charge de certains malentendants. Nos progrès dans la compréhen- sion des mécanismes cellulaires et moléculaires impliqués dans le fonctionnement de l’oreille interne ont contribué à ouvrir la voie à cette recherche à visée thérapeutique, qui consiste le plus souvent à remplacer localement les gènes endogènes altérés. Le but de cet article est de résumer les progrès récents de la thérapie génique dans la restauration des fonctions cochléaire et vestibulaire dans des modèles murins du syndrome d’Usher, principale cause génétique de surdité associée à une cécité. Nous nous concentrerons sur les approches thérapeutiques présentant le plus fort potentiel d’application clinique. < Charlotte Calvet1-3, Ghizlene Lahlou1-3, Saaid Safieddine1-4 Charlotte Calvet1-3, Ghizlene Lahlou1-3, Saaid Safieddine1-4 1Institut Pasteur, Unité de génétique et physiologie de l’audition, 25, rue du Docteur Roux, 75724 Paris, Cedex 15, France. 2Inserm UMRS 1120, 75015 Paris, France. 3Sorbonne Universités, 75005 Paris, France. 4CNRS, UMRS 1120, 75015 Paris, France. ssafiedd@pasteur.fr 1Institut Pasteur, Unité de génétique et physiologie de l’audition, 25, rue du Docteur Roux, 75724 Paris, Cedex 15, France. Les voies possibles d’administration La présence d’une barrière hémato-cochléaire (barrière hémato-péri- lymphatique) empêche la diffusion de nombreux agents thérapeu- m/s n° 10, vol. 34, octobre 2018 https://doi.org/ 10.1051/medsci/2018210 842 au matériel génétique qu’ils hébergent une protection, ce qui permet d’augmenter l’efficacité du transfert de l’agent thérapeutique. Différents vecteurs viraux ont été testés dans l’oreille interne, notamment les lentivirus, les adé- novirus, et les virus adéno-associés (AAV) [9]. Malgré une capacité de transfert limitée aux transgènes thérapeu- tiques qui ne dépassent guère la taille de 4,5 kilobases, les AAV semblent être les vecteurs viraux les plus prometteurs pour une telle thérapie. Les AAV sont en effet caractérisés par une grande stabilité. Ils sont capables de résister à de larges variations de température et de pH, avec peu ou pas de perte d’activité. Ils présentent également un large tropisme pour de nombreux types de cellules et de tissus, faisant d’eux des outils idéaux pour la plupart des applications, y compris la thérapie génique des surdités. D’autres caractéristiques ont contribué à encourager l’uti- lisation des AAV, en particulier la découverte de nouveaux sérotypes dont la spécificité cellulaire permet d’améliorer grandement l’efficacité de la thérapie [9]. La diversité des sérotypes d’AAV permet ainsi d’élargir le champ de cellules à cibler selon la maladie à traiter. Un effort d’ingénierie a d’ores et déjà conduit à une amélioration significative de l’efficacité de transduction des AAV, soit en utilisant des promoteurs spécifiques des cellules ciblées, soit en modifiant génétiquement la capside virale, soit en ajou- tant des séquences régulatrices, comme la séquence WPRE (woodchuck hepatitis virus post-transcriptional regulatory element), qui permettent une meilleure stabilisation des transcrits [10]. Ces recherches ont récemment abouti à la production d’une nouvelle génération d’AAV synthétiques, comme l’Anc80L65 [11], vecteur ayant montré des taux de transduction des cellules ciliées de l’oreille interne inéga- lés à ce jour [12]. tiques ou molécules vers les cellules cibles de l’oreille interne, avec pour conséquence une réduction de l’effet thérapeutique d’une admi- nistration de type systémique. Une thérapie locale intra-cochléaire serait ainsi plus efficace. L’oreille interne est facilement accessible. Elle constitue un compartiment liquidien isolé du reste de l’organisme, ce qui limite la diffusion systémique des agents thérapeutiques et, par conséquent, leurs effets secondaires potentiels. SYNTHÈSE REVUES REVUES Les voies de transfert d’agents thérapeutiques dans l’oreille interne peuvent être divisées en trois catégories principales résumées sché- matiquement dans la Figure 1. Les voies possibles d’administration L’approche périlymphatique peut être réalisée soit par diffusion, soit par injection directe à travers la membrane de la fenêtre ronde. Dans le premier cas, l’agent thérapeutique est déposé dans l’oreille moyenne après une injection trans-tympanique. Il diffuse ensuite de façon passive à travers la membrane de la fenêtre ronde. Dans le deu- xième cas, l’agent thérapeutique est directement injecté dans l’oreille interne, après un abord chirurgical de l’oreille moyenne [1-3]. Il dif- fuse alors dans l’espace périlymphatique, au-delà du site d’injection. La deuxième voie de transfert possible est l’approche endolympha- tique. Elle permet d’atteindre directement le compartiment abritant l’organe de Corti, l’organe sensoriel de l’audition, soit par injection dans le sac endolymphatique, soit par cochléostomie [4], c’est-à-dire directement dans le canal cochléaire. L’injection à travers un canal semi-circulaire (canalostomie) permet une approche à la fois périlymphatique et endolymphatique [5]. L’association de deux approches est également envisageable, notam- ment la combinaison d’une canalostomie et d’une injection à travers la membrane de la fenêtre ronde [6]. Les vecteurs de transfert En thérapie génique, le transfert du matériel génétique nécessite un vecteur qui cible les cellules d’intérêt. L’efficacité de plusieurs vecteurs de transfert a été testée dans l’oreille interne. Les vecteurs non viraux, comme les nanoparticules (liposomes), sont facilement manipulables. Ils présentent l’avantage de protéger et de libérer de façon contrôlée l’agent thérapeutique, mais ces vecteurs ne permettent qu’une expression transi- toire du gène thérapeutique. Ils ne peuvent à eux seuls cibler spécifique- ment certaines cellules de l’oreille interne [7]. Bien que des études in vitro et in vivo aient montré l’utilité de ces nanoparticules comme vecteur de transfert de gènes, seul un nombre relativement faible d’essais cliniques de thérapie génique les utilisant sont en cours de développement [8]. Le nombre d’essais cliniques dans lesquels des vecteurs viraux ont été utilisés comme moyen de transfert de gènes in vivo ne cesse d’augmenter depuis les quinze dernières années3 [17] (➜). (➜) Voir la Synthèse de H. Khabou et D. Dalkara, m/s n° 5, mai 2015 page 529 En thérapie génique, le transfert du matériel génétique nécessite un vecteur qui cible les cellules d’intérêt. L’efficacité de plusieurs vecteurs de transfert a été testée dans l’oreille interne. Les vecteurs non viraux, comme les nanoparticules (liposomes), sont facilement manipulables. Ils présentent l’avantage de protéger et de libérer de façon contrôlée l’agent thérapeutique, mais ces vecteurs ne permettent qu’une expression transi- toire du gène thérapeutique. Ils ne peuvent à eux seuls cibler spécifique- ment certaines cellules de l’oreille interne [7]. Bien que des études in vitro et in vivo aient montré l’utilité de ces nanoparticules comme vecteur de transfert de gènes, seul un nombre relativement faible d’essais cliniques 4 Dans le type 1 (environ 40 % des cas), la surdité est congénitale, profonde, non évolutive, et associée dans la forme typique à une atteinte de la fonction d’équili- bration se manifestant par le retard de certaines acquisitions posturales (tenue de tête, station assise et marche) ; dans le type 2 (environ 60 % des cas), la surdité est prélinguale, moyenne à sévère, lentement évolutive, et sans troubles vestibulaires associés; dans le type 3 (moins de 3 % des cas), la surdité est rapidement évolutive et associée, dans la moitié des cas, à des troubles vestibulaires. La rétinite pigmentaire est généralement diagnostiquée après la surdité. 3 https://clinicaltrials.gov/ct2/results?cond=viral+vector&term=&cntry=&state=&city=&dist= (➜) Voir la Synthèse de A. El-Amraoui et al., m/s, n° 8-9, Thérapie génique du syndrome d’Usher Images obte- nues en microscopie confocale d’un organe de Corti doublement marqué pour la myosine VI (en rouge) et pour la green fluorescent protein (GFP, en vert) après injection intra-cochléaire d’un vecteur viral AAV recombinant permet- tant l’expression de la GFP (gène rapporteur) dans les cellules transduites. Les encarts sont des forts grossissements montrant le profil de transduction des cellules sensorielles auditives par l’AAV8, l’AAV9 et l’Anc80L65. A B C D E F Vestibule Cochlée Rampe vestibulaire (périlymphe) Rampe tympanique (périlymphe) Nerf cochléaire Canal cochléaire (endolymphe) Organe de Corti Membrane basilaire CCI Sans Harmonine Myosine VIIa Lien apical Whirline CCE CCI Anc80L65 CCE CCI AAV8 CCE CCI AAV9 Canalostomie Sac endolymphatique Fenêtre ronde Cochleostomie Membrane tectoriale CCE CCE CCE Cadhérine 23 Protocadhérine 15 A Vestibule Cochlée Canalostomie Sac endolymphatique Fenêtre ronde Cochleostomie A B Rampe vestibulaire (périlymphe) Rampe tympanique (périlymphe) Nerf cochléaire Canal cochléaire (endolymphe) Organe de Corti D E Sans Harmonine Myosine VIIa Lien apical Whirline Cadhérine 23 Protocadhérine 15 C Membrane basilaire CCI Membrane tectoriale CCE CCE CCE D C E C F F CCE CCI Anc80L65 CCE CCI AAV8 CCE CCI AAV9 drome d’USH2D, présentent à la fois une surdité profonde et une atteinte vestibu- laire sévère contrairement aux patients. Ce modèle présente donc des caractéristiques différentes de ce qui est observé chez l’homme. Néanmoins, cette étude a per- mis de montrer que l’administration néo- natale par canalostomie de l’ADN codant la whirline chez ces souris restaure complètement la fonction vestibulaire mais seulement partiellement l’audition. Cette différence d’efficacité pourrait s’ex- pliquer par un faible taux de transduction des cellules sensorielles auditives [14]. drome d’USH2D, présentent à la fois une surdité profonde et une atteinte vestibu- laire sévère contrairement aux patients. Ce modèle présente donc des caractéristiques différentes de ce qui est observé chez l’homme. Néanmoins, cette étude a per- mis de montrer que l’administration néo- natale par canalostomie de l’ADN codant la whirline chez ces souris restaure complètement la fonction vestibulaire mais seulement partiellement l’audition. Cette différence d’efficacité pourrait s’ex- pliquer par un faible taux de transduction des cellules sensorielles auditives [14]. Actuellement, 10 gènes responsables ont été identifiés (Tableau I et Figure 1) et les récentes avancées réalisées dans le cadre de la théra- pie génique permettent désormais d’envisager la possibilité de déve- lopper un traitement curatif de ce syndrome [2, 3, 14]. Thérapie génique du syndrome d’Usher Le syndrome d’Usher (USH) représente la principale cause génétique de surdité associée à une cécité dans le monde, avec une incidence estimée à 1/6 000 naissances [13]. Il en existe trois types cliniques (USH1, USH2 et USH3) classés selon la sévérité et la précocité de l’at- teinte auditive, la présence ou non d’une atteinte de l’équilibration, et l’âge d’apparition de l’atteinte rétinienne4 [18] (➜). (➜) Voir la Synthèse de A. El-Amraoui et al., m/s, n° 8-9, août-septembre 2005, page 737 de thérapie génique les utilisant sont en cours de développement [8]. Le nombre d’essais cliniques dans lesquels des vecteurs viraux ont é é l é d d è été utilisés comme moyen de transfert de gènes in vivo ne cesse d’augmenter depuis les quinze dernières années3 [17] (➜). (➜) Voir la Synthèse de H. Khabou et D. Dalkara, m/s n° 5, i 2015 529 (➜) Voir la Synthèse de H. Khabou et D. Dalkara, m/s n° 5, mai 2015, page 529 (➜) Voir la Synthèse de H. Khabou et D. août-septembre 2005, page 737 Dalkara, m/s n° 5, mai 2015, page 529 mai 2015, page 529 Les vecteurs viraux utilisés en thérapie génique sont des virus dont les séquences de réplication et de virulence ont été rempla- cées par le gène d’intérêt. Ils ont l’avantage d’infecter efficacement aussi bien les cellules mitotiques que post-mitotiques, et leur capside confère mai 2015, page 529 843 m/s n° 10, vol. 34, octobre 2018 Figure 1. A. Représentation schématique de l’oreille interne (cochlée et vestibule) et des différentes voies d’injection : cochléostomie, fenêtre ronde, sac endolymphatique et cana- lostomie. B. Coupe transversale de la cochlée, où on distingue les rampes vestibulaire et tympanique contenant la périlymphe (bleu) ; le canal cochléaire rempli d’endolymphe (vert) et où se loge l’organe de Corti (rouge). C. Fort grossissement du canal cochléaire montrant l’organe de Corti entre les membranes tectoriale (en haut) et basilaire (en bas), et contenant les cellules sensorielles auditives : cellules ciliées internes (CCI) et cellules ciliées externes (CCE). D. Image obtenue au microscope électronique à balayage montrant l’organisation de la touffe ciliaire des CCI encadrée dans (C). E. Illustra- tion schématique des composants moléculaires du lien apical encadré en (D). F. m/s n° 10, vol. 34, octobre 2018 Thérapie génique du syndrome d’Usher Le syndrome d’Usher de type 1G (USH1G) est lié à des mutations dans le gène SANS, codant la protéine du même nom (Sans, scaffold ankyrin and sterile alpha motif-containing protein) [15]. Cette forme clinique est l’une des plus sévères du syndrome d’Usher. Les patients USH1G naissent avec une surdité profonde associée à des troubles sévères de l’équilibration qui sont suivis d’une atteinte rétinienne progressive évoluant vers la cécité. Cette perte visuelle entrave la lecture labiale et limite Des modèles murins des différentes formes génétiques de ce syndrome ont été produits, et des essais de thérapie génique in vivo dans cer- tains de ces modèles ont montré des résultats encourageants pour le développement d’un traitement de la surdité et des troubles de l’équilibration. Une de ces études concerne le syndrome d’Usher de type 2D (USH2D), caractérisé par une surdité progressive moyenne à sévère sans déficit vestibulaire. Il est lié à des mutations du gène WHRN codant la protéine whirline [14]. Les souris dont le gène Whrn a été invalidé (souris Whrn-/-), considérées comme un modèle du syn- m/s n° 10, vol. Thérapie génique du syndrome d’Usher 34, octobre 2018 844 Surdité Phénotype Atteinte vestibulaire Rétinite pigmentaire Locus Gène Protéine Fonction Localisation Usher de type 1 Congénitale profonde Aréflexie vestibulaire bilatérale congénitale Début pré- pubertaire USH1B USH1C MYO7A USH1C myosine VIIa harmonine Protéine motrice : transport des autres protéines USH le long des filaments d’actine du stéréocil Protéine d’échafaudage : lien entre les protéines du lien apical et le cytosquelette d’actine Autour de l’extrémité intracellulaire du lien apical Plaque cuticulaire Autour de l’extrémité intracellulaire du lien apical USH1D CDH23 cadhérine 23 Protéine d’adhérence intercellulaire constitutive du lien apical Partie supérieure du lien apical USH1F PCDH15 protocadhérine 15 Protéine d’adhérence intercellulaire constitutive du lien apical Partie inférieure du lien apical USH1G USH1G Sans Protéine d’échafaudage : lien entre les protéines du lien apical et le cytosquelette d’actine Autour de l’extrémité intracellulaire du lien apical USH1J CIB2 CIB2 Protéine de liaison au Ca2+ et à l’intégrine Autour de l’extrémité intracellulaire du lien apical Usher de type 2 Congénitale moyenne à sévère, d’évolution progressive Normal Début post- pubertaire USH2A USH2C USH2A GPR98 ushérine VGLR1 Protéine d’adhérence intercellulaire impliquée dans le lien basal des stéréocils Protéine G couplée au récepteur impliquée dans le lien basal Expression transitoire à la base du stéréocil durant le développement embryonnaire USH2D WHRN whirline Élongation du stéréocil Extrémité supérieure du stéréocil Usher de type 3 Post- linguale, moyenne d’évolution progressive Variable Variable USH3A CLRN1 clarine-1 Protéine transmembranaire d’interaction impliquée dans l’activité de mécano-transduction et la localisation des composants synaptiques Apex des stéréocils Base des cellules ciliées (synapse) Tableau I. Les syndromes d’Usher : phénotypes, gènes et protéines associés. Comparaison des phénotypes liés à l’atteinte cochléaire, à l’atteinte vestibulaire, et à la rétinite pigmentaire dans chaque type clinique du syndrome d’Usher (types 1, 2 et 3). Les gènes et protéines impliqués sont listés, et la fonction et la localisation de ces protéines sont détaillées. SYNTHÈSE REVUES her : phénotypes, gènes et protéines associés. Comparaison des phénotypes liés à l’atteinte cochléaire, à l’atteinte vestibulaire, et à la rétinite pigmentaire dans chaque sher (types 1, 2 et 3). Les gènes et protéines impliqués sont listés, et la fonction et la localisation de ces protéines sont détaillées. Localisation Localisation REVUES Fonction Un modèle murin du syndrome d’Usher de type USH1C a récemment fait l’objet d’une étude de thérapie génique dans un but curatif. Le syndrome de type USH1C est dû à des mutations du gène codant l’harmonine, une protéine essentielle à la cohésion de la touffe ciliaire des cellules sensorielles auditives et vestibu- laires au cours du développement [19] (➜). (➜) Voir la Nouvelle de N. Grillet, m/s n° 11, novembre 2009, page 903 Un modèle murin du syndrome d’Usher de type USH1C a récemment fait l’objet d’une étude de thérapie génique dans un but curatif. Le syndrome de type USH1C est dû à des mutations du gène codant l’harmonine, une protéine essentielle à la cohésion de la touffe ciliaire des cellules sensorielles auditives et vestibu- laires au cours du développement [19] (➜). (➜) Voir la Nouvelle de N. Grillet, m/s n° 11, novembre 2009, page 903 la compensation des troubles vestibulaires, aggravant ainsi le handicap de ces patients. Comme chez l’homme, les souris invalidées pour le gène SANS (souris Ush1g-/-) présentent une surdité profonde et un déficit ves- tibulaire [15]. Ces anomalies sont dues à la dégénérescence précoce de la touffe ciliaire des cellules sensorielles cochléaires et vestibulaires. Le transfert viral de l’ADNc (ADN complémentaire) codant la protéine Sans aux cellules sensorielles de l’oreille interne à travers la fenêtre ronde chez des souris Ush1g-/- à la naissance restaure la structure des cellules sensorielles auditives et vestibulaires et rétablit durablement la fonction d’équilibration de ces souris, alors qu’il n’améliore que partiellement leurs seuils auditifs (Figure 2). La différence de récupération des fonctions cochléaire et vestibulaire constatée est probablement due à un taux de transduction des cellules cochléaires plus faible que celui des cellules vestibulaires. Un résultat important de cette étude est la démonstration que la fenêtre temporelle pour un traitement efficace de cette forme de surdité est plus large que ce que l’on présupposait, puisque les souris mutantes ont déjà à la naissance de sévères anomalies structurales des cellules sensorielles de l’oreille interne que la thérapie génique a permis de corriger. Ces résultats ouvrent ainsi de nouvelles perspectives pour une thérapie génique des troubles cochléaires et vestibulaires liés à une anomalie de la morphogénèse de l’appareil de transduction mécano- électrique des cellules sensorielles, i.e. leur touffe ciliaire. (➜) Voir la Nouvelle de N. m/s n° 10, vol. 34, octobre 2018 Fonction m/s n° 10, vol. 34, octobre 2018 845 Sauvage A B C D Cochlée Vestibule Ush1g-/- Ush1g-/-injectée Sauvage Ush1g-/- Ush1g-/-injectée 120 100 80 60 40 20 Seuils auditifs aux PEA (dB) Fréquence (kHz) 5 10 15 20 32 40 sauvage sauvage injectée Ush1g-/- injectée Ush1g-/- ns ns ns ns ns * Figure 2. Le transfert viral de l’ADNc codant la protéine Sans restaure la structure et la fonction des cellules sensorielles de l’oreille interne. Images obtenues au microscope électronique à balayage montrant l’organisation de la touffe ciliaire des cellules ciliées externes cochléaires (A) et des cellules ciliées vestibulaires (B) d’une souris sauvage comparée à celle d’une souris Ush1g-/- non traitée et d’une souris Ush1g-/- traitée. C. Histogramme des potentiels évoqués auditifs des souris sauvages non injectées, sauvages injectées, Ush1g-/- non injectées, et Ush1g-/- injec- tées, montrant une amélioration significative des seuils auditifs sur toutes les fréquences testées. D. Suivi vidéo des souris sauvages, sauvages injectées, Ush1g-/- non injectées, et Ush1g-/- injectées, montrant le rétablissement d’un comportement normal chez les souris Ush1g-/- injectées, similaire à celui des souris sauvages. Les souris Ush1g-/- présentent quant à elles un comportement de rotation permanente (circling behavior) dû à l’atteinte vestibulaire. B D Vestibule Sauvage Ush1g-/- Ush1g-/-injectée Ush1g-/- injectée Ush1g-/- B Vestibule Sauvage Ush1g-/- Ush1g-/-injectée Sauvage A Cochlée Ush1g-/- Ush1g-/-injectée A B D Ush1g-/- injectée Ush1g-/- C D C 120 100 80 60 40 20 Seuils auditifs aux PEA (dB) Fréquence (kHz) 5 10 15 20 32 40 sauvage sauvage injectée ns ns ns ns ns * Figure 2. Le transfert viral de l’ADNc codant la protéine Sans restaure la structure et la fonction des cellules sensorielles de l’oreille interne. Images obtenues au microscope électronique à balayage montrant l’organisation de la touffe ciliaire des cellules ciliées externes cochléaires (A) et des cellules ciliées vestibulaires (B) d’une souris sauvage comparée à celle d’une souris Ush1g-/- non traitée et d’une souris Ush1g-/- traitée. C. Histogramme des potentiels évoqués auditifs des souris sauvages non injectées, sauvages injectées, Ush1g-/- non injectées, et Ush1g-/- injec- tées, montrant une amélioration significative des seuils auditifs sur toutes les fréquences testées. D. Suivi vidéo des souris sauvages, sauvages injectées, Ush1g-/- non injectées, et Ush1g-/- injectées, montrant le rétablissement d’un comportement normal chez les souris Ush1g-/- injectées, similaire à celui des souris sauvages. Les souris Ush1g-/- présentent quant à elles un comportement de rotation permanente (circling behavior) dû à l’atteinte vestibulaire. LIENS D’INTÉRÊT́ Les rongeurs en général, et la souris en particulier, restent des modèles incontournables en recherche translationnelle. Mais de tels modèles sont loin d’être parfaits : la taille et le développement de l’oreille interne ainsi que la fonction de certains gènes diffèrent entre les rongeurs et l’homme. Contrairement à l’homme, les rongeurs présentent un système auditif dont la maturation est tardive, et ces animaux naissent sans ouïe (l’audition n’apparaît qu’à environ 12 jours de vie chez la souris). Le développement d’un modèle animal alternatif mimant plus fidèlement la maladie humaine est donc essentiel pour valider l’efficacité des traite- ments potentiels des surdités génétiques chez l’homme et s’assurer de leur tolérance à long terme. Les rongeurs en général, et la souris en particulier, restent des modèles incontournables en recherche translationnelle. Mais de tels modèles sont loin d’être parfaits : la taille et le développement de l’oreille interne ainsi que la fonction de certains gènes diffèrent entre les rongeurs et l’homme. Contrairement à l’homme, les rongeurs présentent un système auditif dont la maturation est tardive, et ces animaux naissent sans ouïe (l’audition n’apparaît qu’à environ 12 jours de vie chez la souris). Le développement d’un modèle animal alternatif mimant plus fidèlement la maladie humaine est donc essentiel pour valider l’efficacité des traite- ments potentiels des surdités génétiques chez l’homme et s’assurer de leur tolérance à long terme. Les auteurs déclarent n’avoir aucun lien d’intérêt concernant les données pubiées dans cet article. RÉFÉRENCES Recent developments and perspectives on gene therapy using synthetic vectors. Ther Deliv 2013 ; 4 : 95-113. 8. Schlenk F, Grund S, Fischer D. Recent developments and perspectives on gene therapy using synthetic vectors. Ther Deliv 2013 ; 4 : 95-113. Enfin, au-delà de la démonstration expérimentale de l’efficacité de la thérapie génique, de sa sécurité, et de la durée de son effet curatif potentiel, d’autres obstacles incluant un cadre réglementaire strict, la difficulté du recrutement de patients volontaires, et des questions éthiques devront être surmontés avant d’entreprendre des essais cli- niques. ‡ 9. Sacheli R, Delacroix L, Vandenackerveken P, et al. Gene transfer in inner ear cells: a challenging race. Gene Ther 2013 ; 20 : 237-47. 9. Sacheli R, Delacroix L, Vandenackerveken P, et al. Gene transfer in inner ear cells: a challenging race. Gene Ther 2013 ; 20 : 237-47. 10. Choi JH, Yu NK, Baek GC, et al. Optimization of AAV expression cassettes to improve packaging capacity and transgene expression in neurons. Mol Brain 2014 ; 7. 10. Choi JH, Yu NK, Baek GC, et al. Optimization of AAV expression cassettes to improve packaging capacity and transgene expression in neurons. Mol Brain 2014 ; 7. 11. Zinn E, Pacouret S, Khaychuk V, et al. In silico reconstruction of the viral evolutionary lineage yields a potent gene therapy vector. Cell Rep 2015 ; 12 : 1056-68. 11. Zinn E, Pacouret S, Khaychuk V, et al. In silico reconstruction of the viral evolutionary lineage yields a potent gene therapy vector. Cell Rep 2015 ; 12 : 1056-68. 12. Landegger LD, Pan B, Askew C, et al. A synthetic AAV vector enables safe and efficient gene transfer to the mammalian inner ear. Nat Biotechnol 2017 ; 35 : 280-4. 12. Landegger LD, Pan B, Askew C, et al. A synthetic AAV vector enables safe and efficient gene transfer to the mammalian inner ear. Nat Biotechnol 2017 ; 35 : 280-4. RÉFÉRENCES 1. Iizuka T, Kanzaki S, Mochizuki H, et al. Noninvasive In vivo delivery of transgene via adeno-associated virus into supporting cells of the neonatal mouse cochlea. Hum Gene Ther 2008 ; 19 : 384-90. 2. Emptoz A, Michel V, Lelli A, et al. Local gene therapy durably restores vestibular function in a mouse model of Usher syndrome type 1G. Proc Natl Acad Sci USA 2017 ; 114 : 9695-700. 3. Pan B, Askew C, Galvin A, et al. Gene therapy restores auditory and vestibular function in a mouse model of Usher syndrome type 1c. Nat Biotechnol 2017 ; 35 : 264-72. 4. György B, Sage C, Indzhykulian AA, et al. Rescue of hearing by gene delivery to inner-ear hair cells using exosome-associated AAV. Mol Ther 2017 ; 25 : 379-91. Il est également primordial d’adopter une approche chirurgicale faci- lement transposable à l’homme. La canalostomie ou l’abord du sac endolymphatique nécessitent une chirurgie invasive et potentiellement à risque pour la préservation de l’intégrité des structures de l’oreille interne humaine. En revanche, une injection à travers la fenêtre ronde ou la fenêtre ovale cochléaires semble être plus appropriée [16]. L’abord chirurgical correspondant, de moins en moins invasif, est déjà pratiqué en routine par les otorhinolaryngologistes pour le traitement de l’otos- pongiose ou la pose d’un implant cochléaire. 5. Guo J, Liu Y, Qu T, et al. Cochleovestibular gene transfer in neonatal mice by canalostomy. Neuroreport 2017 ; 28 : 682-8. 5. Guo J, Liu Y, Qu T, et al. Cochleovestibular gene transfer in neonatal mice by canalostomy. Neuroreport 2017 ; 28 : 682-8. 6. Yoshimura H, Shibata SB, Ranum PT, et al. Enhanced viral-mediated cochlear gene delivery in adult mice by combining canal fenestration with round window membrane inoculation. Sci Rep 2018 ; 8 : 2980. 6. Yoshimura H, Shibata SB, Ranum PT, et al. Enhanced viral-mediated cochlear gene delivery in adult mice by combining canal fenestration with round window membrane inoculation. Sci Rep 2018 ; 8 : 2980. 7. Pyykkö I, Zou J, Zhang W, et al. Nanoparticle-based delivery for the treatment of inner ear disorders. Curr Opin Otolaryngol Head Neck Surg 2011 ; 19 : 388-96. 7. Pyykkö I, Zou J, Zhang W, et al. Nanoparticle-based delivery for the treatment of inner ear disorders. Curr Opin Otolaryngol Head Neck Surg 2011 ; 19 : 388-96. 8. Schlenk F, Grund S, Fischer D. Fonction Grillet, m/s n° 11, novembre 2009, page 903 Comme Sans, l’harmonine fait partie intégrante de la machinerie de transduction mécano-électrique. Les souris modèles d’USH1C sont caractérisées comme chez l’homme par une surdité profonde et une atteinte sévère de l’équilibration. L’injection intra-cochléaire d’un nouvel AAV synthétique, Anc80L65, comme vecteur de transfert du gène de l’harmonine restaure l’expres- sion et la localisation subcellulaire de la protéine et rétablit l’audition et l’équilibration à un niveau quasi normal [3]. Nul doute que ce résultat très prometteur contribuera à accélérer la recherche translationnelle en thérapie génique dans le domaine de la surdité associée ou non à des troubles de l’équilibration. m/s n° 10, vol. 34, octobre 2018 846 Les défis des futures applications cliniques Les défis des futures applications cliniques still lacks an effective curative therapy. Recent break- throughs in preclinical and clinical studies using viral gene therapy suggest that such an approach might succeed in curing many genetic diseases. Our actual understanding and the comprehensive analysis of the molecular bases of genetic deafness forms have provi- ded the multiple bridges toward gene therapy to correct, replace, or modify the expression of defective endoge- nous genes involved in deafness. The aim of this review article is to summarize the recent advances in the resto- ration of cochlear and vestibular functions by local gene therapy in mouse models of Usher syndrome, the leading genetic cause of deafness associated with blindness in the world. We focus herein on therapeutic approaches with the highest potential for clinical application. ‡ Malgré de nombreux revers durant les dernières décennies, la thérapie génique reste un domaine en constante évolution. Les résultats obte- nus au cours de ces dix dernières années permettent d’envisager, dans un futur plus ou moins proche, une application de la thérapie génique pour le traitement curatif de certaines formes de surdité chez l’homme. Bien que la thérapie génique virale apparaisse prometteuse, certaines étapes préalables à son utilisation clinique restent à franchir. Il s’agit notamment de la validation des résultats obtenus dans les modèles murins sur un modèle animal plus proche de l’homme, de la maîtrise de voies d’injection non délétères pour le fonctionnement de la cochlée, et du choix du vecteur de transfert. Il est en effet nécessaire de dévelop- per des vecteurs qui soient plus efficaces pour la transduction et des promoteurs spécifiques des cellules cibles afin d’obtenir de meilleurs taux d’expression protéique et ainsi un effet thérapeutique optimal. L’Anc80L65, vecteur AAV de nouvelle génération, semble très promet- teur pour la thérapie génique des surdités, mais contrairement aux AAV conventionnels son innocuité reste à évaluer. Concernant les nanoparti- cules, des améliorations sont également nécessaires afin d’augmenter leur stabilité et accroître leur efficacité de transfection. REVUES with the highest potential for clinical application. ‡ REMERCIEMENTS Les auteurs remercient chaleureusement le Pr Christine Petit et le Dr Jean-Pierre Hardelin pour la relecture de cette synthèse et la pertinence de leurs remarques. RÉFÉRENCES TIRÉS À PART C. Calvet TIRÉS À PART C. Calvet 17. Hanen Khabou H, Dalkara D. La conception de vecteurs adaptés à la thérapie génique oculaire. Med Sci (Paris) 2015 ; 31 : 529-37. SUMMARY Gene therapy progress: hopes for Usher syndrome 13. Kimberling WJ, Hildebrand MS, Shearer AE, et al. Frequency of Usher syndrome in two pediatric populations: Implications for genetic screening of deaf and hard of hearing children. Genet Med 2010 ; 12 : 512-6. 13. Kimberling WJ, Hildebrand MS, Shearer AE, et al. Frequency of Usher syndrome in two pediatric populations: Implications for genetic screening of deaf and hard of hearing children. Genet Med 2010 ; 12 : 512-6. Hearing and balance impairment are major concerns and a serious public health burden, as it affects millions of people worldwide, but 847 m/s n° 10, vol. 34, octobre 2018 18. El-Amraoui A, Lefèvre G, Hardelin JP, Petit C. Syndrome de Usher de type 1 et développement de la touffe ciliaire des cellules sensorielles de l’oreille interne. Med Sci (Paris) 2005 ; 21 : 737-40. 19. Grillet N. Harmonine est un composant de la machinerie de mécanotransduction auditive. Med Sci (Paris) 2009 ; 25 : 903-6. RÉFÉRENCES 14. Isgrig K, Shteamer JW, Belyantseva IA, et al. Gene therapy restores balance and auditory functions in a mouse model of Usher syndrome. Mol Ther 2017 ; 25 : 780-791. 15. Caberlotto E, Michel V, Foucher I, et al. Usher type 1G protein sans is a critical component of the tip-link complex, a structure controlling actin polymerization in stereocilia. Proc Natl Acad Sci USA 2011 ; 108 : 5825-30. 16. Kang WS, Nguyen K, McKenna CE, et al. Intracochlear drug delivery through the oval window in fresh cadaveric human temporal bones. Otol Neurotol 2016 ; 37 : 218-22. 17. Hanen Khabou H, Dalkara D. La conception de vecteurs adaptés à la thérapie génique oculaire. Med Sci (Paris) 2015 ; 31 : 529-37. TIRÉS À PART C. Calvet 14. Isgrig K, Shteamer JW, Belyantseva IA, et al. Gene therapy restores balance and auditory functions in a mouse model of Usher syndrome. Mol Ther 2017 ; 25 : 780-791. 17. Hanen Khabou H, Dalkara D. La conception de vecteurs adaptés à la thérapie génique oculaire. Med Sci (Paris) 2015 ; 31 : 529-37. 15. Caberlotto E, Michel V, Foucher I, et al. Usher type 1G protein sans is a critical component of the tip-link complex, a structure controlling actin polymerization in stereocilia. Proc Natl Acad Sci USA 2011 ; 108 : 5825-30. 16. Kang WS, Nguyen K, McKenna CE, et al. Intracochlear drug delivery through the oval window in fresh cadaveric human temporal bones. Otol Neurotol 2016 ; 37 : 218-22. 18. El-Amraoui A, Lefèvre G, Hardelin JP, Petit C. Syndrome de Usher de type 1 et développement de la touffe ciliaire des cellules sensorielles de l’oreille interne. Med Sci (Paris) 2005 ; 21 : 737-40. 19. Grillet N. Harmonine est un composant de la machinerie de mécanotransduction auditive. Med Sci (Paris) 2009 ; 25 : 903-6. 18. El-Amraoui A, Lefèvre G, Hardelin JP, Petit C. Syndrome de Usher de type 1 et développement de la touffe ciliaire des cellules sensorielles de l’oreille interne. Med Sci (Paris) 2005 ; 21 : 737-40. 19. Grillet N. Harmonine est un composant de la machinerie de mécanotransduction auditive. Med Sci (Paris) 2009 ; 25 : 903-6. RÉFÉRENCES 14. Isgrig K, Shteamer JW, Belyantseva IA, et al. Gene therapy restores balance and auditory functions in a mouse model of Usher syndrome. Mol Ther 2017 ; 25 : 780-791. 15. Caberlotto E, Michel V, Foucher I, et al. Usher type 1G protein sans is a critical component of the tip-link complex, a structure controlling actin polymerization in stereocilia. Proc Natl Acad Sci USA 2011 ; 108 : 5825-30. 16. Kang WS, Nguyen K, McKenna CE, et al. Intracochlear drug delivery through the oval window in fresh cadaveric human temporal bones. Otol Neurotol 2016 ; 37 : 218-22. 17. Hanen Khabou H, Dalkara D. La conception de vecteurs adaptés à la thérapie génique oculaire. Med Sci (Paris) 2015 ; 31 : 529-37. TIRÉS À PART C. Calvet 14. Isgrig K, Shteamer JW, Belyantseva IA, et al. Gene therapy restores balance and auditory functions in a mouse model of Usher syndrome. Mol Ther 2017 ; 25 : 780-791. 15. Caberlotto E, Michel V, Foucher I, et al. Usher type 1G protein sans is a critical component of the tip-link complex, a structure controlling actin polymerization in stereocilia. Proc Natl Acad Sci USA 2011 ; 108 : 5825-30. 16. Kang WS, Nguyen K, McKenna CE, et al. Intracochlear drug delivery through the oval window in fresh cadaveric human temporal bones. Otol Neurotol 2016 ; 37 : 218-22. 17. Hanen Khabou H, Dalkara D. La conception de vecteurs adaptés à la thérapie génique oculaire. Med Sci (Paris) 2015 ; 31 : 529-37. 18. El-Amraoui A, Lefèvre G, Hardelin JP, Petit C. Syndrome de Usher de type 1 et développement de la touffe ciliaire des cellules sensorielles de l’oreille interne. Med Sci (Paris) 2005 ; 21 : 737-40. m/s n° 10, vol. 34, octobre 2018 848
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A Survey on Temperate Fruit Pests and their Importance in the Highland Areas of North Shewa Zone, Amhara Region, Ethiopia
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Introduction There is a general notion that the Kavango region could be the “Breadbasket” of Namibia if the fields in the area could be productive [1]. This belief is met with challenges due to the harsh climate and the Kalahari sands (arenosols) that dominate most of the area. Terminalia sericea species are dominant in this area and these trees have been known to be an indication of poor sandy soils in an area [2]. The constraints that affect agriculture in The Kavango are the same ones that affect most of the Northern areas of Namibia [1], with poor nutrition status and water retention of the soil, a variable climate and a far distance from the market being the major ones. People’s main source of livelihood in these area is small scale farming [3] despite the poor crop production capacity of the porous soils, hence the need to intervene and study how crops that are widely grown in these regions with harsh conditions can be improved so as to contribute in increasing the fertility of the soils. As the world’s population is on the verge of a dramatic increase that will threaten food security, there is an important need of looking for a long-term food security solution by selection of crops with that are highly nutritious and are high-yielding [4]. Therefore, plant breeders and scientists at large are looking for a crop that can be enhanced or is already adapted to the foreseeable biotic and abiotic environmental changes [4]. With Southern Africa having the highest population of undernourished people in the world [4], cowpea, which is one of the major grain legumes in the region [5], is favourable to be explored to prepare for this threatened food security. Legumes such as cowpea are known to be raw materials that are important in the balancing of the human diet due them being able to provide high proteins, vitamins, minerals and an important source of carbohydrates according to Kiim et al. [6]. They have been known to have multiple physiological effects such as the prevention of metabolic diseases like colon cancer and diabetics and also in the reduction of blood and glucose levels [7]. Vigna unguiculata has been reported to have a high amount of organic matter and generally multiuse properties hence its use by farmers as fodder to feed their animals [8]. Abstract The Kavango region (Northern part of Namibia) were the study was carried out, is extensively involved in agriculture and is also known to be dominated by the sandy aerosols soils. The bad soils in the region, which have poor nutrients and water holding capacity, combined with a fast rate of climate change in the region has contributed in the reduction in yield of most crops grown in the area. The main aim of the study was to determine cowpeas response to bio-inoculants by assessing yield of the pulse. Six different cultivars of Vigna unguiculata (Cow pea) were evaluated for their response to bio-inoculants. These cultivars were subjected to 3 different treatments. One with chemical fertilizer, another with Bradyrhizobium strains (14-3) and (1-7) bio-inoculants and a third which was a negative control with no treatment. After 90 days post seeding the cultivars were harvested and different yield parameters assessed. The cowpeas that were subjected to the bio-inoculant treatments yielded a later grain yield in kg per hectare as compared to the negative control and the fertilizer treatments. The outcome of this study therefore provided the local subsistence farmers with a cheaper eco-friendly alternative to mineral fertilizers. Keywords: Arenosols; Climate-change; Cultivars; Vigna unguiculata; Cowpea, Bio-inoculants; Fertilizer; Bradyrhizobium; Yield Keywords: Arenosols; Climate-change; Cultivars; Vigna unguiculata; Cowpea, Bio-inoculants; Fertilizer; Bradyrhizobium; Yield yields in the area being lower than they were about 30 years ago [1] due to decreasing soil fertility, therefore an urgent need to intervene is required. Despite legumes having to be known to be of wide occurrence during traditionally set cropping settings, they are also deliberately used to manage the soil fertility by most small scale subsistence farmers [9]. Legumes do this by fixing atmospheric nitrogen into ammonia by the help of the nitrogenase enzyme and also by their incorporation into cereal based cropping systems which result into them increasing the soil fertility as was demonstrated by Zahran [10]. Nitrogen fixation is an important process for life forms on earth, biological processes such as the use of legumes, fix about 60% of the world’s nitrogen [10]. Thus, this process is a major source of nitrogen into soils especially for arid environments [11]. for example states that nitrogen fixation by rhizobia on soy bean production in Brazil results in an estimated save of about US$ 10 billion annually instead of the use of chemical fertilizer, this is by using Bradyrhizobium as a bio-inoculant. Review Article Open Access Luchen et al., J Plant Pathol Microbiol 2018, 9:10 DOI: 10.4172/2157-7471.1000456 Journal of Plant Pathology & Microbiology J o u r n a l o f P l a n t P a t h o l o g y & M i c r o b i o l o g y ISSN: 2157-7471 Research Article Open Access Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia Charlie Chaluma Luchen1, Jean-Damascene Uzabikiriho1, Percy M Chimwamurombe2* and Barbara Reinhold-Hurek3 1Department of Biological Sciences, University of Namibia, Namibia 2School of Natural and Applied Health Sciences, Namibian Universities of Science and Technology, Namibia 3Faculty of Biology, Laboratory for General Microbiology, University of Bremen, Germany Review Article Open Access Luchen et al., J Plant Pathol Microbiol 2018, 9:10 DOI: 10.4172/2157-7471.1000456 Journal of Plant Pathology & Microbiology J o u r n a l o f P l a n t P a t h o l o g y & M i c r o b i o l o g y ISSN: 2157-7471 Research Article Open Access Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia Charlie Chaluma Luchen1, Jean-Damascene Uzabikiriho1, Percy M Chimwamurombe2* and Barbara Reinhold-Hurek3 1Department of Biological Sciences, University of Namibia, Namibia 2School of Natural and Applied Health Sciences, Namibian Universities of Science and Technology, Namibia 3Faculty of Biology, Laboratory for General Microbiology, University of Bremen, Germany Luchen et al., J Plant Pathol Microbiol 2018, 9:10 Luchen et al., J Plant Pathol Microbiol 2018, 9:10 DOI: 10.4172/2157-7471.1000456 Journal of Plant Pathology & Microbiology DOI: 10.4172/2157-7471.1000456 Review Article Research Article Abstract The outcome of this study will be significant in providing the subsistence farmers with bio-inoculants that are able to effectively fix biological nitrogen when in symbiosis with cowpea under a climate of low rainfall. This will in turn increase profits and crop productivity at large as less money will be spent on chemicals in trying to enrich the poor soils in the regions and Namibia at large. Introduction Pennisetum glaucum (locally known as mahangu), which is one of Namibia’s staple foods, is widely cultivated in the Kavango region. There have been reports of mahangu Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia arlie Chaluma Luchen1, Jean-Damascene Uzabikiriho1, Percy M Chimwamurombe2* and Barbara Reinhold-Hurek3 1Department of Biological Sciences, University of Namibia, Namibia 2School of Natural and Applied Health Sciences, Namibian Universities of Science and Technology, Namibia 3Faculty of Biology, Laboratory for General Microbiology, University of Bremen, Germany 1Department of Biological Sciences, University of Namibia, Namibia 2School of Natural and Applied Health Sciences, Namibian Universities of Science and Technology, Namibia 3Faculty of Biology, Laboratory for General Microbiology, University of Bremen, Germany J Plant Pathol Microbiol, an open access journal ISSN: 2157-7471 *Corresponding author: Percy M Chimwamurombe, School of Natural and Applied Health Sciences, Namibian University of Science and Technology, Namibia, Tel: +264 61 2063358; E-mail: pchimwa@gmail.com Received October 14, 2018; Accepted October 26, 2018; Published October 29, 2018 Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. doi: 10.4172/2157- 7471.1000456 *Corresponding author: Percy M Chimwamurombe, School of Natural and Applied Health Sciences, Namibian University of Science and Technology, Namibia, Tel: +264 61 2063358; E-mail: pchimwa@gmail.com Materials and Methods The study was conducted by obtaining cowpea cultivars from Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), these were namely (Figure 1) Nakare (Na), Lutembwe (Lu), I2, Bira (Bi), Shindimba (Shi), and Silwana (Si) respectively. Cowpea strains Received October 14, 2018; Accepted October 26, 2018; Published October 29, 2018 Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. doi: 10.4172/2157- 7471.1000456 Copyright: © 2018 Luchen CC, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Volume 9 • Issue 10 • 1000456 Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. doi: 10.4172/2157-7471.1000456 Page 2 of 5 Figure 1: Cowpea cultivars that were used in the study with their indigenous names. Scale bar=1 cm in all the pictures (a) to (f). their indigenous names. Scale bar=1 cm in all the pictures (a) to (f). Figure 1: Cowpea cultivars that were used in the study with their indigenous names. Scale bar=1 cm in all the pictures (a) to (f). exposure to direct sunlight for long hours. Just before planting the bio inoculant treatment, a small amount Polyvinylpyrrolidone (PVP-40) was poured into 25 ml of distilled water. The PVP-40 was used because it is sticky, hence it helped facilitate the sticking of the inoculant better to the seeds. A Small can was used to mix the inoculant, one seed cultivar and the PVP-40, all the six different cultivars were mixed this way before planting. Urea was added on the soils were the nitrogen fertilizer treatment was to be performed. Figure 2: Depicting the cowpea study field at Mashare just before harvesting. Yield assessment Harvest data collection: The yield of the different cowpea cultivars under the three categories of namely: Nitrogen fertilizer, Bio inoculant and No treatment was assessed by comparing the physiological maturity of the different cultivars with the above-named treatments. This assessment was done by selecting 10 cow pea plants from the middle rows of a subplot avoiding the border plants. These were used to calculate the root dry matter, grain and plant dry matter and converted into yield per kilo hectare. Each subplot was expected to have has an estimated 120 plants. With some subplots recording only about half the amount or less during harvesting. This was due to some plants not being so adapted to the local soils and environment in the region and some having been dried up by the time the harvesting took place. Spades were used to dig up the 10 plants from the middle section of each subplot during the flowering phase. This was done carefully to try to excavate as many roots as possible attached to that plant. The none inoculated plots were harvested first and for those subplots that had a few plants growing on them due to some having been dried or not germinated, for these, less than 10 middle plants were harvested such as 7 Nakare plants being excavated. This was followed by the harvesting of the bio inoculant treatment plots. Nakare and Shindimba cultivars had a few cowpea plants growing on the designated subplots during harvesting hence only 5 middle plants of the bio inoculant treatment were dug up. The nitrogen fertilizer treatment plant was the last to be harvested. Figure 2: Depicting the cowpea study field at Mashare just before harvesting. Figure 3: Showing one Lutembwe shoot immediately after harvesting. Figure 3: Showing one Lutembwe shoot immediately after harvesting that are resistant to the ‘witch weed’ Alectra vogelii, which according to Mwaipopo [12] is a parasitic weed that is known to cause major constraints on legumes and most especially cowpea, where obtained from The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) these were named I2. The cowpea was grown under rain fed conditions so as to stimulate the natural environmental conditions of the area. The field was ploughed back and forth to homogenize the plot on which the planting was done. J Plant Pathol Microbiol, an open access journal ISSN: 2157-7471 Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. doi: 10.4172/2157-7471.1000456 J Plant Pathol Microbiol, an open access journal Yield assessment Cultivar Name Shoot wet weight (g) Shoot dry weight (g) Plant dry matter yield (kg/ha) Root wet weight (g) Root dry Weight (g) Root dry Matter yield (kg/ha) Grain yield (g) Grain yield (kg/ha) LUTEMBWE+Bradyrhizobium stain 1-7 Average Yield 2100 966 64400 146.615 40.4025 2693.5 4901.745 2723.191667 LUTEMBWE+Bradyrhizobium strain 14-3 Average Yield 2350 1272.9175 84861.17 135.725 43.775 2918.33 4922.36 2734.64 NAKARE+Bradyrhizobium strain 14-3 Average Yield 850 578 38533.33 209.73 99.46 6630.67 8118 4510 NAKARE+Bradyrhizobium stain 1-7 Average Yield 300 427.5 28500 130.225 62.465 4164.33 4918.5 2732.5 SHINDIMBA+Bradyrhizobium stain 1-7 Average Yield 175 159.25 10616.67 188.8 53.32 3554.67 2921.4 1623 SILWANA+Bradyrhizobium stain 1-7 Average Yield 1900 1148.635 76575.67 129.95 49.965 3331 7185.49 3991.94 SILWANA+Bradyrhizobium strain 14-3 Average Yield 2300 1086.11 72407.33 168.425 41.985 2799 5844.51 3246.95 BIRA+Bradyrhizobium stain 1-7 Average Yield 550 403.335 26889 129.82 31.75 2116.67 3324.88 1847.16 BIRA+Bradyrhizobium strain 14-3 Average Yield 1100 407 27133.33 142.76 35.905 2393.67 2664.01 1480.01 Table 3: Showing the yield data from the bio-inoculant treated plots. Dependent variable: Plant_Dry_Matter_Yield Source Type III sum of squares df Mean square F Sig. Partial Eta squared Corrected Model 39886390060.000a 15 2659092671 4.194 0 0.572 Intercept 73585686100 1 7.3586E+10 116.055 0 0.712 Treatment 1076062735 2 538031367 0.849 0.434 0.035 Cultivar_Name 20984435470 5 4196887093 6.619 0 0.413 Treatment * Cultivar Name 13659285540 8 1707410693 2.693 0.016 0.314 Error 29800844500 47 634060521 --   --  -- Total 1.78973E+11 63  --  --  --  -- Corrected Total 69687234570 62  --  --  -- -- a.R Squared=0.572 (Adjusted R Squared=0.436) Table 4: Tests of between-subjects’ effects (Plant_Dry_Matter_Yield). Table 1: Average yield data per subplot from the negative control (non-inoculated plot). Dependent variable: Plant_Dry_Matter_Yield Source Type III sum of squares df Mean square F Sig. Partial Eta squared Corrected Model 39886390060.000a 15 2659092671 4.194 0 0.572 Intercept 73585686100 1 7.3586E+10 116.055 0 0.712 Treatment 1076062735 2 538031367 0.849 0.434 0.035 Cultivar_Name 20984435470 5 4196887093 6.619 0 0.413 Treatment * Cultivar Name 13659285540 8 1707410693 2.693 0.016 0.314 Error 29800844500 47 634060521 --   --  -- Total 1.78973E+11 63  --  --  --  -- Corrected Total 69687234570 62  --  --  -- -- a.R Squared=0.572 (Adjusted R Squared=0.436) Table 4: Tests of between-subjects’ effects (Plant_Dry_Matter_Yield). Table 4: Tests of between-subjects’ effects (Plant_Dry_Matter_Yield). Table 4: Tests of between-subjects’ effects (Plant_Dry_Matter_Yield). Grain yield: For the grain yield data collection, 10 randomly excavated plants had their pod numbers counted. Yield assessment doi: 10.4172/2157-7471.1000456 Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. doi: 10.4172/2157-7471.1000456 Page 3 of 5 Cultivar Name Shoot wet weight (g) Shoot dry wet (g) Plant dry matter yield (kg/ha) Root wet weight (g) Root dry weight (g) Root dry matter yield (kg/ha) Grain yield (g) Grain yield (kg/ ha) NAKARE Average Yield 383.33 225.21 1501.89 138.73 70.17 4678.22 2273.23 1262.9 SILWANA Average Yield 1125 225 15000 109.055 33.7525 2250.17 2401.86 1334.37 SHINDIMBA Average Yield 300 360 24000 339.24 80.31 5354.22 273.18 151.77 LUTEMBWE Average Yield 2500 1264.71 84313.9 105.3 27.65 1843.33 3560.66 1978.14 BIRA Average Yield 1800 990 66000 158.38 35.5 2366.33 4270.64 2372.58 Table 1: Average yield data per subplot from the negative control (non-inoculated plot). NAKARE Average Yield 383.33 225.21 1501.89 138.73 70.17 4678.22 2273.23 1262.9 SILWANA Average Yield 1125 225 15000 109.055 33.7525 2250.17 2401.86 1334.37 SHINDIMBA Average Yield 300 360 24000 339.24 80.31 5354.22 273.18 151.77 LUTEMBWE Average Yield 2500 1264.71 84313.9 105.3 27.65 1843.33 3560.66 1978.14 BIRA Average Yield 1800 990 66000 158.38 35.5 2366.33 4270.64 2372.58 Table 1: Average yield data per subplot from the negative control (non-inoculated plot). Cultivar Name Shoot wet weight (g) Shoot dry wet (g) Plant dry matter yield (kg/ha) Root wet weight (g) Root dry weight (g) Root dry matter yield (kg/ha) Grain yield (g) Grain yield (kg/ha) LUTEMBWE. Fertiliser Average Yield 2600 732.73 48848.58 118.905 32.53 2168.5 2264.78 1258.21 SHINDIMBA. Fertiliser Average Yield 517 517.5 34500 147.3 33.39 2226 463.97 257.76 NAKARE. Fertiliser Average Yield 966.67 172.07 11471.11 236.5 40.07 2671.33 1873.42 1040.79 SILWANA. Fertiliser Average Yield 2000 600 40000 110.28 29.13 1942.16 3703.37 2057.43 BIRA. Fertiliser Average Yield 2550 493 32866.67 104.38 39.7 2646.65 2460.98 1367.21 NIGERIAN Cultivar. Fertiliser Average Yield 350 105 7000 54.47 13.13 875.58 1652.95 918.31 Table 2: Showing the average yield data for the Subplots with fertilizer treatment. Yield assessment This was used to give an average number of pods per subplot based on the number of plants that were on that subplot. This was carried out for all plots. From these pods, 40 were selected randomly and the number of seeds in these 40 pods counted to get the average seeds per pod. Lastly 100 seeds were selected, from the seeds obtained from the 40 pods, and weighed to get the 100 seed weight per subplot. The seed weight per subplot was also recorded and the above procedure was done for all the subplots. Yield assessment It was divided into 3 sections, with one section having a treatment of the 6 different cowpea cultivars plus nitrogen fertilizer, the other section having the cowpea cultivars plus bio inoculants and the third having only the cowpea cultivars minus any other treatment. This design is illustrated in the diagram below. The inoculant treatment was performed by getting a substantial amount of bacterial inoculant strains called Bradyrhizobium (1-7) and (14-3). The strains were grown fresh Modified Arabinose Gluconate Medium, with peat as a carrier, then packed in Whirl-Pack® sample bags. The bags were stored at room temperature with avoiding their that are resistant to the ‘witch weed’ Alectra vogelii, which according to Mwaipopo [12] is a parasitic weed that is known to cause major constraints on legumes and most especially cowpea, where obtained from The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) these were named I2. The cowpea was grown under rain fed conditions so as to stimulate the natural environmental conditions of the area. The field was ploughed back and forth to homogenize the plot on which the planting was done. It was divided into 3 sections, with one section having a treatment of the 6 different cowpea cultivars plus nitrogen fertilizer, the other section having the cowpea cultivars plus bio inoculants and the third having only the cowpea cultivars minus any other treatment. This design is illustrated in the diagram below. The inoculant treatment was performed by getting a substantial amount of bacterial inoculant strains called Bradyrhizobium (1-7) and (14-3). The strains were grown fresh Modified Arabinose Gluconate Medium, with peat as a carrier, then packed in Whirl-Pack® sample bags. The bags were stored at room temperature with avoiding their Shoot biomass: The harvested middle plants had their shoots separated from their roots. These 10 shoots were then weighed immediately with a balance and the shoot dry mass recorded. They were then dried in an open space in sunlight for 4 days. After the drying, dry weight measurements of these shoots was recorded. These obtained measurements were used to extrapolate the shoot dry matter yield per subplot and were carried out on all the plots. Volume 9 • Issue 10 • 1000456 Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. J Plant Pathol Microbiol, an open access journal ISSN: 2157-7471 Yield in terms of shoot biomass It is of utmost importance to assess the yield of the performed treatments and how these yield components respond so as to reach a conclusion as to which treatment would best suit a farmer’s needs. From the yield assessment of the different cowpea cultivars in terms of plant dry matter yield, there is no statistical difference in the obtained plant dry matter measurements across the three different treatments with a p > 0.05, this is despite there being an observed difference in the obtained mean values of the treatments. This study’s findings in this regard correlates to a study done by Hungria et al. [13], who reported that the use of mineral fertilizer did not have any significant effect on the shoot dry biomass when applied at recommended rates but resulted in a significant increment when applied at 1.5 times the recommended amounts. These obtained results indicate that the use of nitrogen fertilizer to enhance shoot biomass of the bean is not beneficial. Andrade et al., [14] States that previous studies on soybean that was treated with nitrogen fertilizer, did not indicate any benefits as compared to the application of bio-inoculants on the soybean grown in Brazilian soils. With respect to the different cultivars’ relation to plant biomass yield, it was observed that the obtained yield measurements differed significantly depending by the type of cultivar used with a significant p-value less than 0.05. When subjected to all the three different treatments, the cultivar Lutembwe had the largest plant dry yield per hectare as compared to the other cultivars (Figure 3). Hence for farmers that would like to grow cowpea for forage use, this would be the recommended cultivar. This is seconded by Silwana followed by Bira, with the Nigerian cultivar not faring well in terms of shoot yield as compared to the other cultivars. This poor performance of the cultivar could be attributed to it not natively grown in the Southern African soils hence the poor yield. With regards to the interaction between cultivar name and the type of treatment and their effect on shoot dry matter yield, at the 0.05 level of significance, there is a significant interaction between the factors and the shoot dry matter yield of 0.016. Harvesting All the subplots minus the destruction plots were harvested for yield assessment. The samples consisted of roots, shoots and pods. They had to be weighed in grams immediately after harvesting to get the root and shoot wet weights, with a beam balance and a hanging balance respectively. J Plant Pathol Microbiol, an open access journal ISSN: 2157-7471 Volume 9 • Issue 10 • 1000456 Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. doi: 10.4172/2157-7471.1000456 Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. doi: 10.4172/2157-7471.1000456 Page 4 of 5 Dependent variable: Grain_Yield Source Type III Sum of Squares df Mean Square F Sig. Partial Eta Squared Corrected Model 61400644.780a 15 4093376.319 4.758 0 0.603 Intercept 163213020.9 1 163213020.9 189.721 0 0.801 Treatment 22438450.78 2 11219225.39 13.041 0 0.357 Cultivar_Name 14938031.29 5 2987606.259 3.473 0.009 0.27 Treatment *Cultivar_Name 14217142.25 8 1777142.782 2.066 0.059 0.26 Error 40433110.91 47 860278.956 --   -- --  Total 308977495.6 63  -- --   -- --  Corrected Total 101833755.7 62  -- --  --  --  a.R Squared=.603 (Adjusted R Squared=.476) Table 5: Tests of between-subjects’ effects (Grain_Yield). Table 5: Tests of between-subjects’ effects (Grain_Yield). Yield in terms of shoot biomass The cultivars Lutembwe and Nakare had a poor shoot dry matter yield with the fertilizer treatments with Bira and Shindimba reporting the lowest shoot dry matter yield with the bio-inoculant treatment while Silwana and Nakare reported the highest yield with bio-inoculant. The Nigerian cultivar was only subjected to the fertilizer treatment. Therefore with regards to the shoot biomass, with fertilizer treatment maximum yield is achieved by Lutembwe, while with bio- inoculant maximum yields are achieved by the cultivar Silwana. Such information is handy when cowpea is cultivated for its shoot biomass with an indication that the use of fertilizer when cultivating cowpea for this purpose is non-profitable. Data analysis A 2-Way Anova was carried out on the above datasets of namely: Shoot Dry Matter Yield (kg/ha), Root Dry Matter Yield (kg/ha) and Grain yield (kg/ha) after the Anova assumptions were met. This Analysis of variance tested the hypotheses below. 1. H0: There is no significance difference in the Shoot, Root and Grain yields across the 3 different treatments. 1. H0: There is no significance difference in the Shoot, Root and Grain yields across the 3 different treatments. 2. H0: There is no significant difference in the Shoot, Root and Grain yields across the different cultivars. 2. H0: There is no significant difference in the Shoot, Root and Grain yields across the different cultivars. The p-value of treatment to Plant dry matter yield is 0.434, meaning there is no statistical difference between the treatments and shoot biomass yield at the 0.05 level of significance. On the other hand there is a statistical difference between Cultivar name and Plant Dry Matter Yield and the interaction between Treatment and cultivar name at the 0.05 level of significance with p values of 0.00 and 0.016 respectively. The pairwise comparisons of the cultivars is shown in the Annex (Table 4). Therefore, there is insufficient evidence to reject the first null hypothesis and enough evidence to reject the second null hypothesis. Indicating a significant difference in Plant Dry Matter yield across the six different cultivars. Discussion and Conclusion The dry matter yield of the shoots was compared amongst the three treatments of fertilizer, bio-inoculant and a negative control of no treatment to figure out (Figure 2) which was more effective by measuring the yield. The tables (Tables 1-3) that follow are the results of these comparisons in terms of the shoots, roots and the grain yield of each cultivar planted. J Plant Pathol Microbiol, an open access journal ISSN: 2157-7471 Grain yield Cowpea grain yield is considered one of the most important parameters for farmers in terms of assessing how different treatments affect yield [15]. This is due to the proteins having a high protein content for consumption [14] in addition, the more the grain yield the more profits the farmers expects from the legumes and also this entails the farmer has a surplus to plant for the next season. There is a significant difference in the means of the different treatments and cultivars with relation to the grain yields. Our study reviewed a significant mean difference of 1604.14 based on the post hoc tests between the fertilizer treatment and the bio-inoculant treatment, with the bio-inoculant recording a higher grain yield. This is more than a 10% increase in grain yield which is a substantial as an indication that a treatment is working according to Ronner et al. [16]. Our findings are close to the 30% increase in grain yield by bio-inoculant application reported by Martins et al. [17]. If a farmer’s aim is to increase the grain yield of their cowpea then it’s recommended to use bio-inoculant as opposed to mineral fertilizer because not only is it eco-friendly but also is a cheaper alternative, this is supported by our findings. In addition to this, the cultivars Silwana, Nakare and Lutembwe gave the largest grain yield with the bio-inoculant treatment with yields of 3619.45, 3621.25 and 2728.92 kg/ha respectively. Shindimba had the lowest grain yield, a less lower than the Nigerian cultivar. Therefore outcome of this study is significant in providing the subsistence farmers with bio-inoculants that are able to effectively fix biological nitrogen when in symbiosis with cowpea under a climate of low rainfall. This will in turn increase profits and crop productivity at large as less money will be spent on chemicals in trying to enrich the poor soils in the regions and Namibia at large. 5. Hamid S, Muzaffar S, Wani IA, Masoodi FA, Bhat MM (2014) Physical and cooking characteristics of two cowpea cultivars grown in temperate Indian Climate. J Sau Soci Agr Sci 15: 27-134. 6. Kiim YY, Woo KS, Chung HJ (2018) Starch characteristics of cowpea and mungbean cultivars grown in Korea. 7. Hoover R, Hughes T, Chung HJ, Liu Q (2010) Composition, molecular structure, properties and modifaication of luse starches: A review. Food Res Int 43: 339-413. 8. Grain yield For the grain yield statistical analysis, there is a statistical difference across the means of the different treatments and cultivar names at the 0.05 level of significance with p-values of 0.00 and 0.009 respectively. On the contrary there is no statistical difference in means of the interaction of Treatment and Cultivar name with grain yield with a p-value of 0.059. Therefore for Treatment and Cultivar name, the null hypotheses that state: 1. H0: There is no significance difference in the Grain yields across the 3 different treatments. 2. H0: There is no significant difference in the Grain yields across the different cultivars. Are rejected at the 0.05 level of significance (Table 5). J Plant Pathol Microbiol, an open access journal ISSN: 2157-7471 Volume 9 • Issue 10 • 1000456 Volume 9 • Issue 10 • 1000456 Page 5 of 5 Page 5 of 5 Page 5 of 5 4. Mendelsohn J (2009) Land use in Kavango: Past, present and future. Environmental protection and sustainable management of the Okavango River Basin (EPSMO) Project pp: 1-31. 3. Moray C, Game ET, Maxted N (2014) Prioritising in situ conservation of crop resources: A case study of African cowpea (Vigna unguiculata). Sci Rep 4: 5247. J Plant Pathol Microbiol, an open access journal ISSN: 2157-7471 Grain yield Phiri GK, Wellard K, Snapp S (2017) Agricultural systems in a changing world. In: Agr Sys pp: 3-15. 9. Kermah M, Franke AC, Adjei-Nsiah S, Ahiabor BDK, Abaidoo RC, et al. (2018) N2-fixation and N contribution by grain legumes under different soil fertility status and cropping systems in the Guinea savanna of northern Ghana. Elsevier 261: 201-210. 10. Zahran HH (1999) Rhizobium-Legume symbiosis and nitrogen fixation under severe conditions and in an arid climate. Microbiol Mol Biol Rev 63: 968-989. 11. Leite J, Passos SR, Simoes-Araujo JL, Rumjanek NG, Xavier GR, et al. (2017) Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil. Brazil J Microbio 49: 703-713. 12. Mwaipopo BV (2014) Characterization of alectra vogelii (witch weed) strains using molecular markers in selected parts of malawi and tanzania. 13. Hungria M, Franchini JC, Campo RJ, Crispino CC, Moraes JZ, et al. (2006) Nitrogen nutrition of soybean in Brazil: Contributions. Canadian Journal of Plant Science 86: 927-939. 14. Andrade MMM, Stamford NP, Santos Carolina ERS, Freitas ADS, Sousa CA, et al. (2013) Effects of biofertilizer with diazotrophic bacteria and mycorrhizal fungi in soil attribute, cowpea nodulation yield and nutrient uptake in field conditions. Scientia Horticulturae 162: 374-379. 2. Mendelsohn J, Obeid S (2003) Sand and water: A profile of the Kavango region. Cape Town, Windhoek, Struik Publishers and RAISON. Citation: Luchen CC, Uzabikiriho JD, Chimwamurombe PM, Reinhold-Hurek B (2018) Evaluating the Yield Response to Bio-Inoculants of Vigna unguiculata in the Kavango Region in Namibia. J Plant Pathol Microbiol 9: 456. doi: 10.4172/2157-7471.1000456 1. Strohbach BJ, Petersen A (2007) Vegetation of the central Kavango woodlands in Namibia: An example from the Mile 46 Livestock Development Centre. Sou Afri J Bot 73: 391-401. Volume 9 • Issue 10 • 1000456 References 1. Strohbach BJ, Petersen A (2007) Vegetation of the central Kavango woodlands in Namibia: An example from the Mile 46 Livestock Development Centre. Sou Afri J Bot 73: 391-401. 15. Horn L, Shimelis H, Sarsu F, Mwadzingeni L, Lainga MD (2017) Genotype-by- environment interaction for grain. Crop Science Society of China 6: 306-313. 16. Ronner E, Franke AC, Vanlauwe B, Dianda M, Edeh E, et al. (2016) Understanding variability in soybean yield and response to P-fertilizer. Field Crops Res 186: 133-145. 2. Mendelsohn J, Obeid S (2003) Sand and water: A profile of the Kavango region. Cape Town, Windhoek, Struik Publishers and RAISON. 17. Martins LMV, Xavier GR, Range FW, Ribeiro JRA, Neves MCP, et al. (2003) Contribution of biological nitrogen fixation to cowpea: A strategy of improving grain yield in the semi-arid region of Brazil. Bio Fert Soils 38: 333-339. Volume 9 • Issue 10 • 1000456
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Fabrication of Tapered Micropillars with High Aspect-Ratio Based on Deep X-ray Lithography
Materials
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cc-by
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Received: 26 May 2019; Accepted: 25 June 2019; Published: 26 June 2019 Abstract: In this study, a fabrication method of tapered microstructures with high aspect ratio was proposed by deep X-ray lithography. Tapered microstructures with several hundred micrometers and high aspect ratio are demanded owing to the high applicability in the fields of various microelectromechanical systems (MEMS) such as optical components and microfluidic channels. However, as the pattern and gap size were downsized to smaller micro-scale with higher aspect ratio over 5, microstructures were easily deformed or clustered together due to capillary force during the drying process. Here, we describe a novel manufacturing process of tapered microstructures with high aspect ratio. To selectively block the deep X-ray irradiation, an X-ray mask was prepared via conventional ultraviolet (UV) lithography. A double X-ray exposure process with and without X-ray mask was applied to impose a two-step dose distribution on a photoresist. For the clear removal of the exposed region, the product was developed in the downward direction, which encourages a gravity-induced pulling force as well as a convective transport of the developer. After a drying process with the surface additive, tapered microstructures were successfully fabricated with a pattern size of 130 µm, gap size of 40 µm, and aspect ratio over 7. Keywords: tapered micropillars; high aspect-ratio; X-ray lithography; development Fabrication of Tapered Micropillars with High Aspect-Ratio Based on Deep X-ray Lithography Jae Man Park 1, Jong Hyun Kim 2, Jun Sae Han 3, Da Seul Shin 1, Sung Cheol Park 4, Seong Ho Son 4 and Seong Jin Park 1,* 1 Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea 2 Pohang Accelerator Laboratory (PAL), Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea 3 Department of Nano Manufacturing Technology, Korea Institute of Machinery & Materials (KIMM), 156, Gajeongbuk-ro, Yuseong-gu, Daejeon 34103, Korea 4 Surface Treatment R&D Group, Korea Institute of Industrial Technology (KITECH), 156 Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Korea, * C d j k87@ t h k T l +82 54 279 2182 * Correspondence: sjpark87@postech.ac.kr; Tel.: +82-54-279-2182   Materials 2019, 12, 2056; doi:10.3390/ma12132056 materials materials Article 1. Introduction Synchrotron X-ray lithography has emerged as a novel micromachining technology to fabricate nano/micropillars with high aspect ratio and precise optics. The X-ray beam, which has high collimation and intensity, passes through a thick polymer and other materials and allows the materials to be shaped into a nearly vertical structure with good sidewall roughness and high pattern accuracy. With these advantages, X-ray lithography has been used to manufacture a sacrificial polymer mold [1,2], microfluidic channel [3], and tilted polymer structures [4]. As a further process, the nano/micropillars could be metal-electroformed as a mold insert and used for injection molding [5,6] and an embossing process [7]. This sequential process, called LIGA (German abbreviation: Lithographie, Galvanoformung, and Abformung) is beneficial for mass-production of micro-scale polymers and metal/ceramic structures with high aspect ratios. However, severe forces are exerted on the micropillars during the demolding process as the pattern and gap size become smaller Materials 2019, 12, 2056; doi:10.3390/ma12132056 www.mdpi.com/journal/materials www.mdpi.com/journal/materials 2 of 9 Materials 2019, 12, 2056 in micro-scale and as the aspect ratio increases. As a result, the micropillars could be slanted or broken from the mold insert, and these defects deteriorate the quality of the final product. A mold insert with a tapered cavity could be a solution to facilitate the demolding process by reducing the interfacial area between the mold and micropillars. To fabricate a tapered mold insert, the inverted cylindrical microstructures that are pillar-shaped, known as a mandrel, also should be tapered before undergoing the electroforming process. It would be interesting to manufacture the tapered micropillars prior to electroforming because the conventional micromachining process does not realize a tapered shape. To date, as a mandrel, research on the fabrication of tapered micropillars with high aspect ratio has examined the use of various exposure techniques. Klein et al. [8] fabricated 3 mm tapered tall posts using X-ray masks with low contrast during X-ray lithography. Using the same technique, Liu et al. [9] produced micro-scale pyramidal structures with aspect ratio under 5. Matsuzuka et al. [10] adopted a double X-ray exposure technique to attain a tapered microstructure, and tens of micro-scale tapered structures with aspect ratio under 3 were manufactured. Utsumi et al. [11] used an X-ray mask with distributed absorber thickness and replicated the trapezoidal cylindrical structures with aspect ratio below 3. Turner et al. 1. Introduction [12] selected the multiple exposures of SU-8 and achieved a tapered SU-8 post with height over 1 mm. Most of them had an aspect ratio under 5, and the gap size was larger than the pattern size since critical slumping and clustering of micropillars could happen during the drying process. Here, this study proposed and developed a novel technique using X-ray lithography to fabricate tapered micropillars with high aspect ratio. Double X-ray exposure with and without X-ray mask was conducted to impose a two-step dose distribution on photoresist [10]. The exposed region was placed in the downward direction to clearly eliminate a residual resist on the bottom of a substrate during the development process. In the drying process, surface additive was adopted to release a capillary force. Based on the optimized process, tapered micropillars with aspect ratio over 7 were successfully obtained without any visible defects. Samp 2.2. Preparation of X-Ray Mask 2 2 Preparation of X-Ray Mask Samp 2.2. Preparation of X-Ray Mask 2 2 Preparation of X-Ray Mask Samp 2.2. Preparation of X-Ray Mask 2 2 Preparation of X-Ray Mask 2.2. Preparation of X-Ray Mask During deep X-ray lithography, an X-ray mask was used to reduce the irradiated X-ray to a certain state, which cannot collapse a photoresist below the X-ray absorber. The X-ray mask consists of the X-ray absorber material and a substrate. Gold (Au) was adopted as an absorber material with the advantages of short attenuation length and easy process [15]. Polyimide (PI) film was employed as a flexible substrate with high transparency of X-ray and dimensional stability [16]. For the high- precision micropillars with high aspect ratio, it is essential to acquire a delicate X-ray absorber structure. In the present study, the X-ray mask was prepared by a conventional UV-lithography process with negative type photoresist and Au electroplating process Figure 2 displays the brief During deep X-ray lithography, an X-ray mask was used to reduce the irradiated X-ray to a certain state, which cannot collapse a photoresist below the X-ray absorber. The X-ray mask consists of the X-ray absorber material and a substrate. Gold (Au) was adopted as an absorber material with the advantages of short attenuation length and easy process [15]. Polyimide (PI) film was employed as a flexible substrate with high transparency of X-ray and dimensional stability [16]. For the high-precision micropillars with high aspect ratio, it is essential to acquire a delicate X-ray absorber structure. In the present study, the X-ray mask was prepared by a conventional UV-lithography process with negative-type photoresist and Au electroplating process. Figure 2 displays the brief fabrication process of the X-ray mask. p f y During deep X-ray lithography, an X-ray mask was used to reduce the irradiated X-ray to a certain state, which cannot collapse a photoresist below the X-ray absorber. The X-ray mask consists of the X-ray absorber material and a substrate. Gold (Au) was adopted as an absorber material with the advantages of short attenuation length and easy process [15]. Polyimide (PI) film was employed as a flexible substrate with high transparency of X-ray and dimensional stability [16]. For the high- precision micropillars with high aspect ratio, it is essential to acquire a delicate X-ray absorber structure. In the present study, the X-ray mask was prepared by a conventional UV-lithography process with negative-type photoresist and Au electroplating process. Samp 2.2. Preparation of X-Ray Mask 2 2 Preparation of X-Ray Mask Figure 2 displays the brief fabrication process of the X-ray mask. brication process of the X-ray mask. Figure 2. Fabrication process of X-ray mask: (a) deposition of Cr and Au seed layer on polyimide film; Figure 2. Fabrication process of X-ray mask: (a) deposition of Cr and Au seed layer on polyimide film; (b) micropatterning process on the seed layer by UV lithography; (c) Au electroplating between the mask patterns; and (d) X-ray mask detached from the silicon wafer. Figure 2. Fabrication process of X-ray mask: (a) deposition of Cr and Au seed layer on polyimide film; (b) micropatterning process on the seed layer by UV lithography; (c) Au electroplating between the mask patterns; and (d) X-ray mask detached from the silicon wafer. brication process of the X-ra mask. mas on p Figure 2. Fabrication process of X-ray mask: (a) deposition of Cr and Au seed layer on polyimide film; Figure 2. Fabrication process of X-ray mask: (a) deposition of Cr and Au seed layer on polyimide film; (b) micropatterning process on the seed layer by UV lithography; (c) Au electroplating between the mask patterns; and (d) X-ray mask detached from the silicon wafer. Figure 2. Fabrication process of X-ray mask: (a) deposition of Cr and Au seed layer on polyimide film; (b) micropatterning process on the seed layer by UV lithography; (c) Au electroplating between the mask patterns; and (d) X-ray mask detached from the silicon wafer. (b) micropatterning process on the seed layer by UV lithography; (c) Au electroplating between the mask patterns; and (d) X-ray mask detached from the silicon wafer. In the first step, the PI film was laminated on a polished 4-inch silicon wafer using an adhesive dry film resist (DFR). For the electroplating process, a seed layer composed of 20-nm Cr and 100-nm Au was deposited on PI film using an E-beam evaporation. The second step was to formulate a micropatterning on the seed layer. Prior to the patterning process, the Cr/Au seed layer was oxygen plasma-cleaned for 1 min. To create a uniform photoresist layer, a negative-type photoresist solution (SU-8 3010, MicroChem, Westborough, MA, USA) was spin-coated onto the seed layer at 600 rpm for 30 s, resulting in a thickness of about 25 μm. Then, the sample was lightly baked at 95 °C for 18 min. Samp 2.2. Preparation of X-Ray Mask 2 2 Preparation of X-Ray Mask The photoresist layer was exposed to UV source of 10 mW for 17 s using a designed chrome mask, and subsequently post-exposure baking was carried out at 65 °C for 1 min and at 95 °C for 4 min. To In the first step, the PI film was laminated on a polished 4-inch silicon wafer using an adhesive dry film resist (DFR). For the electroplating process, a seed layer composed of 20-nm Cr and 100-nm Au was deposited on PI film using an E-beam evaporation. The second step was to formulate a micropatterning on the seed layer. Prior to the patterning process, the Cr/Au seed layer was oxygen plasma-cleaned for 1 min. To create a uniform photoresist layer, a negative-type photoresist solution (SU-8 3010, MicroChem, Westborough, MA, USA) was spin-coated onto the seed layer at 600 rpm for 30 s, resulting in a thickness of about 25 μm. Then, the sample was lightly baked at 95 °C for 18 min. The photoresist layer was exposed to UV source of 10 mW for 17 s using a designed chrome mask, and subsequently post-exposure baking was carried out at 65 °C for 1 min and at 95 °C for 4 min. To dissolve the unexposed region, the specimen was immersed in SU-8 developer for 5 min, followed In the first step, the PI film was laminated on a polished 4-inch silicon wafer using an adhesive dry film resist (DFR). For the electroplating process, a seed layer composed of 20-nm Cr and 100-nm Au was deposited on PI film using an E-beam evaporation. The second step was to formulate a micropatterning on the seed layer. Prior to the patterning process, the Cr/Au seed layer was oxygen plasma-cleaned for 1 min. To create a uniform photoresist layer, a negative-type photoresist solution (SU-8 3010, MicroChem, Westborough, MA, USA) was spin-coated onto the seed layer at 600 rpm for 30 s, resulting in a thickness of about 25 µm. Then, the sample was lightly baked at 95 ◦C for 18 min. The photoresist layer was exposed to UV source of 10 mW for 17 s using a designed chrome mask, and subsequently post-exposure baking was carried out at 65 ◦C for 1 min and at 95 ◦C for 4 min. To dissolve the unexposed region, the specimen was immersed in SU-8 developer for 5 min, followed by rinsing with isopropyl alcohol for 1 min. 2.1. Experimental Setup Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere Table 1. Experimental setup condition of 9D beamline. Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere 2.2. Preparation of X-Ray Mask Table 1. Experimental setup condition of 9D beamline. Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere 2 2 Preparation of X Ray Mask 2.1. Experimental Setup Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere 2.2. Preparation of X-Ray Mask Figure 1. Schematic diagram of 9D beamline. Table 1. Experimental setup condition of 9D beamline. Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere 2 2 Preparation of X Ray Mask Figure 1. Schematic diagram of 9D beamline. Table 1. Experimental setup condition of 9D beamline. Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere Figure 1. Schematic diagram of 9D beamline. Table 1. Experimental setup condition of 9D beamline. Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere 2.2. Preparation of X-Ray Mask Figure 1. Schematic diagram of 9D beamline. Table 1. Experimental setup condition of 9D beamline. Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere 2 2 Preparation of X-Ray Mask Figure 1. Schematic diagram of 9D beamline. Figure 1. Schematic diagram of 9D beamline. Figure 1. Schematic diagram of 9D beamline. g g Table 1. Experimental setup condition of 9D beamline. Table 1. Experimental setup condition of 9D beamline. Table 1. Experimental setup condition of 9D beamline. 2.1. Experimental Setup In this research, deep X-ray lithography experiments were performed at the 9D X-ray nano/micromachining beamline of the Pohang Accelerator Laboratory (PAL). Figure 1 represents the schematic diagram of the 9D beamline. A polychromatic X-ray beam was injected from a linear accelerator to a storage ring. The linearly accelerated electrons exhibited an energy of 3 GeV with beam current of 360 mA. As a core part in PAL, a bending magnet not only keeps the electrons in the storage ring, but it also delivers the X-ray source directly into the chamber [4]. The horizontal and vertical divergence of the X-ray source were 8 and 0.34 mrad, respectively. Before reaching the target sample in the chamber, the X-ray passes through a double mirror system, slit, and beryllium windows. The mirror system was used to cut offa high-energy-range X-ray, which could cause undesirable secondary effects such as backscattering and Auger electron effect [13]. By using a four-way slit aperture, the beam size on the sample can be adjusted to a square shape with a horizontal size of 100 mm and vertical length of 10 mm, which is sufficient for a 4-inch wafer. Beryllium windows were used for vacuum separation, and were surrounded by helium gas to prevent window oxidation. The chamber was also filled with helium gas to minimize the photon flux degradation and maintain a high X-ray transmission [14]. In addition, this gas gives an efficient convection of heat generation due to its non-zero heat capacity [4]. When the sample was mounted on the jig in the chamber, the sample stage reciprocated vertically to supply a uniform X-ray distribution on the photoresist. Table 1 summarizes the experimental setup condition of the 9D beamline. 3 of 9 3 of 9 f 9 Materials 2019, 12, 2056 Materials 2019 12 x FOR M t i l 2019 12 FO Figure 1. Schematic diagram of 9D beamline. Table 1. Experimental setup condition of 9D beamline. Setup Condition 9D Beamline Original photon energy 3.0 GeV Mirrored photon energy 3.0 to 7.0 KeV Beam current 360 mA Horizontal beam divergence 8 mrad Vertical beam divergence 0.34 mrad Beam size 100 mm (H) × 10 mm (V) Sample environment Vacuum or He atmosphere Figure 1. Schematic diagram of 9D beamline. Table 1. Experimental setup condition of 9D beamline. Samp 2.2. Preparation of X-Ray Mask 2 2 Preparation of X-Ray Mask Finally, residual photoresist was eliminated via oxygen 4 of 9 Materials 2019, 12, 2056 plasma cleaning for 15 s. The third step was to electroplate the Au layer on the developed SU-8 area. An electroplating process was performed at 50 ◦C using a customized electrochemical cell, which is filled with deionized water and electrolyte gold solution. The developed seed layer region was Au electroplated with current density of 1 mA/cm2 for 7 h. Thereafter, the substrate was sufficiently rinsed by distilled water. In the final stage, the X-ray mask was detached from the silicon wafer. Table 2 illustrates the processing conditions of X-ray mask fabrication used in this study. Table 2. Processing conditions of X-ray mask fabrication. Preparation of Substrate Base Substrate 4 inch silicon wafer Seed layer Cr: 20 nm/Au: 100 nm UV lithography Process Surface cleaning by oxygen plasma 300 W for 1 min Spin coating 600 rpm for 30 s (thickness: 25 µm) Soft baking 95 ◦C for 18 min UV exposure energy and time 170 W / 17 s Post exposure baking 65 ◦C for 1 min / 95 ◦C for 4 min Development 5 min Surface cleaning by oxygen plasma 300 W for 15 s Au electroplating Process Applied current 64 mA for 7 h Current density 1 mA/cm2 Table 2. Processing conditions of X-ray mask fabrication. Preparation of Substrate Base Substrate 4 inch silicon wafer Seed layer Cr: 20 nm/Au: 100 nm UV lithography Process Surface cleaning by oxygen plasma 300 W for 1 min Spin coating 600 rpm for 30 s (thickness: 25 µm) Soft baking 95 ◦C for 18 min UV exposure energy and time 170 W / 17 s Post exposure baking 65 ◦C for 1 min / 95 ◦C for 4 min Development 5 min Surface cleaning by oxygen plasma 300 W for 15 s Au electroplating Process Applied current 64 mA for 7 h Current density 1 mA/cm2 Table 2. Processing conditions of X-ray mask fabrication. 3.1. Interaction between X-Ray Source and Photoresist Au X-ray mask on the top of the PMMA shoul Au X-ray mask on the top of the PMMA should be able to efficiently block the deep X-ray as an absorber material. Figure 3a displays the schematic process of X-ray lithography. The X-ray can easily penetrate the SU-8 micropattern on the PI film because the material is transparent to X-rays. On the other hand, the gold layer showed low X-ray transmittance due to the high absorption property of gold to X-ray, as shown in Figure 3b. With the increase of Au thickness, it became more difficult for X-ray to transmit through the Au layer. Before the X-ray reached the X-ray absorber, the photon flux distribution of the light source was analyzed, since it greatly influences the quality of the microstructure. The photon flux distribution was calculated by reference to inherent properties of the beam source. From the analysis, we can predict the desirable Au thickness, and interaction between the electrons and photoresist materials. The photon flux distribution generated from the X-ray at 3.0 GeV showed a wide range of energies from a few volts to tens of kilo-electron volts, as indicated in Figure 3c. When the X-ray passed through two Be windows, its photon flux was reduced to 66% of the original beam source while still maintaining high-energy photons. These high-energy photons were absorbed in the substrate of the photoresist, resulting in creation of photoelectrons, Auger-electrons, and fluorescence photons. Such photons were backscattered to the PMMA layer, which reduced the molecular weight of PMMA on the interfacial surface [19]. Consequently, it caused a poor adhesion between PMMA and the substrate. To eliminate high-energy photons with energies over 7 keV, a double mirror system with angle of 0.45◦was used and revealed a flux distribution with low-energy photon range. absorber material. Figure 3a displays the schematic process of X-ray lithography. The X-ray can easily penetrate the SU-8 micropattern on the PI film because the material is transparent to X-rays. On the other hand, the gold layer showed low X-ray transmittance due to the high absorption property of gold to X-ray, as shown in Figure 3b. With the increase of Au thickness, it became more difficult for X-ray to transmit through the Au layer. Before the X-ray reached the X-ray absorber, the photon flux distribution of the light source was analyzed, since it greatly influences the quality of the microstructure. 2.3. X-Ray Exposure As a positive-type photoresist, a poly(methyl methacrylate) (PMMA; Goodfellow) with a thickness of 980 µm was used for X-ray irradiation by attaching it to a base substrate. The PMMA is generally used for deep X-ray lithography due to its freestanding contrast and process stability. Prior to adhering it on a substrate, PMMA was polished and annealed at 80 ◦C for 1 h to relax its internal stress. As a base substrate, a polished graphite sheet with thickness of 2 mm was prepared because of its high porosity, micro-roughness, and low secondary radiation effect [17]. These properties are advantages for the excellent adhesion with PMMA. The graphite was spin-coated with 1000 rpm using a liquid PMMA (950 PMMA C9; MicroChem, Westborough, MA, USA) and baked at 180 ◦C for 1 h. This process was repeated four times to ensure a sufficient PMMA adhesion layer. Thereafter, the PMMA sheet was chemically bonded to the graphite sheet using a pre-developed solution [18]. An X-ray exposure process was performed on the substrate with the prepared X-ray mask via a scanning system of the 9D beamline. The X-ray mask was placed on the top surface of PMMA in the jig, and the mask was covered by PI film. For the reduction of X-ray diffraction in air atmosphere, the substrate, X-ray mask, and PI film were hard contacted by sucking out the air using a vacuum system. Then, the chamber containing the jig and reciprocating part was filled with helium before X-ray exposure. In this study, double X-ray exposure process with and without X-ray mask was performed to give a two-step dose distribution on the PMMA. First, the PMMA with X-ray mask was exposed to the irradiated X-ray with exposure energy of 4.5 kJ/cm3. Second, both the exposed and unexposed PMMA regions without X-ray mask were X-ray irradiated once more with exposure energy of 0.25 kJ/cm3. The detailed specification of double X-ray exposure is given for Table 3. 5 of 9 Materials 2019, 12, 2056 Table 3. The detailed specification of double X-ray exposure. Controllable Variables 1st Exposure with X-ray Mask 2nd Exposure without X-ray Mask Mirror angle (◦) 0.45 0.40 Exposure energy (kJ/cm3) 4.5 0.25 Filter thickness (µm) 18 0 2.4. Development Materials 2019, 12, x FOR PEER REVIEW 5 of 9 2.4. 2.4. Development To etch out h l 20 l % To etch out the exposed region, a GG-developer consisting of 60 vol.% 2-(2-butoxyethoxy) ethanol, 20 vol.% tetrahydro-1, 4-oxazine, 5 vol.% 2-aminoethanol, and 15 vol.% deionized water was used for 6 h. After the development process, residual PMMA on the substrate was dissolved by GG rinsing solution including 80 vol.% 2-(2-butoxyethoxy) ethanol and 20 vol.% deionized water. Finally, the sample was finished after the cleaning process using a deionized (DI) water mixed with surface additive (BYK-3440; Uni Trading Corporation, Gwangju, Korea). ethanol, 20 vol.% tetrahydro-1, 4-oxazine, 5 vol.% 2-aminoethanol, and 15 vol.% deionized water was used for 6 h. After the development process, residual PMMA on the substrate was dissolved by GG rinsing solution including 80 vol.% 2-(2-butoxyethoxy) ethanol and 20 vol.% deionized water. Finally, the sample was finished after the cleaning process using a deionized (DI) water mixed with surface additive (BYK-3440; Uni Trading Corporation, Gwangju, Korea). 3. Results and Discussion 2.3. X-Ray Exposure Development To etch out the exposed region, a GG-developer consisting of 60 vol.% 2-(2-butoxyethoxy) h l 20 l % h d 1 4 i 5 l % 2 i h l d 15 l % d i i d Table 3. The detailed specification of double X-ray exposure. Table 3. The detailed specification of double X-ray exposure. 3.2. Double X-Ray Exposure 3.2. Double X-Ray Exposure In this research, a double X-ray exposure process with and without an X-ray mask was adopted to acquire tapered micropillars with high aspect ratio. This method gives a two-step dose distribution in the PMMA and results in a tapered shape during the development process [10]. If a single X-ray exposure with X-ray mask were performed on the PMMA, micropillars would have a vertical shape without any taper. In the first step, PMMA adhered to an X-ray mask was irradiated with exposure energy of 4.5 kJ/cm3, which is enough energy to eliminate the exposed PMMA region. During X-ray exposure, a dose on the exposed top surface over 20 kJ/cm3 might cause a thermal swelling of the PMMA. Based on the reference to inherent characters of beam source, the amount of dose on the exposed top surface was calculated and showed a value of 19.98 kJ/cm3. As a result, the exposed region of the PMMA showed a slight amount of thermal swelling because the amount of dose nearly reached the theoretical limit, as shown in Figure 5a. In the second exposure, both exposed and unexposed regions during the first exposure were X-ray irradiated due to the absence of an X-ray mask. The excessive amount of exposure dose not only induced a thermal swelling for the exposed region, but it also drastically lowered the aspect ratio of micropillars for the unexposed region. With the consideration of all requirements, the exposure dose in the second exposure was determined to be 0.25 kJ/cm3. Figure 5b represents the result of double X-ray exposure. The double exposed region having a top dose of 20.02 kJ/cm3 showed more thermal swelling since the dose on the top surface exceeded 20 kJ/cm3. In this research, a double X-ray exposure process with and without an X-ray mask was adopted to acquire tapered micropillars with high aspect ratio. This method gives a two-step dose distribution in the PMMA and results in a tapered shape during the development process [10]. If a single X-ray exposure with X-ray mask were performed on the PMMA, micropillars would have a vertical shape without any taper. In the first step, PMMA adhered to an X-ray mask was irradiated with exposure energy of 4.5 kJ/cm3, which is enough energy to eliminate the exposed PMMA region. During X-ray exposure, a dose on the exposed top surface over 20 kJ/cm3 might cause a thermal swelling of the PMMA. 3.1. Interaction between X-Ray Source and Photoresist Au X-ray mask on the top of the PMMA shoul The number of transmitted X-ray spectrum (sTP) in the perpendicular cross-section of the PMMA can be defined by the following equation [20]. sTP = SM × exp  −µpxp  (1) (1) where SM is the X-ray energy spectrum of the photoresist, µp is the absorption coefficient of photoresist, and xp is the optional depth. Based on the calculation, the dose of the absorber top should be less than 100 J/cm3 to avoid the development. Considering the requirement, the Au thickness of the X-ray mask must be over 8 µm. In this study, the final thickness of the X-ray mask during the electroplating process was set to 21 µm, which is a thick enough layer to prevent the development of the absorber top and minimize the back-scattering effect. Figure 4 reveals the prepared X-ray mask with diameter of 130 µm and gap size of 40 µm. Materials 2019, 12, x FOR PEER REVIEW 6 of 9 should be less than 100 J/cm3 to avoid the development. Considering the requirement, the Au thickness of the X-ray mask must be over 8 μm. In this study, the final thickness of the X-ray mask during the electroplating process was set to 21 μm, which is a thick enough layer to prevent the development of the absorber top and minimize the back-scattering effect. Figure 4 reveals the prepared X-ray mask with diameter of 130 μm and gap size of 40 μm. Figure 4. Fabricated X-ray mask for X-ray exposure: (a) entire image of X-ray mask prepared by UV lithography; and (b) magnified feature of X-ray mask having circle shape. bl E Figure 4. Fabricated X-ray mask for X-ray exposure: (a) entire image of X-ray mask prepared by UV lithography; and (b) magnified feature of X-ray mask having circle shape. Figure 4. Fabricated X-ray mask for X-ray exposure: (a) entire image of X-ray mask prepared by UV lithography; and (b) magnified feature of X-ray mask having circle shape. Figure 4. Fabricated X-ray mask for X-ray exposure: (a) entire image of X-ray mask prepared by UV lithography; and (b) magnified feature of X-ray mask having circle shape. 3.1. Interaction between X-Ray Source and Photoresist Au X-ray mask on the top of the PMMA shoul The photon flux distribution was calculated by reference to inherent properties of the beam source. From the analysis, we can predict the desirable Au thickness, and interaction between the electrons and photoresist materials. The photon flux distribution generated from the X-ray at 3.0 GeV showed a wide range of energies from a few volts to tens of kilo-electron volts, as indicated in Figure 3c. When the X-ray passed through two Be windows, its photon flux was reduced to 66% of the original beam source while still maintaining high-energy photons. These high-energy photons were absorbed in the substrate of the photoresist, resulting in creation of photoelectrons, Auger- electrons, and fluorescence photons. Such photons were backscattered to the PMMA layer, which reduced the molecular weight of PMMA on the interfacial surface [19]. Consequently, it caused a poor adhesion between PMMA and the substrate. To eliminate high-energy photons with energies over 7 keV, a double mirror system with angle of 0.45° was used and revealed a flux distribution with low-energy photon range. Figure 3. Experiment conditions of deep X-ray lithography: (a) schematic diagram of X-ray irradiation into photoresist via X-ray mask; (b) X-ray transmittance with respect to different materials; and (c) calculation of X-ray flux before entering the lithography chamber. Figure 3. Experiment conditions of deep X-ray lithography: (a) schematic diagram of X-ray irradiation into photoresist via X-ray mask; (b) X-ray transmittance with respect to different materials; and (c) calculation of X-ray flux before entering the lithography chamber. Figure 3. Experiment conditions of deep X-ray lithography: (a) schematic diagram of X-ray irradiation into photoresist via X-ray mask; (b) X-ray transmittance with respect to different materials; and (c) calculation of X-ray flux before entering the lithography chamber. Figure 3. Experiment conditions of deep X-ray lithography: (a) schematic diagram of X-ray irradiation into photoresist via X-ray mask; (b) X-ray transmittance with respect to different materials; and (c) calculation of X-ray flux before entering the lithography chamber. Materials 2019, 12, 2056 6 of 9 With the prepared beam source, the thickness of the X-ray mask was calculated using the X-ray flux and dose incident on the PMMA. The number of transmitted X-ray spectrum (sTP) in the perpendicular cross-section of the PMMA can be defined by the following equation [20]. With the prepared beam source, the thickness of the X-ray mask was calculated using the X-ray flux and dose incident on the PMMA. 3.3. Stability of Micro Pillar Structure 3 3 Stability of Micro Pillar Structure 3 3 Stability of Micro Pillar Structure To obtain the final tapered micropillars, the exposed area of PMMA was developed using a GG-developer. The product was mounted in the downward direction to efficiently remove the exposed region. This method uses a gravity-induced pulling force as well as convective transport of the GG-developer and results in more thorough removal of PMMA and reduction of development time [21]. After GG-rinsing, the sample was cleaned by pure deionized (DI) water to dilute a residual GG-solution. However, the micropillars showed slight fracture on the tip and were clustered together due to capillary force when DI water was evaporated offthe surface, as shown in Figure 6. To improve these defects by capillary force, DI water was mixed with surface additives, and the resulting contact angle was compared, as displayed in Figure 7. y f To obtain the final tapered micropillars, the exposed area of PMMA was developed using a GG- developer. The product was mounted in the downward direction to efficiently remove the exposed region. This method uses a gravity-induced pulling force as well as convective transport of the GG- developer and results in more thorough removal of PMMA and reduction of development time [21]. After GG-rinsing, the sample was cleaned by pure deionized (DI) water to dilute a residual GG- solution. However, the micropillars showed slight fracture on the tip and were clustered together due to capillary force when DI water was evaporated off the surface, as shown in Figure 6. To improve these defects by capillary force, DI water was mixed with surface additives, and the resulting contact angle was compared, as displayed in Figure 7. To obtain the final tapered micropillars, the exposed area of PMMA was developed using a GG- developer. The product was mounted in the downward direction to efficiently remove the exposed region. This method uses a gravity-induced pulling force as well as convective transport of the GG- developer and results in more thorough removal of PMMA and reduction of development time [21]. After GG-rinsing, the sample was cleaned by pure deionized (DI) water to dilute a residual GG- solution. However, the micropillars showed slight fracture on the tip and were clustered together due to capillary force when DI water was evaporated off the surface, as shown in Figure 6. To improve these defects by capillary force, DI water was mixed with surface additives, and the resulting contact angle was compared, as displayed in Figure 7. 3.2. Double X-Ray Exposure 3.2. Double X-Ray Exposure Based on the reference to inherent characters of beam source, the amount of dose on the exposed top surface was calculated and showed a value of 19.98 kJ/cm3. As a result, the exposed region of the PMMA showed a slight amount of thermal swelling because the amount of dose nearly reached the theoretical limit, as shown in Figure 5a. In the second exposure, both exposed and unexposed regions during the first exposure were X-ray irradiated due to the absence of an X-ray mask. The excessive amount of exposure dose not only induced a thermal swelling for the exposed region, but it also drastically lowered the aspect ratio of micropillars for the unexposed region. With the consideration of all requirements, the exposure dose in the second exposure was determined to be 0.25 kJ/cm3. Figure 5b represents the result of double X-ray exposure. The double exposed region having a top dose of 20.02 kJ/cm3 showed more thermal swelling since the dose on the top surface exceeded 20 kJ/cm3. 7 of 9 face Materials 2019, 12, 2056 having a top dose d d 20 kJ/ Figure 5. The results of X-ray exposure: (a) first exposure with X-ray mask showing a little thermal swelling; and (b) second exposure without X-ray mask indicating a more thermal swelling. Materials 2019, 12, x FOR PEER REVIEW 7 of Figure 5. The results of X-ray exposure: (a) first exposure with X-ray mask showing a little thermal swelling; and (b) second exposure without X-ray mask indicating a more thermal swelling. Materials 2019, 12, x FOR PEER REVIEW 7 of 9 Figure 5. The results of X-ray exposure: (a) first exposure with X-ray mask showing a little thermal swelling; and (b) second exposure without X-ray mask indicating a more thermal swelling. OR PEER REVIEW OR PEER REVIEW Figure 5. The results of X-ray exposure: (a) first exposure with X-ray mask showing a little thermal swelling; and (b) second exposure without X-ray mask indicating a more thermal swelling. Figure 5. The results of X-ray exposure: (a) first exposure with X-ray mask showing a little thermal swelling; and (b) second exposure without X-ray mask indicating a more thermal swelling. Figure 5. The results of X-ray exposure: (a) first exposure with X-ray mask showing a little thermal swelling; and (b) second exposure without X-ray mask indicating a more thermal swelling. 4. Conclusions 4. Conclusions In this study, a novel fabrication technique of tapered micropillars with high aspect ratio was proposed and demonstrated by X-ray lithography. An X-ray mask with thickness of 21 μm was prepared to efficiently block deep X-rays and minimize back-scattering effect. Double X-ray exposure with and without X-ray mask was conducted by imposing a two-step dose distribution on the PMMA. After the exposure, the top surface of the double-exposed region showed slight thermal swelling because the value exceeded the theoretical limit of 20 kJ/cm3. Thereafter, the exposed region was developed in the downward direction to clearly eliminate the PMMA residual on the bottom surface. To release a capillary force during the drying process, DI water was mixed with surface additive to achieve a smaller contact angle than pure DI water. Taking advantage of the release effect, tapered micropillars with pattern size of 130 μm, gap size of 40 μm, and aspect ratio over 7 did not show any clustering phenomenon or fractures on the tips. Compared with no tapered shape, tapered micropillars would provide an easy demolding process by reducing the surface area between the electroformed mold insert and metal/ceramic micro structures during manufacturing process. In addition, it is expected that this novel method could be used for manufacturing tapered micropillars with high aspect ratio in the MEMS field, including optical components and microfluidic channels. In this study, a novel fabrication technique of tapered micropillars with high aspect ratio was proposed and demonstrated by X-ray lithography. An X-ray mask with thickness of 21 µm was prepared to efficiently block deep X-rays and minimize back-scattering effect. Double X-ray exposure with and without X-ray mask was conducted by imposing a two-step dose distribution on the PMMA. After the exposure, the top surface of the double-exposed region showed slight thermal swelling because the value exceeded the theoretical limit of 20 kJ/cm3. Thereafter, the exposed region was developed in the downward direction to clearly eliminate the PMMA residual on the bottom surface. To release a capillary force during the drying process, DI water was mixed with surface additive to achieve a smaller contact angle than pure DI water. Taking advantage of the release effect, tapered micropillars with pattern size of 130 µm, gap size of 40 µm, and aspect ratio over 7 did not show any clustering phenomenon or fractures on the tips. 3.3. Stability of Micro Pillar Structure 3 3 Stability of Micro Pillar Structure 3 3 Stability of Micro Pillar Structure Figure 8. Fabricated tapered micropillars with high aspect-ratio: (a) top view; and (b) side view. 3.3. Stability of Micro Pillar Structure 3 3 Stability of Micro Pillar Structure 3 3 Stability of Micro Pillar Structure Figure 6. The results of drying process: (a) clustered tapered micropillars each other due to strong capillary force; and (b) magnified image of clustered and fractured micropillars. Figure 6. The results of drying process: (a) clustered tapered micropillars each other due to strong capillary force; and (b) magnified image of clustered and fractured micropillars. Figure 6. The results of drying process: (a) clustered tapered micropillars each other due to strong capillary force; and (b) magnified image of clustered and fractured micropillars. Figure 6. The results of drying process: (a) clustered tapered micropillars each other due to strong capillary force; and (b) magnified image of clustered and fractured micropillars. Figure 6. The results of drying process: (a) clustered tapered micropillars each other due to strong capillary force; and (b) magnified image of clustered and fractured micropillars. Figure 6. The results of drying process: (a) clustered tapered micropillars each other due to strong capillary force; and (b) magnified image of clustered and fractured micropillars. Figure 7. The measurement of contact angle: (a) pure DI water; and (b) DI water mixed with surface addictive. Figure 7. The measurement of contact angle: (a) pure DI water; and (b) DI water mixed with surface addictive. Figure 7. The measurement of contact angle: (a) pure DI water; and (b) DI water mixed with surface addictive. Figure 7. The measurement of contact angle: (a) pure DI water; and (b) DI water mixed with surface addictive. Figure 7. The measurement of contact angle: (a) pure DI water; and (b) DI water mixed with surface addictive. Figure 7. The measurement of contact angle: (a) pure DI water; and (b) DI water mixed with surface addictive. Materials 2019, 12, 2056 8 of 9 The mixed solution resulted in a smaller contact angle, meaning the solution had a weaker capillary force during the evaporation process [22]. Taking advantage of this effect, tapered micropillars were successfully fabricated with pattern size of 130 µm, gap size of 40 µm, and aspect ratio over 7, and showed no fractures or clustering, as revealed in Figure 8. Materials 2019, 12, x FOR PEER REVIEW 8 of 9 Figure 8. Fabricated tapered micropillars with high aspect-ratio: (a) top view; and (b) side view. l i Figure 8. Fabricated tapered micropillars with high aspect-ratio: (a) top view; and (b) side view. l Figure 8. Fabricated tapered micropillars with high aspect-ratio: (a) top view; and (b) side view. 4. Conclusions 4. Conclusions Compared with no tapered shape, tapered micropillars would provide an easy demolding process by reducing the surface area between the electroformed mold insert and metal/ceramic micro structures during manufacturing process. In addition, it is expected that this novel method could be used for manufacturing tapered micropillars with high aspect ratio in the MEMS field, including optical components and microfluidic channels. Author Contributions: Conceptualization, J.M.P., J.H.K. and S.J.P.; methodology, J.M.P., J.S.H. and S.J.P.; validation, J.M.P.; formal analysis, J.M.P.; investigation, J.M.P.; resources, J.M.P.; data curation, J.M.P. and Daseul Shin; writing—original draft preparation, J.M.P., J.H.K. and S.J.P.; writing—review and editing, J.M.P., D S S S C P and S H S ; and visualization J M P and D S S Author Contributions: Conceptualization, J.M.P., J.H.K. and S.J.P.; methodology, J.M.P., J.S.H. and S.J.P.; validation, J.M.P.; formal analysis, J.M.P.; investigation, J.M.P.; resources, J.M.P.; data curation, J.M.P. and D.S.S.; writing—original draft preparation, J.M.P., J.H.K. and S.J.P.; writing—review and editing, J.M.P., D.S.S., S.C.P. and S.H.S.; and visualization, J.M.P. and D.S.S. D.S.S., S.C.P. and S.H.S.; and visualization, J.M.P. and D.S.S. Funding: This work was supported by the Industrial Strategic Technology Development Program (10063459, Development of Powder injection mold with under 150 μm pattern width and high aspect ratio and its molding technology for the fabrication of metal and ceramic micro structures) funded By the Ministry of Trade, Industry & Energy (MOTIE Korea) and the National Research Foundation of Korea (NRF) funded by the Korean Funding: This work was supported by the Industrial Strategic Technology Development Program (10063459, Development of Powder injection mold with under 150 µm pattern width and high aspect ratio and its molding technology for the fabrication of metal and ceramic micro structures) funded By the Ministry of Trade, Industry & Energy (MOTIE, Korea) and the National Research Foundation of Korea (NRF) funded by the Korean government (Grant No. 2017R1D1A1B03032928). The Experiments at PLS-II were supported in part by MSICT and POSTECH. gy ( , ) ( ) y ment (Grant No. 2017R1D1A1B03032928). The Experiments at PLS-II were supported in part by MSICT s of Interest: The authors declare no conflict of interest. gy ( , ) government (Grant No. 2017R1D1A1B03032928). The Experimen Conflicts of Interest: The authors declare no conflict of interest. 1. Han, J.S.; Gal, C.W.; Kim, J.H.; Park, S.J. Fabrication of high-aspect-ratio micro piezoelectric a powder injection molding. Ceram. Int. 2016, 42, 9475–9481, doi:10.1016/j.ceramint.2016.03.011. j g 2. Kim, J.H.; Choi, S.Y.; Jeon, J.H.; Lim, G.; Chang, S.S. Manufacture of a micro-sized piezoelectric structure using a sacrificial polymer mold insert. Microsyst. Technol. 2013, 19, 343–349. [CrossRef] References 1. Han, J.S.; Gal, C.W.; Kim, J.H.; Park, S.J. Fabrication of high-aspect-ratio micro piezoelectric array by powder injection molding. Ceram. Int. 2016, 42, 9475–9481. [CrossRef] References 1. 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Fabrication of high-aspect-ratio micro piezoelectric array by powder injection molding. Ceram. Int. 2016, 42, 9475–9481, doi:10.1016/j.ceramint.2016.03.011. j g 2. Kim, J.H.; Choi, S.Y.; Jeon, J.H.; Lim, G.; Chang, S.S. Manufacture of a micro-sized piezoelectric ceramic structure using a sacrificial polymer mold insert. Microsyst. Technol. 2013, 19, 343–349. [CrossRef] 9 of 9 Materials 2019, 12, 2056 3. Romanato, F.; Tormen, M.; Businaro, L.; Vaccari, L.; Stomeo, T.; Passaseo, T.; Fabrizio, E.D. X-ray lithography for 3D microfluidic applications. Microelectron. Eng. 2004, 73–74, 870–875. [CrossRef] 4. Park, K.; Kim, K.; Lee, S.C.; Lim, G.; Kim, J.H. Fabrication of Polymer Microstructures of Various Angles via Synchrotron X-Ray Lithography Using Simple Dimensional Transformation. Materials 2018, 11, 1460. [CrossRef] [PubMed] 5. Park, J.M.; Han, J.S.; Gal, C.W.; Oh, J.W.; Kim, J.H.; Kate, K.H.; Atre, S.V.; Kim, Y.; Park, S.J. 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[CrossRef] [PubMed] © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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RNA N1-methyladenosine regulator-mediated methylation modification patterns and heterogeneous signatures in glioma
Frontiers in immunology
2,022
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8,167
TYPE Original Research PUBLISHED 22 July 2022 DOI 10.3389/fimmu.2022.948630 TYPE Original Research PUBLISHED 22 July 2022 DOI 10.3389/fimmu.2022.948630 TYPE Original Research PUBLISHED 22 July 2022 DOI 10.3389/fimmu.2022.948630 OPEN ACCESS OPEN ACCESS EDITED BY Jie Mei, Wuxi People’s Hospital Affiliated to Nanjing Medical University, China REVIEWED BY Yutian Zou, Sun Yat-sen University Cancer Center (SYSUCC), China Shixiang Wang, Sun Yat-sen University Cancer Center (SYSUCC), China *CORRESPONDENCE Lin-jian Wang wljgnn@126.com †These authors have contributed equally to this work and share first authorship SPECIALTY SECTION This article was submitted to Cancer Immunity and Immunotherapy, a section of the journal Frontiers in Immunology RECEIVED 20 May 2022 ACCEPTED 04 July 2022 PUBLISHED 22 July 2022 OPEN ACCESS EDITED BY Jie Mei, Wuxi People’s Hospital Affiliated to Nanjing Medical University, China Meng Mao 1,2,3†, Qinjun Chu 1†, Yongli Lou 4, Peipei Lv 5 and Lin-jian Wang 2,3,4* Meng Mao 1,2,3†, Qinjun Chu 1†, Yongli Lou 4, Peipei Lv 5 and Lin-jian Wang 2,3,4* Meng Mao 1,2,3†, Qinjun Chu 1†, Yongli Lou 4, Peipei Lv 5 and Lin-jian Wang 2,3,4* 1Department of Anesthesiology and Perioperative Medicine, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China, 2Research of Trauma Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China, 3Center for Advanced Medicine, College of Medicine, Zhengzhou University, Zhengzhou, China, 4Department of Neurosurgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China, 5Department of Radiology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China N1-methyladenosine (m1A) is ubiquitous in eukaryotic RNA and regulates mRNA translation. However, little is known about its regulatory role in glioma. Here, we identified 4 m1A modification-related patterns based on m1A regulators in the TCGA (The Cancer Genome Atlas) and CGGA (Chinese Glioma Genome Atlas) cohorts. The differences in survival prognosis between different clusters were striking. In addition, stemness, genomic heterogeneity, tumor microenvironment (TME), and immune cell infiltration were also significantly different between the poor and best prognostic clusters. To reveal the underlying mechanism, differentially expressed genes (DEGs) between the poor and best prognostic clusters were identified, and then were integrated for weighted correlation network analysis (WGCNA). After Univariate Cox-LASSO-Multivariate Cox analyses, DEGs PLEK2 and ABCC3 were screened as the risk-hub genes and were selected to construct an m1A-related signature. Moreover, ABCC3 exacerbated glioma proliferation and was associated with temozolomide (TMZ) resistance. Overall, our study provided new insights into the function and potential therapeutic role of m1A in glioma. CITATION Mao M, Chu Q, Lou Y, Lv P and Wang L-j (2022) RNA N1- methyladenosine regulator-mediated methylation modification patterns and heterogeneous signatures in glioma. Front. Immunol. 13:948630. glioma, m1A, heterogeneity, stemness, tumor microenvironment, TMZ-resistance RNA N1-methyladenosine regulator-mediated methylation modification patterns and heterogeneous signatures in glioma OPEN ACCESS EDITED BY Jie Mei, Wuxi People’s Hospital Affiliated to Nanjing Medical University, China REVIEWED BY Yutian Zou, Sun Yat-sen University Cancer Center (SYSUCC), China Shixiang Wang, Sun Yat-sen University Cancer Center (SYSUCC), China *CORRESPONDENCE Lin-jian Wang wljgnn@126.com †These authors have contributed equally to this work and share first authorship SPECIALTY SECTION This article was submitted to Cancer Immunity and Immunotherapy, a section of the journal Frontiers in Immunology RECEIVED 20 May 2022 ACCEPTED 04 July 2022 PUBLISHED 22 July 2022 CITATION Mao M, Chu Q, Lou Y, Lv P and Wang L-j (2022) RNA N1- methyladenosine regulator-mediated methylation modification patterns and heterogeneous signatures in glioma. Front. Immunol. 13:948630. doi: 10.3389/fimmu.2022.948630 COPYRIGHT © 2022 Mao, Chu, Lou, Lv and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. OPEN ACCESS doi: 10.3389/fimmu.2022.948630 COPYRIGHT © 2022 Mao, Chu, Lou, Lv and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. COPYRIGHT © 2022 Mao, Chu, Lou, Lv and Wang. This is an open-access article distributed under the terms of the glioma, m1A, heterogeneity, stemness, tumor microenvironment, TMZ-resistance glioma, m1A, heterogeneity, stemness, tumor microenvironment, TMZ-resistance frontiersin.org Frontiers in Immunology 01 Mao et al. 10.3389/fimmu.2022.948630 Methods The stromal, immune, and ESTIMATE scores of each glioma were calculated based on gene expression using the R package “estimate” (30). The abundance of tumor-infiltrating immune cells in glioma were analyzed using the CIBERSOR algorithm on the TIMER2 platform (http://timer.cistrome.org/) (31). Analysis of stemness features The glioma stemness scores based on RNA expression (RNAss), Epigenetically regulated RNA expression (EREG- EXPss), DNA methylation (DNAss), Epigenetically regulated DNA methylation (EREG-METHs), Differentially methylated probes (DMPss), Enhancer Elements/DNA methylation (ENHss) were calculated according to previous study (26). m1A modification is dynamically regulated in mammalian RNAs. NML, TRMT6, TRMT10C, TRMT61A, and TRMT61B are identified as methylases (16, 17), besides, ALKBH1 and ALKBH3 are responsible for demethylation (18, 19), and YTHDC1, YTHDF1, YTHDF2 and YTHDF3 are m1A binding proteins (20, 21). Here, we identified 4 modification-related clusters based on these m1A regulators in the TCGA and CGGA cohorts. Poor- and best-prognostic clusters differed significantly in stemness, genomic heterogeneity, tumor microenvironment (TME) and immune cell infiltration. An m1A-related signature was constructed using the risk-hub differentially expressed genes (DEGs) PLEK2 and ABCC3, which were identified between clusters with best and worse prognosis and were highly associated with heterogeneity. Furthermore, we found that ABCC3 was significantly associated with temozolomide (TMZ) resistance, and silencing ABCC3 effectively inhibited glioma cell proliferation. Overall, our study focused on the function role of m1A and provided a potential therapeutic strategy for glioma. Introduction (https://xenabrowser.net/datapages/) (22), the CGGA #325 (309 patients included) and CGGA #693 (657 patients included) datasets were obtained from the Chinese Glioma Genome Atlas (CGGA) data portal (http://www.cgga.org.cn/) (23), the data for IMvigor210 cohort (348 patients included) were loaded from R package “IMvigor210CoreBiologies” (24), and the GSE148740, GSE113510 and GSE68071 datasets were downloaded from GEO website (https://www.ncbi.nlm.nih.gov/ geo/). Gliomas are the most common neurological malignancies (1). Currently, surgery followed by chemoradiation is still the standard treatment, but the prognosis is poor (2). In addition, preliminary results from a phase III clinical trial in recurrent glioma suggested that immune checkpoint inhibitor therapy, which has shown promise in tumor therapy, did not significantly improve patient survival (3–6). Extensive intra-tumor and inter- tumor heterogeneity, tumor microenvironment (TME) are particularly critical factors in drug resistance and treatment failure (7, 8). Analysis of genomic heterogeneity The dataset of glioma simple nucleotide variations processed with MuTect2 software (27) was downloaded from GDC (https://portal.gdc.cancer.gov/). TMB (Tumor mutation burden) and MATH (Mutant-allele tumor heterogeneity) for each glioma were calculated using the tmb function and inferHeterogeneity function of the R package “maftools”, respectively. MSI (Microsatellite instability), Neoantigen, purity, ploidy, HRD (Homologous recombination deficiency) and LOH (Loss of heterozygosity) for each glioma were derived from previous studies (28, 29). Consensus clustering analysis To date, more than 160 different types of post-transcriptional modifications have been identified on RNA (9). Breakthroughs in sequencing technologies have greatly improved our knowledge of the location, regulation, and function of RNA modifications in the transcriptome (10, 11), which lead to the birth of epitranscriptomics (12). Notably, RNA modifications, especially N6-methyladenosine (m6A), 5-methylcytidine (m5C) and pseudouridine (Y) modification, affect glioma prognosis and have been proposed as a new class of epigenetic markers for the diagnosis of glioma (13–15). Importantly, a recently identified modification, N1-methyladenosine (m1A), is ubiquitous in eukaryotic tRNA and rRNA, and recent studies have shown that m1A modification can also regulate mRNA translation (16). However, its specific role in glioma remains unclear. Cluster analysis was performed by ConsensusClusterPlus (25), using agglomerative pam clustering with a 1-pearson correlation distances and resampling 80% of the samples for 10 repetitions. The optimal number of clusters was determined using the empirical cumulative distribution function plot. Datasets and samples The TCGA dataset (674 patients included) was downloaded from University of California Santa Cruz (UCSC) Xena browser Frontiers in Immunology frontiersin.org 02 Mao et al. 10.3389/fimmu.2022.948630 Construction of risk signature Weighted correlation network analysis (WGCNA) was performed to construct the scale-free co-expression network using the R software package “WGCNA”, Six co-expression modules were finally obtained after merging modules with distances less than 0.25. Genes with high connectivity in the significant clinical module were identified as hub genes. Univariate, LASSO, and multivariate regression analysis were then sequentially performed to screen for positive hub genes significantly associated with overall survival (OS). The risk score was calculated as follows: Risk score = o n i=1 Coefi*Expi ð Þ DEGs screening and enrichment Analysis and confidence intervals were evaluated using the “ci” function to obtain the final AUC results. GraphPad Prism and R software were used for all statistical analyses, and p values less than 0.05 were considered statistically significant. Differentially expressed genes (DEGs) between different clusters were screened using the R package” limma” (p< 0.05 and |log2FC| ≥1) (32). GO analysis of DEGs was performed using Metascape (33). The GSEA (Gene set enrichment analysis) software was downloaded from the GSEA website (http:// software.broadinstitute.org/gsea/index.jsp) (34), and the c2.cp.kegg.v7.4.symbols.gmt subset was downloaded from the Molecular Signatures Database (http://www.gsea-msigdb.org/ gsea/downloads.jsp) to evaluate related pathways and molecular mechanisms (35). Consensus clustering analysis of m1A regulators in glioma ABCC3 was knocked down using siRNAs (Supplementary Table 1, Shanghai GenePharma Co., Ltd) in LN229 and U87 cells. Control and ABCC3-deficient cells were seed into the 96- well plates or glass bottom cell culture dishes. Cell viability was detected using the CCK-8 kit (Dojindo Molecular Technologies) and EdU kit (Beyotime Biotecnology) according to the manufacturer’s instructions. Based on m1A regulator expression profiles, an unsupervised consensus clustering analysis was performed to identify distinct subtypes in the TCGA dataset. Four clusters were finally determined using the empirical cumulative distribution function plot (Figure 3A and Supplementary Figure 2). We next analyzed the prognosis of the four clusters and found that there were significant differences in overall survival between these clusters. Patients in cluster 4 survived longer, while patients in cluster 3 survived obviously shorter (Figure 3B). It was consistent with the results obtained in unsupervised consensus analysis of the CGGA dataset (Supplementary Figures 3, 4). There were also differences in clinical phenotypes between four clusters, especially the number of GBM, IDH wild-type, older, and MGMT un-methylated phenotypes in cluster 3 (Figure 3C). Furthermore, we studied the expression of m1A regulators in different clusters. Results displayed that comparing with cluster 4, NML, TRMT61B, TRMT6, TRMT10C, ALKBH1, ALKBH3, YTHDF2, and Analysis of m1A regulators in glioma N1-methyladenosine is a unique methylation modification which is ubiquitous and functional in mammalian RNAs. Following the analysis procedure of this study (Figure 1), we first analyzed the expression of m1A regulators between LGG (Low grade glioma) and GBM (Glioblastoma). The results showed that all regulators were differentially expressed between LGG and GBM in the TCGA cohort (Figures 2A, B). Furthermore, except for TRMT61A and ALKBH1, all regulators were also differentially expressed between IDH mutant and IDH wild-type groups (Supplementary Figure 1). The mutational landscape of m1A regulators in glioma was analyzed and displayed as a waterfall plot, with NML mutations present in 2.9% of the samples (Figure 2C). We then studied the interrelationships between m1A regulators and their prognostic roles in the TCGA cohort. Results showed that the expression levels of the regulators were significantly related. (Figure 2D). In addition to TRMT61A, the expression of other m1A regulators was associated with overall survival (OS) in glioma (Figure 2D). Statistical analysis One-way ANOVA, t test and wilcoxon test were used to analyze the significance of differences in heterogeneity and gene expression. Kaplan-Meier analysis was performed using the “survfit” function of the R package “survival”, and the logrank test method was used to evaluate the significance of the prognostic differences between samples from different groups. ROC analyses for 1-, 3-, 5-year time points were performed using the “roc” function of the R package “pROC”, and the AUC Frontiers in Immunology frontiersin.org 03 Mao et al. 10.3389/fimmu.2022.948630 FIGURE 1 Flowchart of this study. Flowchart of this study. YTHDF3 were up-regulated, while YTHDC1 was significantly down-regulated in cluster 3 (Figure 3D). YTHDF3 were up-regulated, while YTHDC1 was significantly down-regulated in cluster 3 (Figure 3D). Extensive intratumoral and interpatient heterogeneity is an underlying cause of treatment failure, especially for the most aggressive and treatment-resistant GBM (8). Here, we analyzed TMB, MATH, MSI, Neoantigen, purity, ploidy, HRD, and LOH of each glioma in different clusters (Figure 5). Cluster 3 with the worst prognosis had higher TMB and LOH than other clusters, while MATH and MSI were lowest (Figures 5A–H). Furthermore, cluster 3 had lower Purity and higher HRD compared to cluster 4 (Figures 5E, G). Correlation analysis showed that m1A regulators were remarkably associated with these heterogenetic scores in the TCGA cohort (Figure 5I). For instance, the m1A writers TRMT6 and NML were most highly related to TMB and MSI, respectively (Figures 5J, K). Stemness, genomic heterogeneity and immune microenvironment analysis in different clusters Tumor progression involves a progressive loss of a differentiated phenotype and the acquisition of progenitor-like, stem-like characteristics. In this study, glioma stemness scores were calculated based on RNA expression and DNA methylation, respectively. The worst-prognostic cluster 3 had lower RNAss but higher EREG-EXPss compared to best-prognostic cluster 4 (Figure 4A, B). Whereas, all stemness scores according to DNA methylation, such as DNAs, EREG-METHs, DMPss, and ENHss, increased in cluster 3 (Figure 4C–F). Correlation analysis showed that m1A regulators were highly associated with stemness scores in the TCGA cohort, especially m1A writers NML, TRMT61B, TRMT6 and readers YTHDC1, YTHDF1, and YTHDF2 (Figure 4G). TME is involved in tumor survival, malignant progression, metastasis and therapy resistance. Therefore, we compared the immune microenvironment of gliomas in different clusters. There were obviously differences in StromalScore, ImmuneScore, and ESTIMATEScore between clusters, with cluster 3 being the highest and cluster 4 being the lowest (Figures 6A–C). Furthermore, m1A regulators were tightly Frontiers in Immunology frontiersin.org 04 Mao et al. 10.3389/fimmu.2022.948630 B C D A FIGURE 2 Analysis of m1A regulators in glioma. (A) Heatmap depicting the expression of m1A regulators in the TCGA cohort. (B) Spilt violin showing the expression of m1A regulators between LGG and GBM. (C) Mutation waterfall chart displaying the mutation on m1A regulators in glioma. (D) The network displaying the relationship and prognosis information of m1A regulators. *, P< 0.05; ****, P< 0.0001. C C C D D B FIGURE 2 Analysis of m1A regulators in glioma. (A) Heatmap depicting the expression of m1A regulators in the TCGA cohort. (B) Spilt violin showing the expression of m1A regulators between LGG and GBM. (C) Mutation waterfall chart displaying the mutation on m1A regulators in glioma. (D) The network displaying the relationship and prognosis information of m1A regulators. *, P< 0.05; ****, P< 0.0001. associated with StromalScore, ImmuneScore, and ESTIMATEScore, especially the writers NML and TRMT10C, the eraser ALKBH3, and the readers YTHDC1 and YTHDF1 (Figure 6D). Analysis of tumor-infiltrating immune cells showed that the abundance of B cell naïve, B cell plasma, Monocyte, and Mast cell resting was dramatically reduced in cluster 3, while Macrophage M0 and Macrophage M2 were dramatically increased (Figure 6E). DMPss, and ENHss, increased in worst-prognostic cluster 3 (Supplementary Figures 5C–G), which were consistent with the entire cohort. Stemness, genomic heterogeneity and immune microenvironment analysis in different clusters Likewise, the genomic heterogeneity analysis ( S u p p l e m e n t a r y F i g u r e s 5 H – L ) a n d i m m u n e microenvironment analysis (Supplementary Figures 5M–O) yielded similar results to the entire cohort. In addition to the differentially infiltrating immune cells identified between clusters 3 and 4 across the entire cohort, we also found T cell CD4+ naïve, T cell CD4+ memory resting, T cell follicular helper, T cell regulatory (Tregs), Myeloid dendritic cell activated, and Neutrophil were differentially infiltrated between cluster 3 and 4 in the LGG subgroup (Supplementary Figure 5P). However, Macrophage M0 and Mast cell resting were not significantly different between clusters 3 and 4 (Supplementary Figure 5P). DMPss, and ENHss, increased in worst-prognostic cluster 3 (Supplementary Figures 5C–G), which were consistent with the entire cohort. Likewise, the genomic heterogeneity analysis ( S u p p l e m e n t a r y F i g u r e s 5 H – L ) a n d i m m u n e microenvironment analysis (Supplementary Figures 5M–O) yielded similar results to the entire cohort. In addition to the differentially infiltrating immune cells identified between clusters 3 and 4 across the entire cohort, we also found T cell CD4+ naïve, T cell CD4+ memory resting, T cell follicular helper, T cell regulatory (Tregs), Myeloid dendritic cell activated, and Neutrophil were differentially infiltrated between cluster 3 and 4 in the LGG subgroup (Supplementary Figure 5P). However, Macrophage M0 and Mast cell resting were not significantly different between clusters 3 and 4 (Supplementary Figure 5P). We re-analyzed stemness, genomic heterogeneity, and immune microenvironment in the LGG subgroup separately. As shown in the Supplementary Figure 5A, there was a clear difference in the OS between cluster 3 and cluster 4. Moreover, the stemness score RNAss decreased in the worst-prognostic cluster 3 compared to the best prognostic cluster 4 (Supplementary Figure 5B), whereas DNAs, EREG-METHs, Frontiers in Immunology frontiersin.org 05 Mao et al. 10.3389/fimmu.2022.948630 B C D A FIGURE 3 Consensus clustering analysis of m1A regulators in glioma. (A) Consensus clustering matrix for the most suitable k = 4. (B) Kaplan-Meier curves displaying prognostic differences between different clusters. (C) Differences in clinical phenotypes between different clusters. (D) Differences in expression of m1A regulators between cluster 3 and cluster 4. Stemness, genomic heterogeneity and immune microenvironment analysis in different clusters ns, no significance; *, P< 0.05; **, P< 0.01; ***, P< 0.001; ****, P< 0.0001. A B B C D FIGURE 3 Consensus clustering analysis of m1A regulators in glioma. (A) Consensus clustering matrix for the most suitable k = 4. (B) Kaplan-Meier curves displaying prognostic differences between different clusters. (C) Differences in clinical phenotypes between different clusters. (D) Differences in expression of m1A regulators between cluster 3 and cluster 4. ns, no significance; *, P< 0.05; **, P< 0.01; ***, P< 0.001; ****, P< 0.0001. Consensus clustering analysis of m1A regulators in glioma. (A) Consensus clustering matrix for the most suitable k = 4. (B) Kaplan-Meier curves displaying prognostic differences between different clusters. (C) Differences in clinical phenotypes between different clusters. (D) Differences in expression of m1A regulators between cluster 3 and cluster 4. ns, no significance; *, P< 0.05; **, P< 0.01; ***, P< 0.001; ****, P< 0.0001. Construction of the risk score signature modules were identified, of which the blue module was most associated with the traits (Figure 8). Seven genes with a module membership greater than 0.85 were identified as hub genes in the blue module. We then sequentially performed Univariate, LASSO, and Multivariate Cox regression analysis to filter variables and reduce model complexity (Figures 9A–C). PLEK2 and ABCC3 were ultimately selected as risk-hub genes (Figure 9C) and used to construct a risk model (Figure 9D). Kaplan Meier curves displayed that higher risk scores were associated with poorer prognosis (Figure 9E). Moreover, the sensitivity and specificity of risk score was greatly high in predicting the survival of glioma patients at 1-, 3- and 5-years (Figure 9F). The results of the risk model were also validated in the CGGA #325 and CGGA #693 datasets (Supplementary To reveal the mechanism leading to differences in prognosis and heterogeneity, DEGs between cluster 3 and cluster 4 were screened using R package “limma”. 997 up-regulated and 418 down-regulated genes were identified (Figure 7A). GO enrichment analysis showed that the DEGs were enriched in the Cytokine-cytokine receptor interaction and Immunoregulatory interactions (Figure 7B). GSEA analysis showed the DEGs were enriched in CELL ADHESION MOLECULES CAMS, JAK STAT signaling pathway, P53 signaling pathway, and immune-related pathways (Figure 7C). DEGs and traits such as stemness, genomic heterogeneity, TME were integrated for WGCNA analysis. Six co-expression Frontiers in Immunology frontiersin.org 06 Mao et al. 10.3389/fimmu.2022.948630 B C D E F G A FIGURE 4 Analysis of stemness features in glioma. (A–F) Difference in stemness scores based on RNA expression and DNA methylation between clusters. (G) Correlation between m1A regulators and stemness scores. *, P < 0.05; **, P < 0.01; ***, P < 0.001. C B C B A C B D E F G F E D E G F F G G FIGURE 4 Analysis of stemness features in glioma. (A–F) Difference in stemness scores based on RNA expression and DNA methylation between clusters. (G) Correlation between m1A regulators and stemness scores. *, P < 0.05; **, P < 0.01; ***, P < 0.001. Figure 6), as well as the LGG subgroup (Supplementary Figure 7). Figure 6), as well as the LGG subgroup (Supplementary Figure 7). were lower than that of the SD/PD group (Supplementary Figure 8). Moreover, low-risk patients had better overall survival (Supplementary Figure 8). Construction of the risk score signature In addition to being associated with stemness, genomic heterogeneity, and TME (Figure 10A), ABCC3 was also significantly correlated with the expression of m1A writers such as NML, TRMT61B, TRMT6 and TRMT10C (Figure 10B). Additionally, ABCC3 was up-regulated in the poor-prognostic cluster 3 relative to cluster 4 (Figures 7A and 10G), and it was also up-regulated in GBM relative to LGG in the TCGA, CGGA #325 and CGGA #693 cohorts (Figures 10C–E). ABCC3 is a member of the MRP subfamily which is involved in multi-drug resistance. We found ABCC3 was up-regulated in the TMZ-resistant PDX model (Figure 10H), TMZ-resistant LN229 cells (Figure 10I), and TMZ-resistant glioma stem cells (GSCs) (Figure 10J) compared to corresponding controls. Furthermore, ABCC3 significantly affected the prognosis of gliomas in the TCGA, CGGA #325, and CGGA #693 cohorts (Figure 10K). Therefore, ABCC3 may be involved in the resistance of TMZ. ABCC3 affects the proliferation of glioma cells changes but without any changes in nucleic acid sequence. RNA modifications play a critical role in regulating multiple metabolic processes of RNA, such as localization, transport, splicing, stabilization, and translation, which also influence phenotype, and thus have been proposed as a new class of epigenetic regulators recently (36, 37). Among all mRNA modifications, N6-methyladenosine (m6A), 5-methylcytidine (m5C) and pseudouridine (Y) modification, have been found to be epigenetic markers for the diagnosis of glioma due to their impact on prognosis (13–15). Surprisingly, m1A also has such potential, as regulators of m1A modification markedly affected glioma prognosis, with NML, TRMT6, TRMT10C, TRMT61B, ALKBH1, ALKBH3, YTHDF1, YTHDF2, and YTHDF3 as risk factors but YTHDC1 as a protective factor (Figure 2). To investigate the effect of ABCC3 on glioma cells, we knocked down it in LN299 and U87 cells, respectively (Figures 11A, F). Then we measured the growth curves of the ABCC3-defficient and control cells using the CCK-8 kit (Figures 11B, G), and detected the proportion of proliferating cells using the EdU kit (Figures 11C, D, H, I). All the results indicated that ABCC3 significantly affected the proliferation of glioma cells. Furthermore, IC50 analysis showed that knockdown of ABCC3 considerably reduced the resistance of glioma cells to TMZ (Figures 11E, J). ABCC3 is associated with tumor stemness, genomic heterogeneity, immune microenvironment and TMZ-resistance We then analyzed the relationship between the traits and the risk score, the prognostic hub genes PLEK2 and ABCC3 (Figure 10A). High associations with stemness, genomic heterogeneity and TME suggested that risk scores might be associated with immunotherapy outcome. Therefore, we selected the most widely used IMVigor210 ICBs cohort, which contains detailed clinicopathological profiles and gene expression data of a large number of patients (n=348) receiving immune checkpoint blockade therapy, to validate the m1A signature. Results showed that the low-risk group had more responders than the high-risk group, and the risk scores of the CR/PR group Frontiers in Immunology frontiersin.org 07 Mao et al. 10.3389/fimmu.2022.948630 B C D E F G H I J K A FIGURE 5 Analysis of genomic heterogeneity in glioma. (A–H) Differences in TMB, MATH, MSI, NEO, Purity, Ploidy, HRD and LOH between clusters. (I) Correlation between m1A regulators and genomic heterogeneity. (J) Representative scatter plot showing the correlation between TRMT6 and TMB. (K) Representative scatter plot showing the correlation between NML and MSI. *, P < 0.05; ****, P < 0.0001. B C A C B D E F G H E I F G H J K J K I J J K FIGURE 5 Analysis of genomic heterogeneity in glioma. (A–H) Differences in TMB, MATH, MSI, NEO, Purity, Ploidy, HRD and LOH between clusters. (I) Correlation between m1A regulators and genomic heterogeneity. (J) Representative scatter plot showing the correlation between TRMT6 and TMB. (K) Representative scatter plot showing the correlation between NML and MSI. *, P < 0.05; ****, P < 0.0001. Discussion According to consensus clustering analysis of all m1A regulators, gliomas could be divided into four clusters with distinct modification patterns (Figure 3 and Supplementary Figure 3). The overall survival of the four clusters was Epigenetic modifications, such as DNA methylation, histone modifications, can result in heritable phenotypic frontiersin.org Frontiers in Immunology 08 Mao et al. 10.3389/fimmu.2022.948630 B C D A B C D E A FIGURE 6 Immune microenvironment analysis in glioma. (A–C) Differences in Stromal, Immune, and ESTIMATE scores between clusters. (D) Correlation between m1A regulators and microenvironment scores. (E) Heatmap and boxplot showing the infiltration of 22 immune cells between different clusters. *, P< 0.05; **, P< 0.01; ***, P< 0.001; ****, P< 0.0001. B C A B A B A D D E FIGURE 6 Immune microenvironment analysis in glioma. (A–C) Differences in Stromal, Immune, and ESTIMATE scores between clusters. (D) Correlation between m1A regulators and microenvironment scores. (E) Heatmap and boxplot showing the infiltration of 22 immune cells between different clusters. *, P< 0.05; **, P< 0.01; ***, P< 0.001; ****, P< 0.0001. E E Immune microenvironment analysis in glioma. (A–C) Differences in Stromal, Immune, and ESTIMATE scores between clusters. (D) Correlation between m1A regulators and microenvironment scores. (E) Heatmap and boxplot showing the infiltration of 22 immune cells between different clusters. *, P< 0.05; **, P< 0.01; ***, P< 0.001; ****, P< 0.0001. significantly different (Figure 3B), suggesting that m1A modification patterns might be used to predict prognosis. Molecular characteristics such as IDH mutation status and MGMT methylation status have been used for pathological diagnosis of glioma. In this study, we found these characteristics differed among the four clusters, with the majority of the worst-prognostic group being IDH wildtype and MGMT un-methylated patients (Figure 3C). Interestingly, tumor cell stemness, heterogeneity, and microenvironment which are associated with malignant progression and therapy resistance (8) also differed significantly between the best and worst prognostic clusters (Figures 4-6). These results raised Frontiers in Immunology frontiersin.org 09 Mao et al. 10.3389/fimmu.2022.948630 B C A FIGURE 7 DEGs screening and enrichment Analysis. (A) Differentially expressed genes between cluster 3 and cluster 4. (B) GO analysis of the differentially expressed genes. (C) GSEA analysis of the differentially expressed genes. C A C B B FIGURE 7 DEGs screening and enrichment Analysis. (A) Differentially expressed genes between cluster 3 and cluster 4. (B) GO analysis of the differentially expressed genes. Discussion (C) GSEA analysis of the differentially expressed genes. B C D A FIGURE 8 Weighted Correlation Network Analysis. (A) Clustering of module genes in the TCGA cohort. (B) Cluster dendrogram of modules. (C) Module- trait relationships. (D) Scatter plot of correlation between GS and MM. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. B A B C D C D D FIGURE 8 Weighted Correlation Network Analysis. (A) Clustering of module genes in the TCGA cohort. (B) Cluster dendrogram of modules. (C) Module- trait relationships. (D) Scatter plot of correlation between GS and MM. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. 10 10 frontiersin.org Frontiers in Immunology Mao et al. 10.3389/fimmu.2022.948630 i h i i i h ’ h l i hi b ll h i i bl i l ( i ) B C D E F A FIGURE 9 Construction of risk score signature. (A) Univariate Cox regression analysis of hub genes in the TCGA cohort. (B) LASSO Cox regression analysis of hub genes in the TCGA cohort. (C) Multivariate Cox regression analysis of hub genes in the TCGA cohort. (D) Distribution of the risk score, survival status, and expression profile of the prognostic genes in the TCGA cohort. (E) Kaplan-Meier curves displaying prognostic differences between high- and low-risk groups in the TCGA cohort. (F) The ROC curves describing the sensitivity and specificity of risk score in predicting OS at 1-, 3- and 5-year time points in the TCGA cohort. B A A C C D E D E F E F F D FIGURE 9 Construction of risk score signature. (A) Univariate Cox regression analysis of hub genes in the TCGA cohort. (B) LASSO Cox regression analysis of hub genes in the TCGA cohort. (C) Multivariate Cox regression analysis of hub genes in the TCGA cohort. (D) Distribution of the risk score, survival status, and expression profile of the prognostic genes in the TCGA cohort. (E) Kaplan-Meier curves displaying prognostic differences between high- and low-risk groups in the TCGA cohort. (F) The ROC curves describing the sensitivity and specificity of risk score in predicting OS at 1-, 3- and 5-year time points in the TCGA cohort. well as their incomparably prognostic roles (Figures 7–9). Frontiers in Immunology Discussion Compared with other epigenetic modification risk models, such as m6A and m5C (15, 38), the risk model constructed in study was very simple but showed high efficiency in TCGA, CGGA #325, and CGGA #693 cohorts (Figure 9 and Supplementary Figure 6). Furthermore, risk model could predict susceptibility to TMZ and outcome of ICBs treatment (Figures 10, 11 and Supplementary Figure 8). some points worth investigating, what’s the relationship between m1A modification and prognostic and heterogeneous features; can m1A shape tumor heterogeneity? Correlation analyses between regulators and features confirmed the possibility of such a relationship (Figures 4G, 5I and 6D), but further elaboration is needed. Herein, PLEK2 and ABCC3 were screened as risk-hub genes for their high connectivity in the significant clinical module as frontiersin.org Frontiers in Immunology 11 Mao et al. 10.3389/fimmu.2022.948630 B C D E F G H I J K A FIGURE 10 ABCC3 is associated with tumor stemness, genomic heterogeneity, immune microenvironment and TMZ-resistance. (A) Correlations between ABCC3 and tumor stemness, genomic heterogeneity, and immune microenvironment. (B) Correlation between ABCC3 and m1A regulators. (C–E) Differences in ABCC3 expression between LGG and GBM in TCGA, CGGA #325 and CGGA #693 cohort, respectively. (F) Differences in ABCC3 expression between primary and recurrent gliomas. (G) Differences in ABCC3 expression between cluster 3 and cluster 4 in the TCGA cohort. (H) Differences in ABCC3 expression between TMZ-sensitive and TMZ-resistant PDX models, (I) LN229 cells, and (J) GSC cells. (K) Kaplan-Meier curves displaying prognostic differences between ABCC3 high and low expression groups in the TCGA, CGGA #325, and CGGA #693 cohort, respectively. *, P < 0.05; **, P < 0.01; ****, P < 0.0001. B C D E F G H I J A A B G K FIGURE 10 ABCC3 is associated with tumor stemness, genomic heterogeneity, immune microenvironment and TMZ-resistance. (A) Correlations between ABCC3 and tumor stemness, genomic heterogeneity, and immune microenvironment. (B) Correlation between ABCC3 and m1A regulators. (C–E) Differences in ABCC3 expression between LGG and GBM in TCGA, CGGA #325 and CGGA #693 cohort, respectively. (F) Differences in ABCC3 expression between primary and recurrent gliomas. (G) Differences in ABCC3 expression between cluster 3 and cluster 4 in the TCGA cohort. (H) Differences in ABCC3 expression between TMZ-sensitive and TMZ-resistant PDX models, (I) LN229 cells, and (J) GSC cells. Discussion (K) Kaplan-Meier curves displaying prognostic differences between ABCC3 high and low expression groups in the TCGA, CGGA #325, and K FIGURE 10 K K ABCC3 is associated with tumor stemness, genomic heterogeneity, immune microenvironment and TMZ-resistance. (A) Correlations between ABCC3 and tumor stemness, genomic heterogeneity, and immune microenvironment. (B) Correlation between ABCC3 and m1A regulators. (C–E) Differences in ABCC3 expression between LGG and GBM in TCGA, CGGA #325 and CGGA #693 cohort, respectively. (F) Differences in ABCC3 expression between primary and recurrent gliomas. (G) Differences in ABCC3 expression between cluster 3 and cluster 4 in the TCGA cohort. (H) Differences in ABCC3 expression between TMZ-sensitive and TMZ-resistant PDX models, (I) LN229 cells, and (J) GSC cells. (K) Kaplan-Meier curves displaying prognostic differences between ABCC3 high and low expression groups in the TCGA, CGGA #325, and CGGA #693 cohort, respectively. *, P < 0.05; **, P < 0.01; ****, P < 0.0001. ABCC3 protein is a member of the ATP-binding cassette transporter that binds and hydrolyzes ATP to enable active transport of various substrates including many toxicants and endogenous compound across extra- and intra-cellular membranes (39–41). ABCC3 protein belongs to the Multidrug Resistance-Associated Protein (MRP) subfamily and confers resistance to various anticancer drugs, methotrexate, tenoposide and etoposide by decreasing accumulation of these drugs in cells (39, 41). ABCC3 was remarkably upregulated in the TMZ-resistant glioma cells (Figures 10H–J) and promoted glioma proliferation (Figure 11), indicating it might be associated with the poor outcome of GBM receiving standard-of-care for concurrent radiotherapy and TMZ-chemotherapy after surgical resection (2, 42). Tumor heterogeneity, especially immunosuppressive TME, was involved in resistance to immune checkpoint blockers therapy (7). Notably, ABCC3 was closely linked to glioma heterogeneity (Figure 10A), low-risk group had more responders than the high-risk group, and low-risk patients had better overall survival (Supplementary Figure 8). Therefore, the relationship between ABCC3 expression and the failure of ICBs therapy needs to be studied. Frontiers in Immunology frontiersin.org 12 Mao et al. 10.3389/fimmu.2022.948630 F G H B C D E F G H I J A FIGURE 11 ABCC3 affects the proliferation of glioma cells. (A) TIMP1 knockdown efficiency in U87 cells. (B) Growth curves of ABCC3-defficient and control U87 cells. (C, D) Proportion of EdU positive cells in ABCC3-defficient and control U87 cells. (E) IC50 analysis of resistance to TMZ in ABCC3- defficient and control U87 cells. (F) TIMP1 knockdown efficiency in LN229 cells. Conclusions In conclusion, we comprehensively analyzed the effect of m1A on glioma, and provided potential targets for improving standard therapy and immunotherapy in glioma. MM, QC and L-JW conceived and designed the experiments. YL and PL contributed data analysis. L-JW wrote the manuscript. MM, QC and L-JW approved final version of manuscript. All authors contributed to the article and approved the submitted version. Discussion (G) Growth curves of ABCC3-defficient and control LN229 cells. (H–I) Proportion of EdU positive cells in ABCC3-defficient and control LN229 cells. (J) IC50 analysis of resistance to TMZ in ABCC3-defficient and control LN229 cells. **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. B F A H C I I D I J E J J E D J GU ABCC3 affects the proliferation of glioma cells. (A) TIMP1 knockdown efficiency in U87 cells. (B) Growth curves of ABCC3-defficient and control U87 cells. (C, D) Proportion of EdU positive cells in ABCC3-defficient and control U87 cells. (E) IC50 analysis of resistance to TMZ in ABCC3- defficient and control U87 cells. (F) TIMP1 knockdown efficiency in LN229 cells. (G) Growth curves of ABCC3-defficient and control LN229 cells. (H–I) Proportion of EdU positive cells in ABCC3-defficient and control LN229 cells. (J) IC50 analysis of resistance to TMZ in ABCC3-defficient and control LN229 cells. **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. Funding The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material. This work was supported by the National Natural Science Foundation of China (82101401). Frontiers in Immunology frontiersin.org 13 Mao et al. 10.3389/fimmu.2022.948630 SUPPLEMENTARY FIGURE 6 Validation of the risk signature in the CGGA #325 and CGGA #693 cohorts. (A) Distribution of the risk score, survival status, and expression profile of the prognostic genes in the CGGA #325 cohort. (B) Kaplan- Meier curves displaying prognostic differences between high- and low- risk groups in the CGGA #325 cohort. (C) The ROC curves describing the sensitivity and specificity of risk score in predicting OS at 1-, 3- and 5-year time points in the CGGA #325 cohort. (D) Distribution of the risk score, survival status, and expression profile of the prognostic genes in the CGGA #693 cohort. (E) Kaplan-Meier curves displaying prognostic differences between high- and low-risk groups in the CGGA #693 cohort. (F) The ROC curves describing the sensitivity and specificity of risk score in predicting OS at 1-, 3- and 5-year time points in the CGGA #693 cohort. SUPPLEMENTARY TABLE 1 (C) Consistency of sample clustering for k = 2 to 10. (D) Consensus clustering matrix for the most suitable k = 4. Primers and siRNAs used in this study. 5. Omuro A, Vlahovic G, Lim M, Sahebjam S, Baehring J, Cloughesy T, et al. Nivolumab with or without ipilimumab in patients with recurrent glioblastoma: results from exploratory phase I cohorts of CheckMate 143. Neuro-oncology (2018) 20:674–86. doi: 10.1093/neuonc/nox208 SUPPLEMENTARY FIGURE 5 Analysis of stemness, genomic heterogeneity and Immune microenvironment features in LGG subgroup. (A) Kaplan-Meier curves displaying prognostic differences between cluster 3 and cluster 4 in the LGG subgroup. (B–G) Differences in stemness score between cluster 3 and cluster 4 in the LGG subgroup. (H–L) Differences in genomic heterogeneity between cluster 3 and cluster 4 in the LGG subgroup. (M–O) Differences in immune microenvironment between cluster 3 and cluster 4 in the LGG subgroup. (P) Differences in infiltration of 22 immune cells between cluster 3 and cluster 4 in the LGG subgroup. *, P < 0.05; **, P < 0.01; ***, P 0.001; ****, P < 0.0001. SUPPLEMENTARY FIGURE 8 Consensus clustering analysis of m1A regulators in the TCGA dataset. (A) Consensus clustering cumulative distribution function for k = 2 to 10. (B) Area under the distribution curve for k = 2 to 10. (C) Consistency of sample clustering for k = 2 to 10. Consensus clustering analysis of m1A regulators in the TCGA dataset. (A) Consensus clustering cumulative distribution function for k = 2 to 10. Validation of the risk score in the IMvigor210 cohort. (A) Boxplot depicting the risk scores between SD/PD and CR/PR groups in the IMvigor210 cohort. (B) Differences in the number responders between high- and low- risk groups in the IMvigor210 cohort. (C) Kaplan-Meier curves displaying prognostic differences between high- and low-risk groups in the IMvigor210 cohort. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. (B) Area under the distribution curve for k = 2 to 10. (C) Consistency of sample clustering for k = 2 to 10. (B) Area under the distribution curve for k = 2 to 10. (C) Consistency of sample clustering for k = 2 to 10. SUPPLEMENTARY FIGURE 4 Kaplan-Meier curves displaying prognostic differences between different clusters in the CGGA #325 cohort. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. SUPPLEMENTARY FIGURE 7 Expression of m1A regulators in glioma. (A) Violin plot showing the expression of m1A regulators between IDH mutant and IDH wildtype groups in the TCGA dataset. (B) Violin plot showing the expression of m1A regulators between LGG and GBM in the CGGA #325 cohort. *, P< 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. Validation of the risk score in LGG subgroup. (A) Kaplan-Meier curves displaying prognostic differences between high- and low-risk groups in the LGG subgroup. (B) The ROC curves describing the sensitivity and specificity of risk score in predicting OS at 1-, 3- and 5-year time points in the LGG subgroup. SUPPLEMENTARY FIGURE 3 Consensus clustering analysis of m1A regulators in the CGGA #325 dataset. (A) Consensus clustering cumulative distribution function for k = 2 to 10. (B) Area under the distribution curve for k = 2 to 10. Consensus clustering analysis of m1A regulators in the CGGA #325 dataset. (A) Consensus clustering cumulative distribution function for k = 2 to 10. (B) Area under the distribution curve for k = 2 to 10. P < 0.0001. ( ) (C) Consistency of sample clustering for k = 2 to 10. (D) Consensus clustering matrix for the most suitable k = 4. 7. Palucka A, Coussens L. The basis of oncoimmunology. Cell (2016) 164:1233– 47. doi: 10.1016/j.cell.2016.01.049 Publisher’s note All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. 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Fine Epitope Mapping of the Central Immunodominant Region of Nucleoprotein from Crimean-Congo Hemorrhagic Fever Virus (CCHFV)
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Fine Epitope Mapping of the Central Immunodominant Region of Nucleoprotein from Crimean-Congo Hemorrhagic Fever Virus (CCHFV) Dongliang Liu1, Yang Li1, Jing Zhao1, Fei Deng2, Xiaomei Duan1, Chun Kou1, Ting Wu1, Yijie Li1, Yongxing Wang1, Ji Ma1, Jianhua Yang1,4, Zhihong Hu2, Fuchun Zhang1, Yujiang Zhang3*, Surong Sun1* 1 Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China, 2 State Key Laboratory of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China, 3 Center for Disease Control and Prevention of the Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang, China, 4 Texas Children’s Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America 1 Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China, 2 State Key Laboratory of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China, 3 Center for Disease Control and Prevention of the Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang, China, 4 Texas Children’s Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America Abstract * Email: xjsyzhang@163.com (YZ); sr_sun2005@163.com (SS) Abstract Crimean-Congo hemorrhagic fever (CCHF), a severe viral disease known to have occurred in over 30 countries and distinct regions, is caused by the tick-borne CCHF virus (CCHFV). Nucleocapsid protein (NP), which is encoded by the S gene, is the primary antigen detectable in infected cells. The goal of the present study was to map the minimal motifs of B-cell epitopes (BCEs) on NP. Five precise BCEs (E1, 247FDEAKK252; E2a, 254VEAL257; E2b, 258NGYLNKH264; E3, 267EVDKA271; and E4, 274DSMITN279) identified through the use of rabbit antiserum, and one BCE (E5, 258NGYL261) recognized using a mouse monoclonal antibody, were confirmed to be within the central region of NP and were partially represented among the predicted epitopes. Notably, the five BCEs identified using the rabbit sera were able to react with positive serum mixtures from five sheep which had been infected naturally with CCHFV. The multiple sequence alignment (MSA) revealed high conservation of the identified BCEs among ten CCHFV strains from different areas. Interestingly, the identified BCEs with only one residue variation can apparently be recognized by the positive sera of sheep naturally infected with CCHFV. Computer-generated three-dimensional structural models indicated that all the antigenic motifs are located on the surface of the NP stalk domain. This report represents the first identification and mapping of the minimal BCEs of CCHFV-NP along with an analysis of their primary and structural properties. Our identification of the minimal linear BCEs of CCHFV-NP may provide fundamental data for developing rapid diagnostic reagents and illuminating the pathogenic mechanism of CCHFV. Editor: Jens H. Kuhn, Division of Clinical Research, United States of America Received February 15, 2014; Accepted August 29, 2014; Published November 3, 2014 Copyright:  2014 Liu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported partly by Science and Technology Basic Work Program 2013FY113500 from Ministry of Science and Technology of China, the National Science Foundation of China (grant no. 81460303, 30860225), and the Open Research Fund Program of Xinjiang Key Laboratory of Biological Resources and Genetic Engineering (grant no. XJDX020l-2014-04). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Citation: Liu D, Li Y, Zhao J, Deng F, Duan X, et al. (2014) Fine Epitope Mapping of the Central Imm Hemorrhagic Fever Virus (CCHFV). PLoS ONE 9(11): e108419. doi:10.1371/journal.pone.0108419 November 2014 | Volume 9 | Issue 11 | e108419 Epitope Prediction Advances have made epitope mapping much easier today than it was before. Many approaches and technologies, including recombinant DNA [23], peptide synthesis [24], and peptide [25] or protein display [26] have highlighted the need for epitope mapping and raised the possibility of mapping to a sufficient level the epitopes of certain antigens of interest [27]. Biosynthetic peptide technology is often used to express several 15–25mer peptide segments covering a certain target protein to determine the presence of an antigenic region or regions for a mAb or pAb by the use of Western blotting. Epitope mapping can be subsequently performed with a set of synthetic overlapping 8mer peptides for the positive segment(s) detected by immunoblotting [28–30]. Herein, based on the findings of a previous study, we describe the fine epitope mapping of immunodominant region NP2372305 of the CCHFV using an improved biosynthetic peptide method [28,29]. p p To predict the B-cell epitopes (BCEs) on the NP2372305 fragment of CCHFV, the corresponding amino acid sequence was analyzed using the DNAStar Protean system. Secondary structure prediction of the truncated protein was performed by using the methods of Garnier and Robson [34] and Chou and Fasman [35]. The surface properties of the structural proteins, namely, hydrophilicity, flexibility, accessibility and antigenicity, were analyzed using the methods of Kyte and Doolittle [36], Karplus and Schulz [37], Emini [38] and Jameson and Wolf [39], respectively. According to the results obtained using these methods, peptides with good hydrophilicity, high accessibility, high flexibility and strong antigenicity were selected as epitope candidates. In general, peptides located in a-spiral and b-sheet regions, which do not readily form epitope regions, were excluded [40]. In this paper, a total of six overlapping 16–22mer peptides (Y1– Y6) and forty-one 8mer peptides (P1–P41), both fused with a truncated carrier protein, were biosynthesized and expressed for minimal epitope mapping of the antigenic properties of NP2372305. Five potential pAb BCEs and one potential mAb BCE were identified and mapped on the stalk region of CCHFV-NP for the first time. In this paper, a total of six overlapping 16–22mer peptides (Y1– Y6) and forty-one 8mer peptides (P1–P41), both fused with a truncated carrier protein, were biosynthesized and expressed for minimal epitope mapping of the antigenic properties of NP2372305. Introduction level of laboratory containment (BSL-4) [11]. Thus, early diagnosis and vaccine development are critical for both patient survival and for the prevention of potential nosocomial infection and transmis- sion in China. The Crimean-Congo hemorrhagic fever virus (CCHFV) is a human pathogenic agent that causes Crimean-Congo hemorrhag- ic fever (CCHF), a severe disease with case-fatality rates up to 30% [1–3]. CCHFV is broadly distributed across much of the Middle East, Africa, and Asia as well and has also been found in parts of Eastern Europe [4–6]. Humans are generally infected through tick bites, direct contact with blood or tissue of infected livestock, or through nosocomial infections [7–9]. In China, the first CCHF cases were reported in 1965 when the CCHFV strain BA66019 was isolated in a patient living in Bachu County of the Xinjiang Autonomous Region, which is now known to have the highest occurrences of CCHF in the country [10]. Despite the high mortality associated with CCHF, the biology and pathogenesis of the disease remain poorly understood for several reasons: CCHF outbreaks are sporadic and have been generally restricted to a relatively small number of cases, limited animal model develop- ment, and the handling of the infectious virus requires the highest CCHFV belongs to the Nairovirus genus within the family Bunyaviridae [2,12]. The genome consists of three negative- stranded RNAs, designated as small (S), medium (M) and large (L) in accordance with their relative nucleotide length, and which encode the viral nucleocapsid protein (NP), the glycoprotein precursor (GP) and the putative RNA-dependent polymerase, respectively [13]. Studies have indicated that NP is the predom- inant protein which is present in high levels early after infection, thereby inducing a high immune response that can be detected in infected cells [14-17]. As a major protein primarily detected during the viral invasion phase, NP has been increasingly regarded as an important target of antivirus and clinical diagnosis [2]. In previous studies, complete NP expressed in bacteria has been used to detect CCHFV immunoglobulin G (IgG) and IgM antibodies; however, the instability of the protein has limited its application for November 2014 | Volume 9 | Issue 11 | e108419 1 PLOS ONE | www.plosone.org Epitope Mapping of CCHFV Nucleoprotein routine use [18–20]. Thus there is a need to develop truncated NP or a multi-epitope peptide for CCHF diagnosis. In a prior study, Saijo et al. Introduction [21] reported that high titer sera of CCHF patients reacted only with amino acid residues 201 to 306 (NP201-306) of the NP central fragment, a highly conserved region among various isolates. In our previous study, the NP region containing amino acid residues 237 to 305 (NP237-305) was found to have remarkable reactivity both with a rabbit polyclonal antibody (pAb) against CCHFV-NP and with a mouse monoclonal antibody (mAb) 14B7 in Western blotting analysis [22]. the study were collected in 2005 and kindly provided by Professor Zhang Yujiang of XJCDC [33]. The serum samples of sheep infected with CCHFV were previously identified by using indirect immunofluorescent assay (IFA) and reverse transcription polymer- ase chain reaction (RT-PCR) [33]. Escherichia coli (E. coli) BL21 (DE3) competent cells, used for expression of recombinant plasmids, were purchased from Beijing TransGen Biotech Co., Ltd. Plasmids, Antibodies and Strains The plasmids pGEX-KG and pXXGST-1 [28] were used to express biosynthetic peptides. The prokaryotic expression plasmid pGEX-KG was maintained by the Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, and pXXGST-1 was donated by Professor Wanxiang Xu of the Shanghai Institute of Planned Parenthood Research. Rabbit polyclonal antibody against CCHFV-NP (pAb) was prepared as previously described [31]. A mouse monoclonal antibody cell line (14B7) secreting IgM type monoclonal antibody 14B7 against CCHFV was obtained from Xinjiang Centers for Disease Control and Prevention (XJCDC). A high titer of mAb was separated from mice ascites [32]. A pooled sheep serum of five samples collected from Bachu County with a confirmed history of CCHFV infection was included in the study and used for reconfirming the antigenicity of identified BCEs of CCHFV-NP in Western blotting assay. Serum sample of one healthy sheep with no history of CCHFV infection was used as negative control. All the sheep sera used in Biosynthesis of 8-22mer Peptides and Recombinant Plasmid Construction Six biosynthetic 16–22mer peptides (designated Y1–Y6) span- ning the NP2372305 segment and overlapping 6 , 9 amino acid residues each other, which all fused with GST or a truncated GST188 carrier protein were expressed in E. coli, respectively [30]. The sequences of the peptides were as follows: Y1 (KLAETEGKGVFDEAKKTVEA), Y2 (AKKTVEALNGYLN- KHK), Y3 (YLNKHKDEVDKASADSM), Y4 (DKASADSMI- TNLLKHI), Y5 (ITNLLKHIAKAQELYK) and Y6 (IAKAQE- LYKNSSALRAQGAQID), which correspond to NP2372256, NP2502265, NP2602276, NP2692284, NP2772292 and NP2842305, respectively. For the immunodominant peptides identified (Y1– Y4), four additional sets of 8mer peptides spanning the Y1 to Y4 fragments overlapping 7 residues each other were generated (totaling 41 biosynthetic peptides designated P1 to P41) for fine epitope mapping (Fig. 1c). Briefly, the synthesized DNA fragments encoding the Y1–Y6 and P1–P41 peptides (based on the S gene sequence [41] were flanked by BamH I and TTA-Sal I sites at the 59 and 39 ends, respectively, then inserted into the BamH I and Sal I sites downstream of the GST or GST188 encoding gene in the pGEX-KG or pXXGST-1 plasmid. Five potential pAb BCEs and one potential mAb BCE were identified and mapped on the stalk region of CCHFV-NP for the first time. Ethics Statement The study was approved by the Research Ethics Committee (Animal Ethics Committee of Xinjiang University) and the procedures that followed were in accordance with the policies and regulations of experimental animals of China. The field studies in Bachu County were permitted by Xinjiang Wildlife Conservation Association (XJWCA). The serum samples were collected using method of random sampling and this process was not involving sacrifice. November 2014 | Volume 9 | Issue 11 | e108419 Expression of Fusion Proteins (b) Epitope predictions of the NP2372305 fra strain based on various principles. (c) Schematic of the BCE mapping strategy with six 16–22mer overlapping biosynt the NP2372305 fragment. The blue band represents the full length nucleoprotein. The red band represents the immunodomin 7 NP. 71/journal.pone.0108419.g001 Figure 1. Prediction and mapping strategy of the epitopes in the central region of CCHFV-NP. (a) Epitope prediction for amino acid residues 237–305 of the NP sequence of the YL04057 strain using DNAStar Protean software. The secondary structure, flexibility plot, hydrophilicity, surface probability, and antigenicity index for NP2372305 were taken into consideration. (b) Epitope predictions of the NP2372305 fragment of the YL04057 strain based on various principles. (c) Schematic of the BCE mapping strategy with six 16–22mer overlapping biosynthetic peptides spanning the NP2372305 fragment. The blue band represents the full length nucleoprotein. The red band represents the immunodominant fragments of YL04057 NP. doi:10 1371/journal pone 0108419 g001 Figure 1. Prediction and mapping strategy of the epitopes in the central region of CCHFV-NP. (a) Epitope prediction for amino acid residues 237–305 of the NP sequence of the YL04057 strain using DNAStar Protean software. The secondary structure, flexibility plot, hydrophilicity, surface probability, and antigenicity index for NP2372305 were taken into consideration. (b) Epitope predictions of the NP2372305 fragment of the YL04057 strain based on various principles. (c) Schematic of the BCE mapping strategy with six 16–22mer overlapping biosynthetic peptides spanning the NP2372305 fragment. The blue band represents the full length nucleoprotein. The red band represents the immunodominant fragments of YL04057 NP. doi:10.1371/journal.pone.0108419.g001 expressed by pGEX-KG or pXXGST-1 as a negative control. All recombinant clones were subsequently sent out for sequencing determination. The cell pellets containing the short peptide fusion proteins were stored at 220uC. expressed by pGEX-KG or pXXGST-1 as a negative control. All recombinant clones were subsequently sent out for sequencing determination. The cell pellets containing the short peptide fusion proteins were stored at 220uC. SDS-PAGE and Western Blotting Expression of Fusion Proteins The resultant recombinant plasmids expressing each 8–22mer peptide fused with GST or GST188 were transformed into E. coli BL21 (DE3) competent cells. Each recombinant clone was cultivated in 3 mL LB medium containing 100 mg/mL ampicillin at 30uC with continuous shaking at 200 rpm overnight. The next day, 30 mL of cell suspension was added to 3 mL fresh LB medium and grown for 4 h until reaching a bacterial density of 0.6–0.8 at OD600. The cells were grown for an additional 4 h with 0.8 mM IPTG (Y1, Y3 and Y6 fusion peptides) or without IPTG (all other fusion peptides) at 42uC to induce the expression of the recombinant proteins. For the screening of positive recombinant clones, an SDS-PAGE gel was run for each harvested cell pellet, with the pellet corresponding to GST or GST188 protein November 2014 | Volume 9 | Issue 11 | e108419 PLOS ONE | www.plosone.org 2 Epitope Mapping of CCHFV Nucleoprotein ed by pGEX-KG or pXXGST-1 as a negative control. All inant clones were subsequently sent out for sequencing ination. The cell pellets containing the short peptide fusion s were stored at 220uC. SDS-PAGE and Western Blotting The cell pellets obtained from 3 mL medium w 400 mL of 16SDS-PAGE loading buffer for 10 m proteins were resolved by SDS-PAGE under reduci using 15% gels [42]. Gels were either stained wit 1. Prediction and mapping strategy of the epitopes in the central region of CCHFV-NP. (a) Epitope prediction s 237–305 of the NP sequence of the YL04057 strain using DNAStar Protean software. The secondary structure, flexibility plot, probability, and antigenicity index for NP2372305 were taken into consideration. (b) Epitope predictions of the NP2372305 fr 7 strain based on various principles. (c) Schematic of the BCE mapping strategy with six 16–22mer overlapping biosynt g the NP2372305 fragment. The blue band represents the full length nucleoprotein. The red band represents the immunodomin 057 NP. 371/journal.pone.0108419.g001 d by pGEX-KG or pXXGST-1 as a negative control. All nant clones were subsequently sent out for sequencing SDS-PAGE and Western Blotting Th ll ll b i d f 3 L di . Prediction and mapping strategy of the epitopes in the central region of CCHFV-NP. (a) Epitope prediction f 237–305 of the NP sequence of the YL04057 strain using DNAStar Protean software. The secondary structure, flexibility plot, robability, and antigenicity index for NP2372305 were taken into consideration. Mapping Epitopes on CCHFV-NP Using pAb fusion proteins or processed for Western blotting by electrotransfer of the proteins onto a 0.2 mm nitrocellulose membrane (Whatman GmbH, Dossel, Germany) [43]. Complete transfer of proteins was ensured by staining the nitrocellulose membrane with 0.1% (w/v) Ponceau S dye liquor. After cleaning and blocking, the nitrocel- lulose membrane was subsequently treated with pAb (1:1000 dilution in PBS containing 0.05% Tween 20 and 1% skim milk powder), mAb 14B7 (1:500 dilution) or a pooled serum (1:100 dilution) collected from sheep with confirmed CCHFV infection. A serum sample from a known healthy sheep with no history of CCHFV infection was used as a negative control. Specific antigen- antibody reactions on the membrane were visualized using goat anti-rabbit IgG, goat anti-mouse IgM, or rabbit anti-sheep IgG conjugated to horseradish peroxidase (HRP) (Proteintech Group, Chicago, USA) at a 1:1000 dilution. The blot was performed using ECL plus Western blotting detection reagent (GE Healthcare, Buckinghamshire, UK) according to the manufacturer’s instruc- tions. All 16–22mer Peptides fused with a GST or GST188 carrier were expressed through constructing short peptide fusion expres- sion plasmids using each synthesized encoding DNA fragments [28]. To define the fine epitopes on the NP2372305 fragment of CCHFV, epitope mapping was performed in two steps. For the first round of antigenic peptide mapping, NP2372305 was divided into six overlapping fragments (Y1–Y6), which were fused with GST/GST188 and expressed in E. coli, respectively. As deter- mined by SDS-PAGE, bands corresponding to the GST-fused proteins (Lane 2, 4 and 7) were approximately 33 kD, and those corresponding to the GST188-fused proteins (Lane 3, 5 and 6) were approximately 25 kD (Fig. 2a). Western blot analysis showed that pAb reacted with polypeptides Y1–Y4 (Fig. 2b). p p yp p ( g ) To further map the epitopes on NP2372305, four sets of 8mer peptides spanning Y1 to Y4 were constructed, which have an overlap of seven amino acid residues each other in second round of fine epitope mapping. A total of 41 recombinant 8mer peptides (designated P1 to P41) were constructed and expressed in E. coli (Fig. 3). Among the 13 recombinant clones corresponding to Y1 (Fig. 3a), Western blot analysis showed that 8mer peptides P9 (GVFDEAKK), P10 (VFDEAKKT) and P11 (FDEAKKTV) were recognized by pAb against NP, suggesting that the epitope minimal motif within Y1 was the FDEAKK (named as epitope 1, E1) according to their shared residues number (Fig. 4). Mapping Epitopes on CCHFV-NP Using pAb Three antigenic peptides Y2–Y4 were similarly identified and analyzed (Fig. 3 and 4): the fine epitopes were the VEAL (E2a) and NGYLNKH (E2b) in Y2, EVDKA (E3) in Y3 and DSMITN (E4) in Y4, respectively. Thus, five specific BCE motifs within the NP2372305 segment were found using rabbit pAb to NP. Epitope Mapping Using mAb 14B7 Against CCHFV-NP 237 305 Epitope Mapping Using mAb 14B7 Against CCHFV-NP In our previous study, NP2372305 was also found to exhibit antigen-antibody reactivity with 14B7. To reveal its antibody- reactive epitope motif, using same strategy described above to map its fine epitope motif. That is, the mAb 14B7 was identified to recognize antigenic peptide Y2 in the first round of mapping (Fig. 2c) and then its epitope motif was confirm as NGYL (designated as E5, amino acid residues 258–261) in the second round of fine mapping (Fig. 5). Interestingly, its epitope motif was located in the E2b identified by the rabbit pAb, suggesting the diversity of antibody production in mouse and rabbit. BCE Prediction and Mapping Strategy Accessibility, variability, fragment mobility, charge distribution and hydrophilicity are important features of antigenic epitopes. The presence of flexible regions, such as coil and turn regions, provide further evidence for epitope identification. In this study, the secondary structure of NP2372305 was predicted using the methods of Garnier and Robson [34] and Chou and Fasman [35] and the NP gene sequence of YL04057 CCHFV. A hydrophilicity plot, flexibility plot, surface probability plot and antigenic index for the truncated protein were obtained using the methods of Kyte and Doolittle [36], Karplus and Schulz [37], Emini [38] and Jameson and Wolf [39], respectively (Fig. 1a). The potential BCEs on NP2372305 were predicted (Fig. 1b) based on the methods mentioned above. The finding that the secondary structure of the NP2372305 fragment consists of five main turn motifs suggested the presence of multiple significant BCEs in this region. In our previous study, the NP2372305 truncated fragment was found to exhibit remarkable antigen-antibody reactivity when either pAb or mAb was used in Western blotting analysis [22]. However, other unpredicted amino acids in this same region should also be considered because they may also contain BCEs, some of which may be predominant BCEs. To identify how many epitopes there are in the fragment of NP, we therefore designed a feasible strategy for BCE mapping of the NP2372305 (Fig. 1c). Briefly, six truncated polypeptides (Y1–Y6) spanning NP2372305 were incorporated into prokaryotic expression plasmids. Based on the results of the Western blotting analysis, sets of 8mer peptides were constructed for each of the immunodominant polypeptides identified for further BCE mapping. Sequence Conservation Analysis and Three-Dimensional Modeling To assess the sequence conservation of the identified epitopes, nine NP amino acid sequences collected from strains in different countries were obtained from GenBank. Amino acid residues 170– 305 of the NP sequences from the nine virus strains were selected for multiple alignment analysis against the corresponding sequence of the YL04057 strain (GenBank code: ACM78470.1) using the ClustalW program (http://www.ebi.ac.uk/services) [44]. Three-dimensional structures of the immunodominant epitopes identified using pAb and 14B7 were simulated using PyMOLTM software [45]. SDS-PAGE and Western Blotting The cell pellets obtained from 3 mL medium were boiled in 400 mL of 16SDS-PAGE loading buffer for 10 min, and the proteins were resolved by SDS-PAGE under reducing conditions using 15% gels [42]. Gels were either stained with Coomassie brilliant blue R-250 to analyze the bands corresponding to the PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org November 2014 | Volume 9 | Issue 11 | e108419 November 2014 | Volume 9 | Issue 11 | e108419 3 Epitope Mapping of CCHFV Nucleoprotein Figure 2. Prokaryotic expression and immunoblotting analysis of Y1–Y6 fused proteins. (a) SDS-PAGE analysis of expressed pXXGST-1 (CK) and Y1-Y6 peptides fused with a GST (Y1, Y3 and Y6) or GST188 tag (Y2, Y4 and Y5). (b) Western blotting of fusion proteins Y1–Y6 using the rabbit polyclonal antibody against CCHFV-NP. (c) Western blotting of fusion proteins Y1–Y6 using the mouse IgM-type monoclonal antibody 14B7 against CCHFV. The arrows represent expressed target peptides in SDS-PAGE and the corresponding positive antigenic-peptides in Western Blotting analysis. doi:10.1371/journal.pone.0108419.g002 Figure 2. Prokaryotic expression and immunoblotting analysis of Y1–Y6 fused proteins. (a) SDS-PAGE analysis of expressed pXXGST-1 (CK) and Y1-Y6 peptides fused with a GST (Y1, Y3 and Y6) or GST188 tag (Y2, Y4 and Y5). (b) Western blotting of fusion proteins Y1–Y6 using the rabbit polyclonal antibody against CCHFV-NP. (c) Western blotting of fusion proteins Y1–Y6 using the mouse IgM-type monoclonal antibody 14B7 against CCHFV. The arrows represent expressed target peptides in SDS-PAGE and the corresponding positive antigenic-peptides in Western Blotting analysis. doi:10.1371/journal.pone.0108419.g002 PLOS ONE | www.plosone.org November 2014 | Volume 9 | Issue 11 | e108419 4 Figure 3. SDS-PAGE identification and Western blotting analysis of the minimal epitopes on NP2372305 using pAb. (a) Thirteen 8mer peptides (P1–P13) corresponding to the Y1 protein. (b) Nine 8mer peptides (P14–P22) corresponding to the Y2 protein. (c) Ten 8mer peptides (P23– P32) corresponding to the Y3 protein. (d) Nine 8mer peptides (P33–P41) corresponding to the Y4 protein. The arrows stand for 8mer peptides which display a positive antigen-antibody reaction in Western Blotting analysis. doi:10.1371/journal.pone.0108419.g003 Epitope Mapping of CCHFV Nucleoprotein Epitope Mapping of CCHFV Nucleoprotein Figure 3. SDS-PAGE identification and Western blotting analysis of the minimal epitopes on NP2372305 using pAb. (a) Thirteen 8mer peptides (P1–P13) corresponding to the Y1 protein. (b) Nine 8mer peptides (P14–P22) corresponding to the Y2 protein. (c) Ten 8mer peptides (P23– P32) corresponding to the Y3 protein. (d) Nine 8mer peptides (P33–P41) corresponding to the Y4 protein. The arrows stand for 8mer peptides which display a positive antigen-antibody reaction in Western Blotting analysis. doi:10.1371/journal.pone.0108419.g003 containing one of the five pAb-identified BCEs, were carried out Western blot test by using sheep sera with or without CCHFV infection (Fig. 6a). As shown in this study, the serum samples of sheep with a confirmed history of CCHFV infection could react with all the five 8-mer peptides to varying degrees, while the Figure 4. The synthetic 8mer peptide sequences derived from a span of the immunodominant peptides Y1, Y2, Y3, and Y4 respectively. The yellow and magenta highlighting represents the common sequences among peptides which react with pAb or mAb using Western blotting analysis. doi:10.1371/journal.pone.0108419.g004 Determination of the Antigenicity of Identified BCEs by CCHFV Antibody-positive Sheep Sera Determination of the Antigenicity of Identified BCEs by CCHFV Antibody-positive Sheep Sera To determine whether the BCEs identified are rabbit/mouse specific or also recognizable by the immune systems of other host species, five randomly selected 8-mer peptides, each of which Figure 4. The synthetic 8mer peptide sequences derived from a span of the immunodominant peptides Y1, Y2, Y3, and Y4 respectively. The yellow and magenta highlighting represents the common sequences among peptides which react with pAb or mAb using Western blotting analysis. doi:10.1371/journal.pone.0108419.g004 Figure 4. The synthetic 8mer peptide sequences derived from a span of the immunodominant peptides Y1, Y2, Y3, and Y4 respectively. The yellow and magenta highlighting represents the common sequences among peptides which react with pAb or mAb using Western blotting analysis. doi:10.1371/journal.pone.0108419.g004 November 2014 | Volume 9 | Issue 11 | e108419 PLOS ONE | www.plosone.org 5 Epitope Mapping of CCHFV Nucleoprotein Figure 5. Minimal epitope identification on CCHFV-NP using mAb 14B7. (a) A reactivity profile of the 8mer peptides P14–P22 corresponding to Y2 using Western blotting analysis. (b) Sequences of the 8mer peptides and their positions in NP. Magenta highlighting indicates the common sequence identified as the minimal BCE (E5) on NP using 14B7. The arrows represent 8mer peptides which display positive antigen- antibody reactions using Western Blotting analysis. doi:10.1371/journal.pone.0108419.g005 Figure 5. Minimal epitope identification on CCHFV-NP using mAb 14B7. (a) A reactivity profile of the 8mer peptides P14–P22 corresponding to Y2 using Western blotting analysis. (b) Sequences of the 8mer peptides and their positions in NP. Magenta highlighting indicates the common sequence identified as the minimal BCE (E5) on NP using 14B7. The arrows represent 8mer peptides which display positive antigen- antibody reactions using Western Blotting analysis. doi:10.1371/journal.pone.0108419.g005 with 90.4% sequence identity. Notably, an even higher sequence identity (92.8%) was found for NP2372305 compared to the other nine strains. The five BCEs (E5 epitope motif was included within E2b) identified were also found to be highly conserved. Only single amino acid differences were found for four BCEs (E1, E2b, E3 and E4) compared with the other strains. To further determine whether the epitope peptides with single residue difference revealed in Fig. 7 could be used as a or all universal diagnostic reagent(s), we prepared four biosynthetic peptides (vE1, FDEAKR; vE2b, NGYLDKH; vE3, EVDRA; vE4, DNMITN) using methods mentioned above and explored their antigenic properties. Determination of the Antigenicity of Identified BCEs by CCHFV Antibody-positive Sheep Sera Specifically, a single amino acid substitution was made within E1 (K252R), E2b (N262D), E3 (K270R), and E4 (S275N). Our investigation demonstrated that the four biosynthetic peptides with one variable residue (vE1, vE2a, vE3, vE4) can remarkably react with CCHFV antibody-positive sheep sera compared with the negative sheep sera panel (Fig. 6b), suggesting that BCEs E1– E4 derived from different CCHFV strains shared conservation in antigenicity aspect. Intriguingly, we found the E2a epitope (VEAL) and E5 epitope (NGYL) identified using mAb 14B7 were highly conserved in a majority of CCHFV isolates (Fig. 7). CCHFV antibody-negative sera could not react with anyone of them. Of the five peptides, P10 (containing E1) and P18 (containing E2a) showed the strongest antigen-antibody reaction activities with CCHFV-infected sheep sera; Meanwhile, P29 (containing E3) and P38 (containing E4) displayed the weakest reaction intensity among the five 8-mer peptides. CCHFV antibody-negative sera could not react with anyone of them. Of the five peptides, P10 (containing E1) and P18 (containing E2a) showed the strongest antigen-antibody reaction activities with CCHFV-infected sheep sera; Meanwhile, P29 (containing E3) and P38 (containing E4) displayed the weakest reaction intensity among the five 8-mer peptides. Sequence Conservation Analysis and Three-Dimensional Modeling The arrows represent 8mer peptides displaying positive antigen-antibody reactions based upon Western Blotting analysis. Sequence Conservation Analysis and Three-Dimensional Modeling To analyze primary structural properties of identified each BCE, the sequence corresponding to amino acid residues 170– 305, which contains the identified BCEs and flanking sequences, was used to conduct multiple sequence alignment (MSA) (Fig. 7). The analysis revealed that this region (using the sequence from Chinese strain YL04057, ACM78470.1) is highly conserved when compared to the corresponding region from other CCHFV strains, Figure 6. Western blot of five 8-mer peptides containing identified BCEs with or without one residue variation per- formed using positive sheep sera with a confirmed history of CCHFV infection. Five randomly selected 8-mer peptides containing identified BCEs (a) or BCEs with one residue variation (b) expressed as GST188 fusion protein in E. coli. A serum sample of healthy sheep with no history of CCHFV infection was used as a negative control. CK was a GST188 protein tag. The arrows represent 8mer peptides displaying positive antigen-antibody reactions based upon Western Blotting analysis. doi:10.1371/journal.pone.0108419.g006 Computer modeling using PyMOLTM software indicated that all of the antigenic motifs are located on the stalk domain of CCHFV-NP (Fig. 8a). Furthermore, the five BCEs are located in a flexible ‘‘helix-turn-helix’’ (HTH) structure (Fig. 8b). According to the surface representations (Fig. 8c and 8d), all of the identified BCEs are located on the surface of NP, which is consistent with the antigenic principles of surface accessibility and hydrophilicity. Figure 6. Western blot of five 8-mer peptides containing identified BCEs with or without one residue variation per- formed using positive sheep sera with a confirmed history of CCHFV infection. Five randomly selected 8-mer peptides containing identified BCEs (a) or BCEs with one residue variation (b) expressed as GST188 fusion protein in E. coli. A serum sample of healthy sheep with no history of CCHFV infection was used as a negative control. CK was a GST188 protein tag. The arrows represent 8mer peptides displaying positive antigen-antibody reactions based upon Western Blotting analysis. Figure 6. Western blot of five 8-mer peptides containing identified BCEs with or without one residue variation per- formed using positive sheep sera with a confirmed history of CCHFV infection. Five randomly selected 8-mer peptides containing identified BCEs (a) or BCEs with one residue variation (b) expressed as GST188 fusion protein in E. coli. A serum sample of healthy sheep with no history of CCHFV infection was used as a negative control. CK was a GST188 protein tag. Discussion Nucleocapsid research is an important branch of viral study, as virus nucleocapsids may stimulate human immune responses, most of which are of the humoral immunity type [46]. Thus, the identification and mapping of minimal BCEs on NP represent significant steps in the development of novel diagnostic tools and multi-epitope peptide vaccines. In a previous study, a bacterially expressed recombinant NP antigen was used to detect IgG doi:10.1371/journal.pone.0108419.g006 November 2014 | Volume 9 | Issue 11 | e108419 November 2014 | Volume 9 | Issue 11 | e108419 PLOS ONE | www.plosone.org 6 Epitope Mapping of CCHFV Nucleoprotein Figure 7. Amino acid sequence comparison of the NP1702305 fragment from the YL04057 strain (ACM78470. 1) and other CCHFV strains using the ClustalW program. The GenBank codes and sources are shown at left. The five minimal epitopes E1, E2a, E2b, E3, and E4 recognized by pAb are highlighted in yellow, and the variable amino acids within the minimal epitopes are highlighted in red. Dots (.) indicate identical amino acids within the ten strains. doi:10.1371/journal.pone.0108419.g007 Figure 7. Amino acid sequence comparison of the NP1702305 fragment from the YL04057 strain (ACM78470. 1) and other CCHFV strains using the ClustalW program. The GenBank codes and sources are shown at left. The five minimal epitopes E1, E2a, E2b, E3, and E4 recognized by pAb are highlighted in yellow, and the variable amino acids within the minimal epitopes are highlighted in red. Dots (.) indicate identical amino acids within the ten strains. doi:10.1371/journal.pone.0108419.g007 Figure 7. Amino acid sequence comparison of the NP1702305 fragment from the YL04057 strain (ACM78470. 1) and other CCHFV strains using the ClustalW program. The GenBank codes and sources are shown at left. The five minimal epitopes E1, E2a, E2b, E3, and E4 recognized by pAb are highlighted in yellow, and the variable amino acids within the minimal epitopes are highlighted in red. Dots (.) indicate identical amino acids within the ten strains. doi:10 1371/journal pone 0108419 g007 antibodies against CCHFV; the instability however, of the protein in soluble expression as well as serological diagnosis restricted the application of this protein [47,48]. The use of non-complete NP or multi-epitope peptides for CCHF diagnosis has attracted increas- ing attention, along with CCHF studies in general. At the same time, there have been increased efforts related to the epitope mapping of CCHFV-NP. For instance, Saijo et al. Discussion reported that in Western blotting analysis, high titer sera of CCHF patients reacted only with the highly conserved NP fragment which contained the amino acid residues 201 to 306 (NP2012306) [21]. Similarly, Burt et al. found that NP1232396 of CCHFV includes a highly antigenic region with application toward the development of antibody detection assays [48]. Previously, our group showed that NP2372305 is an immunogenic region of CCHFV-NP using a polyclonal antibody and two monoclonal antibodies against CCHFV with Western blot analysis [22]. It is worth noting that the NP2372305 region is smaller and more detailed and completely encompassed by the NP2012306 and NP1232396 regions. The consistent finding from these independent research groups suggests that the high antigenicity region of CCHFV-NP is located in the central region of NP rather than the N- or C-terminal regions. Although several antigenic peptides have been mapped on CCHFV-NP, to our knowledge, no minimal motifs have been previously identified, due to methodological limitations. systems on the stability and antigenicity of the recombinant peptides generated. The simplicity, cost effectiveness, reliability, and adaptability of this approach are highly suitable for minimal motif identification [28]. Herein, we demonstrate the use of this method in mapping the minimal motifs of the BCEs of CCHFV- NP. Thus, this methodology may accelerate research requiring the minimal motif mapping of known viral antigenic epitope fragments. In the present study, we mapped six minimal BCEs on NP, five of which were identified by pAb (E1, 247FDEAKK252; E2a, 254VEAL257; E2b, 258NGYLNKH264; E3, 267EVDKA271; and E4, 274DSMITN279) and one by mAb (E5, 258NGYL261). Herein, the antigenicity of the five pAb-identified BCEs was reconfirmed by utilizing natural sera from the sheep with CCHFV infection history, indicating that the identified BCEs may have significant potential in acting as a diagnostic tool to identify whether certain wild animals or even human beings were infected by CCHFV in natural conditions. Additionally, four of the six BCEs were identified in our antigen prediction analysis (Fig. 1b), demonstrating that the epitope prediction tool combined with the biosynthetic peptide method is a reliable approach for epitope mapping and may reduce the experimental effort and expense of identifying and mapping epitopes for immunodiagnostics. antibodies against CCHFV; the instability however, of the protein in soluble expression as well as serological diagnosis restricted the application of this protein [47,48]. Discussion The use of non-complete NP or multi-epitope peptides for CCHF diagnosis has attracted increas- ing attention, along with CCHF studies in general. At the same time, there have been increased efforts related to the epitope mapping of CCHFV-NP. For instance, Saijo et al. reported that in Western blotting analysis, high titer sera of CCHF patients reacted only with the highly conserved NP fragment which contained the amino acid residues 201 to 306 (NP2012306) [21]. Similarly, Burt et al. found that NP1232396 of CCHFV includes a highly antigenic region with application toward the development of antibody detection assays [48]. Previously, our group showed that NP2372305 is an immunogenic region of CCHFV-NP using a polyclonal antibody and two monoclonal antibodies against CCHFV with Western blot analysis [22]. It is worth noting that the NP2372305 region is smaller and more detailed and completely encompassed by the NP2012306 and NP1232396 regions. The consistent finding from these independent research groups suggests that the high antigenicity region of CCHFV-NP is located in the central region of NP rather than the N- or C-terminal regions. Although several antigenic peptides have been mapped on CCHFV-NP, to our knowledge, no minimal motifs have been previously identified, due to methodological limitations. The five minimal BCEs found on NP2372305 span amino acid residues 247 to 279 of CCHFV-NP, and all of them were found to have high sequence similarity among different CCHFV strains according to MSA analysis (88.57% for E2b, 95% for E4, 98% for E3, 98.33% for E1, and 100% for E2a and E5) (Fig. 7). To give specifics, the lysine252 was replaced by arginine within E1 (K252R) in one strain. In certain strains, a single amino acid The biosynthetic peptide method has been successfully used by several research groups to identify the minimal epitopes on human zona pellucida protein [28–30]. In the present study, we used two prokaryotic plasmids for expressing 8–22mer peptides fused with a GST or GST188 tag to avoid the influence of different expression November 2014 | Volume 9 | Issue 11 | e108419 PLOS ONE | www.plosone.org 7 Epitope Mapping of CCHFV Nucleoprotein Figure 8. Location and three-dimensional structure of the epitopes identified using pAb and mAb 14B7 on CCHFV-NP. (a) The ribbon diagram shows the overall secondary structure of CCHFV-NP from strain YL04057 (PDB code: 3U3I). The motifs within the frame indicate the five minimal epitopes E1–E4. Discussion (b) E1–E4 sites on the CCHFV-NP stalk domain. (c) Surface properties of CCHFV-NP. The molecular surfaces of E1 (red), E2a blue), E2b (magenta), E3 (orange) and E4 (yellow) are shown. (d) The structural representations show the location and spatial conformation of epitope E5 (tetrapeptide ‘‘NGYL’’) identified by Amb 14B7. Residues N258, G259, Y260, and L261 are shown in different colors. The figures were generated using the PyMOL molecular graphics system. doi:10.1371/journal.pone.0108419.g008 Figure 8. Location and three-dimensional structure of the epitopes identified using pAb and mAb 14B7 on CCHFV-NP. (a) The ribbon diagram shows the overall secondary structure of CCHFV-NP from strain YL04057 (PDB code: 3U3I). The motifs within the frame indicate the five minimal epitopes E1–E4. (b) E1–E4 sites on the CCHFV-NP stalk domain. (c) Surface properties of CCHFV-NP. The molecular surfaces of E1 (red), E2a (blue), E2b (magenta), E3 (orange) and E4 (yellow) are shown. (d) The structural representations show the location and spatial conformation of epitope E5 (tetrapeptide ‘‘NGYL’’) identified by Amb 14B7. Residues N258, G259, Y260, and L261 are shown in different colors. The figures were generated using the PyMOL molecular graphics system. doi:10.1371/journal.pone.0108419.g008 CCHFV, and using the sera of sheep naturally infected with CCHFV. Thereby, the properties, structure, antigenicity, and immunogenicity of the NP protein, and in particular, identification of human sera infected with CCHFV will be further studied in order to be applied to CCHF diagnosis and therapy in the future. To our knowledge, the ten CCHFV strains used were isolated in countries which were directly affected by at least one of the five CCHF-epidemic areas, namely countries in Europe, Africa, Central Asia, South Asia, and the Middle East (Table S1). As depicted, epitopes E2a and E5 showed 100% conservative properties among all strains from the five CCHF-epidemic areas. CCHFV, and using the sera of sheep naturally infected with CCHFV. Thereby, the properties, structure, antigenicity, and immunogenicity of the NP protein, and in particular, identification of human sera infected with CCHFV will be further studied in order to be applied to CCHF diagnosis and therapy in the future. To our knowledge, the ten CCHFV strains used were isolated in countries which were directly affected by at least one of the five CCHF-epidemic areas, namely countries in Europe, Africa, Central Asia, South Asia, and the Middle East (Table S1). Conclusion In this study, the five highly conserved or 100% conserved B- cell epitopes E1, E2a, E2b (which fully overlaps E5), E3 and E4 do not only react with a prepared polyclonal antibody, but also with the positive sera of sheep naturally infected with CCHFV. More importantly, the four epitope mutants vE1, vE2b, vE3, and vE4 are distinctly recognizable through the use of naturally infected sheep sera. Our discovery has demonstrated a high antigenic- conservation of these identified minimal epitopes, which might be useable as universal epitopes in CCHF diagnosis. It is of great importance that human sera infected with CCHFV be used to test these identified epitopes in future study. Furthermore, these BCEs were determined to be located on the surface of the NP stalk region, suggesting they very well may play significant roles in the process of interaction with the host immune system, being easily recognized by antibodies. These findings would provide funda- mental data for the development of novel diagnostic reagents and the illumination of the pathogenic mechanism of CCHFV. It has been previously reported that the Dugbe virus, another member of the Nairovirus genus, shares some antigenic and genetic properties with CCHFV [49]. Based on our findings, however, the amino acid sequences of NP247-279 of the two viruses (GenBank codes: ACM78470.1 and AAL73396.1) display only a 9.1% similarity, despite a 57.4% sequence similarity between the two complete NP sequences (data not given). These findings suggest that the identified BCEs may be unique to CCHFV and thus highly species specific. To further investigate the structural aspects of the minimal BCEs, the three-dimensional structure of YL04057 NP was retrieved from the Protein Databank (PDB code: 3U3I). The five pAb BCEs and one mAb BCE were all found to be located on the NP stalk domain (BCE surface properties shown in different colors in Fig. 8c and 8d). Structural analyses, particularly of the surface structure of epitopes, provide a good foundation in the search for and creation of structurally complementary drugs with clinical applications. The flexible ‘‘helix-turn-helix’’ structure containing the five BCEs may form a discontinuous epitope and easily react with antibodies or drugs. Human MxA protein has been shown to inhibit the CCHFV replication process [50]. In a protein-protein docking study of MxA with CCHFV-NP emphasizing epitope- based immunoinformatics, Srinivasan et al. [51] showed a complementary wrapping of the NP stalk around the MxA model. Table S1. (DOC) Table S1. (DOC) Acknowledgments We are very grateful to Professor Wanxiang Xu for his technical support and proofreading work. Epitope Mapping of CCHFV Nucleoprotein Epitope E1 was fully conserved in the countries of Europe, Africa, South Asia, the Middle East, and part of Central Asia. Similarly, epitope E3 also displayed complete homology in the different CCHF-epidemic areas, with the exception of Africa. It is worth noting that the epitope E2b from isolate YL04057, though it was not consistent with the other eight strains from different CCHF- epidemic areas, had merely one amino acid difference among ten CCHFV strains. As far as we know, eleven complete NP sequences of CCHFV strains isolated within China have been registered in the GenBank database. To further confirm whether the epitope E2b (258NGYLNKH264) showed high homology among strains from China, the sequences of the eleven Chinese strains corresponding to amino acid residues 241 to 300 of NP were retrieved from the GenBank for sequence alignment using the ClustalW program (Figure S1). Our study indicated that there was only a single difference, which of asparagine changing to aspartic acid (N262D) within epitope E2b in four strains of the eleven, suggesting that asparagine262 may well exist only in the Chinese CCHFV strains. may represent a host defense mechanism against lytic CCHFV infection [56–59]. Interestingly, the occurrence of the DEVD motif is within the epitope-rich region of amino acid residues 247 to 279. Our study also raises the possibility of a combination of caspase-3-dependent apoptosis and intrabody therapy in fighting a CCHFV infection in the future. In the present study, we identified five fine linear BCEs on the stalk region of CCHFV-NP using a peptide biosynthesis strategy, thereby demonstrating the utility of this approach in peptide-based assays aimed at antibody detection. However, it remains a topic of further research whether the antigenic activities, consisting of specificity and sensitivity, can be enhanced by linearly fusing the five BCEs so that they would be more easily and more effectively applied in clinical diagnosis and epidemiological investigation. Author Contributions Conceived and designed the experiments: SRS DLL YJZ FCZ. Performed the experiments: DLL YL JZ XMD CK TW. Analyzed the data: SRS DLL YJL JM YXW. Contributed reagents/materials/analysis tools: DLL SRS YJZ ZHH FD. Wrote the paper: DLL SRS JHY YJZ ZHH. Conclusion Together with the present findings, these results suggest that the CCHFV-NP stalk domain may play a critical role in immune system processes and virus interaction. Intrabodies, or intracellular antibodies, are powerful tools for cell biology studies as well as therapeutic applications [52]. They are commonly used to either block the intracellular antibody target or to image endogenous target dynamics [53,54]. It is reported that intrabodies induced cell death via activation of the caspase-3-mediated apoptotic pathway [55]. In a related vein, recent structural studies of CCHFV-NP revealed that the amino acid residues DEVD at positions 266 to 269 on the NP stalk domain comprise a putative cleavage site of caspase-3, indicating that caspase-3 cleavage of NP Figure S1. (DOC) Figure S1. (DOC) 4. Deyde VM, Khristova ML, Rollin PE, Ksiazek TG, Nichol ST (2006) Crimean- Congo hemorrhagic fever virus genomics and global diversity. J Virol 80: 8834– 8842. 5. Hoogstraal H (1979) The epidemiology of tick-borne Crimean-Congo hemorrhagic fever in Asia, Europe, and Africa. J Med Entomol 15: 307–417. Discussion As depicted, epitopes E2a and E5 showed 100% conservative properties among all strains from the five CCHF-epidemic areas. substitution was also found within E2b (N262D), E3 (K270R), and E4 (S275N). Despite one residue difference, the antigen-antibody reaction was still obvious when using positive sera of sheep naturally infected with CCHFV (Fig. 6b), reflecting highly antigenic conservation. However, ideally, the sera of CCHF patients should be utilized to verify the conservation and specificity of BCEs, which is crucial for future applications in CCHF diagnosis and prevention. In this study, we only provided the fundamental data that the antigenicity of CCHFV-NP was researched using rabbit polyclonal antiserum against the CCHFV-NP, using the mouse monoclonal antibody against the November 2014 | Volume 9 | Issue 11 | e108419 PLOS ONE | www.plosone.org 8 Epitope Mapping of CCHFV Nucleoprotein 6. Maltezou HC, Papa A (2010) Crimean–Congo hemorrhagic fever: Risk for emergence of new endemic foci in Europe? Travel Med Infect Di 8: 139–143. 1. Elliott RM (1990) Molecular biology of the Bunyaviridae. J Gen Virol 71: 501– 522. 2. Ergo¨nu¨l O¨ (2006) Crimean-Congo haemorrhagic fever. Lancet Infect Dis 6: 203–214. 3. World Health Organization (2001) Crimean-Congo haemorrhagic fever. Fact sheet 208. 3. World Health Organization (2001) Crimean-Congo haemorrhagic fever. Fact sheet 208. 4. Deyde VM, Khristova ML, Rollin PE, Ksiazek TG, Nichol ST (2006) Crimean- Congo hemorrhagic fever virus genomics and global diversity. J Virol 80: 8834– 8842. 5. Hoogstraal H (1979) The epidemiology of tick-borne Crimean-Congo hemorrhagic fever in Asia, Europe, and Africa. J Med Entomol 15: 307–417. 6. Maltezou HC, Papa A (2010) Crimean–Congo hemorrhagic fever: Risk for emergence of new endemic foci in Europe? Travel Med Infect Di 8: 139–143. 2. Ergo¨nu¨l O¨ (2006) Crimean-Congo haemorrhagic fever. Lancet Infect Dis 6: 203–214. 1. Elliott RM (1990) Molecular biology of the Bunyaviridae. J Gen Virol 71: 501– 522. Epitope Mapping of CCHFV Nucleoprotein Comput Appl Biosci 4: 181–186. 14. Magurano F, Nicoletti L (1999) Humoral response in Toscana virus acute neurologic disease investigated by viral-protein-specific immunoassays. Clin Vaccine Immunol 6: 55–60. 40. Zhang ZW, Zhang YG, Wang YL, Pan L, Fang YZ, et al. (2010) Screening and identification of B cell epitopes of structural proteins of foot-and-mouth disease virus serotype Asia1. Vet Microbiol 140: 25–33. 15. Schwarz TF, Gilch S, Pauli C, Ja¨ger G (1996) Immunoblot detection of antibodies to Toscana virus. J Med Virol 49: 83–86. ˚ 41. Zhou Z, Meng W, Deng F, Xia H, Li T, et al. (2013) Complete genome sequences of two Crimean-Congo hemorrhagic fever viruses isolated in China. Genome Announc 1: e00571-13. 16. Vapalahti O, Kallio-Kokko H, Na¨rva¨nen A, Julkunen I, Lundkvist A˚ , et al. (1995) Human B-cell epitopes of puumala virus nucleocapsid protein, the major antigen in early serological response. J Med Virol 46: 293–303. 42. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680–685. g y g p 17. Dowall SD, Richards KS, Graham VA, Chamberlain J, Hewson R (2012) Development of an indirect ELISA method for the parallel measurement of IgG and IgM antibodies against Crimean-Congo haemorrhagic fever (CCHF) virus using recombinant nucleoprotein as antigen. J Virol Methods 179: 335–341. 43. Towbin H, Staehelin T, Gordon J (1979) Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci 76: 4350–4354. pp 44. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 13: 3497–3500. 18. Tang Q, Saijo M, Zhang Y, Asiguma M, Tianshu D, et al. (2003) A patient with Crimean-Congo hemorrhagic fever serologically diagnosed by recombinant nucleoprotein-based antibody detection systems. Clin Vaccine Immunol 10: 489–491. 45. DeLano WL (2002) The PyMOL molecular graphics system. ˚ 19. Saijo M, Tang Q, Shimayi B, Han L, Zhang Y, et al. (2005). Recombinant nucleoprotein-based serological diagnosis of Crimean-Congo hemorrhagic fever virus infections. J Med Virol 75: 295-299. 46. Lundkvist A˚ , Meisel H, Koletzki D, Lankinen H, Cifire F, et al. (2002) Mapping of B-cell epitopes in the nucleocapsid protein of Puumala hantavirus. Viral Immunol 1: 177–192. 47. Epitope Mapping of CCHFV Nucleoprotein Samudzi RR, Leman PA, Paweska JT, Swanepoel R, Burt FJ (2012) Bacterial expression of Crimean-Congo hemorrhagic fever virus nucleoprotein and its evaluation as a diagnostic reagent in an indirect ELISA. J Virol Methods 179: 70–76. 20. Garcia S, Chinikar S, Coudrier D, Billecocq A, Hooshmand B, et al. (2006) Evaluation of a Crimean-Congo hemorrhagic fever virus recombinant antigen expressed by Semliki Forest suicide virus for IgM and IgG antibody detection in human and animal sera collected in Iran. J Clin Virol 35: 154–159. 48. Burt FJ, Samudzi RR, Randall C, Pieters D, Vermeulen J, et al. (2013) Human defined antigenic region on the nucleoprotein of Crimean-Congo haemorrhagic fever virus identified using truncated proteins and a bioinformatics approach. J Virol Methods 193: 706–712. 21. Saijo M, Tang Q, Niikura M, Maeda A, Ikegami T, et al. (2002) Recombinant nucleoprotein-based enzyme-linked immunosorbent assay for detection of immunoglobulin G antibodies to Crimean-Congo hemorrhagic fever virus. J Clin Microbiol 40: 1587–1591. 22. Wei PF, Luo YJ, Li TX, Wang HL, Hu ZH, et al. (2010) Serial expression of the.truncated fragments of the nucleocapsid protein of CCHFV and identifica- tion of the epitope region. Virol Sin 25: 45–51. 49. Papa A, Ma B, Kouidou S, Tang Q, Hang C, et al. (2002) Genetic characterization of the M RNA segment of Crimean Congo hemorrhagic fever virus strains, China. Emerg Infect Dis 8: 50–53. ˚ 23. Morrow JF, Cohen SN, Chang AC, Boyer HW, Goodman HM, et al. (1974) Replication and Transcription of Eukaryotic DNA in Esherichia coli. Proc Natl Acad Sci 71: 1743–1747. 50. Andersson I, Bladh L, Mousavi-Jazi M, Magnusson KE, Lundkvist A˚ , et al. (2004) Human MxA protein inhibits the replication of Crimean-Congo hemorrhagic fever virus. J Virol 78: 4323–4329. 24. Merrifield RB (1968) Solid-phase peptide synthesis. Adv Enzymol Relat Areas Mol Biol 32: 221–296. g 51. Srinivasan P, Kumar SP, Karthikeyan M, Jeyakanthan J, Jasrai YT, et al. (2011) Epitope-based immunoinformatics and molecular docking studies of nucleocap- sid protein and ovarian tumor domain of Crimean-Congo hemorrhagic fever virus. Front Gen 2: 72–80. 25. Cwirla SE, Peters EA, Barrett RW, Dower WJ (1990) Peptides on phage: a vast library of peptides for identifying ligands. Proc Natl Acad Sci 87: 6378–6382. 52. Lo AS, Zhu Q, Marasco WA (2008) Intracellular antibodies (intrabodies) and their therapeutic potential. Handb Exp Pharmacol 181: 343–373. 26. Roberts BL, Markland W, Ley AC, Kent RB, White DW, et al. Epitope Mapping of CCHFV Nucleoprotein (1992) Directed evolution of a protein: selection of potent neutrophil elastase inhibitors displayed on M13 fusion phage. Proc Natl Acad Sci 89: 2429–2433. 53. Moutel S, Nizak C, Perez F (2012) Selection and Use of Intracellular Antibodies (Intrabodies). Methods Mol Biol 907: 667–679. p g 27. Ladner RC (2007) Mapping the epitopes of antibodies. Biotechnol Genet Eng 24: 1–30. 54. Stocks M (2005) Intrabodies as drug discovery tools and therapeutics. Curr Opin Chem Biol 9: 359–365. 28. Xu WX, He YP, Tang HP, Jia XF, Ji CN, et al. (2009) Minimal motif mapping of a known epitope on human zona pellucida protein-4 using a peptide biosynthesis strategy. J Reprod Immunol 81: 9–16. 55. Tse E, Rabbitts TH (2000) Intracellular antibody-caspase-mediated cell killing: An approach for application in cancer therapy. Proc Natl Acad Sci USA 97: 12266–12271. y gy J p 29. Xu WX, Bhandari B, He YP, Tang HP, Chaudhary S, et al. (2012) Mapping of Epitopes Relevant for Induction of Acrosome Reaction on Human Zona Pellucida Glycoprotein-4 Using Monoclonal Antibodies. Am. J Reprod Immunol 68: 465–475. 56. Karlberg H, Tan YJ, Mirazimi A (2011) Induction of caspase activation and cleavage of the viral nucleocapsid protein in different cell types during Crimean- Congo hemorrhagic fever virus infection. J Biol Chem 286: 3227–3234. Congo hemorrhagic fever virus infection. J Biol Chem 286: 3227–3 30. Xu WX, He YP, Wang J, Tang HP, Shi HJ, et al. (2012) Mapping of Minimal Motifs of B-Cell Epitopes on Human Zona Pellucida Glycoprotein-3. Available: http://www.hindawi.com/journals/jir/2012/831010/abs/. Accepted 2 Sep- tember 2011. 57. Wang Y, Dutta S, Karlberg H, Devignot S, Weber F, et al. (2012) Structure of Crimean-Congo hemorrhagic fever virus nucleoprotein: superhelical homo- oligomers and the role of caspase-3 cleavage. J Virol 86: 12294–12303. ´ oligomers and the role of caspase-3 cleavage. J Virol 86: 12294–12 ´ 58. Carter SD, Surtees R, Walter CT, Ariza A, Bergeron E´, et al. (2012) Structure, function, and evolution of the Crimean-Congo hemorrhagic fever virus nucleocapsid protein. J Virol 86: 10914–10923. 31. Liu DL, Li Y, Zhao J, Wu T, Sun SR (2013) Preparation of polyclonal antibody to nucleoprotein from Xinjiang hemorrhagic fever virus and its immunological evaluation. Chinese J Cell Mol Immunol 29: 838–841. (In Chinese) p p J 59. Guo Y, Wang WM, Ji W, Deng MP, Sun YN, et al. (2012) Crimean-Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses. Epitope Mapping of CCHFV Nucleoprotein following pretreatment with pristane and Freund’s adjuvant. J Immunol Methods 119: 241–245. following pretreatment with pristane and Freund’s adjuvant. J Immunol Methods 119: 241–245. 7. Swanepoel R, Shepherd AJ, Leman PA, Shepherd SP, McGillivray GM, et al. (1987) Epidemiologic and clinical features of Crimean-Congo hemorrhagic fever in southern Africa. Am J Trop Med Hyg 36: 120–132. ( ) p g in southern Africa. Am J Trop Med Hyg 36: 120–132. 33. Dai X, Muhtar, Feng CH, Sun SR, Tai XP, et al. (2006) Geography and host distribution of Crimean - Congo hemorrhagic fever in the Tarim Basin. Chin J Epidemiol 27: 1048–1052. (In Chinese) J p yg 8. Chinikar S (2009) An overview of Crimean-Congo hemorrhagic fever in Iran. Iran. J Microbiol 1: 7–12. J p ( ) 34. Garnier J, Robson B (1989) The GOR method for predicting secondary structures in proteins. In Prediction of protein structure and the principles of protein conformation. pp. 417–465. 9. Gu¨rbu¨z Y, Sencan I, O¨ ztu¨rk B, Tu¨tu¨ncu¨ E (2009) A case of nosocomial transmission of Crimean–Congo hemorrhagic fever from patient to patient. Int J Infect Dis 13: e105–e107. p pp 35. Chou PY, Fasman GD (1978) Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 47: 45–148. J 10. Sun SR, Dai X, Aishan M, Wang XH, Meng WW, et al. (2009). J Clin Microbiol 47: 2536–2543. ´ q y 36. Kyte J, Doolittle RF (1982) A simple method fo character of a protein. J Mol Biol 157: 105–132. 36. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105–132. 11. Bergeron E´, Albarin˜o CG, Khristova ML, Nichol ST (2010) Crimean-Congo hemorrhagic fever virus-encoded ovarian tumor protease activity is dispensable for virus RNA polymerase function. J Virol 84: 216–226. 37. Karplus PA, Schulz GE (1985) Prediction of chain flexibility in proteins. Naturwissenschaften 72: 212–213. 12. Whitehouse CA (2004) Crimean–Congo hemorrhagic fever. Antivir Res 64: 145–160. 38. Emini EA, Hughes JV, Perlow D, Boger J (1985) Induction of hepatitis A virus- neutralizing antibody by a virus-specific synthetic peptide. J Virol 55: 836–839. 13. Walter CT, Barr JN (2011) Recent advances in the molecular and cellular biology of bunyaviruses. J Gen Virol 92: 2467–2484. 39. Jameson BA, Wolf H (1988) The antigenic index: a novel algorithm for predicting antigenic determinants. References 1. Elliott RM (1990) Molecular biology of the Bunyaviridae. J Gen Virol 71: 501– 522. 2. Ergo¨nu¨l O¨ (2006) Crimean-Congo haemorrhagic fever. Lancet Infect Dis 6: 203–214. 3. World Health Organization (2001) Crimean-Congo haemorrhagic fever. Fact sheet 208. November 2014 | Volume 9 | Issue 11 | e108419 PLOS ONE | www.plosone.org 9 Epitope Mapping of CCHFV Nucleoprotein Epitope Mapping of CCHFV Nucleoprotein Proc Natl Acad Sci 109: 5046–5051. J ( ) 32. 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Genome Sequence of the Heteropolysaccharide-Producing Strain Lactobacillus mucosae DPC 6426
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Genome Sequence of the Heteropolysaccharide-Producing Strain Lactobacillus mucosae DPC 6426 Paul M. Ryan,a,b Caitriona M. Guinane,a Lis E. E. London,c,d Philip R. Kelleher,b Gerald F. Fitzgerald,b,c Noel M. Caplice,c R. Paul Ross,d Catherine Stantona,c Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Irelanda; School of Microbiology, University College Cork, Cork, Irelandb; Centre for Research in Vascular Biology, University College Cork, Cork, Irelandc; Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Irelandd Exopolysaccharide-synthesizing Lactobacillus mucosae DPC 6426 is a heterofermentative strain, which has demonstrated cholesterol-lowering properties in an animal model of lipid-driven atherosclerosis. The genome revealed a plethora of homo- logues linked to carbohydrate metabolism and mucin binding. Received 27 November 2014 Accepted 4 December 2014 Published 15 January 2015 Citation Ryan PM, Guinane CM, London LEE, Kelleher PR, Fitzgerald GF, Caplice NM, Ross RP, Stanton C. 2015. Genome sequence of the heteropolysaccharide-producing strain Lactobacillus mucosae DPC 6426. Genome Announc 3(1):e01350-14. doi:10.1128/genomeA.01350-14. Copyright © 2015 Ryan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Catherine Stanton, catherine.stanton@teagasc.ie. L pression of mucus binding protein (mub) homologues within the species, as well as other adhesin-like proteins (12–14). The L. mu- cosae DPC 6426 genome was found to have predicted CDSs of mucin binding domains with similarities to the mub genes in L. mucosae and L. reuteri strains. Two putative collagen-binding proteins, a fibronectin binding protein (100% coverage and 70% identity to L. fermentum IFO3956 adherence protein), and five LPXTG motifs were also identified. L actobacillus mucosae DPC 6426 is an exopolysaccharide (EPS)- producing strain originally isolated from the bovine gastroin- testinal tract (1). L. mucosae DPC 6426 exhibits technological and biological robustness compared to a non-EPS-producing L. mu- cosae strain, indicating its versatility as an adjunct culture for func- tional food applications (1). Additionally, two recent studies have demonstrated the cholesterol-lowering effects of L. mucosae DPC 6426 in the atherosclerosis-prone apolipoprotein-E-deficient mouse model (2), as well as its application as an adjunct culture in yogurt for improving technofunctional properties (3). A 24-kbp putative EPS operon was identified, which codes for genes common to EPS-synthesizing lactobacilli, including those involved in regulation, chain length determination, repeating unit biosynthesis, and polymerization. Two additional regions (9.8 kbp and 6 kbp), flanked by putative insertion elements, were also identified as coding for putative glycosyltransferases, dextransu- crases, and pectinsucrases. The draft genome of L. Genome Sequence of the Heteropolysaccharide-Producing Strain Lactobacillus mucosae DPC 6426 mucosae DPC 6426 was sequenced by a combined paired-end 454 pyrosequencing on the FLX sequencer and an Illumina MiSeq approach by Beckman Coulter Genomics, with a final coverage of ~24 being achieved. The reads were assembled using the MIRA software (4) into 72 contigs. The order and orientation of the contigs were determined using the Artemis Comparison Tool (ACT) (5, 6) and progressiveMauve software (7) using the reference genomes of Lactobacillus fermentum IFO3956 (GenBank accession no. NC_010610), Lactobacillus reu- teri JCM1112 (GenBank accession no. NC_010609), and L. muco- sae LM1 (8). A combination of Glimmer 3.02, Prokaryotic Dy- namic Programming Genefinding Algorithm (Prodigal) version 1.20 (http://prodigal.ornl.gov) (9, 10), and Rapid Annotations us- ing Subsystems Technology (RAST) (http://rast.nmpdr.org/) (11) was used to identify and annotate predicted coding sequences (CDSs). The draft genome includes 2,079,103 bp, with an average GC content of 46.7%. The genome consists of a single circular chromosome and does not appear to harbor plasmids. A total of 2,045 CDSs were predicted, including five rRNA operons, 47 tRNA genes, and a putative complete novel phage of 40.7 kb, 6426. A total GC-skew analysis and the open reading frame (ORF) orientation identified the oriC proximal to dnaA and the terC at ~1.06 Mb, and the coding density was predicted to be 85.4%. The availability of the genome sequence of L. mucosae DPC 6426 will allow full analysis of the genetics behind its potential health-promoting attributes. Nucleotide sequence accession numbers. This whole- genome shotgun project of L. mucosae DPC 6426 has been de- posited at DDBJ/EMBL/GenBank under the accession number JSWI00000000. The version described here is JSWI01000000. ACKNOWLEDGMENTS P. M. Ryan is in receipt of a Teagasc Walsh Fellowship. P. M. Ryan is in receipt of a Teagasc Walsh Fellowship. This work was supported by the Enterprise Ireland Commercialisation Fund Contract reference CF/2013/3030A/B, European Community’s Sev- enth Framework Programme (FibeBiotics—FP7/2007-2013) under grant agreement no. 289517, and by the Alimentary Pharmabiotic Centre, funded by Science Foundation Ireland (SFI). crossmark smark smark January/February 2015 Volume 3 Issue 1 e01350-14 REFERENCES 1. London LEE, Price NP, Ryan P, Wang L, Auty MA, Fitzgerald GF, Stanton C, Ross RP. 2014. Characterization of a bovine isolate Lactoba- cillus mucosae DPC 6426 which produces an exopolysaccharide composed predominantly of mannose residues. J Appl Microbiol 117:509–517. http://dx.doi.org/10.1111/jam.12542. 1. London LEE, Price NP, Ryan P, Wang L, Auty MA, Fitzgerald GF, Stanton C, Ross RP. 2014. Characterization of a bovine isolate Lactoba- cillus mucosae DPC 6426 which produces an exopolysaccharide composed predominantly of mannose residues. J Appl Microbiol 117:509–517. http://dx.doi.org/10.1111/jam.12542. 1. London LEE, Price NP, Ryan P, Wang L, Auty MA, Fitzgerald GF, Stanton C, Ross RP. 2014. Characterization of a bovine isolate Lactoba- cillus mucosae DPC 6426 which produces an exopolysaccharide composed predominantly of mannose residues. J Appl Microbiol 117:509–517. http://dx.doi.org/10.1111/jam.12542. The L. mucosae species was named as a result of an ability to adhere to intestinal mucosa, due to the apparent ubiquitous ex- The L. mucosae species was named as a result of an ability to adhere to intestinal mucosa, due to the apparent ubiquitous ex- Genome Announcements genomea.asm.org genomea.asm.org Ryan et al. terin and cobalamin production. DNA Res 15:151–161. http://dx.doi.org/ 10.1093/dnares/dsn009. terin and cobalamin production. DNA Res 15:151–161. http://dx.doi.org/ 10.1093/dnares/dsn009. 2. London LEE, Kumar AH, Wall R, Casey PG, O’Sullivan O, Shanahan F, Hill C, Cotter PD, Fitzgerald GF, Ross RP, Caplice NM, Stanton C. 2014. Exopolysaccharide-producing probiotic lactobacilli reduce serum cholesterol and modify enteric microbiota in ApoE-deficient mice. J Nutr 144:1956–1962. http://dx.doi.org/10.3945/jn.114.191627. 9. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. http://dx.doi.org/ 10.1186/1471-2105-11-119. g j 3. London LEE, Chaurin V, Auty MAE, Fenelon MA, Fitzgerald GF, Ross RP, Stanton C. 2015. Use of Lactobacillus mucosae DPC 6426, an exopolysaccharide-producing strain, positively influences the techno- functional properties of yoghurt. Int Dairy J 40:33–38. http://dx.doi.org/ 10.1016/j.idairyj.2014.08.011. 10. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with glimmer. BioInformatics 23:673–679. http://dx.doi.org/10.1093/bioinformatics/btm009. 11. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/ 1471-2164-9-75. j yj 4. 2 genomea.asm.org January/February 2015 Volume 3 Issue 1 e01350-14 REFERENCES Chevreux B. 2005. MIRA: an automated genome and EST assembler. Ph. D. thesis. The Ruprecht-Karls-University Heidelberg, Heidelberg, Ger- many. 5. Carver TJ, Rutherford KM, Berriman M, Rajandream M-A, Barrell BG, Parkhill J. 2005. ACT: the Artemis Comparison Tool. BioInformatics 21:3422–3423. http://dx.doi.org/10.1093/bioinformatics/bti553. 12. Lee JH, Valeriano VD, Shin Y-R, Chae JP, Kim G-B, Ham J-S, Chun J, Kang D-K. 2012. Genome sequence of Lactobacillus mucosae LM1, iso- lated from piglet feces. J Bacteriol 194:4766. http://dx.doi.org/10.1128/ JB.01011-12. 6. Darling AE, Treangen TJ, Messeguer X, Perna NT. 2007. Analyzing patterns of microbial evolution using the mauve genome alignment sys- tem, p 135–152. In Bergman N (ed), Comparative genomics, vol 396. Humana Press, New York, NY. 7. Rissman AJ, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. 2009. Reordering contigs of draft genomes using the mauve aligner. BioInfor- matics 25:2071–2073. http://dx.doi.org/10.1093/bioinformatics/btp356. 13. Roos S, Karner F, Axelsson L, Jonsson H. 2000. Lactobacillus mucosae sp. nov., a new species with in vitro mucus-binding activity isolated from pig intestine. Int J Syst Evol Microbiol 50:251–258. http://dx.doi.org/10.1099/ 00207713-50-1-251. p g p 8. Morita H, Toh H, Fukuda S, Horikawa H, Oshima K, Suzuki T, Murakami M, Hisamatsu S, Kato Y, Takizawa T, Fukuoka H, Yo- shimura T, Itoh K, O’Sullivan DJ, McKay LL, Ohno H, Kikuchi J, Masaoka T, Hattori M. 2008. Comparative genome analysis of Lactoba- cillus reuteri and Lactobacillus fermentum reveal a genomic island for reu- 14. Valeriano VD, Parungao-Balolong MM, Kang DK. 2014. In vitro evalu- ation of the mucin-adhesion ability and probiotic potential of Lactobacil- lus mucosae LM1. J Appl Microbiol 117:485–497. http://dx.doi.org/ 10.1111/jam.12539. January/February 2015 Volume 3 Issue 1 e01350-14 Genome Announcements Genome Announcements
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The Role of Gender in Asking Questions at Cool Stars 18 and 19
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Sarah J. Schmidt,1 Stephanie Douglas,2 Natalie M. Gosnell,3 Philip S. Muirhead,4 Rachel S. Booth,5 James R. A. Davenport,6, 7 and Gregory N. Mace8 Sarah J. Schmidt,1 Stephanie Douglas,2 Natalie M. Gosnell,3 Philip S. Muirhead,4 Rachel S. Booth,5 James R. A. Davenport,6, 7 and Gregory N. Mace8 Sarah J. Schmidt,1 Stephanie Douglas,2 Natalie M. Gosnell,3 Philip S. Muirhead,4 Rachel S. Booth,5 James R. A. Davenport,6, 7 and Gregory N. Mace8 1Leibniz-Institute for Astrophysics Potsdam (AIP), An der Sternwarte 16, 14482, Potsdam, Germany 2Department of Astronomy, Columbia University, MC 5246, 550 West 120th Street, New York, NY 10027 3Department of Physics, Colorado College, 14 East Cache La Poudre St., Colorado Springs, CO 80903 4Department of Astronomy, Boston University, 725 Commonwealth Ave., Boston, MA 02215 5Astrophysics Research Centre, School of Mathematics & Physics, Queen’s University Belfast, University Road, Belfast BT7 1NN, UK 6 , 6Department of Physics & Astronomy, Western Washington University, Bellingham, WA 9822 7NSF Astronomy and Astrophysics Postdoctoral Fellow NSF Astronomy and Astrophysics Postdoctoral Fellow McDonald Observatory & The University of Texas, 2515 Speedway, Stop C1400, Austin, Te 8McDonald Observatory & The University of Texas, 2515 Speedway, Stop C1400, Austin, Texas 78712-1205 8McDonald Observatory & The University of Texas, 2515 Speedway, Stop C1400, Austin, Texas 78712-1205 Draft version April 18, 2017 Typeset using LATEX preprint2 style in AASTeX61 Draft version April 18, 2017 Typeset using LATEX preprint2 style in AASTeX61 ABSTRACT We examine the gender balance of the 18th and 19th meetings of the Cambridge Workshop on Cool Stellar Systems and the Sun (CS18 and CS19). The percent of female attendees at both meetings (31% at CS18 and 37% at CS19) was higher than the percent of women in the American Astronomical Society (25%) and the International Astronomical Union (18%). The representation of women in Cool Stars as SOC members, invited speakers, and contributed speakers was similar to or exceeded the percent of women attending the meetings. We requested that conference attendees assist in a project to collect data on the gender of astronomers asking questions after talks. Using this data, we found that men were over-represented (and women were under-represented) in the question sessions after each talk. Men asked 79% of the questions at CS18 and 75% of the questions at CS19, but were 69% and 63% of the attendees respectively. Contrary to findings from previous conferences, we did not find that the gender balance of questions was strongly affected by the session chair gender, the speaker gender, or the length of the question period. We also found that female and male speakers were asked a comparable number of questions after each talk. The contrast of these results from previous incarnations of the gender questions survey indicate that more data would be useful in understanding the factors that contribute to the gender balance of question askers. We include a preliminary set of recommendations based on this and other work on related topics, but also advocate for additional research on the demographics of conference participants. Additional data on the intersection of gender with race, seniority, sexual orientation, ability and other marginalized identities is necessary to fully address the role of gender in asking questions at conferences. sjschmidt@aip.de Schmidt & Douglas et al. 2 1. INTRODUCTION als with women as principal investigators are less likely to be highly ranked and receive valu- able telescope time (Reid 2014; Patat 2016). Science, technology, engineering, and mathe- matics (STEM) fields have long been dominated by the same group that dominates our culture at large – primarily (white, straight, able, cis-) men. ABSTRACT This is currently the case in Astronomy; The gender balance of the American Astronom- ical Society (AAS) was in 2013 reported to be 25% women and 73% men (Anderson & Ivie 2014), while the gender balance of the Inter- national Astronomical Union (IAU) is recorded to be (as of 1 March 2017) 17% women and 83% men.1 There is no one reason for the gender im- balance in Astronomy (and related fields), but some major factors include the cultural percep- tion of brilliance as a necessary yet exclusively (white) male trait (Leslie et al. 2015), the re- liance on tests like the general and physics GRE that have a documented gender imbalance (as well as a racial imbalance; Levesque et al. 2015; Miller & Stassun 2014) and the persistence of sexual harassment in the field.2 While many of these studies focus on gender (and like our work, address gender as a binary that fails to acknowledge non-binary, agender, intersex, and gender fluid people), these factors are also persistent along other divisions such as race, ability/disability, sexual orientation, gen- der identity. People who are at the intersection of multiple marginalized identities (e.g., women of color, disabled women, disabled women of color, etc.) are usually subject to multiple bar- riers. For example, the study testing the hirabil- ity of lab managers (Moss-Racusin et al. 2012) was based primarily on similar work (Bertrand & Mullainathan 2003) that found resumes with “white” names (Emily and Greg) were strongly favored compared to those with “black” names (Lakisha and Jamal). In practice, an applicant that is both female and black typically experi- ences biases for both identities. Academic conferences act as a microcosm of our field, magnifying some of the most pressing issues for inclusion in astronomy. Yet for many scientists, conferences are an extremely impor- tant opportunity to network and advertise both ourselves and our work, forming important col- laborations and making connections essential to future employment. The participation of all sci- entists in conference settings is thus necessary for an inclusive field. There are a myriad of subtle effects that work in concert with those factors to devalue and de- emphasize the work of women. 1 https://www.iau.org/administration/ membership/individual/distribution/, retrieved 2 March 2017 2 for example https://www. buzzfeed.com/azeenghorayshi/ famous-astronomer-allegedly-sexually-harassed-students, accessed14March2017 ology and Australian Space Research meeting (Casadevall & Handelsman 2014; Horner et al 2016). An announcement of a Nueroscience con ference without any women speakers prompted an initiative to track the gender of all speaker 5 CS 18 website available at http://www2.lowell. edu/workshops/coolstars18/index.html 6 CS19 website available at http://coolstars19. com/ ABSTRACT For example, faculty members reviewing resumes for lab man- agers that were identical except for the name consistently rated male applicants as more com- petent and deserving of more money (an average of $4,000 more per year) than female applicants (Moss-Racusin et al. 2012). Papers by women are cited less, both by themselves (i.e., self- citations; King et al. 2016) and others (Caplar et al. 2016), and a review of Hubble Space Tele- scope and European Southern Observatory tele- scope proposal evaluations reveals that propos- ents, The percent of women speakers is a statistic that has received significant attention, partic- ularly in instances where it is lower than the overall fraction of women in the field, as was the case in these reports from American Microbi- ology and Australian Space Research meetings (Casadevall & Handelsman 2014; Horner et al. 2016). An announcement of a Nueroscience con- ference without any women speakers prompted an initiative to track the gender of all speakers 1 https://www.iau.org/administration/ membership/individual/distribution/, retrieved 2 March 2017 2 for example https://www. buzzfeed.com/azeenghorayshi/ famous-astronomer-allegedly-sexually-harassed-students, accessed14March2017 ology and Australian Space Research meetings (Casadevall & Handelsman 2014; Horner et al. 2016). An announcement of a Nueroscience con- ference without any women speakers prompted an initiative to track the gender of all speakers Gender and Questions at Cool Stars 3 at Neuroscience conferences;3 a similar initia- tive was undertaken by the Committee on the Status of Women in Astronomy (CSWA; https: //cswa.aas.org/percent.html) between 2008 and 2013. Participation in a conference is not limited to giving a talk, however, and each con- ference interaction can be an important net- working opportunity. report on the gender balance at the last two Cool Stars meetings, including that of the or- ganizers, speakers, and attendees, as well as the reported gender of people asking questions. In Section 2, we provide more detail on the Cool Stars meetings. The sources of our data are discussed in Section 3, in Sections 4 and 5 we examine the gender of attendees who asked questions and the differences in the questions asked of female and male speakers. We provide brief resources and recommendations in Sec- tion 6. A python notebook containing most of the analysis presented below can be found on- line at https://github.com/jradavenport/ Gender-in-Astro/blob/master/analysis/ coolstars/douglas_coolstars_analysis. ipynb. After each scientific talk, a brief (2–10 minute) period is allotted for questions from the talk audience. 3 https://biaswatchneuro.com/ 4 https://github.com/jradavenport/ Gender-in-Astro ABSTRACT The main motivation for this period is to foster a public scientific interaction that is not possible in other venues, benefiting the speaker, the questioner, and the audience. Mul- tiple astronomers have noted that the question periods seemed to include more questions from men than warranted given their fractional at- tendance, and at the 2014 winter meeting of the American Astronomical Society (AAS 223), a web form was implemented to track the number of questions from men and women.4 That initial study was described in a white paper (Daven- port et al. 2014), and a similar effort was under- taken at the 2014 annual National Astronomy Meeting (NAM; Pritchard et al. 2014). Both found that the fraction of questions asked by women was lower than their attendance rate by about 10%. This is concerning, as the visibil- ity of asking questions in front of an audience is less available to women; additionally, sociolog- ical studies indicate that speaking more often and/or for longer in a group setting is linked to leadership and power (Mast 2002). 2. COOL STARS OVERVIEW The first Cool Stars meeting was a small work- shop organized at the Harvard Center for As- trophysics in Cambridge, MA in 1980, and the workshop series has continued for over 35 years. In 1993, the workshop series moved from Cam- bridge and started alternating between loca- tions in Europe and the United States. Cool Stars meetings have occurred approximately ev- ery other year since then. In the past decade, Cool Stars meetings have grown to include over 300 participants from the US, Europe, and around the world. In this proceedings, we focus on the previ- ous two Cool Stars meetings: Cool Stars 18 (CS18),5 held 8-13 June 2014 in Flagstaff, AZ and Cool Stars 19 (CS19),6 held 5-10 June 2016 in Uppsala, Sweden. Both conferences had a similar format, with a Sunday opening recep- tion, five mornings of plenary talks, and three afternoons with parallel splinter sessions (split Since the initial results from the Gender Ques- tions project, data has been taken on a variety of meetings, including the last two meetings from the series of Cambridge Workshops on Cool Stellar Systems and the Sun (known as Cool Stars meetings). In this proceedings, we Schmidt & Douglas et al. 4 into three sessions at CS18 and into four ses- sions at CS19) running in the afternoon. Ba- sic information for each Cool Stars meeting, in- cluding Scientific Organizing Committee (SOC) membership, attendees, and the speakers in each session, was available either online or upon request from the organizers. obtained a list of SOC members and the list of speakers from the conference websites of each conference, and we obtained the final partici- pant lists for each conference directly from the conference organizers. In all cases, we assigned gender at first based on name. If the name wasn’t known by our (US based) gender identifiers, a quick internet search was conducted to locate a picture of the attendee or, failing that, find a typical gender for people with that name. We recognize that this method is both imprecise and enforces a false gender binary on individuals who iden- tify as non-binary, genderfluid, intersex, agen- der, and/or in any other way not reflected by the male/female binary. Many of our results are dependent on perception of gender, so this may reflect the biases of some of the conference attendees. 3. DATA FROM COOL STARS To address the role of gender in question/answer dynamics at CS18 and CS19, we gathered data both from conference materials and from a custom-designed webform that has been im- plemented at multiple conferences. 2. COOL STARS OVERVIEW While these two conferences were similar, there were a few differences that may have af- fected gender balance of attendees and fraction of people asking questions. The location of the conference is likely a large factor; CS18 may have drawn a larger fraction of participants from the US, while CS19 drew a larger frac- tion of Europeans. The timing of the plenary sessions was different; CS18 featured slightly longer talks with shorter question periods, while CS19 focused on shorter talks with 5–10 min- utes allowed after each one. Additionally, CS18 provided stand microphones for members of the audience with questions, while CS19 had vol- unteers run microphones to each person with a raised hand. The stand microphones may deter questions from women due to their public place- ment and the pressure of standing and walking to them; microphones with runners may miti- gate that issue and are certainly an otherwise better option because mobility impaired peo- ple may have trouble accessing standing micro- phones. The results of our gender assignment are given in Table 3.1. The total number of attendees rose from 364 to 447 between CS18 and CS19, and both the total number (112 to 176) and the per- centage (31% to 37%) of women rose between the two years (as shown in Figure 1). The frac- tion of women attending both Cool Stars con- ferences is higher than the fraction of women as- tronomers; as reported above, women are 17% of IAU members and 25% of AAS members. The difference between the field-wide statis- tics and the conference attendee fraction could reflect differences in women’s representation be- tween different subfields and at different levels of seniority. Statistics on gender and subfield are difficult to find, but Reid (2014) note that during cycles 17–20 23% of Hubble proposals in the Cool Stars category came from women, com- pared to 22% overall. The combined fraction of female PIs with proposals in the cool stars, star formation, and exoplanet categories (which all participate in Cool Stars meetings to some ex- tent) was 25%. This could indicate a slightly Gender and Questions at Cool Stars 5 CS18 (Flagstaff) CS19 (Uppsala) 0 100 200 300 400 500 Number of attendees 112 176 Women Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Attendees 31% ±3% 37% ±3% Women Men Figure 1. The total number of attendees (top panel) and fraction of female attendees (bottom panel) at CS18 and CS19. The uncertainties are as- signed based on the ambiguities involved in assign- ing gender based on first names. The total number of attendees increased from CS18 to CS19, as did both the number of female attendees and the frac- tion of women. The data for this figure can be found in the first two rows of Table 3.1. CS18 (Flagstaff) CS19 (Uppsala) 0 100 200 300 400 500 Number of attendees 112 176 Women Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Attendees 31% ±3% 37% ±3% Women Men Figure 1. The total number of attendees (top panel) and fraction of female attendees (bottom panel) at CS18 and CS19. The uncertainties are as- signed based on the ambiguities involved in assign- i d b d fit Th t t l b Table 1. Conference Statistics Group Measurement CS18 CS19 Data obtained from conference materials (see Section 3.1) Attendees # total 364 477 % womena 31 ± 3 % 37 ± 3 % SOC # women 7 10 # total 20 25 % women 35% 40% Invited Plenary Speakers # women 4 7 # total 14 10 % women 29% 70% All Plenary Speakers # women 11 18 # total 29 38 % women 38% 47% Total Speakers # women 43 60 # total 113 153 % women 38% 39% Data obtained from web form (see Section 3.2) Speakers with Question Data # women 29 34 # total 76 83 % womenb 38 ± 11 % 41 ± 11 % Recorded Questions # women 46 67 # total 223 264 % womenb 21 ± 5 % 25 ± 5 % Talks With Question Data % All 67% 54% % Plenary 90% 100% % Splinter 60% 37% aUncertainties from gender-ambiguous names. b Uncertainties from binomial confidence intervals. Table 1. Conference Statistics CS18 (Flagstaff) CS19 (Uppsala) CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Attendees 31% ±3% 37% ±3% Women Men CS19 (Uppsala) CS18 (Flagstaff) CS18 (Flagstaff) Figure 1. 3.1. Conference Demographics The gender balances of organizers, attendees, and speakers (both invited and contributed) are essential to understanding both the conference as a whole and as a comparison for the fraction of women asking questions during talks. We Gender and Questions at Cool Stars Gender and Questions at Cool Stars The total number of attendees (top panel) and fraction of female attendees (bottom panel) at CS18 and CS19. The uncertainties are as- signed based on the ambiguities involved in assign- ing gender based on first names. The total number of attendees increased from CS18 to CS19, as did both the number of female attendees and the frac- tion of women. The data for this figure can be found in the first two rows of Table 3.1. b Uncertainties from binomial confidence intervals. divided into those born before and after 1980, the younger group is 40% women and the older group is 21% women. While age and seniority are not interchangeable, they are roughly corre- lated, indicating that a higher fraction of junior astronomers are women while a smaller fraction of senior astronomers are women. larger fraction of women in the Cool Stars sub- field. Scientists who focus on Cool Stars (and those who attend the meetings) could also be dispro- portionately junior. Some of the areas covered by Cool Stars have been topics of study since well before the meetings began (e.g., Solar spec- troscopy) but others have been developed more recently (e.g., brown dwarfs and exoplanets). This is notable because a newer field is typi- cally a field with more women. The 2013 AAS demographics report notes that if members are We also gathered data on the total number and percent of women among the conference Scientific Organizing Committee (SOC), the in- vited speakers, and all speakers. This data was gathered using the conference webpages, and Schmidt & Douglas et al. 6 gender was assigned using the same method as for the attendee list. speaker name, talk number, and/or session, then selecting male or female for the speaker, the session chair (at CS19 - not yet implemented at CS18), and for each person asking questions. The form (shown in Figure 2) was designed to be equally accessible from smartphones, tablets, and computers. The majority of volunteers ac- cessed the form during the question and answer portion of the talk, tapping a button as each question was asked. Each question was rep- resented by a “M” or “F” in the data; a talk with three questions asked by a man, a woman, and then a man would result in a string of “MFM.” Data submitted through the webform were automatically added to a csv file, which was cleaned by hand. Gender and Questions at Cool Stars The SOC grew from a 20 person committee planning CS18 to a 25 person committee for CS19. Both the number and fraction of women on the SOC rose between the two conferences, from 7 (35%) to 10 (40%). This rise is similar to the rise in the fraction of women attendees. The invited plenary speakers for CS18 were 29% women, while the invited plenary speakers for CS19 were 70% women. Both the SOC and the invited speakers are advertised during the reg- istration period for the conference, and as such they can have an effect on the composition of conference attendees. This is explicitly used to select the scientific focus of a conference, and is likely to also impact the conference demograph- ics. While the increase in women between CS18 and CS19 is the result of several factors, the high fraction of female SOC members and in- vited plenary speakers is likely to have played a role. At Cool Stars 18, 223 questions for 76 talks were reported, divided into 87 questions for 26 plenary talks and 136 questions for 50 talks in six splinter sessions. This includes 90% of the total plenary talks, but only 54% of the splinter talks. At Cool Stars 19, 264 ques- tions for 83 talks were reported. These were divided into 151 questions for 40 plenary talks and 113 questions for 43 talks in five splin- ter sessions. This included all plenary talks, but only 37% of splinter talks. Thirty-seven talks at Cool Stars 18 and thirty-six talks at Cool Stars 19 were reported more than once; conflicting reports are noted in the ta- ble, which can be found at https://github. com/jradavenport/Gender-in-Astro/tree/ master/data/cs18 and https://github.com/ jradavenport/Gender-in-Astro/tree/master/ data/cs19. The total number of speakers increased from 113 to 153 between CS18 and CS19, primar- ily as a result of the change from three to four concurrent afternoon parallel sessions. Overall, the fraction of women speakers was remarkably constant, rising from 38% to 39% between the two conferences. In CS18, women were over- represented as speakers compared to confer- ence attendees (38% compared to 31%) while in CS19, the fraction of women speakers was more representative of the conference demographics as a whole (39% compared to 37%). Gender and Questions at Cool Stars Because Cool Stars conference are a series (rather than conferences in isolation), it is possible that the high fraction of women speakers at CS18 en- couraged a larger fraction of women to attend CS19. Overall, women asked 21% of the questions at CS18 and 25% of the questions at CS19. The increase between the two conferences is not sta- tistically significant (as the confidence intervals are 5%). If the rise is a real effect, it may sim- ply be a reflection of the increasing percentage of women attendees (31% at CS18, and 37% at CS19). At both conferences, men asked more Gender and Questions at Cool Stars 7 CS18 (Flagstaff) CS19 (Uppsala) 0 50 100 150 200 250 300 Number of questions 46 67 Asked by Women Asked by Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Questions 21% ±5% 25% ±5% Asked by Women Asked by Men Figure 3. The total number of questions (top panel) and fraction of questions (bottom panel) asked by men and women recorded during CS18 and CS19. The overall number of questions in- creased from CS18 to CS19, as did both the number and fraction of questions asked by women. The 5% uncertainties are based on Poisson counting errors. The total fraction of questions asked by women is low compared to the percent of women attending the conference (21% compared to 31% and 25% compared to 37%). The data shown here can be found in Table 3.1. CS18 (Flagstaff) CS19 (Uppsala) 0 50 100 150 200 250 300 Number of questions 46 67 Asked by Women Asked by Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Questions 21% ±5% 25% ±5% Asked by Women Asked by Men Figure 2. The web form used for CS18 (top) and for CS19 (bottom) to gather data on the gender of the speaker, chair, and questioners. Both forms in- clude a free entry space for Talk ID, “female” and “male” buttons for Speaker Gender, and “female” and “male” buttons for Speaker Gender, and a free entry box for comments. The buttons for Speaker Gender generate a line of text that fills in a text box. The form used for CS18 does not include gen- der buttons for the session chair, while the CS19 form does. CS19 (Uppsala) CS18 (Flagstaff) CS18 (Flagstaff) Figure 3. The total number of questions (top panel) and fraction of questions (bottom panel) asked by men and women recorded during CS18 and CS19. The overall number of questions in- creased from CS18 to CS19, as did both the number and fraction of questions asked by women. The 5% uncertainties are based on Poisson counting errors. The total fraction of questions asked by women is low compared to the percent of women attending the conference (21% compared to 31% and 25% compared to 37%). The data shown here can be found in Table 3.1. Figure 2. 3.2. Gender of Questioners Participants at CS18 and CS19 were given (via twitter) an opportunity to fill out a web form first identifying the talk by inputting the Gender and Questions at Cool Stars Table 2. Talk Statistics by Chair and Speaker Gender One suggestion is that some male audi- ence members feel more strongly they need to provide comments or suggestions for the work of women that they feel they don’t need for men. These and other reasons cannot be evaluated without additional evidence. - or if they are, another factor mediates that effect. One suggestion is that some male audi- ence members feel more strongly they need to provide comments or suggestions for the work of women that they feel they don’t need for men. These and other reasons cannot be evaluated without additional evidence. 4. EXAMINING QUESTIONER GENDER There are multiple factors that may work to encourage (or discourage) questions from women (or men). A close examination of those factors may reveal certain environments that foster a more inclusive question and answer ses- sion. Here, we focus first on the genders of the speaker and the session chair and then on the number of questions in each post-talk question period. No data on session chair gender was taken dur- ing CS18, but during CS19 the gender of the chair was incorporated into the webform. We compare the number of talks, mean questions per talk, and fraction of questions from women based on speaker and chair gender, shown in Figure 5. The total number of talks with fe- male chairs (FC) and male speakers (MS) was the same as those with male chairs (MC) and ei- ther gender of speaker, but the number of talks with both female chairs and female speakers was low. The male chairs allowed a larger number of questions per talk for speakers of any gender - 3.5 compared to 2.5. Both of these results are explained in part by the plenary sessions; they had a high fraction of female speakers and long question periods, but were all chaired by men. Table 2. Talk Statistics by Chair and Speaker Gender Table 2. Talk Statistics by Chair and Speaker Gender Chair Gender Female Male Speaker Gender Female Male Female Male # of talks reported 9 24 25 25 Mean questions per talk 2.6 2.8 3.6 3.4 Questions from women 26±18% 27±11% 28±9% 21±9% astronomers typically ask questions after talks. The percent of questions from women matches more closely to the AAS membership on senior levels (21% women) than overall (30% women) or on junior levels (40% women). Seniority is not the only factor at play, how- ever. Junior astronomers do ask questions, and if they are less well known, they may be less likely to be remembered than the senior as- tronomers asking. Additionally, gender and se- niority cannot be considered as two indepen- dent factors. Research on the joint roles of se- niority and gender in volubility (Brescoll 2011) has found that men with more power/seniority speak more often than junior men, but women with more power/seniority limit themselves to speak only as often as more junior women, pri- marily due to fears that they will be perceived negatively for speaking too much. As part of their study, Brescoll (2011) also found those fears to be justified, as women are frequently penalized for talking too much. questions to male speakers came from women. At CS19 these fractions differed: 22% of ques- tions to female speakers and 28% of questions to male speakers came from women. In each case, female speakers had fewer questions from women than male speakers. This indicates that at Cool Stars meetings, women are not necessar- ily more comfortable asking questions of women - or if they are, another factor mediates that effect. One suggestion is that some male audi- ence members feel more strongly they need to provide comments or suggestions for the work of women that they feel they don’t need for men. These and other reasons cannot be evaluated without additional evidence. questions to male speakers came from women. At CS19 these fractions differed: 22% of ques- tions to female speakers and 28% of questions to male speakers came from women. In each case, female speakers had fewer questions from women than male speakers. This indicates that at Cool Stars meetings, women are not necessar- ily more comfortable asking questions of women - or if they are, another factor mediates that effect. Gender and Questions at Cool Stars The web form used for CS18 (top) and for CS19 (bottom) to gather data on the gender of the speaker, chair, and questioners. Both forms in- clude a free entry space for Talk ID, “female” and “male” buttons for Speaker Gender, and “female” and “male” buttons for Speaker Gender, and a free entry box for comments. The buttons for Speaker Gender generate a line of text that fills in a text box. The form used for CS18 does not include gen- der buttons for the session chair, while the CS19 form does. questions (and women asked fewer questions) than would be expected from their attendance rate. One of the main possibilities suggested for this effect is seniority: the gender balance of senior (faculty and equivalent) astronomers is notably different from that of junior (student and post- doctoral) astronomers. While there is no data on the question balance between junior and se- nior astronomers, many feel that that senior Schmidt & Douglas et al. 8 4.1. Speaker and Chair Gender Over- all, female speakers were asked more questions by men than male speakers. FC FS FC MS MC FS 0 5 10 15 20 25 Number of talks reported FC FS FC MS MC FS 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 Mean questions per talk FC FS FC MS MC FS 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Questions 26% ±18% 27% ±11% 28% ±9 Figure 5. The number of talks (top ber questions per talk (middle), an questions asked by women after each t for talks divided into categories base der of the chair (FC = female chair Gender and Ques CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Qs to Women 19% ±8% 22% ±8% Asked by Women Asked by Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Qs to Men 22% ±7% 28% ±7% Asked by Women Asked by Men Figure 4. The fraction of questions by women ad- dressed to female speakers (top panel) and to male speakers (bottom panel) recorded during CS18 and CS19. At CS18, women asked 19±8% of the ques- tions to women and 22±7% of the questions to men. At CS19, women asked 22±8% of the questions to women and 28±7% of the questions to men. Over- all, female speakers were asked more questions by men than male speakers. FC FS FC MS MC FS MC MS 0 5 10 15 20 25 Number of talks reported FC FS FC MS MC FS MC MS 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 Mean questions per talk FC FS FC MS MC FS MC MS 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Questions 26% ±18% 27% ±11% 28% ±9% 21% ±9% Asked by Women Asked by Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Qs to Women 19% ±8% 22% ±8% Asked by Women Asked by Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Qs to Men 22% ±7% 28% ±7% Asked by Women Asked by Men CS18 (Flagstaff) CS19 (Uppsala) Figure 4. The fraction of questions by women ad- Figure 4. The fraction of questions by women ad- dressed to female speakers (top panel) and to male speakers (bottom panel) recorded during CS18 and CS19. 4.1. Speaker and Chair Gender Women asked 27%±9% of questions in sessions chaired by a woman, while they asked 25% ± 6% of questions in ses- sions chaired by a man. The combinations of female chair and either female of male speaker yielded similar results (26% vs. 27% respec- tively) but the combination of male chair and female speaker yielded more questions from women (28%) than the combination of male chair and male speaker (21%). This difference fi FC FS FC MS MC FS MC MS 0 5 10 15 20 25 Number of talks reported FC FS FC MS MC FS MC MS 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 Mean questions per talk FC FS FC MS MC FS MC MS 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Questions 26% ±18% 27% ±11% 28% ±9% 21% ±9% Asked by Women Asked by Men Figure 5. The number of talks (top), mean num- ber questions per talk (middle), and fraction of questions asked by women after each talk (bottom), for talks divided into categories based on the gen- der of the chair (FC = female chair, MC = male chair) and the gender of the speaker (FS = female speaker, MS = male speaker). Data displayed in this Figure can be found in Table 5. port et al. (2014) found women asked 34% of the questions in sessions with a female chair and 20% of the questions in sessions with a male chair. The same effect was found at NAM (Pritchard et al. 2014), where women asked 22% of the questions in sessions chaired by women and 16% of the questions in sessions chaired by Gender and Questions at Cool Stars CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Qs to Women 19% ±8% 22% ±8% Asked by Women Asked by Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Qs to Men 22% ±7% 28% ±7% Asked by Women Asked by Men Figure 4. The fraction of questions by women ad- dressed to female speakers (top panel) and to male speakers (bottom panel) recorded during CS18 and CS19. At CS18, women asked 19±8% of the ques- tions to women and 22±7% of the questions to men. At CS19, women asked 22±8% of the questions to women and 28±7% of the questions to men. 4.1. Speaker and Chair Gender Previous results indicate that the gender of both the speaker and the chair of the session may have some effect on the number of ques- tions from women and men (Davenport et al. 2014; Pritchard et al. 2014). In Figure 4, we show the fraction of women and men who asked questions of male and female speakers. At CS18, the gender of questioners was similar; 19% of questions to female speakers and 22% of We find that the gender of the session chair has minimal impact on the fraction of ques- Gender and Questions at Cool Stars 9 ons at Cool Stars 9 FC FS FC MS MC FS MC MS 0 5 10 15 20 25 Number of talks reported FC FS FC MS MC FS MC MS 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 Mean questions per talk FC FS FC MS MC FS MC MS 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Questions 26% ±18% 27% ±11% 28% ±9% 21% ±9% Asked by Women Asked by Men Figure 5. The number of talks (top), mean num- ber questions per talk (middle), and fraction of questions asked by women after each talk (bottom), for talks divided into categories based on the gen- der of the chair (FC = female chair, MC = male chair) and the gender of the speaker (FS = female speaker, MS = male speaker). Data displayed in this Figure can be found in Table 5. Gender and Questions at Cool Stars 9 CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Qs to Women 19% ±8% 22% ±8% Asked by Women Asked by Men CS18 (Flagstaff) CS19 (Uppsala) 0.0 0.2 0.4 0.6 0.8 1.0 Fraction of Qs to Men 22% ±7% 28% ±7% Asked by Women Asked by Men Figure 4. The fraction of questions by women ad- dressed to female speakers (top panel) and to male speakers (bottom panel) recorded during CS18 and CS19. At CS18, women asked 19±8% of the ques- tions to women and 22±7% of the questions to men. At CS19, women asked 22±8% of the questions to women and 28±7% of the questions to men. Over- all, female speakers were asked more questions by men than male speakers. tions asked by women. 4.2. Total Question Number The total number of questions allowed after each talk could also be a mitigating factor in the total gender balance of question askers. During a longer question period, women who are shy or unsure of their questions may take time to gain confidence, or may realize their question is just as relevant as the others being asked. At the NAM meeting, there was a strong trend of an increasing fraction of questions from women as the total number of questions increased (see their Figure A; Pritchard et al. 2014). To test for a similar result at the Cool Stars meetings, we examined both the number and fraction of questions asked by women and men as a func- tion of the total questions recorded, shown in Figure 6. We combined data from both meet- ings to decrease the associated uncertainty due to small numbers. Figure 6. The number (top panel) and fraction (bottom panel) of questions asked by women and men at both Cool Stars meetings as a function of question order. The total number of questions de- creases with question order from ∼150 for the first question to ∼40 for the fifth through eight question. Figure 6. The number (top panel) and fraction (bottom panel) of questions asked by women and men at both Cool Stars meetings as a function of question order. The total number of questions de- creases with question order from ∼150 for the first question to ∼40 for the fifth through eight question. The fraction of questions asked by women is is be- low total mean for the first and second questions, then increases for the third and fourth questions. These variations (5–10%) are not significant com- pared to the Poisson uncertainties (10–20%). third questions asked by women still fell slightly below the mean at 22%. The cumulative frac- tion of the fourth and fifth to eighth questions asked by women was 23%. This increase in the fraction of questions asked by women mirrors the trend found by Pritchard et al. (2014), but is not significant compared to the uncertainties. Further data is needed to find if this trend is specific to conference size, type, or subfield. The mean fraction of questions asked by women for CS19 and CS19 combined was 23%, but the fraction of first questions asked by women was 21%. 4.1. Speaker and Chair Gender At CS18, women asked 19±8% of the ques- tions to women and 22±7% of the questions to men. At CS19, women asked 22±8% of the questions to women and 28±7% of the questions to men. Over- all, female speakers were asked more questions by men than male speakers. Figure 5. The number of talks (top), mean num- ber questions per talk (middle), and fraction of questions asked by women after each talk (bottom), for talks divided into categories based on the gen- der of the chair (FC = female chair, MC = male chair) and the gender of the speaker (FS = female speaker, MS = male speaker). Data displayed in this Figure can be found in Table 5. tions asked by women. Women asked 27%±9% of questions in sessions chaired by a woman, while they asked 25% ± 6% of questions in ses- sions chaired by a man. The combinations of female chair and either female of male speaker yielded similar results (26% vs. 27% respec- tively) but the combination of male chair and female speaker yielded more questions from women (28%) than the combination of male chair and male speaker (21%). This difference is not significant compared to the uncertainties, however, nor is it as strong as the differences found in previous work. At AAS 223, Daven- port et al. (2014) found women asked 34% of the questions in sessions with a female chair and 20% of the questions in sessions with a male chair. The same effect was found at NAM (Pritchard et al. 2014), where women asked 22% of the questions in sessions chaired by women and 16% of the questions in sessions chaired by men. port et al. (2014) found women asked 34% of the questions in sessions with a female chair and 20% of the questions in sessions with a male chair. The same effect was found at NAM (Pritchard et al. 2014), where women asked 22% of the questions in sessions chaired by women and 16% of the questions in sessions chaired by men. Schmidt & Douglas et al. 4.1. Speaker and Chair Gender 10 1 2 3 4 5-8 0 20 40 60 80 100 120 140 Number of questions Asked by Women Asked by Men 1 2 3 4 5-8 Question number 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 Fraction of Qs Asked by Women Just that position Cumulative fraction Conference Mean Figure 6. The number (top panel) and fraction (bottom panel) of questions asked by women and men at both Cool Stars meetings as a function of question order. The total number of questions de- creases with question order from ∼150 for the first question to ∼40 for the fifth through eight question. The fraction of questions asked by women is is be- low total mean for the first and second questions, then increases for the third and fourth questions. These variations (5–10%) are not significant com- pared to the Poisson uncertainties (10–20%). 1 2 3 4 5-8 0 20 40 60 80 100 120 140 Number of questions Asked by Women Asked by Men 1 2 3 4 5-8 Question number 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 Fraction of Qs Asked by Women Just that position Cumulative fraction Conference Mean It’s unclear why chair gender would have less impact at Cool Stars when the discrepancy was pronounced at both AAS 223 and NAM. Each of these meetings was a different size, and the community in attendance could be expected to have a different set of relationships. Because Cool Stars is restricted to a single subfield, it is perhaps more likely that the attendees are al- ready familiar with the topic, the speaker, and the chair - a factor that could mitigate gender differences. The splinter sessions were also or- ganized by small committees that typically in- cluded at least one woman; that could miti- gate the effect of a male chair on questions from women. Gathering data from a wide variety of meetings may provide additional insights into this discrepancy. 4.2. Total Question Number The fraction of second ques- tions asked by women was similar (21%), but the fraction of third questions asked by women was 28%. The cumulative fraction of the first to Gender and Questions at Cool Stars 11 0 1 2 3 4 5 6 Number of questions per talk 0 5 10 15 20 Number of talks at CS18 (Flagstaff) 2.6 3.4 Women Men 0 1 2 3 4 5 6 Number of questions per talk 0 2 4 6 8 10 12 14 Number of talks at CS19 (Uppsala) 3.2 3.2 Figure 7. The number of talks where a specific number of questions were asked at CS18 (top) and CS19 (bottom). The data for male (blue) and fe- male (green) speakers are separated, and the mean number of questions per talk for each group is also shown (dashed line). At CS18, men were asked on average one less question then women (2.6 com- pared to 3 4 questions per talk) while as CS19 men 5. QUESTIONS FOR MALE OR FEMALE SPEAKERS 0 1 2 3 4 5 6 Number of questions per talk 0 5 10 15 20 Number of talks at CS18 (Flagstaff) 2.6 3.4 Women Men In addition to quantifying the number and percentage of questions asked by women, we can also use the question data to examine the different numbers and percentages of questions asked the male and female speakers. Figure 7 shows the distribution in the number of ques- tions asked to male and female speakers at both CS18 and CS19. At CS18, men were asked an average of 2.6 questions compared to 3.4 asked to women. Though that is nearly one more question per talk, the difference is not signifi- cant compared to the Poisson uncertainties on the fraction. At CS19, men and women were both asked 3.2 questions on average. 0 1 2 3 4 5 6 Number of questions per talk 0 2 4 6 8 10 12 14 Number of talks at CS19 (Uppsala) 3.2 3.2 While there is no significant difference in the number of questions asked men and women, there are a variety of competing factors that could influence these numbers. A large number of questions could be the result of an interesting, stimulating talk that is generally admired, or a similarly excellent talk that inspires “grilling” from the community. A small number of ques- tions could indicate an unusually clear talk, a talk that was difficult for the majority of the audience to understand, or simply a short ques- tion period. Further classification of the types of questions asked could clarify some of these differences. Number of questions per talk Figure 7. The number of talks where a specific number of questions were asked at CS18 (top) and CS19 (bottom). The data for male (blue) and fe- male (green) speakers are separated, and the mean number of questions per talk for each group is also shown (dashed line). At CS18, men were asked on average one less question then women (2.6 com- pared to 3.4 questions per talk), while as CS19 men and women were asked an equal number of ques- tions (3.2 questions per talk). 6. CONCLUSIONS The last two Cool Stars meetings, CS18 and CS19, included a fraction of female attendees (31% and 37%) larger than that of the astro- nomical field as a whole (27% from the AAS, 17% from the IAU). This could be in part due to the contributions from more junior astronomers, a demographic that has a fraction of women closer to 40%. It is also likely to depend on the fraction of female SOC members (35% and 40%) and invited plenary speakers (38% and 70%), as those are listed on the website before registration is completed. The total fraction of female speakers (38% and 39%) was higher than the fraction of female attendees at both meet- ings, though at CS19 the fractions were closer to equal. Schmidt & Douglas et al. 12 Despite an relatively high overall fraction of women involved in the two meetings, the frac- tion of questions asked by women was low (21% and 25%) compared to the fraction of female at- tendees. The difference between the fraction of women attending the conference and the frac- tion of questions asked by women (31% com- pared to 21% for CS18; 37% compared to 25% for CS19) is in line with the findings from pre- vious results from the AAS and NAM meetings (Davenport et al. 2014; Pritchard et al. 2014). cause the act of collecting data and advertis- ing the project raises awareness that there are strong differences in the participation of men and women in the public forum of a question and answer session. And last, we recommend that the community works to encourage and respect different forms of interaction in addition to the public question forum. Often, the twitter feed of a conference contains not only summaries of the conference talks, but also an array of questions that can be answered in real time by our fellow astron- omy tweeps. We should aim to work in a sci- entific community where each scientist can in- teract and be visible in the ways that are more comfortable and familiar than the public forum of a conference stage. The results from the AAS and NAM meet- ings show strong dependencies of the fraction of questions asked by women on the gender of the speaker and chair as well as on the total num- ber of questions asked. 7 http://arementalkingtoomuch.com/; https:// github.com/cathydeng/are-men-talking-too-much 6. CONCLUSIONS The data from the Cool Stars meetings do not reproduce these differ- ences, indicating that they may not be consis- tent across different meetings sizes and/or sub- fields. We also examined the number of ques- tions asked to male and female speakers, finding that they were nearly the same at CS18 and ex- actly the same at CS19. 6.2. Future Work There are (at least) two ways the current project fails to reflect the astronomical commu- nity. The current incarnation of the survey re- inforces a false gender binary (through the “M” and “F” buttons), further marginalizing people who identify as non-binary, genderfluid, inter- sex, agender, and/or in any other way not cov- ered by those two labels. A third button was considered, but was not implemented because it is unclear that it would be appropriately used by those collecting data. If the questioner has not self-identified to the person recording the data, there would likely be a hesitancy to iden- tify someone as non-binary, with a high chance of misgendering that person. Another strat- egy could be to use a similar strategy as the “Are Men Talking Too Much” site7, which uses “dude” and “not a dude” as the gender classi- fiers. Input on these ideas is welcomed by the authors and can be implemented in future iter- ations of the survey. Gender and Questions at Cool Stars 13 The current incarnation of a survey also fails to recognize intersectionality. Men, women, and non-binary people are not monolithic groups that have the same axes of privilege and op- pression, but are instead made up of a col- lection of people that can be further divided on race/ethnicity, disability, sexual orientation, economic background, culture, national origin, age, and seniority. Each of these factors de- termine not only whether a person is more or less likely to ask a question, but also whether they may be attending the conference in the first place. The proper way to address each classifi- cation is to request that conference participants self-identify, then track questions by name, later matching to demographic data. That undertak- ing would likely require the support of trained sociologists. The authors wish to thank the organizers and sponsors of the Cool Stars 19 Hackathon & Col- laborative Writing Day. Thanks to Gerard Van Belle for providing data from CS18, including a list of attendees. We have made use of the Figure 8. Current implementation of the web form for the ongoing gender in questions project. The majority of the form is the same as those in Fig- ure 2, but buttons are added to capture feedback on whether the audience response is in the form of a question or a comment. A combination of form responses (in the free response box) and feedback from conference at- tendees indicated that some audience members would make a comment instead of a question. Some additionally noted a pattern of men com- menting on the work of women, while male speakers were instead asked questions. If this trend bears out, it could represent a devaluing of the work presented by female speakers i.e., men are trusted to be the experts in their topic, while women are given “advice” or “tips” by a commenter who believes they are the expert. To gather data on this phenomenon, we have imple- mented an updated web form that has separate buttons for “question” and “comment” (shown in Figure 8). The webform was implemented at the January 2016 AAS meeting (AAS 229) but results have not yet been examined. Figure 8. Current implementation of the web form for the ongoing gender in questions project. 9 ADAPTED FROM HTTPS://GITHUB.COM/JRADAVENPORT/GENDER-IN-ASTRO/WIKI/DRAFT-OF-BEST-PRACTICES, A LIVE VERSION OF THIS DOCUMENT. 6.1. Recommendations Due to the lack of correlations between the fraction of questions asked by women and any other examined variable, we have no rec- ommendations based solely on the data for the Cool Stars meetings. As part of this Cool Stars hack day project, we compiled a list of recommendations based on the re- sults of Davenport et al. (2014) and Pritchard et al. (2014), as well as from other sources. A static version of this document is con- tained in Appendix A and a live editable document is available at https://github. com/jradavenport/Gender-in-Astro/wiki/ Draft-of-Best-Practices. We also recommend that further data be col- lected on the gender questions project. This is not only to work towards a better understand- ing of the trends and patterns and their dif- ferences across many conferences, but also be- Gender and Questions at Cool Stars Gender and Questions at Cool Stars The majority of the form is the same as those in Fig- ure 2, but buttons are added to capture feedback on whether the audience response is in the form of a question or a comment. Astropy package (Astropy Collaboration et al. 2013) in our analysis. Astropy package (Astropy Collaboration et al. 2013) in our analysis. A.1. For Conference Organizers Studies indicate that Q&A balance is related to SOC, speaker, chair and attendee balance (Pritchard et al. 2014; Horner et al. 2016). The first step for the conference organizers is to ensure balance when assembling in the SOC. In that case, it is useful to have the demographics of your community. The AAS is 25% women and 73% men (Anderson & Ivie 2014), while the gender balance of the International Astronomical Union (IAU) is recorded to be (as of 1 March 2017) 17% women and 83% men.10 Note that some subfields have a larger representation of women and an SOC drawn from those communities should have a larger representation of women. There is significant material elsewhere on how to achieve speaker gender balance. One good exam- ple is “Ten Simple Rules to Achieve Conference Speaker Gender Balance” (http://www.ncbi.nlm. nih.gov/pmc/articles/PMC4238945/). Scheduling should also include significant time for question sessions, as the fraction of women asking questions increases with the number of questions allowed. If the conference includes independently organized splinter sessions, gender balance should be en- couraged and enforced among the organizers, and they should be made aware of these or similar guidelines. Pritchard et al. (2014) recommends addressing equity directly in a plenary talk during the con- ference. We suggest having this early in a conference, perhaps even in the conference opening, so that more people are exposed to the talk. Certainly this would be a good time to also mention the conference’s code of conduct and standards for behavior. A. BEST PRACTICES FOR ACHIEVING Q&A BALANCE9 Unlike a private interaction during a coffee break, the question and answer (Q&A) interaction that follows a scientific talk is public, so there is the opportunity for everyone in the audience to learn Schmidt & Douglas et al. 14 from a question. There is also the opportunity for discussion, wherein another questioner comments on an exchange between a previous questioner and the speaker. Ultimately the goal is for everyone to learn something from the Q&A interaction, not just the speaker and the questioner. In that case, it is important that we balance our Q&A sessions to not only reflect the ideas and opinions for the most vocal and/or senior people, but to actively engage a broad range of individuals and ideas in our community. This document focuses on gender and seniority because they are two of the most observable dif- ferences in our community and divide it into multiple large groups, but the ultimate goal is to have a conference and Q&A session balance that reflects the underlying community and encourages contributions from marginalized groups. We welcome additional input on this topic. • Moderating Discussion – Do not allow questions to become speeches. Interrupt questioners who talk for a long time to request they shorten or end their time. Some example interventions include: “Perhaps this is better for the coffee break.” or “Apologies, but for the sake of time can you ask your question?” – It is important to keep each Q&A to time; do not continue to call on people when the time is up. • After each talk: – Be strict on time. Use a timer and alarm, and move towards speakers who continue talking after their time is up. If a speaker goes over, penalize their Q&A time, not other speakers. – Be strict on time. Use a timer and alarm, and move towards speakers who continue talking after their time is up. If a speaker goes over, penalize their Q&A time, not other speakers. – Ask specifically for questions, rather than “questions and comments.” Comments often change the topic and tone of the conversation. – Do not begin the Q&A session with making a comment of your own, and reserve your question for the end (or ask in the absence of other questions). – Do not begin the Q&A session with making a comment of your own, and reserve your question for the end (or ask in the absence of other questions). – Ask for names and affiliations of individuals who ask questions (for recording purposes). – Do not immediately select the first hand to go up. Wait a few seconds to see if other hands go up, and take note of the balance. Priority should be given to women, junior scientists, and otherwise underrepresented individuals. – Aim for a total of 4–8 questions per talk, because at that point otherwise reticent ques- tioners may be willing to raise their hands. • Moderating Discussion • Moderating Discussion A.2. Session Chairs The biggest responsibility for Q&A balance falls on session chairs because they shape the discussion. The session chairs should ideally be trained in person on some of the below guidelines and practices. If that is not possible, a list of guidelines should be supplied similar to the ones below. • At the beginning of the session: – The chair can specifically encourage junior scientists to ask questions and prepares senior people for not being called on immediately or at all. For example, “There are many junior scientists in this session. I would like to encourage you to ask questions during the Q&As.” – Set up expectations for keeping talks to time so the question session does not become shortened. 10 https://www.iau.org/administration/membership/individual/distribution/, retrieved 2 March 2017 Gender and Questions at Cool Stars 15 – Reinforce conference guidelines for accessibility (especially microphone use and leaving aisles clear). – Reinforce conference guidelines for accessibility (especially microphone use and leaving aisles clear). – Reinforce conference guidelines for accessibility (especially microphone use and leaving aisles clear). – Reinforce conference guidelines for accessibility (especially microphone use and leaving aisles clear). • After each talk: REFERENCES Anderson, G., & Ivie, R. 2014, Demographics Survey of 2013 US AAS Members Summary Results, https: Horner, J., Gorman, A., Cairns, A., & Short, W. 2016, ArXiv e-prints, arXiv:1605.01498 [astro-ph.IM] C C S Anderson, G., & Ivie, R. 2014, Demographics Survey of 2013 US AAS Members Summary Results, https: //aas.org/files/resources/aas_members_ workforce_survey_final_jan2014v2.pdf Horner, J., Gorman, A., Cairns, A., & Short, W. 2016, ArXiv e-prints, arXiv:1605.01498 [astro-ph.IM] King, M. M., Bergstrom, C. T., Correll, S. J., Jacquet, J., & West, J. D. 2016, ArXiv e-prints, Xi 1607 00376 [ h i h] Horner, J., Gorman, A., Cairns, A., & Short, W. 2016, ArXiv e-prints, arXiv:1605.01498 [astro-ph.IM] Anderson, G., & Ivie, R. 2014, Demographics Survey of 2013 US AAS Members Summary Results, https: //aas.org/files/resources/aas_members_ workforce_survey_final_jan2014v2.pdf King, M. M., Bergstrom, C. T., Correll, S. J., Jacquet, J., & West, J. D. 2016, ArXiv e-prints, arXiv:1607.00376 [physics.soc-ph] Astropy Collaboration, Robitaille, T. P., Tollerud, E. J., et al. 2013, A&A, 558, A33 Astropy Collaboration, Robitaille, T. P., Tollerud, E. J., et al. 2013, A&A, 558, A33 Leslie, S.-J., Cimpian, A., Meyer, M., & Freeland, E. 2015, Science, 347, 262 Leslie, S.-J., Cimpian, A., Meyer, M., & Freeland, E. 2015, Science, 347, 262 Bertrand, M., & Mullainathan, S. 2003, Are Emily and Greg More Employable than Lakisha and Jamal? A Field Experiment on Labor Market Discrimination, Working Paper 9873, National Bureau of Economic Research Bertrand, M., & Mullainathan, S. 2003, Are Emily and Greg More Employable than Lakisha and Jamal? A Field Experiment on Labor Market Discrimination, Working Paper 9873, National Bureau of Economic Research Levesque, E. M., Bezanson, R., & Trembla 2015, ArXiv e-prints, arXiv:1512.03709 [physics.ed-ph] Mast, M. S. 2002, Human Communication Research, 28, 420 Mast, M. S. 2002, Human Communication Research, 28, 420 Brescoll, V. L. 2011, Administrative Science Quarterly, 56, 622 Brescoll, V. L. 2011, Administrative Science Quarterly, 56, 622 Moss-Racusin, C. A., Dovidio, J. F., Brescoll, V. L., Graham, M. J., & Handelsman, J. 2012, Proceedings of the National Academy of Sciences, http://www.pnas.org/content/early/2012/09/14/1211286 Caplar, N., Tacchella, S., & Birrer, S. 2016, ArXiv e-prints, arXiv:1610.08984 [astro-ph.IM] Casadevall, A., & Handelsman, J. 2014, mBio, 5, http://mbio.asm.org/content/5/1/e00846- 13.full.pdf+html // / / / / / / Patat, F. 2016, The Messenger, 165, 2 Pritchard, J., Masters, K., Allen, J., et al. 2014, Astronomy and Geophysics, 55, 6.8 Pritchard, J., Masters, K., Allen, J., et al. 2014, Astronomy and Geophysics, 55, 6.8 Davenport, J. R. A.3. For Question Askers The people who ask questions at conferences can also contribute to a more fair and equitable conference question session. Some evidence indicates that if a women asks the first question, more women are likely to ask the subsequent questions (Pritchard et al. 2014). If you are a woman and/or an otherwise under-represented individual with a question, asking it can not only bring your ideas into the conversation but also encourage others to do the same. Conversely, (primarily male) participants who ask many questions should be conscious of the need to “share the air” with other attendees. Assuming the Cool Stars meeting talks with data were a representative set, we calculate that there were 332 total questions asked at CS18 and 487 at CS19. Given the number of attendees (364 and 477 respectively), that equates to 0.9 and 1 question asked per conference. Naturally, some people ask more and others none at all, but conference attendees who ask more than a few questions should be particularly conscious of asking questions that are of general interest and occasionally holding back to allow others time to participate. There will always be times when an audience member disagrees with the speaker about some scientific question. Even if that is the case, the best questions are both civil and concise and should be limited to information that could be generally useful to the community. One article on asking Schmidt & Douglas et al. 16 good questions11 recommends that you should “Register your dissent and the reasoning behind it without taking up too much time (or unleashing strong emotions). If your point is widely shared in the room, you wont need to labour it; if it is not, a lengthy intervention will not win you many converts. You can always discuss your issues after the session.” 11 https://www.theguardian.com/higher-education-network/2015/nov/11/dont-be-a-conference-troll-a-guide-to- 11 https://www.theguardian.com/higher-education-network/2015/nov/11/dont-be-a REFERENCES A., Fouesneau, M., Grand, E., et al. 2014, ArXiv e-prints, arXiv:1403.3091 [physics.soc-ph] Reid, I. N. 2014, PASP, 126, 923 Miller, C., & Stassun, K. 2014, Nature, 510, 303
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Sediment and carbon deposition vary among vegetation assemblages in a coastal salt marsh Jeffrey J. Kelleway1,2, Neil Saintilan2, Peter I. Macreadie1,3, Jeffrey A. Baldock4, and Peter J. Ralph1 1Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia 2Department of Environmental Sciences, Macquarie University, Sydney, NSW 2109, Australia 3School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Victoria 3216, Australia 4CSIRO Agriculture and Food, Glen Osmond, SA 5064, Australia Correspondence to: Jeffrey J. Kelleway (jeffrey.kelleway@mq.edu.au) Received: 19 January 2017 – Discussion started: 3 February 2017 Revised: 15 June 2017 – Accepted: 10 July 2017 – Published: 17 August 2017 Received: 19 January 2017 – Discussion started: 3 February 2017 Revised: 15 June 2017 – Accepted: 10 July 2017 – Published: 17 August 2017 Elemental (C : N), isotopic (δ13C), mid-infrared (MIR) and 13C nuclear magnetic resonance (NMR) analyses re- vealed little difference in either the source or character of materials being deposited among neap versus spring tidal periods. Instead, these analyses point to substantial redistri- bution of materials within the Sarcocornia and Sporobolus assemblages, compared to high retention and preservation of organic inputs in the Juncus assemblage. By combining medium-term accretion quantification with short-term depo- sition measurements and chemical analyses, we have gained novel insights into above-ground biophysical processes that may explain previously observed regional differences in sur- face dynamics among key salt marsh vegetation assemblages. Our results suggest that Sarcocornia and Sporobolus assem- blages may be particularly susceptible to changes in sea level, though quantification of below-ground processes (e.g. root production, compaction) is needed to confirm this. Abstract. Coastal salt marshes are dynamic, intertidal ecosystems that are increasingly being recognised for their contributions to ecosystem services, including carbon (C) accumulation and storage. The survival of salt marshes and their capacity to store C under rising sea levels, however, is partially reliant upon sedimentation rates and influenced by a combination of physical and biological factors. In this study, we use several complementary methods to assess short-term (days) deposition and medium-term (months) accretion dy- namics within a single marsh that contains three salt marsh vegetation types common throughout southeastern (SE) Aus- tralia. We found that surface accretion varies among vegeta- tion assemblages, with medium-term (19 months) bulk ac- cretion rates in the upper marsh rush (Juncus) assem- blage (1.74 ± 0.13 mm yr−1) consistently in excess of esti- mated local sea-level rise (1.15 mm yr−1). Sediment and carbon deposition vary among vegetation assemblages in a coastal salt marsh Accretion rates were lower and less consistent in both the succulent (Sarcocornia, 0.78 ± 0.18 mm yr−1) and grass (Sporobo- lus, 0.88 ± 0.22 mm yr−1) assemblages located lower in the tidal frame. Short-term (6 days) experiments showed deposition within Juncus plots to be dominated by au- tochthonous organic inputs with C deposition rates rang- ing from 1.14 ± 0.41 mg C cm−2 d−1 (neap tidal period) to 2.37 ± 0.44 mg C cm−2 d−1 (spring tidal period), while minerogenic inputs and lower C deposition dominated Sar- cocornia (0.10 ± 0.02 to 0.62 ± 0.08 mg C cm−2 d−1) and Sporobolus (0.17 ± 0.04 to 0.40 ± 0.07 mg C cm−2 d−1) as- semblages. Biogeosciences, 14, 3763–3779, 2017 https://doi.org/10.5194/bg-14-3763-2017 © Author(s) 2017. This work is distributed under the Creative Commons Attribution 3.0 License. Biogeosciences, 14, 3763–3779, 2017 https://doi.org/10.5194/bg-14-3763-2017 © Author(s) 2017. This work is distributed under the Creative Commons Attribution 3.0 License. 1.1 Coastal salt marshes Coastal salt marshes are dynamic ecosystems, vegetated by herbs, grasses and rushes, that are found in a range of sedi- mentary settings along low-energy coastlines. Globally, veg- etation type and floristic assemblage have been used to clas- sify general types of salt marsh (Adam, 1990, 2002). On the local scale, vegetation zonation is one of the most striking ecological features of many salt marshes, reflecting the ele- J. J. Kelleway et al.: Salt marsh surface deposition 3764 vation requirements of a small number of dominant species, although mosaics of species within a zone are also com- mon (Adam, 2002; Hickey and Bruce, 2010). Whilst the bio- diversity values and exceptionally high productivity of salt marshes have long been recognised, increasing attention is now being focused upon ecosystem services such as carbon (C) accumulation and storage (Chmura et al., 2003; Duarte et al., 2013) and the response of these coastal ecosystems to changes in climate (Kirwan and Mudd, 2012) and sea level (Rogers et al., 2014). coastal ecosystems, with a mean ± standard error (SE) accu- mulation rate of 0.024 ± 0.003 g C cm−2 yr−1 (Ouyang and Lee, 2014). While much of this OM is produced below- ground by roots and rhizomes, contributions from above- ground sources may be significant (Boschker et al., 1999; Zhou et al., 2006). Sources of above-ground C may include both autochthonous (produced within the community) and al- lochthonous (deposited from outside the community) OM, although their relative contributions may vary within and among salt marsh settings (Kelleway et al., 2016a). The con- tribution of C redistributed within the community (i.e. within and among different species assemblages) to surface depo- sition and longer-term C accumulation remains unquantified and may vary with vegetation structure and geomorphic po- sition. Regardless of OM source, the capacity of salt marshes to store carbon in the long-term remains dependent upon the balance between OM input and its decay (Mueller et al., 2016). While there is considerable debate as to which fac- tors most influence the long-term retention of C in soils, litter quality has long been identified as a key driver of decay rates (Cleveland et al., 2014; Enríquez et al., 1993; Hemminga and Buth, 1991; Josselyn and Mathieson, 1980; Kristensen, 1994) and is of particular relevance to C stock accumulation in surface soils. Sedimentation dynamics partially determine the survival of salt marshes under rising sea level (Baustian et al., 2012; Kirwan and Megonigal, 2013; Kirwan et al., 2016) and the delivery and storage of organic matter (OM; Duarte et al., 2013; Lovelock et al., 2013). Salt marsh soils may be minero- genic (dominated by mineral inputs) or organogenic (domi- nated by biomass and litter production and/or allochthonous OM inputs), although most comprise both mineral and or- ganic fractions (Adam, 2002; Baustian et al., 2012). 1.3 Measuring surface deposition and accretion A variety of methods have been developed for measuring and monitoring surface dynamics in tidal wetlands (for re- views see Nolte et al., 2013; Thomas and Ridd, 2004). These include techniques relevant to short-term deposition events (of sediments and plant litter) through to medium- and long- term measures of accretion or accumulation (the net effect of multiple deposition and removal events) as well as surface elevation change. Because methods vary in their effective- ness of trapping and retaining different materials, a combi- nation of techniques may be required to identify the differ- ent physical and biotic influences on deposition and accretion (Nolte et al., 2013). In this study, we combine several meth- ods to assess short-term (days) deposition and medium-term (months) accretion dynamics within three salt marsh vegeta- tion assemblages common throughout SE Australia. Our aim is to use three different measurement methods to identify the role of vegetation and physical factors in surface deposition and/or accretion. We hypothesise that (1) mineral deposition and accretion will be highest in lower-elevation assemblages but organic deposition and accretion will be highest in the Juncus assemblage; (2) the source and character of material deposited will vary temporally according to tidal inundation patterns, with a greater proportion of allochthonous mate- rial deposited during times of high inundation frequency; and (3) there will be no difference in biomass–litter–sediment de- cay patterns among the vegetation assemblages. Together, we expect this information will improve our understanding of how materials (including C) are deposited and accumulate in Numerous studies have investigated the interactions be- tween vegetation and marsh surface dynamics (Langley et al., 2009; Rooth et al., 2003), although the majority of these stud- ies have focussed on the genus Spartina (e.g. Baustian et al., 2012; Mudd et al., 2010, 2009; Nyman et al., 2006). Gener- ally, these studies have shown that the presence of vegetation may have a significant positive influence on surface accretion through (1) accumulating organic matter and (2) facilitating sediment trapping (Morris et al., 2002; Mudd et al., 2010; Nyman et al., 2006). Findings of comparative studies of the effect of vegetation composition on deposition rates, how- ever, vary from no difference in accretion among different vegetation species (e.g. Culberson et al., 2004) to substan- tial differences among mangroves and different salt marsh species (e.g. Saintilan et al., 2013). J. J. Kelleway et al.: Salt marsh surface deposition Conse- quently, soil properties and surface dynamics may be influ- enced by both physicochemical and biological factors. Phys- ical drivers of accretion (the vertical accumulation of sedi- ments) in intertidal wetlands include the suspended sediment supply of inundating waters (Zhou et al., 2007), the tidal range of a site and position within the tidal range (Ouyang and Lee, 2014; Saintilan et al., 2013; van Proosdij et al., 2006). High tides may play an important role in importing sediment into salt marshes (Rosencranz et al., 2016), while low-tide rainfall may act to redistribute or export materials, including particulate organic carbon (Chen et al., 2015). 1.3 Measuring surface deposition and accretion Little is known about the extent to which surface materials are redistributed among neighbouring salt marsh species assemblages, though stable isotope approaches have been used to demonstrate the small- scale (i.e. a few metres) movement of OM at mangrove–salt marsh interfaces (Guest et al., 2004, 2006). Published by Copernicus Publications on behalf of the European Geosciences Union. Published by Copernicus Publications on behalf of the European Geosciences Union. Published by Copernicus Publications on behalf of the European Geosciences Union. J. J. Kelleway et al.: Salt marsh surface deposition www.biogeosciences.net/14/3763/2017/ J. J. Kelleway et al.: Salt marsh surface deposition J. J. Kelleway et al.: Salt marsh surface deposition Figure 1. Location of experimental plots within Weeney Bay salt marsh of Towra Point Nature Reserve (a), located along the southern shoreline of Botany Bay (b) in SE Aus- tralia (c). Location of the nearest tidal gauge is marked by an X in inset B. SARC = Sarcocornia quinqueflora assemblage; SPOR = Sporobolus virginicus assemblage; JUNC = Juncus kraus- sii assemblage. The salt marsh within this site comprises two broad vege- tation communities. The lower and middle marsh is charac- terised by an association of the perennial succulent Sarcocor- nia quinqueflora (C3 photosynthetic pathway) and the peren- nial grass Sporobolus virginicus (C4 photosynthetic path- way). The upper marsh assemblage is dominated by the rush Juncus kraussii (C3), with S. virginicus (C4) ubiquitous as a subdominant lower stratum across this assemblage. On the basis of salt marsh vegetation zonation, 15 plots were selected – five plots randomly chosen within the Juncus-dominated assemblage and 10 plots strategically se- lected within the Sarcocornia–Sporobolus association (five plots vegetated exclusively by Sarcocornia, and five vege- tated exclusively by Sporobolus). Hereafter, these three as- semblages are referred to by genus (Sarcocornia, Sporobo- lus, Juncus), while reference to the plant species themselves involves the species name (S. quinqueflora, S. virginicus, J. kraussii). Figure 1. Location of experimental plots within Weeney Bay salt marsh of Towra Point Nature Reserve (a), located along the southern shoreline of Botany Bay (b) in SE Aus- tralia (c). Location of the nearest tidal gauge is marked by an X in inset B. SARC = Sarcocornia quinqueflora assemblage; SPOR = Sporobolus virginicus assemblage; JUNC = Juncus kraus- sii assemblage. Data previously collected within the study region showed a substantial difference in above-ground biomass of the rush assemblage (Juncus mean = 1116 g DW m−2; range = 51– 4832 g DW m−2), compared to that of the non-rush assem- blages (Sarcocornia mean = 320 g DW m−2, range = 52– 1184 g DW m−2; Sporobolus mean = 350 g DW m−2, range = 148–852 g DW m−2). Moreover, there do not appear to be distinct seasonal patterns of biomass stock for any of these species (Clarke and Jacoby, 1994). Both Sarcocornia and Sporobolus are perennial species, while J. kraussii culms undergo initiation and senescence throughout the year, but with peak culm initiation before and after summer flowering and fruiting (Clarke and Jacoby, 1994). J. J. Kelleway et al.: Salt marsh surface deposition Below-ground biomass data are rare, though on the basis of 0–20 cm depth data presented by Clarke and Jacoby (1994) we have calculated a mean above-ground : below-ground biomass ratio of 1.5 for Juncus. No below-ground data have been reported for either Sarcocornia and Sporobolus. coastal wetlands and how these ecosystems might respond under rising sea levels. 2.1 Study setting Broadly, the salt marshes of SE Australia have been classi- fied within the temperate group of salt marshes, which also includes those of Europe, the Pacific coast of North Amer- ica, Japan and South Africa (Adam, 1990). These are distinct from the well-studied Spartina-dominated marshes of North America’s Atlantic coast. Towra Point Nature Reserve is lo- cated within the oceanic embayment Botany Bay, approx- imately 16 km south of central Sydney, Australia’s largest city. The intertidal estuarine wetland complex at this site is the largest remaining within the Sydney region and is listed as a Ramsar Wetland of International Importance. Within the site, a large salt marsh area adjacent to Weeney Bay was cho- sen as a study site as this area exhibits vegetation zonation typical of SE Australian salt marshes (Fig. 1). The lower salt marsh is bordered by the mangrove species Avicennia ma- rina, beyond which seagrass meadows (including Posidonia australis) occur within the subtidal zone. In some areas, the upslope limit of the salt marsh extends into small patches of the supratidal trees Casuarina glauca and Melaleuca ericifo- lia, but for the most part the salt marsh is bordered by a levee, which was constructed between 1947 and 1951. Previous in- vestigation has revealed vegetation zonation across the site coinciding with ranges in elevation and tidal extent (Hickey and Bruce, 2010). Tides along the New South Wales coast are semidiurnal (two flood and two ebb periods each lunar day) with a max- imum spring tidal range of 2.0 m (Roy et al., 2001). Astro- nomical (i.e. predicted) maxima occur during the new moon in summer and during the full moon in winter (spring tides). Tidal inundation of and recession from the study area oc- curs via Weeney Bay, with the causeway acting as a barrier to surface water exchange with the western section of the Nature Reserve and Woolooware Bay. The linear rate of sea- level rise in Botany Bay since local records commenced in 1981 is 1.15 mm yr−1 (Kelleway et al., 2016b). Rainfall in the region is spread throughout the year, with an annual rain- fall of 1084 mm yr−1 in Botany Bay (Bureau of Meteorology, 2016). 1.2 C storage Average global rates of soil carbon accumulation is ex- tremely high in salt marshes, relative to most terrestrial and Biogeosciences, 14, 3763–3779, 2017 www.biogeosciences.net/14/3763/2017/ www.biogeosciences.net/14/3763/2017/ 3765 2.2 Surface elevation measurements Plot elevation was recorded to assess relationships between deposition dynamics and plot position within the tidal frame. Biogeosciences, 14, 3763–3779, 2017 2.3 Feldspar marker horizons The feldspar marker horizon (MH) technique (Cahoon and Turner, 1989) has been proposed as a suitable method to investigate the effects of above-ground vegetation structure on the accretion (vertical accumulation) of material on the marsh surface over the medium term (Nolte et al., 2013). The feldspar MH technique was used to record the amount of ac- cretion of bulk materials at each plot on the temporal scale of multiple months. A total of 45 feldspar MHs were installed across the study site on 23 January 2014, comprising three replicates in each of the 15 study plots. Accretion was de- termined at later dates as the height difference between the marsh surface and the feldspar (i.e. the material accumulated above the MH) and was recorded as the mean of three repli- cate measurements from within the marker horizon at each sampling event. Measurements were taken 11, 13, 15, 17 and 19 months after installation. During the later sampling events, many MHs in Sarcocornia and Sporobolus plots be- came increasingly difficult to discern within the soil, proba- bly due to bioturbation and mixing of sediments (Cahoon and Turner, 1989; Krauss et al., 2003). Consequently, monitoring of all plots was terminated after 19 months. Short-term traps were deployed for 6-day (12 high tides) periods on four instances on the basis of tide chart predic- tions. Two neap (“December neap” and “January neap”) pe- riods were selected to reflect periods when high tides were at their lowest. While these neap periods were intended to mea- sure periods without any inundation, higher than predicted tides occurred in both neap periods. Although unconfirmed, inundation of some plots within lower-elevation zones of the study area were expected to have occurred at least once dur- ing the December neap (up to 80 % of Sarcocornia plots and 100 % of Sporobolus plots) and/or the January neap (up to 60 % of Sarcocornia plots only; Table S1 in the Supple- ment). Two other periods (“December spring” and “January spring”) were selected as maximum salt marsh inundation events with between five and 10 high tides inundating each plot in each period (Table S1). Although unintended, the fact that a small number of inundations were likely captured dur- ing neap tides more accurately reflects the differences in tidal behaviour that naturally occur among the three vegetation as- semblages (i.e. 2.3 Feldspar marker horizons lower-elevation assemblages are subject to a greater number of high tides throughout the year than higher- elevation assemblages). Consequently, all results from short- term measures were considered in the context of these varied inundation patterns. J. J. Kelleway et al.: Salt marsh surface deposition 3766 Elevation was measured using a modified version of the tidal inundation method described by English et al. (1994), whereby three vertical rods marked with water-soluble dye were inserted into the ground immediately prior to a sum- mer spring tide (23 January 2015; measured tidal height of 1.897 m above lowest astronomical tide (LAT) datum at near- est tidal gauge). Depth of inundation above the salt marsh surface was measured immediately after the tide receded and was subtracted from the measured tide height to obtain an estimate of surface elevation. Care was taken during the measurement procedure and in the selection of a calm day (to minimise wind and wave effects) to minimise discrepan- cies between measurements at different plots. Comparison of three replicate rods revealed a SE of the mean < 1.3 cm for each plot. including large fragments of plant litter. Second, a modified version of the filter paper method described by Reed (1989) and Adame et al. (2010) was used to quantify passive sedi- mentation and litter accretion on the salt marsh surface. Pre- weighed 90 mm hydrophilic nylon filters (pore size 0.45 µm) were placed over 90 mm upturned plastic Petri dishes and attached to the salt marsh surface by two small staples, so that the nylon filter lay level with the surface. The resolu- tion of this method (i.e. the smallest accumulation incre- ment detectable), using a 90 mm filter, has been calculated as 0.0015 mg cm−2 (Thomas and Ridd, 2004). Three replicates of each short-term trap were installed at the centre of each of the study areas described above dur- ing the summer of 2014/15. We chose to base our sampling strategy upon expected tidal inundation patterns rather than capturing seasonal variability for several reasons. First, based on relevant literature (Rogers et al., 2014) we expect tidal in- undation patterns to be of primary importance to deposition and accretion dynamics. Second, we do not expect there to be substantial seasonal variability due to factors other than tidal pattern variation. That is, the study region does not ex- perience high seasonal variability in rainfall, nor are there clear seasonal patterns in terms of biomass standing stock or senescence (Clarke and Jacoby, 1994). www.biogeosciences.net/14/3763/2017/ www.biogeosciences.net/14/3763/2017/ Biogeosciences, 14, 3763–3779, 2017 2.7 13C NMR Solid-state 13C nuclear magnetic resonance (NMR) spec- troscopy was used to quantify the contribution of C func- tional groups to live plant biomass, litter and residue samples. This was carried out to identify what compositional changes occurred between the different sample types and to what ex- tent this differed between vegetation assemblages and inun- dation periods. Residue samples were treated with 2 % hy- drofluoric acid (HF) according to the method of Skjemstad et al. (1994) to remove paramagnetic materials and concentrate organic C for 13C NMR analyses. Cross-polarisation 13C NMR spectra were acquired using a 200 MHz Avance spec- trometer (Bruker Corporation, Billerica, MA, USA) follow- ing the instrument specifications, experimental procedures and spectral processing outlined by Baldock et al. (2013b). The 13C NMR data are presented as the proportion of in- tegral area under each of eight chemical shift regions cor- responding to the main types of organic functional group- ings found in natural organic materials: alkyl C (0–45 ppm), N-alkyl/methoxyl (45–60 ppm), O-alkyl (60–95 ppm), di- O-alkyl (95–110 ppm), aryl (110–145 ppm), O-aryl (145– 165 ppm), amide/carboxyl (165–190 ppm) and ketone (190– 215 ppm; Baldock and Smernik, 2002). J. J. Kelleway et al.: Salt marsh surface deposition 3767 Oslo, Norway) before conducting principal component anal- ysis (PCA). Oslo, Norway) before conducting principal component anal- ysis (PCA). and allochthonous) materials were retained for analysis as we considered these to be largely unaffected by crab excavation. In the laboratory, vials were centrifuged, the supernatant decanted and the vial was placed in an oven for drying. All samples and vessels (filters and centrifuge vials) were dried at 60 ◦C until constant weight was achieved (≤72 h) and sub- tracted from initial vessel mass to obtain the dry weight of material collected. In addition, all identifiable litter was re- moved from each filter, identified to the species level and weighed. Litter samples of the main salt marsh species en- countered (S. quinqueflora, S. virginicus and J. kraussii), wrack of the seagrass Posidonia australis and macroalga Hormosira banksii, fresh leaves of the mangrove Avicen- nia marina, and composite samples of all residual deposits (mineral component and unidentified organic matter; referred to hereafter as residues) from filters were also prepared for chemical analyses. 2.8 Statistical analyses Separate simple linear regression analyses were conducted using all feldspar MH measurements for each of the three vegetation assemblages for the purpose of obtaining accu- mulation rates over 19 months and to assess the strength of linear fits for these data. We chose to use regression mod- els that do not force a y intercept of 0, as doing so would place an unrealistic weight upon nil accretion values at time t0. We present a comparison of regression statistics with and without y-intercept forcing in Table S2. 2.5 Elemental and isotopic analysis Elemental C and N content was measured in order to quantify C deposition rates and infer biomass, litter and soil consump- tion quality (C : N, by weight). To infer the source of sam- ples relative to reference source material and literature val- ues, δ13C was analysed. Dried above-ground plant biomass, litter and residues were homogenised and ground into a fine powder using a ball mill. The Champagne test (Jaschinski et al., 2008) was used to determine that no residue samples contained inorganic C. Consequently, acidification of sam- ples was deemed unnecessary. Organic %C, %N and δ13C were measured for all samples using an isotope ratio mass spectrometry – elemental analyzer (Thermo Delta V) at the University of Hawaii (HILO). 2.4 Sediment traps Two complementary types of sediment trap were installed concurrently for the purpose of quantifying short-term (days) deposition of materials among the three vegetation assem- blages. These types of traps were selected on the basis of the types of materials that they are most likely to collect, with the aim of providing insights into the processes driving de- position among assemblages. First, pre-weighed 50 mL cen- trifuge vials (30 mm mouth diameter, 115 mm depth) were placed into the ground, so that the “lip” of each tube was 10 mm above the ground surface. This vial method has a bias towards the collection of non-buoyant materials wash- ing over the mouth of the tube (i.e. mineral matter) and a bias against collection of coarse and/or buoyant materials, Great care was taken not to disturb sediments or litter col- lected on or surrounding the removable traps during their in- stallation and collection. Filters with visible crab-excavated sediment (n = 23/180) or that were physically upturned dur- ing inundation (n = 3 January spring inundation only) were excluded from analysis, although all plant (autochthonous www.biogeosciences.net/14/3763/2017/ www.biogeosciences.net/14/3763/2017/ Biogeosciences, 14, 3763–3779, 2017 J. J. Kelleway et al.: Salt marsh surface deposition www.biogeosciences.net/14/3763/2017/ 2.6 MIR Diffuse reflectance mid-infrared (MIR) spectroscopy was used to assess the composition of biomass, litter and residue samples. MIR spectroscopy characterises the bulk compo- sition and is therefore inclusive of both mineral and or- ganic components. Spectra were acquired using a Nico- let 6700 Fourier transform infrared (FTIR) spectrometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) follow- ing the specifications and procedures outlined by Baldock et al. (2013a). Spectra were acquired over 8000–400 cm−1 with a resolution of 8 cm−1, but were truncated to 6000– 600 cm−1. This spectral range was chosen to include signifi- cant signal intensity (including the first near-infrared over- tones of the MIR spectra) in the range 4000–6000 cm−1 and allow appropriate baseline correction, but also to ex- clude noise in the acquired signal intensity outside the se- lected spectral range. Spectra were baseline corrected using a baseline-offset transformation and were then mean centred using the Unscrambler 10.2 software (CAMO Software AS, Bulk short-term deposition variables (bulk material col- lected in vials, bulk material collected on filters) were log- transformed to achieve normality and analysed with sepa- rate linear mixed models to test main and interactive effects of vegetation assemblage (Sarcocornia, Sporobolus, Juncus) and tidal event (repeated measures: December neap, Decem- ber spring, January neap, January spring) on the amount of material retained at the end of a deployment period. Elevation was included as a covariate for each of these analyses. Co- variance structure was selected for each model through com- parison of Akaike’s information criterion (AIC) of four co- variance structures (unstructured, compound symmetry, di- agonal, scaled identity). Where main effects presented sig- nificance differences (P < 0.05), post hoc tests (with conser- vative Bonferroni adjustment) were used to determine the difference among levels of vegetation and tidal event fac- 2.8.2 MIR analysis PCA was performed using the transformed MIR spectra to (1) identify differences in composition among samples due to sample type and vegetation assemblage and (2) define the MIR spectral components most important to differentiating the samples. Loadings were plotted for the first two principal components to assist in the latter and to guide interpretation of differences in composition among samples. Figure 2. Surface accretion above feldspar marker horizons. Data are presented as the mean ± standard error of three replicate plots at each of five locations for each vegetation assemblage. A linear fit was applied on the basis of all data points (n = 90) for each vegeta- tion assemblage. 3.1 Feldspar MHs Net accretion (i.e. vertical surface accumulation) was mea- sured among Juncus plots throughout the entire 19 months, reflected in the moderate-strong linear fit (R2 = 0.68, P < 0.001) and a mean accumulation rate with relatively low variance (1.74 ± 0.13 mm yr−1). In contrast, accumu- lation above the feldspar MHs was more varied and slower overall in the Sarcocornia (R2 = 0.16, P < 0.001, 0.76 ± 0.18 mm yr−1) and Sporobolus plots (R2 = 0.14, P < 0.001, 0.88 ± 0.22 mm yr−1; Fig. 2). Accretion varied both spatially and temporally within the Sarcocornia and Sporobolus assemblages. Across Sporobolus plots, there was relatively high accretion recorded at the 11-month interval, followed by multiple peaks and troughs in the height of ma- terial measured above MHs, with some similarity among replicate plots in the timing of these (Fig. 2b). After mod- est gains at the 11-month interval, Sarcocornia accretion di- verged among plots with two plots (Sarcocornia 2 and 5) ex- periencing continued accretion, whilst Sarcocornia 3 and 4 appeared to lose surface material through the remainder of the study. The pattern of accumulation and loss observed be- tween 13 and 19 months at Sarcocornia 1 was mirrored in the nearby Sporobolus 1 plot. 2.8.1 Isotope mixing model A two-source, single-isotope mixing model (Phillips, 2012) was used to estimate the proportion of C3 (f1 in Eq. 1) and C4 (f2 in Eq. 2) plants to the unidentified organic residue (i.e. the material leftover after macrolitter was removed): f1 = δ13Cresidue −δ13CC4 δ13CC3 −δ13CC4 (1) f2 = 1 −f1, (2) (1) (1) (2) (2) in which δ13C denotes the isotopic signal of different sources of organic C: Cresidue (the residue organic C), CC3 (rel- evant C3 plants – S. quinqueflora litter for Sarcocornia– Sporobolus association residues or J. kraussii litter for Jun- cus assemblage residues) and CC4 (litter of the C4 species S. virginicus). in which δ13C denotes the isotopic signal of different sources of organic C: Cresidue (the residue organic C), CC3 (rel- evant C3 plants – S. quinqueflora litter for Sarcocornia– Sporobolus association residues or J. kraussii litter for Jun- cus assemblage residues) and CC4 (litter of the C4 species S. virginicus). J. J. Kelleway et al.: Salt marsh surface deposition Figure 2. Surface accretion above feldspar marker horizons. Data are presented as the mean ± standard error of three replicate plots at each of five locations for each vegetation assemblage. A linear fit was applied on the basis of all data points (n = 90) for each vegeta- tion assemblage. tors. Data are presented as the mean ± SE as there was some minor variation in sample numbers among assemblages and events (as described above). Statistical analyses were performed using SPSS v19 (IBM, USA), Origin Pro 2015 (Originlab, USA) and PRIMER v6 (PRIMER-E, UK). www.biogeosciences.net/14/3763/2017/ www.biogeosciences.net/14/3763/2017/ Biogeosciences, 14, 3763–3779, 2017 3768 J. J. Kelleway et al.: Salt marsh surface deposition Table 1. Summary of sedimentation measurement techniques; mean and standard error values for feldspar marker horizon (MH), vial and filter bulk sediment measures; mean and standard error of organic C deposition rates; and contributions of C3 and C4 vegetation to depo- sition among vegetation assemblages. Accretion rates slower than local sea-level rise (1.15 mm yr−1) are in red. DN: December neap; DS: December spring; JN: January neap; JS: January spring. Table 1. Summary of sedimentation measurement techniques; mean and standard error values for feldspar marker horizon (MH), vial and filter bulk sediment measures; mean and standard error of organic C deposition rates; and contributions of C3 and C4 vegetation to depo- sition among vegetation assemblages. Accretion rates slower than local sea-level rise (1.15 mm yr−1) are in red. DN: December neap; DS: December spring; JN: January neap; JS: January spring. Technique Parameter Period Measurement Temporal scale Biases/issues Feldspar MH Bulk measure sediment accumulation mean SE mean SE mean SE mid-term (days to years) 0 19 mo. J. J. Kelleway et al.: Salt marsh surface deposition 0.78 0.18 0.88 0.22 1.74 0.13 95% CI lower 0.42 0.44 1.48 95% CI upper 1.14 1.32 2.00 Vial Bulk measure sediment deposition mean SE mean SE mean SE short-term (hours to days) DN 9.33 3.12 7.49 2.48 10.37 3.41 DS 68.97 10.63 182.11 28.67 49.63 8.94 JN 105.88 25.18 51.59 15.02 13.66 3.65 JS 275.93 89.62 221.61 24.43 40.85 5.86 Filter Bulk measure mean SE mean SE mean SE sediment deposition DN 4.03 0.52 2.99 0.72 3.40 2.7E-03 short-term (hours to days) DS 5.97 0.95 3.59 0.27 6.49 6.7E-03 JN 2.18 0.55 1.19 0.13 2.81 5.6E-03 JS 8.31 2.15 6.84 1.27 6.97 7.7E-03 Filter + material identification composition of material deposited Filter + elemental analysis organic C deposition rate mean SE mean SE mean SE DN 0.27 0.04 0.21 0.05 1.21 0.17 DS 0.25 0.06 0.34 0.06 2.37 0.44 JN 0.10 0.02 0.17 0.04 1.14 0.41 JS 0.62 0.08 0.40 0.07 1.99 0.46 Filter + isotopic analysis sources contributing to soil organic C C3 C4 C3 C4 C3 C4 DN 59.6 40.4 38.3 61.7 80.2 19.8 DS 77.5 22.5 25.0 75.0 84.6 15.4 JN 67.9 32.1 19.9 80.1 81.0 19.0 JS 72.4 27.6 26.0 74.0 78.8 21.2 Filter + MIR & 13C NMR character of deposited materials isotope mixing model - plant contribution (%) see also Table 2 see Figure 4 & Table 2 see also Figure 2 Sarcocornia Juncus Sporobolus bulk deposition rate (mg cm-2 d-1) accretion rate (mm y-1) MH may be lost through erosion or bioturbation Biased towards materials entrained by water. Biased against coarse litter larger than vial mouth bulk deposition rate (mg cm-2 d-1) see Figure 3 organic C deposition rate (mg C cm-2 d-1) a - Vial riods (Fig. S1b–d). That is, there were broad trends of higher sedimentation at lower-elevation plots than higher-elevation plots during these periods. each event as significantly different from the others. De- spite large differences in mean deposition among the three vegetation assemblages during December spring, January neap and January spring events (Table 1), vegetation assem- blage was not a significant factor when elevation was in- cluded as a covariate (F2, 45.8 = 1.06, P = 0.36). J. J. Kelleway et al.: Salt marsh surface deposition There was, however, a significant event times assemblage interaction (F6, 42 = 10.01, P < 0.001), with deposition in Sarcocornia vials higher during January neap relative to December spring for Sarcocornia plots, but not so for Sporobolus and Jun- cus vials (Table 1). Deposition into vials was lowest for all three assemblages during December neap (Table 1) and was highest overall in Sarcocornia vials during January spring (275.93 ± 89.62 mg cm−2 d−1). 3.2.1 Vials Mean bulk material deposition rates as determined by vials were higher than filter bulk deposition rates across all sam- pling events and vegetation assemblages (Table 1). Obser- vations of materials retained within vials suggested a domi- nance of mineral matter and unidentified detritus, except in Juncus plots in which Juncus kraussii fragments were the dominant material. Deposition varied significantly among tidal events (F6, 42 = 10.01, P < 0.001), with post hoc tests revealing Biogeosciences, 14, 3763–3779, 2017 www.biogeosciences.net/14/3763/2017/ 3769 3.2.2 Filters Retention of bulk materials on filters also varied among all four tidal periods (F3, 109.3 = 48.82, P < 0.001), with overall deposition highest in January spring, followed by December spring (Table 1, Fig. 3). Bulk depo- sition on filters varied among vegetation assemblages (F2, 30.85 = 48.82, P = 0.004), with significantly lower de- position in Sporobolus plots relative to both Sarcocor- nia (Bonferroni-adjusted P value = 0.010) and Juncus (Bonferroni-adjusted P value = 0.023) plots across all tidal events (Fig. 3, Table 1). In contrast to the vials, there was no clear relationship between bulk material retained on filter papers and plot surface elevation during either of the neap or spring tidal events (Fig. S2). Regression of the log (mass of material retained within vials) versus plot surface elevation revealed no clear relation- ship between the two variables during the December neap pe- riod (Fig. S1a in the Supplement), but negative relationships (P < 0.001, R2 = 0.35 to 0.59) existed for all other time pe- J. J. Kelleway et al.: Salt marsh surface deposition 3770 Figure 3. Mean mass of autochthonous litter, allochthonous litter and mineral matter–organic residue retained on filters at the end of a 6-day deployment during December neap (a), December spring (b), January neap (c) and January spring (d) tidal periods. Error bars are presented for each component and represent 1 standard error each side of the mean. biomass and litter samples of the C4 grass Sporobolus were more enriched in 13C relative to those of the C3 species Sar- cocornia and Juncus (Table 2). This distinction, however, was not as great for the unidentified residue samples, with δ13C values from all assemblages sitting between the δ13C values of the C3 and C4 salt marsh plants. Outputs from the isotope mixing model (Table 1) high- lighted differences in source contribution among the vege- tation assemblages. Sarcocornia residues showed a higher contribution of C3 plant material during spring tides rela- tive to the neap tides. Further, similar contribution from the host plant (i.e. C3 in Sarcocornia and C4 in Sporobolus) to residues was apparent for all tidal periods except January neap, when the C4 contribution to Sporobolus residue was higher. Overall, contributions of the host plant ranged from 59.6 to 77.5 % in Sarcocornia plots and from 61.7 to 80.1 % in Sporobolus plots. Source contributions across the four tidal periods were most consistent in the Juncus assemblage, in which esti- mates ranged between 78.8–84.6 % for C3 plant material and 15.4–21.2 % for C4 plant material. These contributions aligned well with visual observations of plant cover across plots (in which the C3 plant J. kraussii is dominant over the C4 plant S. virginicus in approximately an 80 : 20 % biomass mix). Quantification of litter fall onto filters, however, high- lighted a skew towards J. kraussii litter (85.9–97.0 %) over S. virginicus litter (3.0–14.1 %) across the Juncus assem- blage. Residue C : N ratios were also highest for Juncus, fol- lowed by Sporobolus and then Sarcocornia. While Juncus litter samples had a higher C : N, relative to all other Juncus biomass (Table 2), this difference was not noted for Sarco- cornia or Sporobolus. Figure 3. Mean mass of autochthonous litter, allochthonous litter and mineral matter–organic residue retained on filters at the end of a 6-day deployment during December neap (a), December spring (b), January neap (c) and January spring (d) tidal periods. J. J. Kelleway et al.: Salt marsh surface deposition Error bars are presented for each component and represent 1 standard error each side of the mean. Although the mass of bulk material retained on filters was similar across Sarcocornia and Juncus plots, Fig. 3 demon- strates that different materials were contributing to surface accumulation among the two vegetation assemblages. In Jun- cus plots, autochthonous plant litter (that is, from the dom- inant species Juncus kraussii and the subdominant species Sporobolus virginicus) contributed between 66 % (December neap) and 78 % (both December spring and January neap) of all deposited material mass. In contrast, litter contributions were low (≤12 % of all deposited material) in both Sarcocor- nia and Sporobolus assemblages, regardless of the tidal pe- riod. Contributions from identifiable allochthonous materials were low in all cases, with negligible quantities of Posidonia australis litter (recorded in five out of all 60 Sporobolus fil- ters) and a single large piece of Hormosira banksii deposited on a Sporobolus filter during December spring – the latter was considered an outlier and was therefore excluded from Fig. 3. 3.4 MIR and 13C NMR Together, the first two principal components explained 96.4 % of the variation in MIR spectra of all samples as- sessed. A clear separation of residue samples from litter and biomass is apparent along PC1 (Fig. 4a) with inspec- tion of the loadings plot (Fig. 4b) highlighting variation in the range of 600–2000 cm−1 (quartz) and distinct troughs at 3400 cm−1 (water) and 2900 cm−1 (OM-alkyl). Residue samples are separated along PC2, with differentiation among vegetation assemblages, regardless of tidal event. The load- ings plot for PC2 (Fig. 4C) also exhibits variation in the range of 600–2000 cm−1 (quartz), a peak at 2900 cm−1 (OM-alkyl) and 3600–3700 cm−1 (kaolinite). Chemical analysis of the unidentified portion of material deposited on filters also highlights differences between the vegetation assemblages. The organic content (%C, %N) of unidentified material pooled across Juncus plots was much higher than for the other assemblages (Table S3), with this difference also apparent in the disparity between C accumu- lation rates in Juncus versus Sarcocornia and Sporobolus as- semblages (Table 1). The proportions of C within each of eight organic func- tional groupings for each sample analysed with 13C NMR are presented in Table 2. For all samples O-alkyl C was the most abundant. O-alkyl C content was higher in live plant biomass than litter for both Sarcocornia, but less so for Sporobolus and essentially unchanged for Juncus. Generally, residues were higher in alkyl C, and amide/carboxyl C, and lower in O-alkyl, di-O-alkyl and aromatics relative to litter and www.biogeosciences.net/14/3763/2017/ Biogeosciences, 14, 3763–3779, 2017 J. J. Kelleway et al.: Salt marsh surface deposition S: spring tide samples; N: neap tide samples; H: Hormosira banksii (macroalga) wrack; P: Posidonia australis (seagrass) wrack; A: Avicennia marina (mangrove) leaf; al: benthic algae mat. Figure 4. Principal component analysis of MIR spectra with the proportion of variance explained by each component given in parentheses (a); spectral loading plots for PC1 (b) and PC2 (c). S: spring tide samples; N: neap tide samples; H: Hormosira banksii (macroalga) wrack; P: Posidonia australis (seagrass) wrack; A: Avicennia marina (mangrove) leaf; al: benthic algae mat. Figure 4. Principal component analysis of MIR spectra with the proportion of variance explained by each component given in parentheses (a); spectral loading plots for PC1 (b) and PC2 (c). S: spring tide samples; N: neap tide samples; H: Hormosira banksii (macroalga) wrack; P: Posidonia australis (seagrass) wrack; A: Avicennia marina (mangrove) leaf; al: benthic algae mat. 3.3 Elemental and isotopic ratios Elemental C : N ratios and δ13C values of plant biomass, lit- ter and unidentified residues are presented in Table 2. The Biogeosciences, 14, 3763–3779, 2017 www.biogeosciences.net/14/3763/2017/ 4 Discussion biomass samples. There were differences in residue C com- position according to which vegetation assemblage they were collected from – aromatics (higher in Juncus and Sporobo- lus), alkyl C and amide/carboxyl (higher in Sarcocornia). There was high similarity between residues collected under the two different tides, however, for both the Sarcocornia and Sporobolus assemblages. These similarities among tides are mirrored in the similarity of the residue C : N values. There was insufficient residue material available for analysis from Juncus neap tide, even though samples were pooled across a large number of filters, further highlighting the small contri- bution of unidentifiable sedimentary components within this assemblage. In this study we have compared sediment and C accre- tion dynamics among three vegetation assemblages within a single intertidal wetland complex. Our findings, across a range of methods, showed that there were substantial differ- ences among assemblages in (1) the types of materials de- posited on the marsh surface in the short term (days) and (2) the quantities of material accumulated over the medium term (19 months). Here, we first consider the accumulation differences among assemblages over the medium term and then discuss the interactions among vegetation, physical and degradation processes that are likely driving short-term and J. J. Kelleway et al.: Salt marsh surface deposition 3771 Table 2. Results of 13C NMR, δ13C and elemental (C : N) analyses for each component of three salt marsh plant assemblages and other potential sources. 13C NMR outputs are the average of two samples for each of the biomass and litter components (except Sporobolus litter, for which only one reliable spectrum was obtained). δ13C and C : N values are the mean (± SE) of biomass (n = 3) and litter (n = 4) samples. Residue samples were pooled from 15 filters in each vegetation assemblage. The tidal period was deemed not appropriate (n/a) for live biomass sample collection. Table 2. Results of 13C NMR, δ13C and elemental (C : N) analyses for each component of three salt marsh plant assemblages and other potential sources. 13C NMR outputs are the average of two samples for each of the biomass and litter components (except Sporobolus litter, for which only one reliable spectrum was obtained). δ13C and C : N values are the mean (± SE) of biomass (n = 3) and litter (n = 4) samples. Residue samples were pooled from 15 filters in each vegetation assemblage. The tidal period was deemed not appropriate (n/a) for live biomass sample collection. J. J. Kelleway et al.: Salt marsh surface deposition Principal component analysis of MIR spectra with the proportion of variance explained by each component given in parentheses (a); spectral loading plots for PC1 (b) and PC2 (c). S: spring tide samples; N: neap tide samples; H: Hormosira banksii (macroalga) wrack; P: Posidonia australis (seagrass) wrack; A: Avicennia marina (mangrove) leaf; al: benthic algae mat. biomass samples. There were differences in residue C com- 4 Discussion Community Component Tide 13C NMR chemical assignment and region (ppm) δ13C C : N Alkyl N-alkyl/methoxyl O-alkyl Di-O-alkyl Aryl O-aryl Amide/carboxyl Ketone (0–45) (45–60) (60–95) (95–110) (110–145) (145–165) (165–190) (190–215) Sarcocornia biomass n/a 14.4 6.6 45.0 10.6 10.5 4.4 7.1 1.4 −26.5 ± 0.5 38.0 ± 4.2 litter combined 10.2 5.1 34.0 9.0 16.3 8.6 13.2 3.6 −25.7 ± 0.1 33.0 ± 1.2 residue neap 23.1 8.2 33.7 7.3 11.3 4.3 11.0 1.1 −22.1 ± 0.3 14.2 ± 0.4 spring 25.1 8.1 32.8 7.1 10.5 4.0 11.3 1.1 −23.3 ± 0.2 14.2 ± 0.7 Sporobolus biomass n/a 8.6 4.6 51.0 12.0 11.5 4.6 6.5 1.3 −14.9 ± 0.1 59.8 ± 6.3 litter spring 5.2 4.5 47.1 12.0 14.6 6.6 8.0 2.0 −15.8 ± 0.2 59.4 ± 5.2 residue neap 19.2 7.9 36.5 8.3 12.6 5.0 9.4 1.2 −18.7 ± 0.6 15.5 ± 0.5 spring 18.5 7.3 36.6 8.4 13.0 5.2 9.5 1.4 −18.4 ± 0.0 16.3 ± 1.1 Juncus biomass n/a 8.6 5.4 51.8 12.2 11.2 4.6 5.2 1.1 −24.8 ± 0.3 61.3 ± 5.6 litter combined 5.6 5.4 52.2 12.8 11.9 5.4 5.4 1.3 −25.6 ± 0.1 89.9 ± 4.5 residue neap Insufficient material available for 13C NMR analysis −23.7 ± 0.0 19.6 ± 0.0 spring 15.4 7.2 35.7 8.8 15.4 6.6 9.2 1.7 −23.8 ± 0.2 18.2 ± 0.4 Other sources algal mat n/a 14.3 5.6 37.5 8.7 11.5 4.9 14.8 2.6 −15.0 ± 0.4 13.2 ± 0.1 mangrove leaf n/a 16.4 6.4 40.6 9.1 12.8 4.8 8.7 1.1 −28.7 ± 0.3 24.8 ± 1.7 seagrass wrack spring 11.6 3.9 33.3 8.0 14.4 7.7 16.4 4.6 −12.3 29.2 macroalga wrack spring 6.0 2.6 52.5 14.0 5.5 6.6 11.5 1.3 −17.7 57.8 Figure 4. Principal component analysis of MIR spectra with the proportion of variance explained by each component given in parentheses (a); spectral loading plots for PC1 (b) and PC2 (c). J. J. Kelleway et al.: Salt marsh surface deposition Community Component Tide 13C NMR chemical assignment and region (ppm) δ13C C : N Alkyl N-alkyl/methoxyl O-alkyl Di-O-alkyl Aryl O-aryl Amide/carboxyl Ketone (0–45) (45–60) (60–95) (95–110) (110–145) (145–165) (165–190) (190–215) Sarcocornia biomass n/a 14.4 6.6 45.0 10.6 10.5 4.4 7.1 1.4 −26.5 ± 0.5 38.0 ± 4.2 litter combined 10.2 5.1 34.0 9.0 16.3 8.6 13.2 3.6 −25.7 ± 0.1 33.0 ± 1.2 residue neap 23.1 8.2 33.7 7.3 11.3 4.3 11.0 1.1 −22.1 ± 0.3 14.2 ± 0.4 spring 25.1 8.1 32.8 7.1 10.5 4.0 11.3 1.1 −23.3 ± 0.2 14.2 ± 0.7 Sporobolus biomass n/a 8.6 4.6 51.0 12.0 11.5 4.6 6.5 1.3 −14.9 ± 0.1 59.8 ± 6.3 litter spring 5.2 4.5 47.1 12.0 14.6 6.6 8.0 2.0 −15.8 ± 0.2 59.4 ± 5.2 residue neap 19.2 7.9 36.5 8.3 12.6 5.0 9.4 1.2 −18.7 ± 0.6 15.5 ± 0.5 spring 18.5 7.3 36.6 8.4 13.0 5.2 9.5 1.4 −18.4 ± 0.0 16.3 ± 1.1 Juncus biomass n/a 8.6 5.4 51.8 12.2 11.2 4.6 5.2 1.1 −24.8 ± 0.3 61.3 ± 5.6 litter combined 5.6 5.4 52.2 12.8 11.9 5.4 5.4 1.3 −25.6 ± 0.1 89.9 ± 4.5 residue neap Insufficient material available for 13C NMR analysis −23.7 ± 0.0 19.6 ± 0.0 spring 15.4 7.2 35.7 8.8 15.4 6.6 9.2 1.7 −23.8 ± 0.2 18.2 ± 0.4 Other sources algal mat n/a 14.3 5.6 37.5 8.7 11.5 4.9 14.8 2.6 −15.0 ± 0.4 13.2 ± 0.1 mangrove leaf n/a 16.4 6.4 40.6 9.1 12.8 4.8 8.7 1.1 −28.7 ± 0.3 24.8 ± 1.7 seagrass wrack spring 11.6 3.9 33.3 8.0 14.4 7.7 16.4 4.6 −12.3 29.2 macroalga wrack spring 6.0 2.6 52.5 14.0 5.5 6.6 11.5 1.3 −17.7 57.8 Community Component Tide 13C NMR chemical assignment and region (ppm) δ13C C : N Alkyl N-alkyl/methoxyl O-alkyl Di-O-alkyl Aryl O-aryl Amide/carboxyl Ketone (0–45) (45–60) (60–95) (95–110) (110–145) (145–165) (165–190) (190–215) Sarcocornia biomass n/a 14.4 6.6 45.0 10.6 10.5 4.4 7.1 1.4 −26.5 ± 0.5 38.0 ± 4.2 litter combined 10.2 5.1 34.0 9.0 16.3 8.6 13.2 3.6 −25.7 ± 0.1 33.0 ± 1.2 residue neap 23.1 8.2 33.7 7.3 11.3 4.3 11.0 1.1 −22.1 ± 0.3 14.2 ± 0.4 spring 25.1 8.1 32.8 7.1 10.5 4.0 11.3 1.1 −23.3 ± 0.2 14.2 ± 0.7 Sporobolus biomass n/a 8.6 4.6 51.0 12.0 11.5 4.6 6.5 1.3 −14.9 ± 0.1 59.8 ± 6.3 litter spring 5.2 4.5 47.1 12.0 14.6 6.6 8.0 2.0 −15.8 ± 0.2 59.4 ± 5.2 residue neap 19.2 7.9 36.5 8.3 12.6 5.0 9.4 1.2 −18.7 ± 0.6 15.5 ± 0.5 spring 18.5 7.3 36.6 8.4 13.0 5.2 9.5 1.4 −18.4 ± 0.0 16.3 ± 1.1 Juncus biomass n/a 8.6 5.4 51.8 12.2 11.2 4.6 5.2 1.1 −24.8 ± 0.3 61.3 ± 5.6 litter combined 5.6 5.4 52.2 12.8 11.9 5.4 5.4 1.3 −25.6 ± 0.1 89.9 ± 4.5 residue neap Insufficient material available for 13C NMR analysis −23.7 ± 0.0 19.6 ± 0.0 spring 15.4 7.2 35.7 8.8 15.4 6.6 9.2 1.7 −23.8 ± 0.2 18.2 ± 0.4 Other sources algal mat n/a 14.3 5.6 37.5 8.7 11.5 4.9 14.8 2.6 −15.0 ± 0.4 13.2 ± 0.1 mangrove leaf n/a 16.4 6.4 40.6 9.1 12.8 4.8 8.7 1.1 −28.7 ± 0.3 24.8 ± 1.7 seagrass wrack spring 11.6 3.9 33.3 8.0 14.4 7.7 16.4 4.6 −12.3 29.2 macroalga wrack spring 6.0 2.6 52.5 14.0 5.5 6.6 11.5 1.3 −17.7 57.8 Figure 4. 4.1 Accretion varies among vegetation assemblages Surface accretion above feldspar MHs over a period of 19 months and deposition measured with short-term sedi- ment traps provide evidence of the multiple ways in which deposition and accretion dynamics differ between salt marsh vegetation assemblages. First, feldspar MHs highlight a record of continued and consistent accretion across the upper marsh Juncus assemblage, amounting to a reliable (R2 = 0.68) accretion rate of 1.74 ± 0.13 mm yr−1 (Fig. 2). This value is remarkably similar to the mean accretion rate measured over 10 years above feldspar MHs of 1.76 mm yr−1 by Saintilan et al. (2013) for Juncus salt marshes across a range of sites in SE Australia. In contrast, accretion above MHs in Sarcocornia and Sporobolus assemblages varied sub- stantially – both spatially and temporally – in our study (Fig. 2), possibly due in part to the influence of erosion, bioturbation and sediment mixing above MHs (Cahoon and Turner, 1989; Krauss et al., 2003). While our mean accre- tion estimates for both Sarcocornia and Sporobolus are lower than the regional estimate for Sarcocornia–Sporobolus asso- ciations (1.11 ± 0.08 mm yr−1; Saintilan et al., 2013), this re- gional mean is within the 95 % confidence interval for both species at Towra Point (Table 1). Critically, medium-term accretion rates in the Juncus assemblage consistently ex- ceed contemporary rates of sea-level rise within Botany Bay (1.15 mm yr−1), while mean accretion rates for both Sarco- cornia and Sporobolus (including the upper 95 % confidence interval of Sarcocornia) are below the contemporary rate of sea-level rise. These patterns of high marsh versus lower marsh accretion are also atypical of results reported outside of the study region (see Sect. 4.2.2), and while in general agreement within previous data from our region, these accre- tion patterns would benefit from validation across a broader network of sites. In the following sections we interpret the influence of bio- logical, physical and interactive processes on salt marsh sur- face dynamics on the sub-site scale. We do so by assessing the response of different surface deposition measures (two short term, one medium term) among the three vegetation assemblages studied. 4.2.1 The influence of vegetation on salt marsh surface deposition The results of this study partially support our first hypothesis. That is, there were broad differences among the vegetation assemblages regarding the amount and type of materials de- posited in the short term and rates of accretion in the medium term. The high spatial and temporal variability in marker horizon measurements across Sarcocornia and Sporobolus plots (Table 1; Fig. 2a, b) limit interpretation of medium-term processes between these two assemblages. In contrast, the relative stability of medium-term accretion patterns in Jun- cus plots (Fig. 2b) and unique short-term deposition results from Juncus plots (Table 1, Fig. 3, plus Sect. 4.3.2) allow some interpretation of the potential role of vegetation struc- ture on surface dynamics. J. J. Kelleway et al.: Salt marsh surface deposition 3772 medium-term differences among assemblages. We conclude with an assessment of the implications for C accumulation and response to relative sea-level rise (RSLR). butions of autochthonous litter and the residual sediment (comprising mineral and organic residue components) were stark. There was further evidence of this in the short-term vial results, where mineral-biased deposition was high in the lower-elevation, non-rush assemblages and low in the higher- elevation Juncus assemblage during multiple experimental periods (Table 1, Fig. S1). Although higher-than-predicted tides likely influenced some short-term traps during neap ex- perimental periods (Table S1), the fact that deposition into vials was lower during December neap (when up to 80 % of Sarcocornia plots and 100 % of Sporobolus plots would have been subjected to at least one tidal inundation) relative to Jan- uary neap (up to 60 % of Sarcocornia plots; no inundation of Sporobolus plots) suggests that this had a small impact rela- tive to other influences. Non-tidal processes, such as rain- or wind-driven sedimentation and/or bioturbation, are the most likely factors behind sedimentation when inundation was ab- sent. Although filters with visible crab-excavated sediment (n = 23/180) were excluded from analysis, such clear iden- tification was not able to be determined for sediments de- posited in vials. www.biogeosciences.net/14/3763/2017/ www.biogeosciences.net/14/3763/2017/ Biogeosciences, 14, 3763–3779, 2017 J. J. Kelleway et al.: Salt marsh surface deposition mineral-specific deposition results are largely supportive of the role of the physical position within the salt marsh towards differences among assemblages. also be indirect vegetation effects on the deposition and accu- mulation of surface materials. For instance, the tall (∼1 m), dense structure of the Juncus assemblage is likely to en- hance (1) the retention of autochthonous litter (Fig. 3), which may have otherwise been exported during tidal recession, and (2) the capture of mineral particles on plant stems (Morris et al., 2002; Mudd et al., 2004). Dense salt marsh vegeta- tion also has the capacity to enhance sedimentation by reduc- ing the turbulent energy of inundating waters, with Mudd et al. (2010) demonstrating that this phenomenon was respon- sible for virtually all of the sedimentation increase observed when standing plant biomass of Spartina alterniflora was ar- tificially increased. The high short-term litter deposition rates we observed during neap tides (Fig. 3a, c) and the increased contribution of both mineral and litter components during spring tides (Fig. 3b, d) suggested that each of these direct and indirect plant mechanisms may be contributing to the relatively high medium-term accretion rates observed within Juncus assemblages. also be indirect vegetation effects on the deposition and accu- mulation of surface materials. For instance, the tall (∼1 m), dense structure of the Juncus assemblage is likely to en- hance (1) the retention of autochthonous litter (Fig. 3), which may have otherwise been exported during tidal recession, and (2) the capture of mineral particles on plant stems (Morris et al., 2002; Mudd et al., 2004). Dense salt marsh vegeta- tion also has the capacity to enhance sedimentation by reduc- ing the turbulent energy of inundating waters, with Mudd et al. (2010) demonstrating that this phenomenon was respon- sible for virtually all of the sedimentation increase observed when standing plant biomass of Spartina alterniflora was ar- tificially increased. The high short-term litter deposition rates we observed during neap tides (Fig. 3a, c) and the increased contribution of both mineral and litter components during spring tides (Fig. 3b, d) suggested that each of these direct and indirect plant mechanisms may be contributing to the relatively high medium-term accretion rates observed within Juncus assemblages. Importantly, the deposition–elevation relationship ex- pressed by the mineral component did not apply when bulk results of the passive short-term filter method were consid- ered. J. J. Kelleway et al.: Salt marsh surface deposition With the mineral bias effectively removed, no clear re- lationship between elevation and bulk deposition (i.e. min- eral plus organic matter) was observed across any of the tidal periods (see Fig. S2). Instead, total deposition was sim- ilar between the minerogenic, lower-elevation Sarcocornia– Sporobolus plots, and the organogenic higher-elevation Jun- cus plots. p The lack of an elevation relationship in terms of bulk ma- terial deposition is somewhat contrary to spatial patterns ex- pected on the basis of physical sedimentary processes in the tidal zone. This disparity extended to medium-term accretion results, in which lower marsh (Sarcocornia and Sporobolus) assemblages accrete at a slower rate than upper marsh (Jun- cus), both in our study and regionally (Saintilan et al., 2013). This relationship does not necessarily downplay the impor- tance of tidal influence on surface dynamics in SE Australian salt marshes. An alternative explanation is that these physi- cal processes, in interaction with biological factors, instead remobilise and redistribute materials across the lower marsh assemblages, rather than depositing significant amounts of new allochthonous material. 4.2.2 The influence of physical factors on salt marsh surface deposition Differences in suspended sediment supply and tidal flooding characteristics (tidal range, position within the tidal prism) have been identified as key physical drivers of salt marsh ac- cretion (Chmura and Hung, 2004; Rogers et al., 2014). Gen- erally, lower elevation within the tidal frame and closer prox- imity to the source of tidal inundation result in higher sedi- mentation rates. This is because (1) greater flooding depth al- lows for greater suspended sediment volume and higher sedi- mentation, (2) the increase in flooding duration increases the time for sediment deposition to occur and (3) flooding fre- quency is higher at lower elevations (Baustian et al., 2012; Harter and Mitsch, 2003; Morris, 2007; Oenema and De- Laune, 1988). If these processes were operating at our site, we would have expected to observe higher sedimentation rates in the Sarcocornia and Sporobolus assemblages, which were generally both lower in the tidal frame (Table S1) and nearer to tidal sources (Fig. 1). Indeed, when measurements relevant to the mineral component were considered, our re- sults appeared to be consistent with this. First, overall min- eral retention on filters (Fig. 3) was highest in the Sarcocor- nia and Sporobolus assemblages. Second, short-term vials (i.e. the method that is biased toward retention of heavy min- erals over organic matter) showed a significant log-linear re- lationship between deposition and elevation during the peri- ods of greatest tidal inundation (December spring, January spring) and during January neap when significant rainfall (Fig. S3) as well as some inundation of low-elevation sites likely occurred (Table S3). Further, observations made dur- ing the first measurement of feldspar MHs at 11 months sug- gested a high mineral contribution in all Sporobolus and Sar- cocornia plots, though it is unclear why this accretion trend reversed in many plots after this sampling event. Overall, 4.2 Processes driving spatial variability in deposition and accretion One of the key strengths of using short-term deposition meth- ods is the ability to identify and quantify the composition of inputs that may be contributing to differences observed over the medium term. In this study, a distinction was ob- served between the Juncus assemblage (in which medium- term accretion rates were consistently high and organic de- position was higher) and the Sarcocornia and Sporobolus assemblages (in which medium-term accretion rates were generally lower but more varied and deposition was dom- inated by mineral material; Table 1, Fig. 3). This distinc- tion was best exemplified by the results of the short-term filter method (Fig. 3), in which differences in the contri- There are fundamental differences in vegetation structure and function that can at least partly account for the vari- ations in the quantity and type of materials being retained in rush (Juncus) versus non-rush (Sarcocornia and Sporobo- lus) assemblages. First, Juncus assemblages have large po- tential for litter production through the annual replacement of their significant above-ground biomass (1116 g m−2; Clarke and Jacoby, 1994). No clear patterns of annual turnover have been observed in Sarcocornia and Sporobolus assemblages, in which standing biomass is only about one-third that of the Juncus assemblage (Clarke and Jacoby, 1994). There may Biogeosciences, 14, 3763–3779, 2017 www.biogeosciences.net/14/3763/2017/ 3773 www.biogeosciences.net/14/3763/2017/ J. J. Kelleway et al.: Salt marsh surface deposition In contrast, the constancy of isotope signatures and their overall similarity with the mix of C3- and C4-derived biomass in the Juncus plots provide further evidence of the autochthonous nature and trapping capacity of this assemblage. Next, it was not expected that tidal inundation would substantially increase salt marsh plant litter production. We therefore interpret the increased concentration of au- tochthonous litter in Juncus plots during spring tides relative to neap tides (Fig. 3) as evidence of the redistribution and trapping of autochthonous material within this assemblage. That is, the extra spring tide litter was material that had been remobilised by inundating water and redistributed within the same community, resulting in a larger amount of material be- ing caught on the Juncus filters. The fact that no identifiable Juncus litter was collected on any of the Sporobolus short- term filters, despite their position being within the expected path of receding tides (Fig. 1), further highlights the retain- ing capacity within the Juncus assemblage. While it is not known over what scale the litter redistribution occurs in the Juncus assemblage, we expect it to be highly localised, given the dense structure of standing vegetation here and its capac- ity to impede movement of coarse litter particles. Together, these findings allow several hypotheses about re- distribution of surface materials to be made. First, short-term deposition measures may capture a significant proportion of within-marsh redistribution and therefore may not necessar- ily equate with longer-term accretion. Second, the capacity of vegetation to retain autochthonous materials appears to vary substantially among species assemblages. Third, redistribu- tion is likely to be greatest in more exposed, lower-biomass assemblages. These findings also highlight the importance of considering redistributed materials in quantifications of wet- land surface dynamics and likely shortcomings for studies that attempt to assess surface dynamics using only short-term methods. y p p Finally, by placing our Sarcocornia and Sporobolus plots within small patches vegetated exclusively by either the C3 species (S. quinqueflora) or the C4 species (S. virginicus), we are able to estimate the contribution of each resident plant to the short-term residue collected from within its assemblage. While the dominance of resident plant signatures suggested a strong autochthonous contribution in all instances (see mix- ing model results in Table 1), residue signatures across all tidal periods reveal a mixture of sources both present (i.e. the resident plant) or neighbouring (i.e. J. J. Kelleway et al.: Salt marsh surface deposition 3774 distribution of materials over time in this assemblage. Such movement of materials within the Sarcocornia and Sporobo- lus assemblages also fits with the expectation that hydrody- namic energy, and therefore potential for sediment redistri- bution, would be highest in the salt marsh zones lower in the tidal frame and located closer to tidal sources (Fig. 1, Ta- ble S1). We also attribute the fading of feldspar horizons in many Sarcocornia and Sporobolus plots over time to mixing of sediments (Cahoon and Turner, 1989) in this active zone, with assistance from bioturbation (Cahoon and Turner, 1989; Krauss et al., 2003). In contrast, these temporal discrepancies and variations (including fading of MHs) were not observed in the Juncus assemblage, in which hydrodynamic energy is expected to be greatly reduced as a result of both its position within the marsh and the influences of plant biomass (see discussion in Sect. 4.2.2). count for any degradation-related kinetic fractionation from plants to litter and sediments. Data in Table 2 suggest little to no fractionation between fresh biomass and partially decom- posed litter samples, consistent with other studies compar- ing δ13C between fresh and decomposing leaves of estuarine plant species (e.g. Zieman et al., 1984; Fry and Ewel, 2003; Saintilan et al., 2013). We cannot rule out the potential for isotopic fractionation occurring in the decay from litter to residue samples, however, and we recommend this as an area of future research. A two-source (C3 plant vs. C4 plant) mixing model prob- ably presents an overly simplified estimate of source mat- ter contributions. This is because it does not account for other potential sources that have δ13C values within or near the range of salt marsh plant sources prescribed in the mix- ing model. These include mangroves (−28.7 ± 0.3 ‰), sea- grass (−12.3 ‰), macroalgae (−17.7 ‰) and benthic algae (−15.0 ± 0.4 ‰). Of these, benthic algae would have the greatest potential for contributing to Sarcocornia residue, as vegetation is sparsest here (and therefore light penetration to benthos the greatest), while the MIR PC plot (Fig. 4) also points to a similarity in chemical composition between the two. However, the fact that Sporobolus residues are consis- tently depleted in 13C, relative to both the resident plant (S. virginicus) and benthic algae, shows that our interpretation of mixing between both C3 and C4 sources is warranted at least in that assemblage. J. J. Kelleway et al.: Salt marsh surface deposition the other co-dominant plant in the association) to the plots. The fact that contri- butions of sources other than the resident plant were of the order of 20–40 % (Table 1) during the neap tides suggests significant mixing across scales greater than the monospe- cific patches (i.e. several metres or more). While some of this movement of materials may have been due to the creep of the highest neap period tides into the lower elevation plots (though this appears small – see Sect. 4.2), non-tidal agents such as redistribution by rainfall (Chen et al., 2015) and fau- nal activity (Guest et al., 2004) may have also contributed. It should be noted that our isotopic mixing model does not ac- 4.2.3 Redistribution of surface materials The second hypothesis of our study was that the source and character of materials deposited would vary temporally with tidal inundation patterns. For the most part, however, this was not observed, with high degrees of within-assemblage similarity for neap and spring tide samples across the vari- ous analyses undertaken (Table 2, Fig. 4). Instead, our results provide multiple lines of evidence that suggest a redistribu- tion of surface materials across the salt marsh, mediated by a range of biological, physical and interactive processes. The first indication of redistribution of surface materials was the mismatch between rates of short-term bulk deposi- tion and patterns of medium-term accretion among vegeta- tion assemblages. This was best exhibited in the Sarcocornia plots, in which short-term measures showed deposition to be as high or higher in Sarcocornia plots relative to the other assemblages (Table 1, Fig. 3), while medium-term accretion was actually lowest here (Fig. 2). This suggests that short- term measures in this assemblage were capturing materials that were being moved or redistributed across the salt marsh but not necessarily retained in a given location over longer time periods (i.e. months). While the short- versus medium- term discrepancy was not as large for the Sporobolus assem- blage, the temporal variability in medium-term feldspar MH measurements (i.e. multiple peaks and troughs across the 19- month period for most plots) also suggested significant re- www.biogeosciences.net/14/3763/2017/ Biogeosciences, 14, 3763–3779, 2017 J. J. Kelleway et al.: Salt marsh surface deposition 4.3.1 C deposition and accumulation rates pounds (carbohydrates more broadly, as well as lignin) were retained within the Juncus litter and residue relative to the other species (Table 2). In contrast, the higher proportions of alkyl-C and amide/carboxyl-C within Sarcocornia and Sporobolus residues were indicative of higher protein and lipid contents, consistent with bacterial biomass and marine algae signatures (Dickens et al., 2006). However, they may also be partly explained by the selective retention of resistant plant waxes, such as suberin and cutan. We therefore reject our third hypothesis that decay patterns would show no dif- ferences among the vegetation assemblages. The distinction between organogenic and minerogenic de- posits, and their respective locations within the tidal frame, has important implications for surface C deposition and ac- cumulation rates. Here we estimate mean C deposition rates ranging from 0.10 to 0.62 mg C cm−2 d−1 across the four tidal periods for the minerogenic Sarcocornia and Sporobo- lus assemblages and from 1.14 to 2.37 mg C cm−2 d−1 for the organogenic Juncus assemblage (Table 1). It should be noted that such short-term C deposition rates inclusive of plant lit- ter will likely represent a massive overestimation of C that is retained and sequestered over longer timescales, due to dia- genesis of deposited OM (Duarte and Cebrian, 1996), and the potential for materials to be redistributed or even exported by tidal and non-tidal processes (see Sect. 4.2.3). Therefore, these deposition rates are not directly comparable to C ac- cumulation rates determined by medium-term (e.g. feldspar MH) or longer-term (e.g. radiometric dating) techniques. Notwithstanding this, the magnitude of the differences we re- port among assemblages above fit broadly with differences in regional estimates of C accumulation over the medium term (10-year MH experiments), which have been estimated as 4.5 times higher in Juncus relative to Sarcocornia–Sporobolus salt marsh (Saintilan et al., 2013). Similarly, our results are also in agreement with findings further north in Moreton Bay, where Lovelock et al. (2013) reported much higher C seques- tration rates on oligotrophic sand island marshes dominated by J. kraussii than S. quinqueflora-dominated marshes on the western side of that bay. g g g There are multiple mechanisms that may explain the greater retention of plant-derived C along the biomass–litter– residue pathway for Juncus, relative to the other assem- blages. 4.3.1 C deposition and accumulation rates The simplest explanation is that a high turnover of Juncus biomass (and its exclusion of other sources through shading and/or structural impedance) ensures ample supply of plant-derived C to the benthos. Our data, however, reveal an important biomass to litter transformation in Juncus that was not observed in either the Sarcocornia or Sporobolus as- semblage. That is, the C : N of Juncus litter increased sub- stantially relative to live biomass. Such an increase is com- monly observed in terrestrial (McGroddy et al., 2004) and marine (Stapel and Hemminga, 1997) plants and may be ex- plained by the selective resorption of nutrients (but not car- bon) by the plant prior to, or during, senescence (McGroddy et al., 2004; Stapel and Hemminga, 1997). Such a mechanism was supported by the constancy of molecular C composition between Juncus biomass and litter (Table 2). The selective resorption of N by a plant has important implications for the fate and processing of the resulting litter and residue, as tis- sue C : N is considered a primary determinant on salt marsh OM decomposition (Minden and Kleyer, 2015). By retain- ing nutrients within the living tissues, the plant effectively decreases the lability of resulting litter and residual soils and makes them less attractive to the microbial decomposer com- munity (Hessen et al., 2013; Sterner and Hessen, 1994). This will have the effect of lowering OM remineralisation rates in Juncus relative to other assemblages, a result that also coin- cides with the bacterial and/or marine algae signatures (Dick- ens et al., 2006) inferred for Sarcocornia and Sporobolus but not apparent within the more recalcitrant Juncus residues (Table 2). 4.3 Implications for wetland functioning Understanding the biological and physical feedbacks that af- fect surface dynamics is critical to predict the survival of in- tertidal wetlands and their associated ecosystem services un- der changing environmental conditions (Kirwan and Mego- nigal, 2013). To this end, the data collected as part of this study reveal patterns of how C deposition and accumulation, organic matter decomposition and vulnerability to sea-level rise vary among salt marsh assemblages. Biogeosciences, 14, 3763–3779, 2017 www.biogeosciences.net/14/3763/2017/ 3775 www.biogeosciences.net/14/3763/2017/ 4.3.3 Vulnerability to sea-level rise maintenance is also required, including in relation to ex- pected non-linear increases in sea level. By combining medium-term accretion quantification with short-term deposition measurements and chemical analyses, we have gained insights into the various processes behind ob- served differences in accretion among salt marsh vegetation assemblages. While our study highlights assemblage-scale differences in potential response to RSLR, it represents only a small part of the information needed to accurately predict the future of SE Australian salt marsh assemblages. Further measures of short-term deposition and medium-term accre- tion across a broader range of sites and geographical settings, longer-term studies of surface elevation change among as- semblages and modelling of vegetation response thresholds are all required. There is growing evidence of the capacity of coastal wetlands to maintain surface elevation with relative sea-level rise, in certain situations, by increasing surface elevation through below-ground production, enhanced trapping of sediments or a combination of the two (Baustian et al., 2012; Kelleway et al., 2016b; McKee et al., 2007). Where wetland assemblages are unable to maintain a suitable elevation relative to inun- dating water levels, vegetation shifts may occur, including the loss of marsh vegetation (Day et al., 1999, 2011; Rogers et al., 2006). While wetland surface elevation is a function of multiple factors, including below-ground production and decomposition, groundwater dynamics, and sedimentary and regional subsidence (Cahoon et al., 1999; Rogers and Sainti- lan, 2008), the retention of above-ground inputs plays a criti- cal role in wetland survival under changing hydrological con- ditions (Day et al., 2011). Data availability. It is intended that data from this research will be made public as part of the CSIRO Coastal Carbon Cluster. With this in mind, medium-term accretion data suggest that Sporobolus and Sarcocornia assemblages at our study site may be particularly vulnerable to current RSLR. That is, mean surface accretion rates were either lower (Sarco- cornia = 0.92 mm yr−1) or only marginally higher (Sporobo- lus = 1.30 mm yr−1) than contemporary rates of local sea- level rise within Botany Bay (1.15 mm yr−1). Across much of the Towra Point Nature Reserve (as well as elsewhere in the region) upslope encroachment of mangrove shrubs into Sarcocornia–Sporobolus association is occurring, pos- sibly in response to sea-level rise (Kelleway et al., 2016b). 4.3.3 Vulnerability to sea-level rise In contrast, vegetation change (either in the form of man- grove encroachment or dieback) has not been widely re- ported for Juncus assemblages across SE Australia over re- cent decades, suggesting relative stability during a time of changing sea levels. While below-ground biomass produc- tion likely plays a role, average Juncus surface accretion rates (1.70 mm yr−1 in this study, 1.76 mm yr−1 regionally) in excess of local RSLR suggest a potential role of above- ground inputs towards maintaining surface elevation. Depen- dence upon organogenic inputs for accretion, however, also means that the response of Juncus assemblages to RSLR may vary with shifts in productivity or decomposition dynam- ics (e.g. changes in climate and/or nutrient status). Under present conditions, at least, our analyses have shown these organic inputs to be relatively resistant to early decompo- sition. In all, our findings are also supportive of recent re- search that suggests organic accretion may be of critical im- portance in marsh survival under RSLR, particularly in areas most removed from inorganic sediment delivery (D’Alpaos and Marani, 2015). Whether below-ground organic matter production makes substantial contributions to Australian salt marsh surface elevation dynamics and vulnerability to sea- level rise remains unknown and represents an important area for further research. Better understanding of the temporal dynamics of organic and mineral contributions to elevation The Supplement related to this article is available online at https://doi.org/10.5194/bg-14-3763-2017-supplement. Competing interests. The authors declare that they have no conflict of interest. Acknowledgements. Charlie Hinchcliffe, Mikael Kim, Sarah Meoli and Frederic Cadera assisted with field measurements. Janine Mc- Gowan and Bruce Hawke assisted with sample preparation and spectroscopic methods. Field collections were undertaken in ac- cordance with NSW Office of Environment and Heritage scientific licence SL101217 and NSW Department of Primary Industries Scientific permit P13/0058-1.0. We also thank NSW National Parks and Wildlife Service for supporting access to Towra Point Nature Reserve. This research was supported by the CSIRO Coastal Carbon Cluster. Peter I. Macreadie was supported by an Australian Research Council DECRA fellowship (DE130101084). Edited by: Steven Bouillon Reviewed by: two anonymous referees Edited by: Steven Bouillon Reviewed by: two anonymous referees 4.3.2 Chemical composition of deposits varies among assemblages We have assessed the chemistry of above-ground biomass, litter and unidentified residues through elemental (C : N) and spectrometric (MIR spectroscopy, 13C NMR) methods. Most importantly, our results highlight assemblage differences in the transformation of OM along the biomass–litter–soil de- cay continuum. Shifts in the bulk composition of materials were best seen in the principal component plots of MIR spec- tra, in which biomass, litter and soil residue samples varied across PC1 (Fig. 4a). Broadly, the separation of residues from litter and biomass was primarily due to the addition of min- eral components in the residues; however, there was also ev- idence of a shift in alkyl OM. Specifically, the presence of a single peak at ∼2900 cm−1 in the loadings plot (Fig. 4b) was indicative of a declining cellulose content across PC1, that is, in the general order live biomass – litter – residue. Importantly, cellulose also appears to be a factor in the sepa- ration of residues from the three different salt marsh assem- blages along PC2 (Fig. 4c), suggesting higher content in the two Juncus samples, followed by Sporobolus and then Sar- cocornia samples. This finding was confirmed by 13C NMR data, which showed that greater proportions of plant com- Together, these data from SE Australia contribute to a broader pattern of plant assemblage differences in salt marsh surface dynamics and C sequestration potential (Minden and Kleyer, 2015; Saintilan et al., 2013; Wang et al., 2003). They also highlight short-term processes that may contribute to the high capacity of Juncus salt marshes to accumu- late significant C stocks globally (0.034 g C cm−2 yr−1 or 0.093 mg C cm−2 d−1), relative to most other salt marsh gen- era (mean C accumulation rate = 0.024 g C cm−2 yr−1 or 0.066 mg C cm−2 d−1; Ouyang and Lee, 2014). Biogeosciences, 14, 3763–3779, 2017 www.biogeosciences.net/14/3763/2017/ 3776 Edited by: Steven Bouillon Reviewed by: two anonymous referees J. J. Kelleway et al.: Salt marsh surface deposition Feldspar marker horizon technique, Estuaries, 12, 260–268, 1989. Guest, M. A., Connolly, R. M., and Loneragan, N. R.: Carbon move- ment and assimilation by invertebrates in estuarine habitats at a scale of metres, Mar. Ecol.-Prog. Ser., 278, 27–34, 2004. Cahoon, D. R., Day Jr, J. W., and Reed, D. J.: The influence of sur- face and shallow subsurface soil processes on wetland elevation: A synthesis, Current Topics In Wetland Biogeochemistry, 3, 72– 88, 1999. 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D.: Accretion rates in salt marshes in the Eastern Scheldt, south-west Netherlands, Estuar. Coast. Shelf Sci., 26, 379–394, 1988. Kirwan, M. L., Temmerman, S., Skeehan, E. E., Guntenspergen, G. R., and Fagherazzi, S.: Overestimation of marsh vulnerability to sea level rise, Nature Climate Change, 6, 253–260, 2016. Ouyang, X. and Lee, S. Y.: Updated estimates of carbon accumula- tion rates in coastal marsh sediments, Biogeosciences, 11, 5057– 5071, https://doi.org/10.5194/bg-11-5057-2014, 2014. Krauss, K. W., Allen, J. A., and Cahoon, D. R.: Differential rates of vertical accretion and elevation change among aerial root types in Micronesian mangrove forests, Estuar. Coast. Shelf Sci., 56, 251–259, 2003. Phillips, D. L.: Converting isotope values to diet composition: the use of mixing models, J. Mammal., 93, 342–352, 2012. Reed, D. J.: Patterns of sediment deposition in subsiding coastal salt marshes, Terrebonne Bay, Louisiana: the role of winter storms, Estuaries, 12, 222–227, 1989. Kristensen, E.: Decomposition of macroalgae, vascular plants and sediment detritus in seawater – use of stepwise thermogravime- try, Biogeochemistry, 26, 1–24, 1994. Rogers, K. and Saintilan, N.: Relationships between surface eleva- tion and groundwater in mangrove forests of southeast Australia, J. Coast. Res., 24, 63–69, 2008. Langley, J. A., McKee, K. L., Cahoon, D. R., Cherry, J. A., and Megonigal, J. P.: Elevated CO2 stimulates marsh elevation gain, counterbalancing sea-level rise, P. Natl. Acad. Sci. USA, 106, 6182–6186, 2009. Rogers, K., Wilton, K. M., and Saintilan, N.: Vegetation change and surface elevation dynamics in estuarine wetlands of south- east Australia, Estuar. Coast. Shelf Sci., 66, 559–569, 2006. Lovelock, C. E., Adame, M. F., Bennion, V., Hayes, M., O’Mara, J., Reef, R., and Santini, N. S.: Contemporary Rates of Carbon Sequestration Through Vertical Accretion of Sediments in Man- grove Forests and Saltmarshes of South East Queensland, Aus- tralia, Estuar. Coast., 37, 763–771, 2013. Rogers, K., Saintilan, N., and Copeland, C.: Managed Retreat of Saline Coastal Wetlands: Challenges and Opportunities Identi- fied from the Hunter River Estuary, Australia, Estuar. J. J. Kelleway et al.: Salt marsh surface deposition Coast., 37, 67–78, 2014. McGroddy, M. E., Daufresne, T., and Hedin, L. O.: Scaling of C: N: P stoichiometry in forests worldwide: implications of terrestrial Redfield-type ratios, Ecology, 85, 2390–2401, 2004. Rogers, K., Saintilan, N., and Woodroffe, C. D.: Surface eleva- tion change and vegetation distribution dynamics in a subtrop- ical coastal wetland: Implications for coastal wetland response to climate change, Estuar. Coast. Shelf Sci., 149, 46–56, 2014. McKee, K. L., Cahoon, D. R., and Feller, I. C.: Caribbean man- groves adjust to rising sea level through biotic controls on change in soil elevation, Global Ecol. Biogeogr., 16, 545–556, 2007. Rooth, J. E., Stevenson, J. C., and Cornwell, J. C.: Increased sedi- ment accretion rates following invasion by Phragmites australis: the role of litter, Estuar. Coast., 26, 475–483, 2003. Minden, V. and Kleyer, M.: Ecosystem multifunctionality of coastal marshes is determined by key plant traits, J. Veg. Sci., 2015. Rosencranz, J. A., Ganju, N. K., Ambrose, R. F., Brosnahan, S. M., Dickhudt, P. J., Guntenspergen, G. R., MacDonald, G. M., Takekawa, J. Y., and Thorne, K. M.: Balanced Sediment Fluxes in Southern California’s Mediterranean-Climate Zone Salt Marshes, Estuar. Coast., 39, 1035–1049, 2016. Morris, J. T.: Ecological engineering in intertidial saltmarshes, Hy- drobiologia, 577, 161–168, 2007. Morris, J. T., Sundareshwar, P., Nietch, C. T., Kjerfve, B., and Ca- hoon, D.: Responses of coastal wetlands to rising sea level, Ecol- ogy, 83, 2869–2877, 2002. Roy, P., Williams, R., Jones, A., Yassini, I., Gibbs, P., Coates, B., West, R., Scanes, P., Hudson, J., and Nichol, S.: Structure and function of south-east Australian estuaries, Estuar. Coast. Shelf Sci., 53, 351–384, 2001. Mudd, S. M., Fagherazzi, S., Morris, J. T., and Furbish, D. J.: Flow, sedimentation, and biomass production on a vegetated salt marsh in South Carolina: Toward a predictive model of marsh morpho- logic and ecologic evolution, Coast. Estuar. Stud., 59, 165–188, 2004. Saintilan, N., Rogers, K., Mazumder, D., and Woodroffe, C.: Al- lochthonous and autochthonous contributions to carbon accumu- lation and carbon store in southeastern Australian coastal wet- lands, Estuar. Coast. Shelf Sci., 128, 84–92, 2013. Mudd, S. M., Howell, S. M., and Morris, J. T.: Impact of dynamic feedbacks between sedimentation, sea-level rise, and biomass production on near-surface marsh stratigraphy and carbon accu- mulation, Estuar. Coast. Shelf Sci., 82, 377–389, 2009. J. J. 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Day Jr, J., Rybczyk, J., Scarton, F., Rismondo, A., Are, D., and Cecconi, G.: Soil accretionary dynamics, sea-level rise and the survival of wetlands in Venice Lagoon: a field and modelling ap- proach, Estuar. Coast. Shelf Sci., 49, 607–628, 1999. Day, Jr, J., Kemp, G. P., Reed, D. J., Cahoon, D. R., Boumans, R. M., Suhayda, J. M., and Gambrell, R.: Vegetation death and rapid Biogeosciences, 14, 3763–3779, 2017 www.biogeosciences.net/14/3763/2017/ J. J. Kelleway et al.: Salt marsh surface deposition Skjemstad, J., Clarke, P., Taylor, J., Oades, J., and Newman, R.: The removal of magnetic materials from surface soils-a solid state 13C CP/MAS NMR study, Soil Res., 32, 1215–1229, 1994. Mudd, S. M., D’Alpaos, A., and Morris, J. T.: How does vegetation affect sedimentation on tidal marshes? Investigat- ing particle capture and hydrodynamic controls on biolog- ically mediated sedimentation, J. Geophys. Res.-Earth, 115, https://doi.org/10.1029/2009JF001566, 2010. Stapel, J. and Hemminga, M.: Nutrient resorption from seagrass leaves, Mar. Biol., 128, 197–206, 1997. Sterner, R. W. and Hessen, D. O.: Algal nutrient limitation and the nutrition of aquatic herbivores, Annu. Rev. Ecol. Syst., 25, 1–29, 1994. Mueller, P., Jensen, K., and Megonigal, J. P.: Plants Mediate Soil Organic Matter Decomposition In Response To Sea Level Rise, Glob. Change Biol., 22, 404–414, 2016. Thomas, S. and Ridd, P. V.: Review of methods to measure short time scale sediment accumulation, Mar. Geol., 207, 95–114, 2004. Nolte, S., Koppenaal, E. C., Esselink, P., Dijkema, K. S., Schuerch, M., De Groot, A. V., Bakker, J. P., and Temmerman, S.: Measur- ing sedimentation in tidal marshes: a review on methods and their applicability in biogeomorphological studies, J. Coast. Conserv., 17, 301–325, 2013. van Proosdij, D., Davidson-Arnott, R. G. D., and Ollerhead, J.: Con- trols on spatial patterns of sediment deposition across a macro- tidal salt marsh surface over single tidal cycles, Estuar. Coast. Shelf Sci., 69, 64–86, 2006. Biogeosciences, 14, 3763–3779, 2017 www.biogeosciences.net/14/3763/2017/ www.biogeosciences.net/14/3763/2017/ Zieman, J., Macko, S., and Mills, A.: Role of seagrasses and man- groves in estuarine food webs: temporal and spatial changes in stable isotope composition and amino acid content during de- composition, B. Mar. Sci., 35, 380–392, 1984. J. J. Kelleway et al.: Salt marsh surface deposition 3779 Zieman, J., Macko, S., and Mills, A.: Role of seagrasses and man- groves in estuarine food webs: temporal and spatial changes in stable isotope composition and amino acid content during de- composition, B. Mar. Sci., 35, 380–392, 1984. Wang, X. C., Chen, R. F., and Berry, A.: Sources and preservation of organic matter in Plum Island salt marsh sediments (MA, USA): long-chain n-alkanes and stable carbon isotope compositions, Es- tuar. Coast. Shelf Sci., 58, 917–928, 2003. Zhou, J., Wu, Y., Zhang, J., Kang, Q., and Liu, Z.: Carbon and nitrogen composition and stable isotope as potential indicators of source and fate of organic matter in the salt marsh of the Changjiang Estuary, China, Chemosphere, 65, 310–317, 2006. Zhou, J., Wu, Y., Kang, Q., and Zhang, J.: Spatial variations of carbon, nitrogen, phosphorous and sulfur in the salt marsh sedi- ments of the Yangtze Estuary in China, Estuar. Coast. Shelf Sci., 71, 47–59, 2007. Biogeosciences, 14, 3763–3779, 2017
https://openalex.org/W2327015813
https://periodicos.uninove.br/dialogia/article/download/877/751
Portuguese
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Porque o samba é fi lho da dor (a comemoração dos 500 anos do “descobrimento” do Brasil e a opinião da imprensa portuguesa)
Dialogia
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cc-by
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Dialogia, São Paulo, v. 4, p. 101-113, 2005 1 Introdução mático, um tempo cuja especificidade se forma na essência do ritmo do jornal, fundamentalmente sensível à conjuntura diária. Em 1998, comemorou-se em Portugal os 500 anos da chegada da frota de Vasco da Gama à Índia. No verão desse mesmo ano, realizou-se a Exposição Universal de Lisboa e um ano depois, em 1999, sucederam os épicos acontecimentos relativos à in­ dependência do Timor Leste. Posteriormente, deu-se a retirada total do Estado português de Macau e a subseqüente entrega do território à administração chinesa. Por fim, em 2000, foi a vez das comemo­ rações dos 500 anos do “descobrimento” do Brasil. Em pouco mais de dois anos, estiveram em jogo várias imagens da história de Portugal e muito con­ cretamente do passado imperial do país. Este artigo debruça-se sobre um dos campos de jogo: os artigos de opinião que, de março a maio de 2000, foram publicados em dois jornais diários portugueses de “referência”, tendo por assunto temas suscitados pelas comemorações do “descobrimento” do Brasil. No caso em estudo, é desde logo muito evi­ dente que as contestações dos movimentos sociais brasileiros às comemorações dos 500 anos do “descobrimento” marcaram a agenda da opinião publicada nos jornais portugueses. Em grande medida, a opinião publicada sobre o “descobri­ mento” começa como uma resposta a críticas que chegam do Brasil. Porque o samba é filho da dor (a comemoração dos 500 anos do “descobrimento” do Brasil e a opinião da imprensa portuguesa) José Manuel Viegas Neves Doutorando em História da Cultura – Instituto Superior de Ciências do Trabalho e da Empresa [Portugal]. nevesze@hotmail.com, Lisboa [Portugal] A partir da análise de artigos de opinião publicados na imprensa portuguesa por ocasião da comemoração dos 500 anos do “des­ cobrimento” do Brasil, procura-se situar as relações complexas entre história, poder e identidade, esboçando-se, assim, alguns traços dominantes do nacionalismo português. Em concreto, procura-se perceber o lugar do passado imperial do país nas nar­ rativas históricas e na imaginação sociológica de intelectuais. Igualmente central é a análise dos eixos norteadores da moderni­ dade política que dominaram a abordagem das relações de poder no contexto colonial e hoje permeiam essas relações em contex­ to pós-colonial, no que se refere à relação de colonização e de contestação à comemoração dos 500 anos do “descobrimento” protagonizada por diferentes movimentos sociais no Brasil. Palavras-chave: Comemorativismo. Historiografia. Nacionalismo. Dialogia, São Paulo, v. 4, p. 101-113, 2005 Artigos Artigos 101 Dialogia, São Paulo, v. 4, p. 101-113, 2005 2 A resposta à crítica A “coisa” é complexa – este é um pressuposto central à abordagem de muitos artigos de opinião. Essa generalizada consideração inicial revela uma precaução que é rara no discurso do artigo de opinião e que é mais freqüente como prefácio ao discurso científico. Todavia, nos artigos de opinião que analisamos, o reconhecimento da complexi­ dade não inicia a construção de um problema, mas antes acaba por legitimar que o “descobri­ mento” seja parcelado em dimensões negativas e positivas. A negatividade ou positividade depen­ dem de julgadas conseqüências históricas, isto é, de um tempo posterior ao próprio acontecimento, concluindo-se, em regra, por uma prevalência de uma carga positiva sobre uma outra negativa, ou seja, a reconhecida complexidade que precede o parcelamento, que quebra a consistência do fenô­ meno histórico, é superada por uma síntese final, cuja economia nos restringe ao que de positivo houve no “descobrimento”. Público e Diário de Notícias são jornais com circulação (entre 40 e 60 mil exemplares diários) e público leitor socialmente semelhan­ tes. Os articulistas que aí escrevem têm também origens profissionais parecidas: políticos, acadê­ micos ou jornalistas de prestígio. Esta semelhança genérica não é significativamente perturbada por um eventual posicionamento político-ideológico específico. Os artigos de opinião a seguir foram analisa­ dos privilegiando uma leitura que dialoga com as principais idéias por eles propostas. Constituíram, assim, a um só tempo, material a ser analisado e instrumento de análise, simultaneamente “fonte” e “bibliografia”. Esta ambivalência caracteriza, desde logo, o artigo de opinião como discurso compara­ tivamente ao texto científico: o artigo de opinião compreende um tempo mais precário e mais dra­ A maioria das opiniões acaba, assim, por fazer da história do encontro, da narrativa do sincretismo e do elogio do progresso técnico-científico as ques­ Dialogia, São Paulo, v. 4, p. 101-113, 2005 102 tões centrais, ou seja, as opiniões que se preocupam em afirmar que a história do “descobrimento” e das relações históricas entre Portugal e Brasil não pode ser reduzida à consideração das opressões dão aí um primeiro passo para que nem sequer se fale dessas opressões, ou para que, num balanço geral, se acabe redimindo-as. 2 A resposta à crítica Na maior parte dos casos, não nos parece que se trate de compreender histo­ ricamente a violência, mas, sim, de aceitá-la como manifestação inevitável da História, legitimando-se a narrativa do sacrifício que, uma vez submetido a uma teleologia, acaba por ser integrado numa me­ tafísica do progresso – todo o crescimento tem as suas dores, como escreve Vasco Pulido Valente1: opinião, da autoria de José Gonçalves (2000, p. 12). Aqui, contudo, o programa da crítica é bem dife­ rente. Gonçalves, à época correspondente do Diário de Notícias na África Austral, começa igualmen­ te por equacionar a questão da culpa dos “males” atuais do Brasil – questão que, em regra, é pensada ou em termos de uma culpa que reside ou no pre­ sente nacional brasileiro ou no passado imperial português – e logo critica o discurso da herança colonial por se dar como álibi convocado pelos go­ vernos nacionais de hoje, a fim de escamotearem as suas próprias responsabilidades na presente situ­ ação social do país que governam. Gonçalves, todavia, acrescenta um ponto importante à visão de Fernandes, ao sublinhar que o debate sobre a implicação do passado imperial português no presente nacional brasileiro tende também a secundarizar o fato de, no momento atual, manter-se ou acentuar-se a relação de desi­ gualdade entre Norte e Sul. Gonçalves remete-nos, assim, para uma visão dos conflitos e das desigual­ dades que não obedece estritamente a critérios de relação entre nações e traz à superfície da escrita a trama histórica da convivência das elites do Norte e do Sul, também em tempos pós-coloniais. [...] a civilização Européia não se ex­ pandiu, evidentemente, sem uma invul­ gar barbaridade. Resta saber se, no fim, o mundo ficou pior ou melhor. Eu não hesito em responder que ficou melhor, o que não faz de mim nem um racista, nem um xenófobo [...] (PULIDO VALENTE, 2000, p. 30). Ainda no quadro dessa metafísica do pro­ gresso, constrói-se a crítica da percepção do “descobrimento” como conflito. Em parte, ela se faz na negação da importância dessa conflituosi­ dade e de seus efeitos na situação atual do Brasil. Por exemplo, José Manuel Fernandes, diretor do jornal Público, afirma: “Estivemos 300 anos no Brasil, saímos de lá há 200. Se o Brasil continua a ter problemas sociais [...] isso não é seguramen­ te devido à ‘pesada dívida’ que lá deixamos [...]” (FERNANDES, 2000, p. 3). Dialogia, São Paulo, v. 4, p. 101-113, 2005 2 A resposta à crítica Critica-se assim o dis­ curso que valora o peso da herança colonial. Na compreensão das razões do discurso sobre a herança colonial produzido pelas elites na­ cionalistas dos países do Sul, o questionamento de Gonçalves não é, todavia, predominante. Muitos dos que, como Fernandes, recusam a importân­ cia da violência e da opressão na relação imperial passada respondem ao discurso sobre a herança, invocando a tese que define a colonização por­ tuguesa como tendo sido diferente das restantes colonizações ocidentais: teria sido menos opresso­ ra e menos violenta que suas congêneres. A esse propósito é exemplar a opinião de Miguel Sousa Tavares:2 A crítica do discurso sobre a herança pode também ser encontrada num outro artigo de Dialogia, São Paulo, v. 4, p. 101-113, 2005 Artigos Artigos 103 nos avisa do perigo do anacronismo das análises e dos julgamentos, ponto sublinhado por Fernandes e Sousa Tavares ao considerarem inaceitável que se leia o passado à luz de éticas presentes. A questão in­ terroga também o historiador Fernando Rosas4 que situa o problema inicial precisamente na distinção entre julgamento e análise. Embora concorde com a idéia de que não se pode compreender o passado à luz de éticas presentes, Rosas critica a linha de Fernandes e de Sousa Tavares ao sublinhar que, quando se trata de discursar politicamente no pre­ sente, de comemorar, trata-se de algo mais do que fazer história. Trata-se da Já vi este tipo de argumentação, sobre o extermínio dos índios pelos coloniza­ dores portugueses e espanhóis, usado várias vezes e sobretudo por historiadores anglo-saxónicos. Mas, curiosamente, onde Portugal e Castela estiveram, sobravam e sobram nativos e por onde passaram os outros, não sobra nada [...] (SOUSA TAVARES, 2000, p. 13).3 Está então aberto o caminho à insinuação de que as críticas brasileiras à comemoração do “descobrimento” são devidas ao desgosto brasi­ leiro de celebrar sua “descoberta” por uma nação tão pequena como Portugal, ou seja, a motivação dos brasileiros que contestam a comemoração não estaria tanto numa sua oposição à colonização, mas, sim, no fato de essa colonização-descoberta não ter sido protagonizada por países mais desen­ volvidos. Diz-nos Sousa Tavares (2000, p. 13) que, “[...] pese a alguns brasileiros, não foi a Inglaterra, nem a França ou a Holanda, nem sequer a Espanha, a matriz Européia do Brasil [...]”. 2 A resposta à crítica Sendo certo que a insinuação de Sousa Tavares corresponde a certas teses brasileiras sobre a formação do Brasil, ela acomoda muito especificamente o orgulho nacio­ nal (português) pelo heroísmo que, supostamente, resulta da tantas vezes reiterada desproporção da empresa imperial portuguesa: como um país tão pequeno protagonizou tão grandes feitos. [...] identidade nacional, construída a partir de mitos identitários que usam a matéria-prima do passado à luz de juízos políticos e morais de hoje para fabricar, com valores actuais e com propósitos pre­ sentes e futuros, visões legitimadoras a partir da História. Relativizar o esclava­ gismo e o genocídio índio no quadro deste propósito não é um exercício de compre­ ensão histórica, é uma sua falsificação branqueadora com vista a obter efeitos políticos para o presente e no futuro [...] (ROSAS, 2000, p. 13). No cerne dessa problemática, encontramos o debate sobre a possibilidade de um pedido de desculpas. Tanto Sousa Tavares quanto Fernandes reagem com negativa veemência à hipótese de um pedido de desculpas a ser apresentado por Portugal ao Brasil: rejeitam-na remetendo sua motivação à “moda do politicamente correto”, acrescentan­ do ainda Fernandes que a política da desculpas acentua uma dicotomização da história, isto é, a visão de um mundo feito de índios e de cowboys.5 Dialogia, São Paulo, v. 4, p. 101-113, 2005 3 Culpa: rejeição e esvaziamento A argumentação que visa destituir de racio­ nalidade a crítica do “descobrimento” tece-se ainda por uma outra linha: um acentuado relativismo moral. Este se apresenta sob o senso comum que Dialogia, São Paulo, v. 4, p. 101-113, 2005 104 Havendo autores que afirmam ser inútil pedir desculpas porque semelhante ato em nada transformará o passado, a verdade é que a maioria rejeita simplesmente a idéia de culpa. Para essa maioria, não parece que a questão se ponha entre saudar ou criticar os valores dos portugueses co­ lonizadores de antanho, mas de ressaltar que a noção de culpa só é atribuível a um entendimento de hoje: à luz dos padrões de ontem, a questão da culpa não era imaginável, sequer chegava a existir. Mais do que rejeitar a culpa, assistimos agora ao seu esvaziamento. Ora, é precisamente aqui que se inscreve o significado do relativismo moral: tal como hoje se relativizam relações de dominação em partes do mundo decorrentes de identificadas culturas locais assim imaginadas, relativizam-se, igualmente, relações de domi­ nação em momentos históricos anteriores como conseqüência de atrasadas culturas de época assim imaginadas. Pedir desculpas aos índios, aos africanos, aos indianos e aos timorenses obrigaria a definir lucidamente a posição de Portugal na história e no mundo, ajudaria a impedir a nossa alegre deriva colectiva para o ano­ nimato, forçaria os outros (os descenden­ tes das antigas vítimas) a vitimizarem-se um pouco menos (GOMES, 2000, p. 9). Além de criticado por Gomes pela sua cumpli­ cidade com o passado imperial português, Sampaio também o é por não elogiar suficientemente esse mesmo passado. Luís Delgado,9 reagindo a notí­ cias sobre as contestações dos movimentos índios, acusa Sampaio de ter vergonha do “descobrimen­ to”. O móvel da acusação de Delgado é o fato de Sampaio se manifestar grato por um convite do Estado brasileiro solicitando seu comparecimen­ to às comemorações oficiais. Afirma Delgado que, se o Brasil não quer comemorar o ato, então Portugal deve fazê-lo sozinho, pois, na gratidão de Sampaio, Delgado vê submissão. A opinião de Delgado interessa-nos por expressar os “pontos de honra” de uma tradição política de direita, tida por mais conservadora, uma tradição que não parece disposta a admitir a falibilidade da nação ou qualquer outro indício de questionamento do passado do país. Como proclama Delgado (2000a, p. 2), “[...] a história não se justifica, assume-se. Com força e orgulho [...]”. Dialogia, São Paulo, v. 4, p. 101-113, 2005 3 Culpa: rejeição e esvaziamento É em artigos como os de Miguel Portas6 (2000) e de Paulo Varela Gomes7 que encon­ traremos uma interpretação dissonante e, em grande medida, contraposta à de Sousa Tavares e de Fernandes. Ambos os autores refutam, desde logo, a idéia da inconseqüência do pedido de desculpas. Portas dá o exemplo de como, “nos Balcãs, uma batalha ocorrida há 500 anos foi ontem”, isto é, o pedido de desculpas pode fazer parte de uma memória crítica. Gomes insiste nesse ponto, contrastando a atitude do presi­ dente português, Jorge Sampaio, no Brasil, com a de João Paulo II, ao publicar o documento Memória e reconciliação.8 Gomes sublinha que o pedido de desculpas é um ato para o futuro, definindo uma mudança na posição dos interlo­ cutores por meio de um gesto que aponta novas responsabilidades para todos: A excepcionalidade de Delgado resiste à com­ paração com outros rasgados elogios tecidos ao “descobrimento”. Pedro Rebelo de Sousa, então presidente da Fundação Luso-Brasileira para o Desenvolvimento do Mundo de Língua Portuguesa, fala-nos do cumprimento da tarefa “lusíada”, estando certo “[...] de que soubemos deixar a men­ sagem do universalismo [...]” (REBELO DE SOUSA, Dialogia, São Paulo, v. 4, p. 101-113, 2005 Artigos Artigos 105 2000, p. 12). Carlos Magno, em editorial do Diário de Notícias, reforça a retórica do “Pai Portugal”: “[...] estamos a comemorar o melhor produto made in Portugal. O Brasil é o maior feito dos portugueses [...]” (MAGNO, 2000, p. 3). Esse nexo causal, esta idéia do Brasil de hoje como fruto e como filho do “descobrimento” português, perpassa o sentido de muitos dos artigos aqui analisados bem como o de muitas reportagens e notícias publicadas então na imprensa. De forma mais ou menos assumida, mais ou menos banal, reitera-se assim a crença na necessidade e na responsabilidade de civilização, concretizada quer na imaginação dos portugue­ ses como um povo designado a ser um elo entre mundos diferentes, quer na metáfora da dívida do filho brasileiro para com o pai português. Também de exemplos menos flagrantes se faz a persistência dos tópicos lusotropicalistas. Adriano Moreira (2000) justifica a contestação índia do “descobrimento” dizendo que os índios já não se comportam como num passado em que eram povos mudos por quem outros falavam, ou seja, em Moreira narra-se um passado em que a culpa não é uma questão, uma vez que a vítima não se fazia existir. 3 Culpa: rejeição e esvaziamento Moreira, ministro do Ultramar no regime fascista e atualmente uma figura “senatorial” da democracia portuguesa, não aventa a hipótese de, no passado que imagina, os índios terem sido impedidos de falar ou de não terem sido ouvidos. A modernidade política abraçada por Moreira, alicerçando-se na sua ambição universalizan­ te aplicável tanto no contexto colonial quanto no pós-colonial, somente reconhece as críticas expressas na sua própria linguagem, ignoran­ do sua surdez etnocêntrica ao atribuir a mudez ao “outro”. Como fundantes dessa modernidade política, encontramos os princípios elementares de um racionalismo iluminista que apenas reco­ nhece a aptidão histórica do “outro” à custa da identificação desse mesmo “outro” com o próprio racionalismo iluminista, o que depende do “pro­ cesso civilizatório”, seja em tempo colonialista ou pós-colonial. Moreira, ministro do Ultramar no regime fascista e atualmente uma figura “senatorial” da democracia portuguesa, não aventa a hipótese de, no passado que imagina, os índios terem sido impedidos de falar ou de não terem sido ouvidos. Decorre assim um jogo vivo de imagens que é apenas uma batalha de uma guerra maior: o debate sobre a identidade nacional portuguesa. Sobre esse jogo paira um espectro que, tão etéreo quanto visível, assola igualmente boa parte das opiniões publicadas – um espectro adensado por temas usualmente ligados ao lusotropicalis­ mo. Em nome da “cultura lusíada,” Rebelo de Sousa fala-nos de um povo que soube “conviver com índios e negros”. Extasiado diante do espe­ táculo do Sambódromo carioca, afirma “[...] que orgulho olhar aquela mistura de raças, a dançar o samba celebrando o descobrimento, mesmo com o que ele trouxe de crítico para o índio e para o negro [...]” (REBELO DE SOUSA, 2000, p. 12). Não se trata, portanto, do que de trágico e de opressor o “descobrimento” trouxe à vida do índio e do negro, mas, sim, do aspecto “crítico”: a relação entre portugueses, índios e negros não foi tão marcada pelo conflito e pelo poder quanto o foi pela “mistura” e pelo “conviver”. A dor resume-se ao prazer. O samba não é filho da dor. O absolutismo universalista inicia-se, por­ tanto, no relativismo moral. O “outro” só existe como sujeito se for igual ao “eu”, porque a sua alteridade é de tal forma irredutível que não deixa lugar para entendimento e interação entre o “outro” e o “eu”. Não é possível uma relação de homem para homem. 4 Políticas de identidade: a atualidade do lusotropicalismo e que todos subscrevemos –, acaba-se por ter a própria idéia da culpa como um atributo sem ca­ bimento nessa mesma época histórica passada, como se a noção de culpa fosse apenas um atri­ buto representado no discurso de intelectuais críticos do presente, aos quais se pede que rela­ tivizem. Essa situação é possível apenas porque um processo de desvalorização da história social do passado silencia a resistência dos colonizados à colonização, abrindo o campo à percepção de que os colonizados não estão aptos a sentir sub­ jetivamente as dores de crescimento objetivas do progresso. O “conviver” que Rebelo de Sousa convoca leva-nos diretamente à tese fulcral de Freyre, quando este nos diz que o ambiente social do império português era, grosso modo, marcado pela forte reciprocidade cultural que permitia ao coloni­ zado aprender mais facilmente com o colonizador. Essa “lusíada” característica da “pedagogia” como marca fundadora da relação entre os portugueses e os povos do império derivaria do fato de o povo português ser o privilegiado elo entre diferentes mundos – entre civilização e barbárie –, o que seria já decorrente dos momentos iniciais de uma etnia lusa em que o traço árabe teria sido tranqüilamen­ te incorporado. Portugal como país de “vocação ecumênica” – eis uma imagem que nem a vio­ lenta guerra colonial dos anos 1960 e 1970, com toda a sua escancarada materialidade, conseguiu destruir. Sendo a recepção portuguesa do lusotro­ picalismo de Freyre circunscrita a uma conjuntura política específica – as transformações que perfa­ zem uma nova abordagem do Estado português ao império, no limiar do segundo pós-guerra – seus tópicos são ainda atuais no modo português inte­ lectualmente dominante de ver “o modo português de estar no mundo”.11 E, como agora sublinham os trabalhos de alguns cientistas sociais, a atualidade desses tópicos antecede mesmo o tempo do próprio regime fascista, remetendo ao pensamento de di­ versos intelectuais portugueses nos séculos XIX e XX (CASTELO, 1998). Hoje, depois das comemorações de 1940 (com O “conviver” que Rebelo de Sousa convoca leva-nos diretamente à tese fulcral de Freyre, quando este nos diz que o ambiente social do império português era, grosso modo, marcado pela forte reciprocidade cultural que permitia ao coloni­ zado aprender mais facilmente com o colonizador. 3 Culpa: rejeição e esvaziamento Começando por en­ tender os sentidos da culpa como algo relativo à época histórica passada – princípio de análise que nos vacina contra o perigo do anacronismo Dialogia, São Paulo, v. 4, p. 101-113, 2005 106 Dialogia, São Paulo, v. 4, p. 101-113, 2005 4 Políticas de identidade: a atualidade do lusotropicalismo O termo “descobrimento”, instituindo, mais ou menos pro­ nunciadamente, a desigualdade em nível da aptidão histórica dos agentes – por um lado, o ativo, viril e masculino colonizador; por outro, a doce, passiva e feminina colônia –, perde agora terreno para o termo “encontro”, o qual obscurece novamente a dimensão do conflito e de desigualdade no processo de construção de uma memória que se procura par­ tilhada. Nesse contexto, os temas lusotropicalistas renovam a sua atualidade: retoma-se a imagem de um Portugal naturalmente ecumênico e, ao mesmo tempo, afastamo-nos da problemática atual da de­ sigualdade Norte/Sul. Mas, para além disso, Sampaio reconhece que o que está em causa nas comemorações não é somente um debate histórico em que a compreen­ são se deve mostrar como condição sine qua non da leitura histórica: ele lamenta que não se valo­ rize mais o ensino da história de Portugal – base da identidade nacional. Sampaio revela claramen­ te que a visão atual do passado é já um campo de jogo político e que, para além do trabalho neces­ sariamente compreensivo do historiador, há um discurso político presente em todo o ato comemo­ rativo. Todos estão cientes da promiscuidade entre passado e presente implícito no ato comemorativo. Talvez poucos, porém, terão abordado a questão em termos tão claros e instrumentais quanto os do pre­ sidente da Comissão Nacional para a Comemoração dos Descobrimentos Portugueses (CNCDP), o histo­ riador Romero de Magalhães (2001, p. 11): Em razão de ser produzido por alguém que desempenha o cargo institucional mais alto na hie­ rarquia do poder nacional em Portugal, o diário da viagem do presidente da República ao Brasil, por ocasião das celebrações do “descobrimento” – pu­ blicado no jornal Público ao longo de vários dias –, é um curioso objeto de análise e um ponto de abertura do debate da relação entre história, polí­ tica e identidade. Reagindo às manifestações que a comemoração oficial do “descobrimento” suscita no Brasil, Sampaio afirma inicialmente que as compreende e que crê que o momento deva ser apro­ veitado para discutir o presente e o futuro. Contudo, essa compreensão de Sampaio não mais ressurge nos seus relatos e ele desde cedo afirma que a con­ Portugal é hoje, a despeito de todos os seus problemas, um país a caminhar para uma modernização que vai dar-lhe uma feição diferente, já advinhável de resto em algumas coisas. 4 Políticas de identidade: a atualidade do lusotropicalismo De um modo que extrema ainda mais a relação identidade/diferença, Delgado conclui sua crítica ao presidente Sampaio, assumindo o valor da identidade sobre o da alteridade, isto é, proclamando que toda a alteridade é irredu­ tível e, portanto, identitária: “Nós, e eles, somos a mesma coisa [...]” (DELGADO, 2000b, p. 2). O valor da identidade, todavia, não se resume à vontade identitária de Delgado; ele também pre­ valece em narrativas em que uma retórica da alteridade se afirma muito energicamente. É o que sucede quando Edson Athayde10 retoma os tópicos do lusotropicalismo de Gilberto Freyre e se assume, ele próprio, como fruto de um “[...] milk shake genético [...]” (ATHAYDE, 2000, p. 14). Se já no passado a imagem da alteridade em Freyre presidira tanto a um discurso identitário sobre o Brasil quanto a um discurso identitário sobre Portugal – com a leitura positiva do lusotropica­ lismo pelo fascismo português –, hoje ela se afina igualmente com os diversos discursos identitários do nacionalismo português e brasileiro. Em qual­ quer um dos casos, o “outro” é imaginado como diferente do “eu”, sendo a diferença motivo para a celebração ou para o confronto. Hoje, depois das comemorações de 1940 (com destaque para a Exposição do Mundo Português) e após as comemorações henriquinas da década de 1960 (em que, num contexto de integração do regime na nova ordem internacional do pós-guerra, Dialogia, São Paulo, v. 4, p. 101-113, 2005 Artigos 107 testação do “descobrimento” que ocorre no Brasil em nada diminui o brilho do passado português. Em texto ou em declarações públicas, Sampaio não mais se referirá a essas mesmas contestações. “Lamento que a história, no que teve de negativo, tenha sido o que foi [...]”, disse Sampaio, mostran­ do que o ponto decisivo não é ter uma visão crítica do passado, e sim a importância dada a essa visão crítica por contraponto a uma outra celebratória (SAMPAIO, 2000, p. 3). a retórica da “missão” adquiriu maior relevância no contexto da colonização), as comemorações dos descobrimentos portugueses parecem ter mergulha­ do num novo ciclo. Perdidas as colônias africanas e caído o império, a questão da identidade nacio­ nal instala-se agora na retórica da “lusofonia”, conceito que é o rosto de uma comunidade que se imagina com uma língua comum e uma cultura harmoniosa – “todos diferentes, todos iguais” – que sustentam a tolerância racial. Dialogia, São Paulo, v. 4, p. 101-113, 2005 4 Políticas de identidade: a atualidade do lusotropicalismo E é esse Portugal que nos convém que seja visto e apreciado [...] O historiador pode garantir-se na dissociação entre o tempo passado e o tempo presente, procu­ Dialogia, São Paulo, v. 4, p. 101-113, 2005 108 corpo/razão atualiza-se: o imaginário português dominante na área da sensualidade – da destreza da arte futebolística de um Ronaldinho à beleza da “mulher brasileira” – está indelevelmente marcado pelo universo do made in Brazil, do carnaval à te­ lenovela e da música ao futebol.12 rando assim, em nome da objetividade científica, preservar o passado dos olhares categorizadores e moralistas presentes; no entanto, para aquele que hoje se encontra a tutelar os espaços dos poderes do­ minantes, a ciência não tem como se furtar a servir à política: o passado é o código de conduta que an­ tecede a ação presente que assim se legitima como simples procedência. A história é aqui uma presta­ ção de serviço à política. Este mapa cartesiano da história mundial – no Norte, o elemento racional; no Sul, o elemen­ to corporal –, configurando igualmente uma face feminina e outra masculina da História, restringe os agentes do passado aos Estados, às nações ou às chamadas civilizações, ignorando os confrontos sociais ou culturais no interior e à margem daque­ las entidades e silenciando a diversidade de agentes históricos em jogo. É na construção desse silêncio que a evocação metafórica da família se revela tão importante na frase de Athayde, já que é difícil en­ contrar uma instituição que seja dominantemente imaginada como mais coesa, unificada e impene­ trável: “[...] houve sim massacres e explorações. Mas e daí? O que passou, passou. Todas as famílias têm os seus podres. Mas nem assim deixam de ser família [...]” (ATHAYDE, 2000, p. 14). 5 Políticas de identidade: história, identidade e movimento “São 500 anos de cópula, uma das maiores orgias da história. Com o Brasil a ser continuamen­ te fecundado por gerações infinitas de imigrantes portugueses.” A frase é todo um épico slogan, não fosse de autoria de um profissional do marketing como o brasileiro Athayde (2000, p. 14). Não sendo inovador o recurso à metáfora do corpo na história dos povos, reconheçamos a carnosidade do retrato de Athayde, o qual nos permite observar, sem grande esforço, como o discurso do racismo e da etnicização se dá como uma outra face do discurso do sexismo e da feminização. Na metáfora de Athayde podemos de fato observar como se cruzam os tópicos retóricos da “raça” e do gênero: a idéia da colônia como o espaço passivo, virginal, desprotegido e selvagem que “pede” para ser domado é corrente no imaginário colonialista europeu. Tal idéia articula-se com uma outra que lhe é oposta mas afim, a idéia do estado- nação europeu como o agente ativo, fecundador, viril e civilizador que não pode fugir à responsabi­ lidade da iniciativa e da educação, conceitos que aqui assumem, respectivamente, suas feições mais voluntaristas e paternalistas. No contexto presente das relações entre Portugal e Brasil, essa dicotomia Raros são os artigos de opinião que propõem uma narrativa alternativa à que é produzida nas esferas de influência dos poderes políticos e culturais dominantes. Mesmo quem recusa a comemoração do “descobrimento” aceita a necessidade de narrar uma identidade nacional. Tal é o caso de Rosas que reivindica a importância de uma identidade da democracia portuguesa construída a partir da Revolução de Abril e em oposição às tradicionais narrativas nacionais. Deslocados do “olho da nação” encon­ tramos apenas alguns artigos de opinião, entre os quais se encontra o texto do historiador Luiz Felipe de Alencastro (2000), publicado no jornal Público, em que aborda as relações históricas Dialogia, São Paulo, v. 4, p. 101-113, 2005 Artigos 109 ao movimento indígena ou aos sem-terra, mas antes remete para a relação geral dos cronistas citados com as dinâmicas político-sociais que não se subordinem ao enquadramento normativo da modernidade política. Essa relação se expressa na opinião que outros movimentos sociais e experi­ ências políticas suscitam àqueles articulistas, dos novos movimentos globais anticapitalistas, tidos como “antiglobalização”, aos movimentos do universo lésbico, gay, bissexual e transgênero. 5 Políticas de identidade: história, identidade e movimento A oposição dos articulistas a esses movimentos se ex­ pressa, na maior parte das vezes, destituindo-os de atributos de racionalidade política, o que em regra antecede a sua irracionalização. entre Portugal e Brasil, mostrando como as elites políticas, comerciais e econômicas de ambos os países, por meio do escravismo, contribuíram para a situação angolana presente. Já o antropólogo Miguel Vale de Almeida preocupa-se em perceber as diferenças manifestas na adesão ao fenômeno comemorativo, diferenças que situa além do senti­ mento nacional. A propósito do movimento negro, do “renascimento indígena” ou do Movimento dos Trabalhadores Rurais Sem-Terra (MST), Almeida (2000a, p. 8) escreve no Público: “[...] para eles, ou os 500 anos não têm a menor importância, ou são uma oportunidade para contestar as bases co­ loniais das desigualdades sociais.” A contestação de movimentos de índios, do movimento negro e do MST à comemoração do “descobrimento”, despertando, de alguma forma, a opinião portuguesa publicada para um debate do qual se encontrava, até então, relativamente distante, nem sempre é explícita e diretamente dis­ cutida. A exceção mais clara é Fernandes (2000, p. 3) que afirma: “[...] por mais índios e sem-terra que se manifestem por estes dias, eu não vou deixar de me orgulhar de pertencer ao povo que empre­ endeu tais viagens e lançou raízes de tão longe.” Saliente-se que Fernandes, ainda que por outros caminhos, evita, por vezes, a lógica de represen­ tação exclusivamente nacional dos conflitos – ele assegura-nos que tanto Sampaio quanto Fernando Henrique Cardoso deram provas de maturidade por contraponto aos movimentos sociais brasileiros. Uma vez mais, ele mostra o seu incômodo perante os movimentos sociais brasileiros. Aqui e ali esse desconforto será explicitamente assumido por outros articulistas, como Delgado, Moreira, Magno ou Sousa Tavares. Dialogia, São Paulo, v. 4, p. 101-113, 2005 6 Considerações finais Num contexto geral em que a idéia de co­ nhecimento é fortemente submetida à de ciência, o processo de construção da irracionalidade do mo­ vimento social analisado mobiliza regularmente a legitimidade científica e acadêmica do sujeito que analisa. Essa legitimidade dá-se como um or­ namento cujo simbolismo protege o discurso do poder político dominante. É isso que está em jogo nas declarações acima citadas de Magalhães, um historiador de méritos científicos notórios e reco­ nhecidos que presidiu à CNCDP. O encontro entre a tarefa científica do historiador e a tarefa políti­ ca do comissário13 expõe-nos a sua problemática compatibilidade: enquanto o historiador é inter­ rogado pelo caos e pela disparidade, o comissário é solicitado pela ordem e pela identidade. O lugar que se quer simultaneamente ocupado pelo co­ missário e pelo historiador é um lugar resistente à competência do segundo. E o inverso não deixa de ser também verdade, isto é, o lugar do historiador O problema que nos apresenta a aborda­ gem desses articulistas não é uma questão restrita Dialogia, São Paulo, v. 4, p. 101-113, 2005 110 Why the samba is a pain’s son (the 500 years Brazil’s “discovery” celebration and the Portuguese press’ opinion) revela-se resistente à função do comissário, e isso se verifica mesmo quando o historiador António Hespanha, que antecedeu Magalhães na presidên­ cia da CNCDP, recusa a idéia do pedido de desculpas de Portugal ao Brasil, por rejeitar a carga de iden­ tidade nacional que transporta a própria noção da culpa, por ele tida como impessoal e transmissível ao afetar outro que não o diretamente responsável (HESPANHA, 2000). Starting from the analysis of opinion articles published in the Portuguese press during the 500 years Brazil’s “discovery” celebration, one searches to place the complex relations among history, power and identity, outlining some dominant characteristics of the Portuguese nationalism. Concretely, one tries to notice the place occupied by the imperial past in the country on the historical narratives and on the scholars’ sociological imagination. Equally central is the analysis of the guiding points of the political modernity which dominated the approach about the power relations in the colonial context and nowadays permeates these relations in the post- colonial context, concerning the colonization relation and the protest against the 500 years Brazil’s “discovery” celebration leaded by different social movements in Brazil. Foi com a vantagem de partir de um lugar, porventura, mais convidativo ao historiador, mas também arcando com a desvantagem de dispor­ mos de uma qualidade científica em tudo menor à de Magalhães e de Hespanha, que iniciamos este trabalho. Observando o debate sobre a herança colonial e os sentidos da culpa, descrevemos a mobilização do ideário lusotropicalista no atual contexto de construção de uma identidade na­ cional portuguesa que continua a encontrar, no legado imperial, o lugar dos “outros” que definem o “eu”. Essa mobilização e esta definição são o re­ sultado de processos intelectuais em que as políticas de identidade presentes inspiram as aproximações históricas ao passado. Fazem-no propondo certas substâncias culturais como conteúdos de uma identidade, mas fazem-no igualmente, desde logo, propondo o princípio da identidade como forma de representação das relações sociais tanto de ontem quanto de hoje. Key words: Celebrationism. Historiography. Nationalism. Key words: Celebrationism. Historiography. Nationalism. ALMEIDA, M. V. de. Comemorar o futuro. Público, Lisboa, p. 8, 22 abr. 2000a. ALMEIDA, M. V. de. Comemorar o futuro. Público, Lisboa, p. 8, 22 abr. 2000a. 5 Paradoxalmente, depois de 11 de setembro de 2001, e a propósito quer da Guerra do Afeganistão quer da Guerra do Iraque, Fernandes – que em ambos os casos apoiou a política do governo dos Estados Unidos – foi objeto de críticas que denunciaram a dicotomização moral da história subjacente à sua opinião. 5 Paradoxalmente, depois de 11 de setembro de 2001, e a propósito quer da Guerra do Afeganistão quer da Guerra do Iraque, Fernandes – que em ambos os casos apoiou a política do governo dos Estados Unidos – foi objeto de críticas que denunciaram a dicotomização moral da história subjacente à sua opinião. ______. Um mar da cor da terra: raça, cultura e política da identidade. 1. ed. Oeiras: Celta, 2000b. ATHAYDE, E. Inconsciente colectivo. Diário de Notícias, Lisboa, p. 14, 23 abr. 2000. CASTELO, C. O modo português de estar no mundo: o luso-tropicalismo e a ideologia colonial portuguesa (1933-1961). 1. ed. Porto: Afrontamento, 1998. 6 Portas é jornalista e mantém uma página de opinião no Diário de Notícias. Tal como Rosas, hoje é um dos principais rostos do Bloco de Esquerda. Atualmente é deputado do Parlamento Europeu. DELGADO, L. A honra de Cabral. Diário de Notícias, Lisboa, p. 2, 24 abr. 2000a. 7 Gomes é historiador de arte. Politicamente situa-se também numa área pós-comunista, embora as suas posições não possam ser balizadas nos clássicos termos esquerda e direita. ______. Gratos? Diário de Notícias, Lisboa, p. 2, 25 abr. 2000b. FERNANDES, J. M. Sem complexos. Público, Lisboa, p. 3, 22 abr. 2000. 8 Autoria do agora papa Bento XVI. 8 Autoria do agora papa Bento XVI. 9 Delgado é um dos mais importantes jornalistas portugueses, ocupando vários cargos de direção em grupos de mídia. GOMES, P. V. A herança do presidente. Público, Lisboa, p. 9, 2 maio 2000. GONÇALVES, J. Os grandes equívocos da “lusofonia”. Diário de Notícias, Lisboa, p. 12, 24 abr. 2000. 10 Athayde foi uma importante figura na vida política portuguesa na década de 1990. Este publicitário brasileiro foi considerado elemento fundamental nos triunfos eleitorais do Partido Socialista. HESPANHA, A. M. Há 500. 1. ed. Lisboa: Comissão Nacional para a Comemoração dos Descobrimentos Portugueses, 2000. Notas 1 Pulido Valente é um dos mais prestigiados cronistas portugueses. Em 2000, escrevia regularmente para o Diário de Notícias e atualmente é cronista do jornal Público. Historiador de profissão, sua evolução política levou-o da esquerda à direita, embora suas posições não possam ser simplesmente balizadas dessa forma. A História, uma vez que se entregue como conhecimento que se submete ao ponto de vista do Estado, afirma-se como princípio por excelência, da identidade e como um precioso instrumento nas relações de poder actuais, revelando a sua instru­ mentalidade e colocando-nos perante a urgência de debater os limites de sua autonomia enquanto pro­ cesso de conhecimento. 2 Tavares foi jornalista e é hoje um dos mais prestigiados articulistas portugueses. 3 O tema dos “brandos costumes” da colonização portuguesa é recorrente na produção intelectual portuguesa, a ponto de se poder detectar sua presença na própria historiografia marxista portuguesa (NEVES, 2004a). Dialogia, São Paulo, v. 4, p. 101-113, 2005 Artigos 111 4 Rosas mantém há alguns anos uma página de opinião no jornal Público. É atualmente deputado nacional pelo Bloco de Esquerda (partido que poderíamos grosseiramente classificar como pós- comunista), mas seu prestígio intelectual advém do fato de ser provavelmente o historiador português que mais se destacou no estudo do Estado Novo. 4 Rosas mantém há alguns anos uma página de opinião no jornal Público. É atualmente deputado nacional pelo Bloco de Esquerda (partido que poderíamos grosseiramente classificar como pós- comunista), mas seu prestígio intelectual advém do fato de ser provavelmente o historiador português que mais se destacou no estudo do Estado Novo. Referências ALENCASTRO, L. F. de. Destinos cruzados. Público, Lisboa, p. 9, 9 mar. 2000. Dialogia, São Paulo, v. 4, p. 101-113, 2005 ALMEIDA, M. V. de. Comemorar o futuro. Público, Lisboa, p. 8, 22 abr. 2000a. 11 Para uma análise das principais concepções atuais do “ser português”, do ensaísmo de Eduardo Lourenço ao pensamento sociológico de Boaventura de Souza Santos (ALMEIDA, 2000b; LEAL, 2000). LEAL, J. Etnografias populares (1870-1970): cultura popular e identidade nacional. 1. ed. Lisboa: Dom Quixote, 2000. 12 Sobre o trabalho das representações nacionais no futebol, em Portugal como no Brasil, veja Neves (2004b). MAGALHÃES, R. de. O fim de Macau e as comemorações dos 500 anos do Brasil. História, Lisboa, n. 21, p. 11, 2001. 13 Designação em Portugal para o responsável máximo por uma entidade ou por um determinado projeto. O responsável máximo pela CNCDP, delegado de vastos poderes que lhe eram conferidos pelo Estado, era designado como comissário. MAGNO, C. Made in Portugal. Diário de Notícias, Lisboa, p. 3, 23 abr. 2000. MOREIRA, A. Os índios do Brasil brasileiro. Diário de Notícias, Lisboa, p. 14, 2 maio 2000. Dialogia, São Paulo, v. 4, p. 101-113, 2005 112 NEVES, J. A imaginação da nação na historiografia comunista portuguesa. Ler História, Lisboa, n. 46, 2004a. PULIDO VALENTE, V. O Brasil. Diário de Notícias, Lisboa, p. 30, 30 abr. 2000. REBELO DE SOUSA, P. Obrigado, Rio. Diário de Notícias, Lisboa, p. 12, 23 mar. 2000. ______. O eterno fado dos últimos trinta metros: futebol, nacionalismo e corpo. In: NUNO DOMINGOS, J. N. (Ed.). A época do futebol: o jogo visto pelas Ciências Sociais. 1. ed. Lisboa: Assírio e Alvim, 2004b. ROSAS, F. Do mito à fraternidade. Público, Lisboa, p. 13, 26 abr. 2000. SAMPAIO, J. Diário de viagem do PR: a descoberta foi um feito notável. Público, Lisboa, p. 3, 21 abr. 2000. PORTAS, M. Culpas & desculpas. Diário de Notícias, Lisboa, p. 19, 23 mar. 2000. SOUSA TAVARES, M. Desculpem lá o Cabral. Público, Lisboa, p. 13, 3 mar. 2000. Artigos recebido em: 17 jun. 2005 / aprovado em: 30 out. 2005 Para referenciar este texto: NEVES, J. M. V. Porque o samba é filho da dor (a comemoração dos 500 anos do “descobrimento” do Brasil e a opinião na imprensa portuguesa). Dialogia, São Paulo, v. 4, p. 101-113, 2005. recebido em: 17 jun. 2005 / aprovado em: 30 out. 2005 recebido em: 17 jun. 2005 / aprovado em: 30 out. 2005 Para referenciar este texto: NEVES, J. M. V. Porque o samba é filho da dor (a comemoração dos 500 anos do “descobrimento” do Brasil e a opinião na imprensa portuguesa). ALMEIDA, M. V. de. Comemorar o futuro. Público, Lisboa, p. 8, 22 abr. 2000a. Dialogia, São Paulo, v. 4, p. 101-113, 2005. Para referenciar este texto: NEVES, J. M. V. Porque o samba é filho da dor (a comemoração dos 500 anos do “descobrimento” do Brasil e a opinião na imprensa portuguesa). Dialogia, São Paulo, v. 4, p. 101-113, 2005. Dialogia, São Paulo, v. 4, p. 101-113, 2005 Artigos 113
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Calcium Influx and Male Fertility in the Context of the Sperm Proteome: An Update
BioMed research international
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Hindawi Publishing Corporation BioMed Research International Volume 2014, Article ID 841615, 13 pages http://dx.doi.org/10.1155/2014/841615 Hindawi Publishing Corporation BioMed Research International Volume 2014, Article ID 841615, 13 pages http://dx.doi.org/10.1155/2014/841615 Hindawi Publishing Corporation BioMed Research International Volume 2014, Article ID 841615, 13 pages http://dx.doi.org/10.1155/2014/841615 Md Saidur Rahman, Woo-Sung Kwon, and Myung-Geol Pang Department of Animal Science and Technology, Chung-Ang University, 4726 Seodong-daero, Anseong, Gyeonggi-Do 456-756, Republic of Korea Department of Animal Science and Technology, Chung-Ang University, 4726 Seodong-daero, Anseong, Gyeonggi-Do 456-756, Republic of Korea Correspondence should be addressed to Myung-Geol Pang; mgpang@cau.ac.kr Received 17 December 2013; Accepted 14 January 2014; Published 27 April 2014 Copyright © 2014 Md Saidur Rahman et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Freshly ejaculated spermatozoa are incapable or poorly capable of fertilizing an oocyte. The fertilization aptness of spermatozoa depends on the appropriate and time-dependent acquisition of hyperactivation, chemotaxis, capacitation, and the acrosome reaction, where calcium (Ca2+) is extensively involved in almost every step. A literature review showed that several ion channel proteins are likely responsible for regulation of the Ca2+ uptake in spermatozoa. Therefore, manipulation of the functions of channel proteins is closely related to Ca2+ influx, ultimately affecting male fertility. Recently, it has been shown that, together with different physiological stimuli, protein-protein interaction also modifies the Ca2+ influx mechanism in spermatozoa. Modern proteomic analyses have identified several sperm proteins, and, therefore, these findings might provide further insight into understanding the Ca2+ influx, protein functions, and regulation of fertility. The objective of this review was to synthesize the published findings on the Ca2+ influx mechanism in mammalian spermatozoa and its implications for the regulation of male fertility in the context of sperm proteins. Finally, Pathway Studio (9.0) was used to catalog the sperm proteins that regulate the Ca2+ influx signaling by using the information available from the PubMed database following a MedScan Reader (5.0) search. Review Article Calcium Influx and Male Fertility in the Context of the Sperm Proteome: An Update Md Saidur Rahman, Woo-Sung Kwon, and Myung-Geol Pang Department of Animal Science and Technology, Chung-Ang University, 4726 Seodong-daero, Anseong, Gyeonggi-Do 456-756, Republic of Korea 1. Introduction acrosome reaction and facilitates the spermatozoa reaching and fertilizing of an oocyte [3–8]. Therefore, understanding the mechanism that regulates the Ca2+ influx in spermatozoa is a matter of utmost importance. Spermatozoa are atypical cells with peculiar functionality: they are produced in one organism and released, and then they invade another organism and deliver their genetic material into a host cell to produce offspring by sexual reproduction. It is a well-known fact that only about 1 in 25,000 spermatozoa finally reaches the fallopian tube and gets the opportunity to fertilize an oocyte. In the mid-20th century, it had been claimed that mammalian spermatozoa are unable to fertilize an oocyte before achieving functional maturation, which occurs during their journey through the female reproductive tract for a finite period of time [1, 2]. This fundamental maturational process is chiefly regulated by numerous signaling cascades, and calcium (Ca2+) plays a dynamic role in this process, as an intracellular second messenger. Several studies have hypothesized that elevation of sperm intracellular Ca2+ ([Ca2+]i)/Ca2+ influx regulates motility, hyperactivation, chemotaxis, capacitation, and the p Previous studies have shown that the Ca2+ entry mecha- nisms are regulated via numerous Ca2+ permeable channel proteins in spermatozoa [6, 9, 10]. Therefore, the factors that regulate the functions of those channels will ulti- mately help us understand how male fertility is regulated. Recent applications of proteomic approaches such as two- dimensional polyacrylamide gel electrophoresis, mass spec- trometry, and differential in-gel electrophoresis have yielded the identification of several sperm-specific proteins [11, 12]. These discoveries have provided new insight into protein functions and enabled us to recognize diverse sperm-specific processes in order to differentiate normal from abnormal spermatozoa [11]. Mature spermatozoa are widely known to be silent in both transcription and translation [11, 13, 14] or poorly capable of translation [15]; therefore, studies on 2 2 BioMed Research International BioMed Research International BioMed Research International individual sperm proteomes have described the importance of spermatozoal posttranslational modifications and their ability to induce physiological changes as a prerequisite for successful fertilization. The literature reviewed shows that the primary source of Ca2+ for spermatozoa is the external environment: the fallop- ian tube in the female reproductive tract (in vivo) and culture media (in vitro) [8], and simultaneously increasing [Ca2+]i regulates the release of Ca2+ into the cell. Therefore, how Ca2+ crosses into cells through the sperm plasma membrane is a matter of paramount importance. 1. Introduction In eukaryotic cells, the Ca2+ influx occurs through specific Ca2+ permeable ion chan- nel proteins located on the plasma membrane [43, 44] such as classical voltage-gated (high and low) Ca2+ (Cavs), transient receptor potential (TRP), and cyclic nucleotide-gated (CNG) channels [9]. Recently, Ren and Xia have proposed four criteria to identify sperm ion channel proteins: detectability in sperm, preferably with knockout sperm as a negative control; ability to produce ion channel current detectable by patch-clamp recording; blocking of the channels that impairs normal sperm function; and mutations of gene encoding the ion channel proteins leading to sperm malfunctions [10].h Torres-Flores et al. [16] have shown that human sperma- tozoa exposed to the phosphodiesterase inhibitor papaverine cause activation of protein kinase A (PKA) and stimulate the progesterone-induced Ca2+ influx via the cyclic adenosine monophosphate- (cAMP-) dependent pathway. Although these authors did not evaluate the relationship between in vitro fertility and Ca2+ influx, changes in intracellular pH and increased tyrosine phosphorylation ultimately provide a potential clue regarding sperm fertility competence. In another study, to evaluate hamster spermatozoa capacitation capability, comparative association was observed between pyruvate dehydrogenase A, Ca2+ influx, cAMP, and reactive oxygen species [17]. Additionally, Breitbart et al. [18] reported that polymerization of globular- (G-) actin to filamentous- (F-) actin occurs during capacitation. As capacitation and the acrosome reaction are Ca2+-mediated events [4, 5], one can, without considering further signaling cascade, assume that remodeling the actin structure might be linked with the regulation of Ca2+ influx in spermatozoa. p g p [ ] The CatSper family of channels is the newest and only family of voltage-gated Ca2+ channels that meets most of the aforementioned criteria and essentially regulates Ca2+ entry into cells and is therefore crucial for sperm fertility [9, 45]. Four pore-forming CatSper channel proteins, CatSper 1–4, and at least two auxiliary subunits, CatSper𝛽and CatSper𝛾, have been identified in a wide range of animals, including humans and mice [46, 47]. Physiologically, CatSper members are permeable to Ca2+,whereas the CatSper knockdown sperm does not have the channel current that is detected in the principal piece of wild-type sperm [20, 48]. Most of the channel proteins, including CatSper members, have been identified in the principal piece of spermatozoa [20, 46, 47, 49] (Figure 1). 1. Introduction Although the explanation of such subcellular localization is still debated, it might be because of interactions among the channel proteins and with the auxiliary subunits, although a further study is needed to resolve this issue. Collectively, these proteins play a key role in various cellular processes via regulation of the membrane potential and intracellular ionic balance. Carlson et al. [50] and Quill et al. [51] have conclusively proved that CatSper1 and CatSper2 null mice are sterile owing to their inability to generate the sperm-hyperactivated motility prerequisite for penetration of an oocyte extracellular matrix. In effect, the complete or partial absence of single or multiple Ca2+ channels is responsible for infertility or subfertility, although their underlying signaling cascade has not been properly studied. Recently, in our laboratory, we found that the manip- ulation of sperm proteins such as ubiquinol-cytochrome-c reductase core protein 2 (UQCRC2) [39], voltage-dependent anion channels proteins (VDACs) [4], and arginine vaso- pressin [5] could control the Ca2+ influx in spermatozoa and regulate capacitation, the acrosome reaction, and fertility. Therefore, design and construction of a similar study with most of the identified sperm proteins available from several protein databases might provide a more realistic insight into the Ca2+ influx, protein functions, and fertility. The present work reviews the latest information published by other labo- ratories as well as our research team on the aforementioned aspects of spermatozoa and their potential implications for diagnosis and prognosis of male fertility. 2. Mechanism of Ca2+ Influx in Mammalian Spermatozoa The different channel proteins that are depicted in the diagram include the Na+-coupled HCO3 −transporter (NBC) family, soluble adenylyl cyclase (sACY), adenosine triphosphate (ATP), cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), cyclic nucleotide-gated ion channel (CNG), hyperpolarization-activated cyclic nucleotide-gated channel (HCN), zona pellucida (ZP), the voltage-gated proton channel (Hv1), glutamate receptor family class-C (GPCRC), and an unknown mechanism (?). GPCRC ? Alkalinization CatSper 𝛾 𝛽 Ca2+ [Ca 2+]i sACY ATP cAMP cGMP ZP receptors HCN Stimulate ? ? ? Opening ? CNG K+ Ca2+ ? Progesterone Spermatozoa Principal piece H+ Extracellular space Intracellular space Na+ NBC Na+ Follicle nHCO3 − HCO3 − Hv1 pH Figure 1: Possible signal transduction mechanisms of mammalian sperm Ca2+ influx through the Ca2+ permeable channel proteins. Previously published studies were used as references to summarize the list of channel proteins in spermatozoa. The channel proteins are localized mainly in the principle piece of spermatozoa. The follicular fluid and several factors in the fallopian tube (in vitro media) stimulate the receptors for spermatozoa Ca2+ influx. Ca2+ influx in spermatozoa is principally regulated by CatSper channels; however, the possible interaction between other channels that are responsible for controlling the opening of CatSper and allowing the Ca2+ into cells is indicated by arrow signs (red circle). The different channel proteins that are depicted in the diagram include the Na+-coupled HCO3 −transporter (NBC) family, soluble adenylyl cyclase (sACY), adenosine triphosphate (ATP), cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), cyclic nucleotide-gated ion channel (CNG), hyperpolarization-activated cyclic nucleotide-gated channel (HCN), zona pellucida (ZP), the voltage-gated proton channel (Hv1), glutamate receptor family class-C (GPCRC), and an unknown mechanism (?). important role in Ca2+ influx mechanisms in mammalian spermatozoa by regulating the opening of CatSper members, including the flagellar voltage-gated proton channel (Hv1) [21], Ca2+-ATPase pump [33], several cyclic nucleotide-gated ion channels (CNG) [27, 54], hyperpolarization-activated cyclic nucleotide-gated (HCN) channels [27], and G-protein coupled receptors (GPCRs).l successful fertilization. In mammalian spermatozoa, numer- ous Ca2+ permeable channel proteins control intracellular pH, and the pH-dependent Ca2+ influx is measured by the whole-cell patch clamp technique [9, 20]. A review of the literature showed that a potential functional interaction exists between the sperm proteins and Ca2+ permeable chan- nel proteins, thus modulating the Ca2+ influx mechanism [4, 5, 39] and playing a vital role in adjusting male fertility. 2. Mechanism of Ca2+ Influx in Mammalian Spermatozoa The ultimate goal of fertilization of mammalian sperm is to fuse with and deliver their genetic materials into an oocyte [2, 40, 41]. For fertilization to occur completely, the spermatozoa must experience various obstacles both in vitro and in vivo [40, 41]. Ca2+ ions act as central signaling molecules; once they enter the spermatozoa, they exert allosteric regulatory effects on enzymes and many proteins [10, 21, 42]. Indeed, numerous elegant research findings have contributed signif- icantly to our understanding of the molecular signaling of Ca2+ influx, especially through monitoring the activity of individual cells. However, most of the studies are discrete and often do not represent a cumulative idea. This section presents a compilation of some basic information regarding the Ca2+ entry mechanism into mammalian spermatozoa by recapitulating scientific evidence. Previously, it has been reported that CatSper-dependent increases of [Ca2+]i in spermatozoa are induced by several psychological stimuli such as cyclic nucleotides (e.g., cAMP and cGMP) [29, 30, 52], soluble adenylyl cyclase [29, 52], zona pellucida glycoprotein [34, 35, 38], serum albumin [37, 38], secretion of cumulus oophorus [38], intracellular alkalization [3, 53], and pH [6, 21]. A recent study showed that endocrine disruptors such as p,p󸀠- dichlorodiphenyldichloroethylene (p,p󸀠-DDE) promoted Ca2+ entry into spermatozoa by activating CatSper channels, even at a physiological concentration [36]. In addition, several other components are also known to play an 3 BioMed Research International 3 GPCRC ? Alkalinization CatSper 𝛾 𝛽 Ca2+ [Ca 2+]i sACY ATP cAMP cGMP ZP receptors HCN Stimulate ? ? ? Opening ? CNG K+ Ca2+ ? Progesterone Spermatozoa Principal piece H+ Extracellular space Intracellular space Na+ NBC Na+ Follicle nHCO3 − HCO3 − Hv1 pH Figure 1: Possible signal transduction mechanisms of mammalian sperm Ca2+ influx through the Ca2+ permeable channel proteins. Previously published studies were used as references to summarize the list of channel proteins in spermatozoa. The channel proteins are localized mainly in the principle piece of spermatozoa. The follicular fluid and several factors in the fallopian tube (in vitro media) stimulate the receptors for spermatozoa Ca2+ influx. Ca2+ influx in spermatozoa is principally regulated by CatSper channels; however, the possible interaction between other channels that are responsible for controlling the opening of CatSper and allowing the Ca2+ into cells is indicated by arrow signs (red circle). 2. Mechanism of Ca2+ Influx in Mammalian Spermatozoa However, the mechanism by which Ca2+ triggers intracellular signaling to regulate physiological events in spermatozoa and the role of sperm proteins in adjustment of Ca2+ influx into cells remains unclear. This topic is emphasized below. A hypothetical signaling cascade of Ca2+ influx pathways and interaction of several channel proteins is depicted in Figure 1. Although the functions of several ion channel proteins together with their concurrent relationship with numerous stimuli have been well studied [21, 27, 38], several fundamental questions remain unanswered; for example, how do these channels/stimuli regulate the Ca2+ influx during spermatozoa processes such as capacitation, the acrosome reaction, and fertilization? Do they work alone or together with other channel proteins to regulate Ca2+ influx? More- over, which other parameters that remain undetected could have an effect on Ca2+ influx? Therefore, future research should focus on resolving these issues. Table 1 summarizes the proposed effect of Ca2+ ion channels and their physio- logical role that ultimately helps Ca2+ influx into mammalian spermatozoa. 3.1. Ca2+ Influx, Sperm Hyperactivation, Chemotaxis, and Protein Functions. In general, mature spermatozoa are held immotile within the epididymis. However, they quickly begin to swim following release. This is known as activation of motility and is characterized by symmetrical flagellar beats [55, 56]. The terms sperm activation and hyperactivation have quite different meanings. The spermatozoa become hyperac- tivated when the amplitude of the flagellar bend increases and produces a highly asymmetrical beat. In vivo, hyperactivation of spermatozoa facilitates the release of sperm from oviductal storage and boosts them through mucus in the oviductal lumen and matrix of the cumulus oophorus during fertiliza- tion [7]. In contrast, chemotaxis is a form of sperm movement in which spermatozoa move toward a concentration gradient of a chemoattractant released from the oocyte [57, 58]. 3. Effect of Ca2+ Influx on Male Fertility Ca2+ triggers multiple physiological events in sperma- tozoa, such as hyperactivation, chemotaxis, capacitation, and the acrosomal reaction, all of which are essential for 4 BioMed Research International Table 1: Summary of published works on ion channels and physiological stimuli of mammalian spermatozoa that regulate the Ca2+ influx mechanism. Name of channel/stimuli Localization on spermatozoa/availability Role in Ca2+ influx Role in sperm physiology Effect of knocking down/absence Reference CatSper CatSper 1 CatSper 2 CatSper 3 CatSper 4 CatSper𝛽 CatSper𝛾 Principal piece Regulates Ca2+ influx Ca2+ uptake, hyperactivated motility Sterile Barratt and Publicover, [19]; Qi et al. [20] Hv1 Principal piece Intracellular pH, alkalization thus stimulate Ca2+ influx Extrudes protons from flagella, alkalization Fertile Lishko et al. [21], Lishko et al. [22] 𝐼ATP Midpiece Selectively transports the Ca2+ Ca2+ influx, alkalization Fertile Navarro et al. [23] TRPC Principal piece, midpiece Stimulates opening of CatSper Ca2+ influx, cell depolarization Fertile Gees et al. [24], Castellano et al. [25] CNG Sperm flagellum, head Stimulates opening of CatSper via cAMP/cGMP Ca2+ influx Fertile Biel and Michalakis [26] HCN Flagellum Depolarization and opening of CatSper Ca2+ influx Fertile Wiesner et al. [27] SOC Plasma membrane ZP-induced Ca2+ influx Sperm chemotactic Subfertile Yoshida et al. [28] sACY cAMP/cGMP Intracellular space and cell membrane Activates CatSper, CNG, and HCN to regulate Ca2+ influx Ca2+ influx, alkalization Sterile Esposito et al. [29], Hess et al. [30] GPCR(s) Principal piece, midpiece ZP-induced Ca2+ influx increases in [Ca2+]i Maintains fertilization Subfertile Fukami et al. [31] Fukami et al. [32] PLC𝛿 Acrosome ZP induced increases in [Ca2+]i Ca2+ influx Subfertile Fukami et al. [32] Ca2+-ATPase pump Principal piece Intracellular pH and alkalization Ca2+ influx, capacitation Motility loss results in infertility Wennemuth et al. [33] ZP glycoproteins Follicle Induced Ca2+-dependent increase in [Ca2+]i Hyperactivation, capacitation Delayed capacitation Florman [34], Florman et al. [35] Endocrine disruptor (p,p󸀠-DDE) Female reproductive tract Activates CatSper Ca2+ influx Motility loss, delayed capacitation Tavares et al. 3. Effect of Ca2+ Influx on Male Fertility [36] BSA Extracellular space Similar to ZP glycoprotein In vitro capacitation Motility loss, subfertility Xia and Ren [37] Bailey and Storey [38] Oviductal and follicular fluid Extracellular space (in vivo) Ca2+-dependent increase in [Ca2+]i in sperm Ca2+ influx Motility loss delayed capacitation Xia and Ren [37] Hv1: voltage-gated proton channel; 𝐼ATP: ATP-gated channel; TRPC: transient receptor potential channels; CNG: cyclic nucleotide-gated ion channel; HCN: hyperpolarization-activated cyclic nucleotide-gated channel; SOC: store-operated Ca2+ channel; cAMP: cyclic adenosine monophosphate; cGMP: cyclic guanosine monophosphate; sACY: soluble adenylyl cyclase; GPCR: glutamate receptor family class-C; PLC𝛿: phospholipase C zeta; ZP: zona pellucida; p,p󸀠- DDE: p,p󸀠-dichlorodiphenyldichloroethylene; BSA: bovine serum albumin. Table 1: Summary of published works on ion channels and physiological stimuli of mammalian spermatozoa that regulate the Ca2+ influx mechanism. However, the molecular event that characterizes spermatozoa chemotaxis is only partially known [57].h by using the fluorescent Ca2+ indicator indo-1 proved that spermatozoa hyperactivation is potentially regulated by Ca2+ influx. However, it is unknown whether Ca2+ influx indepen- dently induces hyperactivation/chemotaxis in mammalian spermatozoa. Ho and Suarez [56] proposed that sperm hyper- activation induced by Ca2+ influx is mainly pH-dependent because sperm require a pH of 7.9–8.5 for hyperactivation, whereas activation can occur at a pH < 7.0. The proposed There is strong evidence to support that sperm hyper- activation and chemotaxis are required for penetrating the zona pellucida [48, 57, 59, 60]. Incubation of spermatozoa with an extracellular Ca2+ source induces hyperactivation in mammalian spermatozoa [61, 62] and chemotaxis in starfish [57]. In addition, measuring cytoplasmic Ca2+ levels BioMed Research International 5 model of Ca2+-induced hyperactivation is represented in Figure 2. The term “capacitation” was proposed by Austin in 1952 [1], although this concept was initially described by both Chang and Austin in 1951 [2, 41]. In fact, in vivo capacitation takes place in the female reproductive tract; however, it is also possible to capacitate spermatozoa in vitro by using particular media containing appropriate electrolytes and pH [2]. In an elegant review, Visconti summarized that the early stage of capacitation mainly comprises the bicarbonate-mediated activation of sperm motility, whereas the late stages include intracellular alkalinization, increase in protein tyrosine phos- phorylation, and preparation for the acrosomal reaction [63]. These temporal differences in capacitation and the acrosome reaction require numerous mechanisms, and Ca2+ influx plays a significant role in the process [63, 64]. 3. Effect of Ca2+ Influx on Male Fertility Fraser [65] reported that capacitation is a comparatively slow event that requires several hours to complete and is mainly regulated by a modest rise in [Ca2+]i, whereas the acrosome reaction is an exocytosis process that occurs very rapidly (within a minute) and is triggered by a large influx of [Ca2+]i [65, 66]. g It has recently been found by our laboratory that treatment of mouse spermatozoa with nutlin-3a, a small molecule antagonist of the mouse double minute 2 repressor, potentially downregulates the functions of the ubiquinol- cytochrome-c reductase complex component UQCRC2 and correlated with significantly reduced [Ca2+]i and sperm hyperactivation. This study provided insight that the Ca2+ influx in spermatozoa is partially regulated by UQCRC2 protein. Kwon et al. [4] reported that blocking VDAC with 4,4󸀠-diisothiocyanostilbene-2,2󸀠-disulfonic acid (DIDS) significantly decreased sperm hyperactivation. A signifi- cant decrease in [Ca2+]i was observed in (−) DIDS con- ditions, while [pH]i significantly increased in (−) DIDS, regardless of Ca2+. Simultaneously, a significantly elevated [pH]i was observed in (+) Ca2+. This study provides strong evidence that the modulation of Ca2+ influx by VDACs is pH-dependent, which is consistent with the result of a previous study by Ho and Suarez [56]. Moreover, another study proposed that deamino [Cys 1, d-ArgS] vaso- pressin (dDAVP), an AVPR2 agonist, significantly decreased sperm motility and intracellular pH, but, interestingly, it increased [Ca2+]i by regulating the function of arginine vasopressin in mice spermatozoa. However, it remains to be clarified as to why spermatozoa motility is decreased even in increased [Ca2+]i conditions.i Although the biochemical phenomenon of Ca2+ regulated capacitation and the acrosome reaction have been known for the last two decades, the molecular basis of this process is still poorly understood. For capacitation, the cholesterol influx initially stimulates the elevation of [Ca2+]i and bicarbonate into the spermatozoa and finally activates PKA and tyrosine phosphorylation, respectively, via the production of the cAMP [66–68]. In addition, binding to the zona pellucida causes additional activation of cAMP/PKA and protein kinase C (PKC) [68–70]. Spermatozoa need [Ca2+]i influx to proceed further, and they are believed to be activated by PKC through the opening of the calcium channels. Interestingly, PKA together with a secondary messenger, inositol trisphosphate, activates calcium channels localized in the outer acrosomal membrane and increases the calcium concentration in the cytosol. 3. Effect of Ca2+ Influx on Male Fertility Further increase of cytosolic Ca2+ influx occurs through a store-operated calcium entry mechanism in the plasma mem- brane, resulting in further depletion of Ca2+ in the acrosome [68, 69]. i On the basis of the findings of the aforementioned studies, it is tempting to hypothesize that spermatozoa hyperactivation is mostly controlled by Ca2+ influx. How- ever, potential interactions exist between protein func- tions. Therefore, Ca2+ influx, protein interaction, and hyperactivation might give numerous different annotations of upcoming research in this field. We have illustrated a schematic representation of different signaling path- ways involving sperm proteins by using Pathway Studio. These proteins exhibit significant modifications to induce sperm hyperactivation and chemotaxis in spermatozoa by regulating Ca2+ influx (Figure 3). In support of the aforesaid studies, several recent stud- ies on the same topic have also hypothesized that, after the morphological maturation of spermatozoa for sperm- oocyte fusion, [Ca2+]i decreases because acrosome-reacted spermatozoa release a substantial amount of Ca2+ from their inner cell layers [71, 72]. Ca2+-mediated capacitation and the acrosome reaction have been illustrated in Figure 2 for better understanding. However, for a more in-depth understanding, we recommend reading some excellent reviews on this topic [63, 67, 73–77]. 3.2. Ca2+ Influx versus Capacitation, the Acrosomal Reaction, Fertilization, and Sperm Proteome. Mammalian fertilization is a species-specific episode that is accomplished by a complex set of molecular events. To fertilize an oocyte, multiple extreme changes occur in spermatozoa that begin from its formation in the testes of the male reproductive tract to its penetration and fusion with an egg in the female reproductive tract. Although spermatozoa are motile as well as morphologically normal after ejaculation, they are unable to fertilize an oocyte [59]. They gain the fertilization ability only after educating in the female reproductive tract [40], and the modifications that spermatozoa experience during this time are collectively known as “capacitation.” Only capacitated spermatozoa can undergo the acrosome reaction through binding to the egg zona pellucida, and they finally become capable of penetrating and fertilizing the egg [4, 18, 39]. 3.2. Ca2+ Influx versus Capacitation, the Acrosomal Reaction, Fertilization, and Sperm Proteome. Mammalian fertilization is a species-specific episode that is accomplished by a complex set of molecular events. 3. Effect of Ca2+ Influx on Male Fertility Activated G-proteins stimulate the H+ transporter to increase intracellular pH, ultimately inducing the acrosomal reaction and hyperactivation by catalyzing the acrosomal enzymes [91]. Cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) are produced from adenosine triphosphate (ATP) owing to enzymatic catalysis by soluble adenylate cyclase (sAC) and guanylate cyclase (sGC), respectively, in mature spermatozoa. The bicarbonate ions activate the sAC; however, follicular fluid also stimulates the sAC through release of Ca2+ ions via the CatSper channel (principal piece). However, G-protein mediated signal transduction activates sAC and phospholipase-C (PLC) that ultimately causes tyrosine phosphorylation [51, 92], which is responsible for events such as capacitation and the acrosomal reaction. Likewise, extracellular signals such as nitric oxide (NO) and carbon monoxide (CO) stimulate membrane-bound GC (mGC) and sGC, respectively, to synthesize cGMP. Increases in cGMP level evoke a concomitant increase in cAMP by inhibiting its PDE3. However, the increased Ca2+ level can also directly catalyze cAMP [93, 94]. Activated sAC, sGC, and PLC stimulate the generation of the second messengers’ inositol trisphosphate (IP3) like cAMP, cGMP. The IP3 binds to the IP3 receptor (IP3R) to increase [Ca2+]i via the release of the [Ca2+]i storage ions. Concurrently, the second messengers activate protein kinases (PKA, PKC, and PKG), in turn gating ions through the T-type calcium channels, cyclic-nucleotide gated ion channel (CNG), and so on, that together with the activation of protein tyrosine kinases (PTK) and serine/threonine protein kinase (STK) cause increased protein phosphorylation [93, 94]. Additionally, the CatSper Ca2+ activates calmodulin (Calm), phospholipase-A (PLA), and phospholipase-D (PLD) with increased generation of other second messengers during the acrosome reaction. Ca2+ influx together with increased protein phosphorylation brings about the capacitation response that is responsible for the waveform asymmetry of motility termed hyperactivation during fertilization. Both hyperactivation and the acrosomal reaction boost flagellar beating, ultimately resulting in the penetration of the outer egg coat and subsequent fertilization of the mature ovum [91–95]. capacitation, and it is therefore tempting to hypothesize that organizational modification of F-actin in spermatozoa together with interacting with other sperm proteins has potential influence on Ca2+ influx. A similar finding has been established more precisely by another study [78], where boar sperm capacitation was studied by combined applica- tion of computational and experimental approaches. 3. Effect of Ca2+ Influx on Male Fertility To fertilize an oocyte, multiple extreme changes occur in spermatozoa that begin from its formation in the testes of the male reproductive tract to its penetration and fusion with an egg in the female reproductive tract. Although spermatozoa are motile as well as morphologically normal after ejaculation, they are unable to fertilize an oocyte [59]. They gain the fertilization ability only after educating in the female reproductive tract [40], and the modifications that spermatozoa experience during this time are collectively known as “capacitation.” Only capacitated spermatozoa can undergo the acrosome reaction through binding to the egg zona pellucida, and they finally become capable of penetrating and fertilizing the egg [4, 18, 39]. A review of the literature showed that several sperm proteins potentially regulate the Ca2+-dependent capacita- tion and the acrosome reaction in mammalian spermato- zoa [4, 5, 39]. However, how these proteins regulate the Ca2+ influx in spermatozoa is a matter that remains to be elucidated. Breitbart et al. [18] reported that forma- tion of F-actin mostly depends on PKA, protein tyrosine phosphorylation, and phospholipase D activation during capacitation. Ca2+ is one of the principle regulators of 6 BioMed Research International 6 Acrosome reaction Protein phosphorylation Flagellarbeating hyperactivation CatSper sAC ATP cAMP CNG Calm MPL PLD PLD Acrosomal enzymes Acrosome IP3R ZRK G- proteins Flagellar beating PLC Anion transport sAC mAC T-type calcium channel PKC PTK PKG mGC GTP cGMP sGC CO NO NO CO STK PDE3 Nucleus IP3 Fallopian tube (follicular fluid) Sperm head Principle piece Transporter [pH]i ZP3 Ca2+ Ca2+ Ca2+ Ca2+ Ca2+ Ca2+ Ca2+ Ca2+ G- proteins H+ H+ Ca2+ HCO − 3 ZP3 ATP cAMP PKA Figure 2: Schematic diagram showing the mechanism of Ca2+ regulated hyperactivation, capacitation, and the acrosome reaction of spermatozoa, which are three principal events of fertilization. Ca2+ together with ZP3 (zona pellucida glycoprotein-3) exhibits the most important role in sperm binding and acrosomal reaction. Ca2+ triggers the zona pellucida (ZP) receptors of cell membrane that activate G-proteins in the sperm head. Activated G-proteins stimulate the H+ transporter to increase intracellular pH, ultimately inducing the acrosomal reaction and hyperactivation by catalyzing the acrosomal enzymes [91]. Cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) are produced from adenosine triphosphate (ATP) owing to enzymatic catalysis by soluble adenylate cyclase (sAC) and guanylate cyclase (sGC), respectively, in mature spermatozoa. 3. Effect of Ca2+ Influx on Male Fertility The bicarbonate ions activate the sAC; however, follicular fluid also stimulates the sAC through release of Ca2+ ions via the CatSper channel (principal piece). However, G-protein mediated signal transduction activates sAC and phospholipase-C (PLC) that ultimately causes tyrosine phosphorylation [51, 92], which is responsible for events such as capacitation and the acrosomal reaction. Likewise, extracellular signals such as nitric oxide (NO) and carbon monoxide (CO) stimulate membrane-bound GC (mGC) and sGC, respectively, to synthesize cGMP. Increases in cGMP level evoke a concomitant increase in cAMP by inhibiting its PDE3. However, the increased Ca2+ level can also directly catalyze cAMP [93, 94]. Activated sAC, sGC, and PLC stimulate the generation of the second messengers’ inositol trisphosphate (IP3) like cAMP, cGMP. The IP3 binds to the IP3 receptor (IP3R) to increase [Ca2+]i via the release of the [Ca2+]i storage ions. Concurrently, the second messengers activate protein kinases (PKA, PKC, and PKG), in turn gating ions through the T-type calcium channels, cyclic-nucleotide gated ion channel (CNG), and so on, that together with the activation of protein tyrosine kinases (PTK) and serine/threonine protein kinase (STK) cause increased protein phosphorylation [93, 94]. Additionally, the CatSper Ca2+ activates calmodulin (Calm), phospholipase-A (PLA), and phospholipase-D (PLD) with increased generation of other second messengers during the acrosome reaction. Ca2+ influx together with increased protein phosphorylation brings about the capacitation response that is responsible for the waveform asymmetry of motility termed hyperactivation during fertilization. Both hyperactivation and the acrosomal reaction boost flagellar beating, ultimately resulting in the penetration of the outer egg coat and subsequent fertilization of the mature ovum [91–95]. Acrosome reaction Protein phosphorylation Flagellarbeating hyperactivation CatSper sAC ATP cAMP CNG Calm MPL PLD PLD Acrosomal enzymes Acrosome IP3R ZRK G- proteins Flagellar beating PLC Anion transport sAC mAC T-type calcium channel PKC PTK PKG mGC GTP cGMP sGC CO NO NO CO STK PDE3 Nucleus IP3 Fallopian tube (follicular fluid) Sperm head Principle piece Transporter [pH]i ZP3 Ca2+ Ca2+ Ca2+ Ca2+ Ca2+ Ca2+ Ca2+ Ca2+ G- proteins H+ H+ Ca2+ HCO − 3 ZP3 ATP cAMP PKA Figure 2: Schematic diagram showing the mechanism of Ca2+ regulated hyperactivation, capacitation, and the acrosome reaction of spermatozoa, which are three principal events of fertilization. Ca2+ together with ZP3 (zona pellucida glycoprotein-3) exhibits the most important role in sperm binding and acrosomal reaction. Ca2+ triggers the zona pellucida (ZP) receptors of cell membrane that activate G-proteins in the sperm head. 3. Effect of Ca2+ Influx on Male Fertility These authors reported that the boar spermatozoa capacitation network contains several connecting cascades, whereas only three nodes bound to all the subcellular compartments are involved in spermatozoa postejaculatory signaling, such as [Ca2+]i, ATP, and actin polymerization. Removal of the actin polymerization node from this aforesaid network causes disorganization of the network topography and affects capac- itation, and this has been confirmed by zona pellucida- induced capacitation and the acrosomal reaction in an in vitro demonstration [78]. In another study, Patrat et al. [79] showed that pro- gesterone (P4) that is secreted by cumulus cells directly acts on the sperm plasma membrane and triggers the 7 BioMed Research International 7 AVP AVPR2 CNR1CATSPE RB Motility/hyperactivation CATSPE R1 CATSPE R2 CATSPE RG Calmoduli- n MARCKS BASP 1 MAPK1 PRKCSH CALR ITPR1 ADC Y SRC DLD HSPA2 AKAP3 RON1 CABYR SPINLW1 SEMG1 RAPGEF 4 TNF PLCZ1 Ca + 2 PLC PKC PIP2 NSF PTPN1 SNAP receptor SYT6 RAB3A RAPGEF 3 GEF SLC8A1 NPR1 NPPA Chemotaxis Progest- erone Protein tyrosine kinase Protein Cell process Functional class Small molecule Regulation Mol. synthesis Mol. transport Binding Prot. modifcation Figure 3: Schematic representation of interactions among ∼35 proteins related to Ca2+ regulated spermatozoa hyperactivation chemotaxis. The figure was produced by use of Pathway Studio (9.0) following the MedScan Reader (5.0) protein search from PubMed datab 12]. Figure 3: Schematic representation of interactions among ∼35 proteins related to Ca2+ regulated spermatozoa hyperactivation and chemotaxis. The figure was produced by use of Pathway Studio (9.0) following the MedScan Reader (5.0) protein search from PubMed database [12]. ras-related protein Rab-3A (RAB3A) is also necessary for Ca2+-dependent exocytosis. Interestingly, Rab3A activation of acrosomal exocytosis requires active NSF. Therefore, protein-protein interaction might also play a potential role in regulating Ca2+ influx. All of these observations seem to be consistent with the idea that Ca2+ functions are regulated by sperm proteins during fertilization. However, the key question is how do these proteins modify Ca2+ influx in spermatozoa? intracellular signals and enzymatic pathways involved in the acrosome reaction. P4 regulates the acrosome reaction and is mediated by a compulsory Ca2+ increase. This study found that P4 induced the activation of Gi/Go protein- coupled and protein tyrosine kinase receptors, and it affected capacitation and the acrosome reaction. In contrast, Ca2+ reg- ulated exocytosis of spermatozoa requires active acrosomal proteins such as N-ethylmaleimide-sensitive factor (NSF) [66]. 3. Effect of Ca2+ Influx on Male Fertility Additionally, the same research team showed that the 8 8 BioMed Research International SEMG1 AVP PGR CATSPE R1 CATSPE R2 ZP3 CDC42 DNM1 CHR NA7 PLCB1 PLCD4 GNA13 F- actin Spinkl GSN IP3 PIP2 Protein tyrosine kinase MAPK1 cAMP Sperm capacitation PKA PRKAR2 A ADCY10 PLC PKC Actin flament PLCZ1 L-tyrosine CAMP AKAP3 ADCY RON1 LY6G6C SLC8A1 OR10J5 CAMK2B SRC PLCG1 CS ABCC1 NPPA ABCB1 CAPN1 VDAC Phospholipa- Intracellular pH Acrosome reaction se A2 Ca2+ Fertilization Protein Cell process Functional class Small molecule Regulation Complex Axone- mal dynein igure 4: Schematic representation of interactions among ∼40 proteins related to Ca2+ regulated spermatozoa capacitation, the acroso eaction, and fertilization. The figure was produced by use of Pathway Studio (9.0) following the MedScan Reader (5.0) protein search fr ubMed database [12]. Figure 4: Schematic representation of interactions among ∼40 proteins related to Ca2+ regulated spermatozoa capacitation, the acrosome reaction, and fertilization. The figure was produced by use of Pathway Studio (9.0) following the MedScan Reader (5.0) protein search from PubMed database [12]. of Pathway Studio helped us represent over 40 proteins that are potentially implicated in Ca2+ mediated regulation of capacitation, the acrosome reaction, and male fertility (Figure 4). Recently, in our laboratory, we used mice spermatozoa to evaluate the interrelationship of proteins related to Ca2+ influx, including UQCRC2 [39], arginine vasopressin [5], and VDACs [4], and evaluate their effects on capacitation and the acrosome reaction. It is likely that a sustained phase of Ca2+ is required for fertilization and might be regulated by the complex interaction of numerous sperm proteins. Therefore, studies to identify proteins that might have the ability to induce such a change are worth undertaking. Application 3.3. Ca2+ Influx and Postfertilization Egg Activation in Con- text of Sperm Proteome. Ca2+ influx in spermatozoa is not only important for sperm maturation, but it is also equally 3.3. Ca2+ Influx and Postfertilization Egg Activation in Con- text of Sperm Proteome. Ca2+ influx in spermatozoa is not only important for sperm maturation, but it is also equally BioMed Research International 9 9 Ca2+ Ca2+ PLC𝜁 InsP3 + + Endoplasmic reticulum Perivitelline space Zona pellucida Oocyte Sperm Figure 5: Schematic representation showing the Ca2+ influx mechanism in mammalian eggs stimulated by mature spermatozoa. Spermatozoa donate the phospholipase C isoform zeta (PLC𝜁) protein within a few minutes of sperm-egg fusion (represented by green color circle). 3. Effect of Ca2+ Influx on Male Fertility Inositol 1,4,5-trisphosphate (InsP3) is produced due to the hydrolysis of PLC𝜁, which subsequently triggers the nsP3 receptor-mediated Ca2+ release (indicated by red color circle) from the endoplasmic reticulum of the oocyte. Simultaneously, the increased cytoplasmic Ca2+ leads to further PLC𝜁stimulation, leading to the positive feedback loop of Ca2+ and InsP3 rise. The hypothesis has been modified from Swann [96] and Swann et al. [97]. Figure 5: Schematic representation showing the Ca2+ influx mechanism in mammalian eggs stimulated by mature spermatozoa. Spermatozoa donate the phospholipase C isoform zeta (PLC𝜁) protein within a few minutes of sperm-egg fusion (represented by green color circle). Inositol 1,4,5-trisphosphate (InsP3) is produced due to the hydrolysis of PLC𝜁, which subsequently triggers the nsP3 receptor-mediated Ca2+ release (indicated by red color circle) from the endoplasmic reticulum of the oocyte. Simultaneously, the increased cytoplasmic Ca2+ leads to further PLC𝜁stimulation, leading to the positive feedback loop of Ca2+ and InsP3 rise. The hypothesis has been modified from Swann [96] and Swann et al. [97]. have similar effects. We illustrated the relevant signaling and metabolic pathways by using sperm proteins to facilitate the understanding of the mechanisms behind Ca2+ mediated activation of oocytes (Figure 6). important for activation and development of the oocyte. A study of egg activation by Ca2+ was conducted by Steinhardt and colleagues in 1974 and showed remarkable findings [80]. Steinhardt et al. [80] reported that administration of Ca2+ ionophores induced the early events of hamster egg activation. Thus far, it has been shown that the eggs of almost all species are activated by an increase in Ca2+ oscillation by spermatozoa during fertilization [81, 82]. However, how the spermatozoa trigger the oocyte Ca2+ oscillation remains to be elucidated. Several hypotheses have been proposed to describe these mechanisms [83–86]. 4. Future Prospects The maturational events of mammalian spermatozoa are strictly regulated through the well-coordinated Ca2+ influx. It is the central regulator of many key activities in spermatozoa, all of which are necessary for fertilization. However, our current understanding at the molecular level concerning Ca2+ signaling in the spermatozoa is insufficient. Therefore, a better understanding of such an event can provide a more complete comprehension of Ca2+ regulated sperm functions and fertility optimization. It has been reported previously [83] that the spermatozoa introduce Ca2+ influx into oocytes by a specific protein called oscillogen in hamsters. Recent studies have shown that phospholipase C zeta (PLC𝜁), a novel sperm-specific agent, is responsible for induction of Ca2+ oscillation in eggs after sperm-egg membrane fusion [87–89]. According to this mechanism, the sperm protein PLC𝜁causes the release of [Ca2+]i in eggs and is mediated via inositol 1,4,5- trisphosphate (InsP3) receptors (hypothetical depiction in Figure 5). Even when the InsP3 or its derivatives are injected into unfertilized, mature eggs, oscillation occurs due to the unique feedback properties of the InsP3 receptors in mouse eggs [90]. However, it is still unknown whether there are any other factors/proteins available in spermatozoa that also A large number of Ca2+ permeable ion channel proteins have been identified [10, 43] that collectively regulate the Ca2+ influx mechanism in spermatozoa. Although the recent application of patch-clamp recordings of channel current significantly improves our understanding of the functions of these channel proteins, several basic aspects remain unsolved, such as identifying the functions of individual channels in spermatozoa and how these channels coordinate Ca2+ influx. 10 BioMed Research International 10 BioMed Research Internatio Disease Chemical reaction Direct regulation Expression EGF KIT PLCZ1 KCNMA1 PLCG1 PLCB1 PLCG1 MAPK1 PAEP GiCR PKA Calmod- ulin CATSPE OR10J5 R1 ADCY PIP2 Glutamyl Ovarian neoplasms PDGF PDGF PLCG2 VPS54 ZP3 CS TPA Phorbol esters Microtu- bule PKC PLC RYR YES1 CCNB1 CDK1 Guanine nucleotide- s SRC receptor Embryonal development Egg activation endopepti- dase G- protein H2O2 HCO − 3 L- tyrosin- e Cation channel Calcium channel Ca2+ Na+/H+ antiporter Voltage- gated Ca2+ channel Progester- one Intracell- ular pH Sperm capacitation G-Actin Phosphol- ipase D Phospho- diesteras- e Protein Cell process Functional class Small molecule Regulation Mol. synthesis Mol. transport Binding Prot. 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Future Prospects modifcation Complex Figure 6: Schematic representation of interactions among ∼30 proteins related to Ca2+ regulated egg activation and embryonic developme The figure was produced by the use of Pathway Studio (9.0) following the MedScan Reader (5.0) protein search from PubMed database [ Figure 6: Schematic representation of interactions among ∼30 proteins related to Ca2+ regulated egg activation and embryonic development. The figure was produced by the use of Pathway Studio (9.0) following the MedScan Reader (5.0) protein search from PubMed database [12]. Figure 6: Schematic representation of interactions among ∼30 proteins related to Ca2+ regulated egg activation and embryonic development. The figure was produced by the use of Pathway Studio (9.0) following the MedScan Reader (5.0) protein search from PubMed database [12]. although the underlying mechanism is less clearly defined. Protein-protein interactions also potentially regulate the Ca2+ uptake mechanism in spermatozoa. Although recently applied proteomic approaches have identified several sperm- specific proteins, their functions in Ca2+ regulation and interaction with channel proteins are unclear. Therefore, future research should target this topic to provide a robust understanding of Ca2+ and male fertility in both humans and other animal species. Therefore, production of knockdown animals and using them as negative controls compared with their wild counterparts might provide more specific ideas about channel functions. CatSper is the one of the well-studied channel proteins [10] and the functions of different pore-forming CatSper channels (1–4) and auxiliary subunits (CatSper𝛽and CatSper𝛾) remain a matter to be elucidated. Therefore, production of knockdown animals and using them as negative controls compared with their wild counterparts might provide more specific ideas about channel functions. although the underlying mechanism is less clearly defined. Protein-protein interactions also potentially regulate the Ca2+ uptake mechanism in spermatozoa. Although recently applied proteomic approaches have identified several sperm- specific proteins, their functions in Ca2+ regulation and interaction with channel proteins are unclear. Therefore, future research should target this topic to provide a robust understanding of Ca2+ and male fertility in both humans and other animal species. i CatSper is the one of the well-studied channel proteins [10] and the functions of different pore-forming CatSper channels (1–4) and auxiliary subunits (CatSper𝛽and CatSper𝛾) remain a matter to be elucidated. 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Acknowledgments This study was financially supported by the Cooperative Research Program for Agriculture Science and Technology Development (Project no. PJ008415), Rural Development Administration, Republic of Korea. Md Saidur Rahman was supported through the “Chung-Ang University Young Scientist Scholarship (CAYSS),” Chung-Ang University, Republic of Korea. This study was financially supported by the Cooperative Research Program for Agriculture Science and Technology Development (Project no. PJ008415), Rural Development Administration, Republic of Korea. Md Saidur Rahman was supported through the “Chung-Ang University Young Scientist Scholarship (CAYSS),” Chung-Ang University, Republic of Korea. [17] V. Kumar, V. Kota, and S. Shivaji, “Hamster sperm capacitation: role of pyruvate dehydrogenase A and dihydrolipoamide dehy- drogenase,” Biology of Reproduction, vol. 79, no. 2, pp. 190–199, 2008. [18] H. Breitbart, G. Cohen, and S. Rubinstein, “Role of actin cytoskeleton in mammalian sperm capacitation and the acro- some reaction,” Reproduction, vol. 129, no. 3, pp. 263–268, 2005. References Ren, “CatSper𝛽, a novel transmembrane protein in the CatSper channel complex,” The Journal of Biological Chemistry, vol. 282, no. 26, pp. 18945– 18952, 2007. [47] H. Wang, J. Liu, K.-H. Cho, and D. Ren, “A novel, single, trans- membrane protein CATSPERG is associated with CATSPER1 channel protein,” Biology of Reproduction, vol. 81, no. 3, pp. 539– 544, 2009. [31] K. Fukami, K. Nakao, T. Inoue et al., “Requirement of phospho- lipase C𝛿4 for the zona pellucida-induced acrosome reaction,” Science, vol. 292, no. 5518, pp. 920–923, 2001. [32] K. Fukami, M. Yoshida, T. Inoue et al., “Phospholipase C𝛿4 is required for Ca2+ mobilization essential for acrosome reaction in sperm,” The Journal of Cell Biology, vol. 161, no. 1, pp. 79–88, 2003. [48] D. Ren, B. Navarro, G. 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Radiofrequency ablation
SA journal of radiology
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EDITORIAL Radiofrequency ablation Leonie Scholtz MB ChB, MMedRad (D) Department of Radiology University of Pretoria he exciting developments in magnetic resonance imaging are leading us towards the fetus, the female breast and the prostate gland, resulting in a smiling contented look on the face of radiology, not to mention the prospect of regaining imaging of the coronary arteries (that has been the sole and dearly cherished possession of the cardiologists for decades), with multi-slice computed tomography approaching resolution comparable to digital angiography. Despite all the commotion surrounding the MR and CT consoles we can always rely on the interventional magicians to invent new fascinating, sometimes frightening and occasionally totally impractical procedures to stimulate the everlasting repressed surgical pulses in our blood. We have dilated, embolised, occluded, excluded, infiltrated and biopsied almost everything. With radiofrequency ablation (RFA),‘cooking’ is definitely the new kid on the block. RFA has been employed for some time for the treatment of primary and metastatic liver tumours. Pancreatic tumours, bone metastases and intra-pulmonary tumours are being treated similarly and RFA has recently entered phase 2 clinical trials for the treatment of small renal tumours. RFA involves the use of high-frequency electrical current to cause heat-based tissue destruction through needle electrodes of varying diameters depending on the size of the tumour treated. Limitations include tumours larger than 5 cm in diameter as well as proximity to vascular structures and other visceral organs. Treatment of liver tumours can be done percutaneously or as an open procedure during which the tumour can be visualised with an ultrasound probe placed directly on the surface of the liver. RFA is still in its infancy. The initial results are promising and have certainly caught the imagination of interventional radiologists, surgeons and oncologists. The length of treatment varies considerably, depending on the size and number of lesions treated. It would seem that we are facing long sessions of coagulating various lesions, hopefully with excellent results, whilst in the process broadening our musical repertoire, listening to Bach, the Beatles or Britney, depending on the age of the interventional radiologist hanging on to the end of the electrode. T Leonie Scholtz Editor 2 SA JOURNAL OF RADIOLOGY • May 2004
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English
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Murine CD4 T Cells Produce a New Form of TGF-β as Measured by a Newly Developed TGF-β Bioassay
PloS one
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Abstract Funding: This work was supported by the National Institutes of Health Grants AI435801 and NS38037. The funders had no role in st and analysis, decision to publish, or preparation of the manuscript. supported by the National Institutes of Health Grants AI435801 and NS38037. The funders had no role in study design, data collection publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Competing Interests: The authors have declared that no competing interests exist. * E-mail: hweiner@rics.bwh.harvard.edu * E-mail: hweiner@rics.bwh.harvard.edu ¤ Current address: BioLegend Inc., San Diego, California, United States of America TGF-b. Latent TGF-b is a non-covalently associated complex consisting of latency-associated peptide (LAP) which is the N- terminal portion of pro-TGF-b, and mature TGF-b which is made of the C-terminal of pro-TGF-b. Latent TGF-b cannot bind TGF- b receptors and thus further activation processes are required for biological activity [12]. It is unknown how T cell-produced TGF-b is activated. Takatoku Oida¤, Howard L. Weiner* r for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America Murine CD4 T Cells Produce a New Form of TGF-b as Measured by a Newly Developed TGF-b Bioassay Takatoku Oida¤, Howard L. Weiner* Abstract Background: It is generally assumed that T cells do not produce active TGF-b since active TGF-b as measured in supernatants by ELISA without acidification is usually not detectable. However, it is possible that active TGF-b from T cells may take a special form which is not detectable by ELISA. Methodology/Principal Findings: We constructed a TGF-b bioassay which can detect both soluble and membrane-bound forms of TGF-b from T cells. For this bioassay, 293T cells were transduced with (caga)12 Smad binding element-luciferase along with CD32 (Fc receptor) and CD86. The resulting cells act as artificial antigen presenting cells in the presence of anti- CD3 and produce luciferase in response to biologically active TGF-b. We co-cultured pre-activated murine CD4+CD252 T cells or CD4+CD25+ T cells with the 293T-caga-Luc-CD32-CD86 reporter cells in the presence of anti-CD3 and IL-2. CD4+CD252 T cells induced higher luciferase in the reporter cells than CD4+CD25+ T cells. This T cell-produced TGF-b is in a soluble form since T cell culture supernatants contained the TGF-b activity. The TGF-b activity was neutralized with an anti- mouse LAP mAb or an anti-latent TGF-b/pro-TGF-b mAb, but not with anti-active TGF-b Abs. An anti-mouse LAP mAb removed virtually all acid activatable latent TGF-b from the T cell culture supernatant, but not the ability to induce TGF-b signaling in the reporter cells. The induction of TGF-b signaling by T cell culture supernatants was cell type-specific. Conclusions/Significance: A newly developed 293T-caga-Luc-CD32-CD86 reporter cell bioassay demonstrated that murine CD4 T cells produce an unconventional form of TGF-b which can induce TGF-b signaling. This new form of TGF-b contains LAP as a component. Our finding of a new form of T cell-produced TGF-b and the newly developed TGF-b bioassay system will provide a new avenue to investigate T cell function of the immune system. Citation: Oida T, Weiner HL (2011) Murine CD4 T Cells Produce a New Form of TGF-b as Measured by a Newly Developed TGF-b Bioassay. PLoS ONE 6(4): e18365. doi:10.1371/journal.pone.0018365 Editor: Jean Kanellopoulos, University Paris Sud, France Received October 12, 2010; Accepted March 5, 2011; Published April 11, 2011 Received October 12, 2010; Accepted March 5, 2011; Published April 11, 2011 Copyright:  2011 Oida, Weiner. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. PLoS ONE | www.plosone.org Introduction TGF-b is an immunoregulatory cytokine that controls immune responses by multiple mechanisms [1]. TGF-b-deficient mice manifest an autoimmune syndrome and do not survive longer than 3–4 wks after birth [2], [3]. Moreover, it has been shown that TGF-b initiates Th17 differentiation in combination with IL-6 or IL-21 [4], [5], [6], [7], [8]. Although IL-17 is a dominant factor in the induction of autoimmune diseases such as experimental autoimmune encephalomyelitis [9] and collagen-induced arthritis [10], IL-17 production is not seen in TGF-b1 2/2 mice [5]. Although many cell types produce TGF-b, T cell-produced TGF- b is plays an important role in the control of autoimmune responses and Th17 differentiation. Thus, T cell-specific TGF-b conditional knockout mice develop fatal autoimmune disease even though they survive longer than TGF-b2/2 mice [11], and Th17 differentiation is hampered in these mice [11], indicating that TGF-b produced by T cells themselves is required for Th17 differentiation. Murine T cell culture supernatants usually do not contain active TGF-b when measured by ELISA without acidification. Thus, it is generally believed that T cells do not produce active TGF-b. Nakamura et al. [13] first reported that murine CD4+CD25+ regulatory T cells (Tregs) expressed surface LAP and/or TGF-b (LAP/TGF-b), and they proposed that the membrane-bound TGF-b mediated suppressive activity of Tregs. We also confirmed that Foxp3+ Tregs express surface LAP/TGF-b by using our newly developed anti-mouse LAP/TGF-b mAbs [14]. Human FOXP3+ Tregs have also been shown to express surface LAP [15], [16], [17]. It is possible that surface LAP/TGF-b on T cells can trigger TGF-b signaling in target cells by a cell-cell contact manner, give that active TGF-b is usually not detectable from T cell culture supernatants by ELISA. Alternatively, active TGF-b may be a rapidly-consumed, TGF-b is produced as a pro-form (pro-TGF-b), and is intracellularly processed by furin proprotein convertase into latent PLoS ONE | www.plosone.org 1 April 2011 | Volume 6 | Issue 4 | e18365 A New Form of T Cell Derived TGF-b short-lived cytokine in T cell culture. Although there is no experimental evidence thus far, it is also possible that T cells produce biologically active TGF-b in a form that is not detectable by ELISA. TGF-b Abs. TGF-b activity remained in culture supernatants even after the culture supernatant was treated with immobilized anti- LAP mAb by which latent TGF-b detected by TGF-b ELISA after acidification was virtually all depleted. Introduction Thus, T cell-produced TGF-b takes a unique molecular form which contains LAP as a component, and from which 25 kDa mature TGF-b is not released even after acidification. T cell-produced TGF-b initiated TGF-b signaling not in all cell types, suggesting that cell type- specific factors are required to sense the T cell-produced TGF-b. Given these possibilities, we developed a bioassay system which detects TGF-b activity, rather than the specific molecular form (the 25 kDa free TGF-b dimer) that an ELISA detects. This new bioassay consists of reporter cells that have direct contact with T cells and which can sense both short-lived and membrane-bound forms of TGF-b. 293T cells were transduced with a TGF-b reporter vector which has repeated the CAGA Smad binding elements in the promoter followed by luciferase, and with CD32 (Fc receptor) and CD86. Generation of a TGF-b reporter cell line doi:10.1371/journal.pone.0018365.g001 April 2011 | Volume 6 | Issue 4 | e18365 PLoS ONE | www.plosone.org 2 A New Form of T Cell Derived TGF-b (Figure 1B). To make the 293T-caga-Luc cells function as artificial antigen presenting cells, the 293T-caga-Luc cells were transduced with mouse CD32 (Fc receptor) and mouse CD86 retroviral vectors (Figure 1C). Serpinb9 (granzyme B inhibitor) and Serpinb9b (granzyme M inhibitor) were also retrovirally expressed. These granzyme inhibitor genes suppressed CD4 T cell-mediated killing of CD32- and CD86-transduced mink lung epithelial cells (MLEC) (data not shown), and it is expected that the granzyme inhibitor genes protect 293T cells from CD4 T cell-mediated killing, too, although 293T cells are relatively resistant to CD4 cell-mediated killing without these gene transductions. The transduced 293T cells were cloned at each step and high responding or high expressing clones were selected. The resulting TGF-b reporter cell line is termed as 293T-caga-Luc-CD32-CD86. (Figure 2A). As shown Figure 2B, CD4 T cells induced high luciferase activity in a cell number dependent manner. Interestingly, although the response to recombinant TGF-b became saturated above 200 pg/ml, CD4 T cells often induced higher luciferase activity than the saturation point. It should be noted that the re- stimulation at this time point minimally induced activation-induced cell death, while re-stimulation at later time points induced notable cell death under microscopic observation. Higher luciferase signal was observed at later time points when anti-FasL mAb was added to block the activation-induced cell death (Figure S1). Thus, it is not likely that the TGF-b activity is generated from dying T cells. Generation of a TGF-b reporter cell line ( p ) By using the newly developed 293T-caga-Luc-CD32-CD86 reporter cells, we found that pre-activated murine CD4 T cells induced high luciferase signals in the reporter cells. Although Foxp3+ T cells expressed surface LAP/TGF-b [14], pre-activated CD4+CD252 T cells induced much higher TGF-b signal than pre-activated CD4+CD25+ T cells. The T cell-produced TGF-b was a soluble form since T cell culture supernatants contained TGF-b activity. The T cell-produced TGF-b is not the canonical 25 kDa mature TGF-b since a TGF-b ELISA did not detect the 25 kDa mature TGF-b form in the same T cell culture supernatants. Surprisingly, the TGF-b activity in T cell culture supernatants was neutralized with an anti-LAP mAb and with an anti-pro-TGF-b/latent TGF-b mAb, but not with anti-mature It has been reported that CAGA is a Smad binding element and a promoter assay vector containing tandem repeats of CAGA in the minimum promoter region ((caga)12-MLP-Luc) is a sensitive and specific TGF-b reporter vector [18], [19]. We inserted the (caga)12-MLP-Luc segment into a promoterless lentiviral vector (pSMPUW) to construct a lentivirus based universal TGF-b reporter vector (pSMPUW-(caga)12-MLP-Luc-UbC-EGFP.puro- RRE) (Figure 1A). Human embryonic kidney 293T cells were then transduced with the TGF-b reporter vector (293T-caga-Luc cells). The response curve of 293T-caga-Luc cells to recombinant TGF-b was able to detect as little as 2 pg/ml recombinant human TGF-b Figure 1. Generation of a TGF-b reporter cell line. (A) Schematic diagram of pSMPUW-(caga)12-Luc lentivirus based TGF-b reporter vector. (B) Representative luciferase response of 293T-caga cells to recombinant TGF-b. 293T cells were transduced with the pSMPUW-(caga)12-Luc vector, and cultured in the presence of recombinant human TGF-b for 16 hrs. Luciferase activity was measured from the cell lysates. Mean 6 S.D. from duplicates are shown. (C) Schematic diagram of generation of 293T-caga-Luc-CD32-CD86 cells and how the cells function as artificial antigen presenting cells. doi:10.1371/journal.pone.0018365.g001 Figure 1. Generation of a TGF-b reporter cell line. (A) Schematic diagram of pSMPUW-(caga)12-Luc lentivirus based TGF-b reporter vector. (B) Representative luciferase response of 293T-caga cells to recombinant TGF-b. 293T cells were transduced with the pSMPUW-(caga)12-Luc vector, and cultured in the presence of recombinant human TGF-b for 16 hrs. Luciferase activity was measured from the cell lysates. Mean 6 S.D. from duplicates are shown. (C) Schematic diagram of generation of 293T-caga-Luc-CD32-CD86 cells and how the cells function as artificial antigen presenting cells. TGF-b activity from Tregs We previously reported that activated Fox3+ CD4 T cells express surface LAP/TGF-b using our newly developed anti- mouse LAP/TGF-b mAbs [14]. We tested whether these surface LAP/TGF-b-expressing Foxp3+ CD4 T cells were CD4 T cells with TGF-b activity. CD4+CD25+ (.90% Foxp3+) cells and CD4+CD252 (.98% Foxp32) cells were isolated and stimulated with plate-bound anti-CD3/CD28 in the presence of IL-2 for two days and rested for one day in presence of IL-2. They were then co-cultured with 293T-caga-Luc-CD32-CD86 TGF-b reporter cells in presence of anti-CD3 and IL-2 for 16 hrs. The T cells have tight cell to cell contact with the reporter cells both by the CD32- anchored anti-CD3 Ab and by CD86; thus the reporter cells should be able to sense membrane-bound TGF-b activity if Detection of TGF-b activity from CD4 T cells in coculture We tested whether murine CD4 T cells have TGF-b activity by using the 293T-caga-Luc-CD32-CD86 TGF-b reporter cells. For these experiments we co-cultured T cells with 293T-caga-Luc- CD32-CD86 TGF-b reporter cells in presence of anti-CD3 antibody. In preliminary experiments, we found that freshly prepared CD4 T cells barely induced luciferase during 24 hr co- culture. Then, we tested pre-activated CD4 T cells. Thus, mouse CD4 T cells were stimulated with plate-bound anti-CD3/CD28 for two days, rested for one day and then co-cultured with 293T-cgga- Luc-CD32-CD86 TGF-b reporter cells with anti-CD3 for 16 hrs Figure 2. TGF-b bioassay in co-culture. Mouse CD4 T cells were stimulated with plate-bound anti-CD3/CD28 for 2 days, and rested for 1 day. The pre-activated CD4 T cells were recovered, and the indicated numbers of T cells were added to 293T-caga-Luc-CD32-CD86 cells with 0.5 mg/ml anti- CD3 antibody. Recombinant human TGF-b was also added as a standard. After 16 hr of culture, the reporter cells were lysed and the luciferase activity was measured. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g002 Figure 2. TGF-b bioassay in co-culture. Mouse CD4 T cells were stimulated with plate-bound anti-CD3/CD28 for 2 days, and rested for 1 day. The pre-activated CD4 T cells were recovered, and the indicated numbers of T cells were added to 293T-caga-Luc-CD32-CD86 cells with 0.5 mg/ml anti- CD3 antibody. Recombinant human TGF-b was also added as a standard. After 16 hr of culture, the reporter cells were lysed and the luciferase activity was measured. Error bars represent mean 6 S.D. of duplicates. TGF-b activity from Tregs doi:10.1371/journal.pone.0018365.g002 April 2011 | Volume 6 | Issue 4 | e18365 PLoS ONE | www.plosone.org 3 A New Form of T Cell Derived TGF-b present. As shown in Figure 3, CD4+CD25+ T cells had less TGF- b activity in the co-culture bioassay than CD4+CD252 T cells. These results demonstrate that non-Tregs are the main CD4 T cells with TGF-b activity by the reporter assay. the T cell culture supernatant from the 16105 cells/well induced luciferase activity equivalent to approximately 200 pg/ml of recombinant human TGF-b. Thus, TGF-b activity accumulates in T cell culture supernatants. We also measured the same culture supernatant by TGF-b ELISA without acidification which detects the 25 kDa free TGF-b dimer and found that the amount of active TGF-b as measured by the TGF-b ELISA was 10 pg/ml. ‘‘Total’’ TGF-b as measured by ELISA after acidification was found to be 486 pg/ml (Table 1). These results indicate that the T cell- produced TGF-b activity takes an unconventional form which is different from the 25 kDa free TGF-b dimer and is not detectable by ELISA. T cell-produced TGF-b activity induces Smad2 phosphorylation in 293T-caga-Luc-CD32-CD86 cell To confirm that the luciferase activity was a consequence of TGF-b signaling, we determined Smad2 phosphorylation in 293T-caga-Luc-CD32-CD86 cells after exposure to T cell culture supernatants. T cell culture supernatants from anti- CD3/CD28-stimulated cultures of pre-activated CD4+CD252 T cells contained higher TGF-b activity (2–3 ng/ml recombi- nant TGF-b equivalent) than cultures re-stimulated with 293T- caga-Luc-CD32-CD86 reporter cells/anti-CD3 (data not shown). Thus, we used culture supernatants from plate-bound anti-CD3/CD28 re-stimulated CD4+CD252 T cells for further studies. 1 ng/ml recombinant human TGF-b or a diluted T cell culture supernatant adjusted to the equivalent TGF-b activity determined by the 293T-caga-Luc-CD32-CD86 TGF-b bioas- say was added to 293T-caga-Luc-CD32-CD86 cells for the indicated time, and the cell lysates were run on SDS-PAGE and blotted with anti-phospho-Smad2 antibody. Although the T cell culture supernatant was diluted to normalize the TGF-b activity, the T cell culture supernatant induced stronger Smad2 phosphorylation than recombinant TGF-b at all the time points (Figure 6). This result suggests that T cell-produced TGF-b activity is qualitatively different from the 25 kDa free TGF-b dimer. No requirement for direct contact with T cells for induction of TGF-b signaling Although we initially anticipated that membrane-bound TGF-b on Foxp3+ CD4 T cells would trigger TGF-b signaling in the reporter cells, as described above, this was not the case. To further investigate the role of membrane-bound TGF-b, we asked whether direct contact between T cells and the reporter cells was required to initiate TGF-b signaling. In order to address this question, 293T-caga-Luc cells that did not have surface CD32 or CD86 were mixed with CD32- and CD86-trandsduced 293T cells that did not have the (caga)12-Luc reporter (Figure 4B). If T-reporter contact was required to present T cell-produced TGF-b to TGF-b receptors on the reporter cells, there would be diminished induction of luciferase in this condition. We found, however, that pre-activated CD4 T cells stimulated with 293T-CD32-CD86 cells in presence of anti-CD3 induced TGF-b signaling in 293T-caga- Luc cells as well as or better than the condition in which 293T- caga-Luc-CD32-CD86 cells were used as reporter cells (Figure 4A). This result indicates that the T cell-produced TGF-b that results in TGF-b activity as measured in our reported system is soluble and can diffuse to adjacent cells. TGF-b activity in T cell culture supernatants Under this condition the 293T-caga reporter cells have minimal contact with CD4 T cells. doi:10.1371/journal.pone.0018365.g004 A New Form of T Cell Derived TGF-b A New Form of T Cell Derived TGF-b Figure 4. Investigation of requirement for direct contact between T cells and TGF-b reporter cells. (A) 293T-caga-Luc-CD32-CD86 cells were mixed with an equal number of un-manipulated 293T cells. Under this condition, a single 293T-caga-Luc-CD32-CD86 cell stimulates CD4 T cells and responds to TGF-b activity produced by the same T cells. (B) 293T-caga cells that did not have CD32 or CD86 were mixed with 293T-CD32-CD86 cells lacking the (caga)12-Luc reporter. Under this condition the 293T-caga reporter cells have minimal contact with CD4 T cells. doi:10.1371/journal.pone.0018365.g004 Figure 4. Investigation of requirement for direct contact between T cells and TGF-b reporter cells. (A) 293T-caga-Luc-CD32-CD86 cells were mixed with an equal number of un-manipulated 293T cells. Under this condition, a single 293T-caga-Luc-CD32-CD86 cell stimulates CD4 T cells and responds to TGF-b activity produced by the same T cells. (B) 293T-caga cells that did not have CD32 or CD86 were mixed with 293T-CD32-CD86 cells lacking the (caga)12-Luc reporter. Under this condition the 293T-caga reporter cells have minimal contact with CD4 T cells. doi:10.1371/journal.pone.0018365.g004 TGF-b activity in T cell culture supernatants After demonstrating that T cell-produced TGF-b is in a soluble form, we next asked whether this form accumulates in culture supernatants. To address this, pre-activated CD4+CD252 T cells (anti-CD3/28 for 3 days) were re-stimulated with the reporter cells plus anti-CD3 for 16 hrs as the co-culture assay (Figure 5A), and the culture supernatants were also taken at the end of the assay. The culture supernatants were added to fresh 293T-caga-Luc- CD32-CD86 TGF-b reporter cells (without live T cells), and the reporter cells were cultured for 9 hrs (Figure 5B). We found that Figure 3. TGF-b bioassay of CD4+CD25+ Tregs. Mouse CD4+CD25+ T cells and CD4+CD252 T cells were stimulated with plate-bound anti-CD3/ CD28 for 2 days, and rested for 1 day in presence of 100 U/ml IL-2. These pre-activated CD4 T cells were recovered, and the indicated numbers of T cells were added to 293T-caga-Luc-CD32-CD86 cells with 0.5 mg/ml anti-CD3 antibody and 100 U/ml IL-2 for 16 hrs after which luciferase activity was measured. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g003 Figure 3. TGF-b bioassay of CD4+CD25+ Tregs. Mouse CD4+CD25+ T cells and CD4+CD252 T cells were stimulated with plate-bound anti-CD3/ CD28 for 2 days, and rested for 1 day in presence of 100 U/ml IL-2. These pre-activated CD4 T cells were recovered, and the indicated numbers of T cells were added to 293T-caga-Luc-CD32-CD86 cells with 0.5 mg/ml anti-CD3 antibody and 100 U/ml IL-2 for 16 hrs after which luciferase activity was measured. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g003 April 2011 | Volume 6 | Issue 4 | e18365 April 2011 | Volume 6 | Issue 4 | e18365 PLoS ONE | www.plosone.org 4 T cell-produced TGF-b activity is not found in the ELISA detectable ‘‘total’’ TGF-b fraction TGF-b measured by ELISA after acidification is termed ‘‘total’’ isotype control mAb MOPC21) to deplete latent TGF-b in the supernatant. The amount of ‘‘total’’ TGF-b detected by ELISA after acidification in control MOPC21-treated T cell culture supernatant Figure 4. Investigation of requirement for direct contact between T cells and TGF-b reporter cells. (A) 293T-caga-Luc-CD32-CD86 cells were mixed with an equal number of un-manipulated 293T cells. Under this condition, a single 293T-caga-Luc-CD32-CD86 cell stimulates CD4 T cells and responds to TGF-b activity produced by the same T cells. (B) 293T-caga cells that did not have CD32 or CD86 were mixed with 293T-CD32-CD86 cells lacking the (caga)12-Luc reporter. T cell-produced TGF-b activity is not found in the ELISA detectable ‘‘total’’ TGF-b fraction These data indicate that T cell-produced TGF-b activity is not contained in the ELISA detectable ‘‘total’’ TGF-b fraction. expected anti-TGF-b Abs neutralized recombinant TGF-b activity, whereas anti-LAP/anti-latent TGF-b/pro-TGF-b mAbs did not (Figure 8A). Surprisingly, anti-TGF-b Abs did not neutralize TGF-b activity in the T cell culture supernatant (Figure 8B). The ALK5 inhibitor II [14] completely blocked luciferase induction by the T cell culture supernatant (Figure 8B), confirming that the luciferase production was downstream of the TGF-b signaling. On the other hand, anti-LAP mAb TW7-20B9 and anti-latent TGF-b/pro-TGF-b TW7-28G11 inhibited TGF-b activity in the culture supernatant (Figure 8B). Thus, T-cell T cell-produced TGF-b activity is not found in the ELISA detectable ‘‘total’’ TGF-b fraction isotype control mAb MOPC21) to deplete latent TGF-b in the supernatant. The amount of ‘‘total’’ TGF-b detected by ELISA after acidification in control MOPC21-treated T cell culture supernatant was 1,318 pg/ml, whereas the anti-LAP TW7-16B4-treated T cell culture supernatant contained 126 pg/ml ‘‘total’’ TGF-b (Figure 7A). Since anti-murine LAP TW7-16B4 mAb does not cross-react with bovine LAP (data not shown), we conclude that all T cell-derived ‘‘total’’ TGF-b was removed by the TW7-16B4-coupled magnetic bead treatment. However, TGF-b activity in the TW7- 16B4-treated T cell culture supernatant was intact since the anti- LAP TW7-16B4-treated T cell culture supernatant induced an identical TGF-b response in 293T-caga-Luc-CD32-CD86 reporter cells as the control MOPC21-treated T cell culture supernatant TGF-b measured by ELISA after acidification is termed ‘‘total’’ TGF-b. This is based on the assumption that following acidification, the 25 kDa free TGF-b dimer is released from any form of TGF-b, such as the small latent TGF-b complex and the large latent TGF-b complexes. We thus asked whether T-cell produced TGF-b activity resides in the ‘‘total’’ TGF-b fraction. Since FBS-derived latent TGF-b affects TGF-b ELISA after acidification, we used TGF-b- depleted FBS for the culture medium [20]. The background bovine TGF-b remaining in the 10% TGF-b-depleted FBS-supplemented medium was 148 pg/ml. We treated a T cell culture supernatant with anti-LAP mAb TW7-16B4-coupled magnetic beads (or an IgG1 PLoS ONE | www.plosone.org PLoS ONE | www PLoS ONE | www.plosone.org April 2011 | Volume 6 | Issue 4 | e18365 5 A New Form of T Cell Derived TGF-b Figure 5. TGF-b bioassay from T cell culture supernatants. (A) Pre-activated CD4+CD252 T cells were re-stimulated with 293T-caga-Luc-CD32- CD86 cells in the presence of anti-CD3 as a co-culture assay. (B) Supernatants were taken from the co-culture assay, added to new wells of 293T-caga- Luc-CD32-CD86 reporter cells and luciferase activity was measured. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g005 Figure 5. TGF-b bioassay from T cell culture supernatants. (A) Pre-activated CD4+CD252 T cells were re-stimulated with 293T-caga-Luc-CD32- CD86 cells in the presence of anti-CD3 as a co-culture assay. (B) Supernatants were taken from the co-culture assay, added to new wells of 293T-caga- Luc-CD32-CD86 reporter cells and luciferase activity was measured. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g005 (Figure 7B). These data indicate that T cell-produced TGF-b activity is not contained in the ELISA detectable ‘‘total’’ TGF-b fraction. (Figure 7B). Neutralization of T cell-produced TGF-b activity with anti-LAP/latent TGF-b mAbs Since our results above indicate that T cell-produced TGF-b activity takes a form that is different from the 25 kDa free TGF-b dimer, we tested anti-active TGF-b Abs and anti-mouse LAP/ latent TGF-b mAbs to better understand the structure of T cell- produced TGF-b. Recombinant TGF-b (100 pg/ml) and a T cell culture supernatant diluted to the equivalent activity were treated with 50 mg/ml of anti-TGF-b Abs (1D11 or chicken polyclonal anti-TGF-b), anti-mouse LAP mAb (TW7-20B9), or anti-latent TGF-b/pro-TGF-b mAb (TW7-28G11), and then tested for TGF-b activity by the 293T-caga-Luc-CD32-CD86 bioassay. As Figure 6. Smad2 phosphorylation by T cell culture superna- tants. Recombinant TGF-b (1 ng/ml) or a T cell culture supernatant containing equivalent amount of TGF-b activity was added to 293T- caga-Luc-CD32-CD86 cells. After 2, 5, 15, and 30 min, the cells were lysed, and the lysates were run on SDS-PAGE. After transfer to a PVDF membrane, the membrane was blotted with anti-phospho-Smad2 Ab, and reblotted with anti-Smad2/3 Ab. doi:10.1371/journal.pone.0018365.g006 Table 1. TGF-b in a T cell culture supernatant was measured by the 293T-caga-CD32-CD86-caga bioassay (TGF-b activity), by ELISA without acidification (the 25 kDa free TGF-b dimer), and by ELISA after acidification ( ‘‘total TGF-b’’). TGF-b in culture supernatant 293T-(caga)12-Luc ELISA ELISA bioassay without acidification after acidification (activity) (25 kDa free dimer) (‘‘total’’) ,200 pg/ml 10 pg/ml 486 pg/ml doi:10.1371/journal.pone.0018365.t001 TGF-b in culture supernatant 293T-(caga)12-Luc ELISA ELISA bioassay without acidification after acidification (activity) (25 kDa free dimer) (‘‘total’’) ,200 pg/ml 10 pg/ml 486 pg/ml doi:10.1371/journal.pone.0018365.t001 Figure 6. Smad2 phosphorylation by T cell culture superna- tants. Recombinant TGF-b (1 ng/ml) or a T cell culture supernatant containing equivalent amount of TGF-b activity was added to 293T- caga-Luc-CD32-CD86 cells. After 2, 5, 15, and 30 min, the cells were lysed, and the lysates were run on SDS-PAGE. After transfer to a PVDF membrane, the membrane was blotted with anti-phospho-Smad2 Ab, and reblotted with anti-Smad2/3 Ab. doi:10.1371/journal.pone.0018365.g006 after acidification April 2011 | Volume 6 | Issue 4 | e18365 6 A New Form of T Cell Derived TGF-b Figure 7. Immunologic depletion of ‘‘total’’ TGF-b from culture supernatants. (A) A T cell culture supernatant from plate-bound anti-CD3/ CD28 re-stimulated CD4+CD252 T cells cultured in 10% TGF-b-depleted FBS IMDM was treated with control IgG1 mAb-coated magnetic beads or anti- mouse LAP TW7-16B4 mAb-coated magnetic beads. The remaining ‘‘total’’ TGF-b in the culture supernatant was measured by TGF-b ELISA after acidification. Error bars represent mean 6 S.D. of duplicates. (B) TGF-b activity in the same control IgG1-treated or anti-LAP TW7-16B4-treated T cell culture supernatant was measured by the 293T-caga-Luc-CD32-CD86 bioassay after 630, 660 and 6120 dilutions. doi:10.1371/journal.pone.0018365.g007 Figure 7. Immunologic depletion of ‘‘total’’ TGF-b from culture supernatants. (A) A T cell CD28 re-stimulated CD4+CD252 T cells cultured in 10% TGF-b-depleted FBS IMDM was treated with c mouse LAP TW7-16B4 mAb-coated magnetic beads. The remaining ‘‘total’’ TGF-b in the culture s acidification. Error bars represent mean 6 S.D. of duplicates. (B) TGF-b activity in the same control culture supernatant was measured by the 293T-caga-Luc-CD32-CD86 bioassay after 630, 660 and doi:10 1371/journal pone 0018365 g007 Figure 7. Immunologic depletion of ‘‘total’’ TGF-b from culture supernatants. (A) A T cell culture supernatant from plate-bound anti-CD3/ CD28 re-stimulated CD4+CD252 T cells cultured in 10% TGF-b-depleted FBS IMDM was treated with control IgG1 mAb-coated magnetic beads or anti- mouse LAP TW7-16B4 mAb-coated magnetic beads. T cell-produced TGF-b is not latent TGF-b b b Since the T cell-produced TGF-b contains LAP, it may simply represent the latent TGF-b complex and the 293T-caga-Luc- CD32-CD86 reporter cells have a TGF-b activation machinery which can initiate TGF-b signaling in response to latent TGF-b. To exclude this possibility, we added a commercially available recombinant human latent TGF-b or a culture supernatant of mouse TGF-b-transduced P3U1 cells to the 293T-caga-Luc-CD32- CD86 reporter cells. We found that mouse TGF-b-transduced P3U1 cells produced high amounts of latent TGF-b, as judged by a TGF-b ELISA with or without acidification. However, both latent TGF-b samples barely induced TGF-b signaling in the 293T-caga- Luc-CD32-CD86 cells (Figure 9). Even at 4,000 pg/ml, recombi- nant human latent TGF-b and mouse latent TGF-b-containing supernatants induced only faint luciferase signals (equivalent to less than 10 pg/ml recombinant TGF-b), which is likely explained by the presence of contaminating active TGF-b which was detected by ELISA without acidification (data not shown). The remaining ‘‘total’’ TGF-b in the culture supernatant was measured by TGF-b ELISA after acidification. Error bars represent mean 6 S.D. of duplicates. (B) TGF-b activity in the same control IgG1-treated or anti-LAP TW7-16B4-treated T cell culture supernatant was measured by the 293T-caga-Luc-CD32-CD86 bioassay after 630, 660 and 6120 dilutions. doi:10.1371/journal.pone.0018365.g007 produced TGF-b activity as measured by the 293T-caga-Luc- CD32-CD86 bioassay takes a molecular form that contains LAP as a component. Since anti-LAP mAb TW7-20B9 does not cross- react with human LAP (Figure S2), the new form of active TGF-b is truly produced from murine CD4 T cells, but not from the human 293T reporter cells. Cell type-specific responses to T cell-produced TGF-b Since T cell-produced TGF-b activity takes an unconventional TGF-b form, it is possible that it requires specific sensing machineries and that only certain cell types respond to T cell- produced TGF-b. To test this, we assayed T cell culture supernatants on other TGF-b reporter cell lines. The Mv1Lu- (caga)12-Luc cell line has the same the (caga)12-Luc reporter as the 293T-caga-Luc-CD32-CD86 cell line, and responds to recombi- nant TGF-b in a dose-dependent manner. However, we found that Mv1Lu-(caga)12-Luc cells did not respond to T cell culture supernatants (Figure 10, middle). Another well-known TGF-b bioassay reporter line is the mink lung epithelial cell (MLEC)-PAI- 1-Luc cell line which has a PAI-1 promoter-driven luciferase reporter [21]; we found that MLEC-PAI-1-Luc cells also did not respond to T cell-produced TGF-b (Figure 10, bottom). These results indicate that T cell-produced TGF-b does not initiate TGF- b signaling in all cell types, but it requires cell type-specific molecular machineries to initiate TGF-b signaling. Discussion We have previously reported [22] a TGF-b bioassay for T cells using the MLEC-PAI-1-Luc cell line, in which T cells were cocultured with reporter cells and stimulated with anti-CD3/CD28- coated beads attached to the reporter cell surface. This bioassay PLoS ONE | www.plosone.org April 2011 | Volume 6 | Issue 4 | e18365 PLoS ONE | www.plosone.org 7 A New Form of T Cell Derived TGF-b Figure 8. Effects of anti-LAP or anti-latent TGF-b/pro-TGF-b mAbs on TGF-b activity in T cell culture supernatants. (A) Recombinant human TGF-b was pre-mixed with anti-active TGF-b Abs (1D11 or chicken anti-TGF-b), an anti-LAP mAb (TW7-20B9), an anti-latent TGF-b/pro-TGF-b mAb (TW7-28G11) (final 50 mg/ml), or ALK5 inhibitor II (final 1 mM), and then added to 293T-caga-Luc-CD32-CD86 reporter cells. (B) A T cell culture supernatant containing an equivalent amount of TGF-b was pre-mixed with the indicated Abs or the ALK5 inhibitor, and added to 293T-caga-Luc- CD32-CD86 cells. The luciferase activity was measured after 16 hr culture. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g008 Figure 8. Effects of anti-LAP or anti-latent TGF-b/pro-TGF-b mAbs on TGF-b activity in T cell culture supernatant human TGF-b was pre-mixed with anti-active TGF-b Abs (1D11 or chicken anti-TGF-b), an anti-LAP mAb (TW7-20B9), an anti-late mAb (TW7-28G11) (final 50 mg/ml), or ALK5 inhibitor II (final 1 mM), and then added to 293T-caga-Luc-CD32-CD86 reporter cells supernatant containing an equivalent amount of TGF-b was pre-mixed with the indicated Abs or the ALK5 inhibitor, and adde CD32-CD86 cells. The luciferase activity was measured after 16 hr culture. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g008 Figure 8. Effects of anti-LAP or anti-latent TGF-b/pro-TGF-b mAbs on TGF-b activity in T cell culture supernatants. (A) Recombinant human TGF-b was pre-mixed with anti-active TGF-b Abs (1D11 or chicken anti-TGF-b), an anti-LAP mAb (TW7-20B9), an anti-latent TGF-b/pro-TGF-b mAb (TW7-28G11) (final 50 mg/ml), or ALK5 inhibitor II (final 1 mM), and then added to 293T-caga-Luc-CD32-CD86 reporter cells. (B) A T cell culture supernatant containing an equivalent amount of TGF-b was pre-mixed with the indicated Abs or the ALK5 inhibitor, and added to 293T-caga-Luc- CD32-CD86 cells. The luciferase activity was measured after 16 hr culture. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g008 the presence of anti-CD3. Thus, we chose 293T cell line as TGF-b reporter cells as this cell line is resistant to CD4-mediated killing. Discussion We made a lentivirus based TGF-b reporter vector which contains repeated CAGA Smad binding elements in the promoter region linked luciferase (pSMPUW-(caga)12-Luc). 293T cells were trans- duced with (caga)12-Luc, mouse CD32 and mouse CD86. Serpinb9 and Serpinb9b were also transduced as we found in preliminary experiments that these granzyme inhibitor genes acted to lessen CD4-mediated killing in MLEC-PAI-1-Luc cells. demonstrated that CD4+CD25+ Tregs produced active TGF-b which was neutralized with anti-TGF-b mAb 1D11. In order to improve on this bioassay, we first modified the bioassay so that the reporter cells behaved as artificial antigen presenting cells by transducing MLEC-PAI-1-Luc cells with mouse CD32 (Fc receptor) for anti-CD3 capture and with mouse CD86 for costimulation. Preliminary experiments showed that these CD32/CD86-trans- duced MLEC-PAI-1-Luc cells were killed by murine pre-activated CD4 T cells when T cells were co-cultured with the reporter cells in Figure 9. Response of 293T-caga-Luc-CD32-CD86 cells to latent TGF-b. Recombinant TGF-b, commercially available recombinant human latent TGF-b or a diluted culture supernatant of mouse Tgfb1-transduced P3U1 cells was added to 293T-caga-Luc-CD32-CD86 cells and the resultant luciferase activity was measured after 11 hrs. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g009 Figure 9. Response of 293T-caga-Luc-CD32-CD86 cells to latent TGF-b. Recombinant TGF-b, commercially available recombinant human latent TGF-b or a diluted culture supernatant of mouse Tgfb1-transduced P3U1 cells was added to 293T-caga-Luc-CD32-CD86 cells and the resultant luciferase activity was measured after 11 hrs. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g009 April 2011 | Volume 6 | Issue 4 | e18365 PLoS ONE | www.plosone.org 8 A New Form of T Cell Derived TGF-b Figure 10. Cell type-specific responses to T cell-produced TGF-b. 293T-caga-Luc-CD32-CD86 cells (top), Mv1Lu-(caga)12-Luc cells (middle), or MLEC-PAI-1-Luc cells (bottom) were exposed to recombinant TGF-b or diluted T cell culture supernatants. The luciferase activity was measured after 11 hr culture. Error bars represent mean 6 S.D. of duplicates. doi:10.1371/journal.pone.0018365.g010 Figure 10. Cell type-specific responses to T cell-produced TGF-b. 293T-caga-Luc-CD32-CD86 cells (top), Mv1Lu-(caga)12-Luc cells (middle), or MLEC-PAI-1-Luc cells (bottom) were exposed to recombinant TGF-b or diluted T cell culture supernatants. The luciferase activity was measured after 11 hr culture. Error bars represent mean 6 S.D. of duplicates. Discussion doi:10.1371/journal.pone.0018365.g010 When we used this new 293T-caga-Luc-CD32-CD86 reporter cell to assay activated T cells, we found that activated T cells produced high TGF-b activity in the 293T-caga-Luc-CD32-CD86 reporter cell assay even though we could not detect active TGF-b production by ELISA. Furthermore, we found that activated Foxp3+ CD4 T cells that express surface LAP/TGF-b [14] had lower TGF-b activity in the 293T-caga-Luc-CD32-CD86 reporter cell assay than activated CD252 T cells. This TGF-b activity was detected in T cell culture supernatants indicating that the T cell- produced TGF-b was in the soluble form and was not membrane- bound. These findings are in contrast to our previous observations using MLEC-PAI-1-Luc cells [22] that when compared to CD4+CD252 T cells, activated CD4+CD25+ T cells had higher TGF-b activity and this activity was linked to membrane bound TGF-b. We believe that this difference is because the T cell- produced TGF-b activity we observed using the 293T-caga-Luc- CD32-CD86 reporter cell assay consists of an unconventional form of TGF-b which can be measured by the 293T-caga reporter cells but not by MLEC-PAI-1-Luc cells. Thus it appears that Foxp3+ Tregs produce the canonical form of mature TGF-b which can be neutralized with anti-TGF-b mAb 1D11, whereas Foxp32 non-Tregs produce a new form of TGF-b which we have identified with our new reporter assay and which can induce TGF-b signaling in a cell type-specific manner. Whether all activated CD4+CD252 T cells produce this newly described form of TGF-b or it is produced by a subset of CD4+CD252 cells is an important question. In addressing this question, we found that CD4 T cells that produce this new form of TGF-b reside primarily in the CD62L2CD44hi memory fraction as opposed to the CD62L+CD44lo naive fraction (Figure S3). Whether differentiated Th cell subsets such as Th1, Th2, Th17, or Tr1 cells preferentially produce this form of TGF-b is an interesting future question. g q The molecular structure and/or composition of this new form of TGF-b are unknown. It contains LAP as a component since the TGF-b activity measured by the 293T-caga-Luc-CD32-CD86 reporter cell is neutralized by an anti-LAP mAb and by an anti- latent TGF-b/pro-TGF-b mAb. Since mature TGF-b is not released from the new form of TGF-b by acidification, this suggests strong binding of the LAP segment to the TGF-b segment. This may be because LAP is linked to TGF-b by covalent bonding. PLoS ONE | www.plosone.org CD4 T cell preparation and stimulation Mice were housed in a pathogen-free environment and the animal protocols were approved by the Committee on Animals of Harvard Medical School (Harvard Medical Area Standing Committee on Animals, Protocol No. 02683). CD4 T cells were separated from BALB/c mice (The Jackson Laboratories) using a MACS CD4 purification kit (Miltenyi Biotec). When CD4+CD252 T cells were prepared, biotinylated anti-CD25 antibody (7D4, BD Biosciences) was additionally mixed to the MCAS antibody cocktail. CD4+CD25+ T cells were prepared from the CD4 fraction by staining CD25-FITC (7D4, BD Biosciences) followed by anti-FITC MACS beads (Miltenyi Biotec), and by MS column separation. T cells were stimulated with plate-bound anti-CD3 and anti-CD28 (5 mg/ul each) for 2 days in 10% FBS-supplemented IMDM. In case of CD4+CD25+ Detection of Smad2 phosphorylation 293T-caga-Luc-CD32-CD86 cells were exposed to recombi- nant human TGF-b (1 ng/ml) or a T cell culture supernatant diluted by TGF-b activity determined by the 293T-caga-Luc- CD32-CD86 bioassay equivalent to 1 ng/ml TGF-b. After 2, 5, 15, and 30 min, the cells were lysed with 1% Triton X-100, 0.25% deoxycholate, 0.1% SDS, 1 mM NaVO4, protease inhibitor cocktail (Pierce/Thermo), 25 mM Tris buffered saline. The lysates were clarified by centrifugation at 13,000 rpm for 15 min, and run on SDS-PAGE under reducing conditions. Western blot was conducted with rabbit anti-phospho-Smad2(Ser465/467) antibody (Cell Signaling) and with rabbit anti-Smad2/3 antibody (Cell Signaling). Cell lines, Plasmids, and antibodies The (caga)12-MLP-Luc vector was kindly provided from Dr. D. Vivien (the Universite’ de Caen, Daix, France). Mv1Lu cells (ATCC) were stably transfected with the (caga)12-MLP-Luc plasmid (Mv1Lu-(caga)12-Luc cells). The mink lung epithelial cell line transfected with the Smad-responsive plasminogen activator inhibitor-1 promoter driving a luciferase reporter gene (MLEC- PAI-1-Luc) (originally developed by Abe et al. [21]) was obtained from Dr. L. van de Water (Massachusetts General Hospital, Boston, MA, USA). A lentivirus based TGF-b reporter vector was constructed by inserting the (caga)12-MLP-Luc segment into a promoterless lentiviral vector pSMPUW (Cell Biolabs) along with ubiquitin C promoter-driven a GFP-puro fusion gene as a selection marker (pSMPUW-(caga)12-Luc). pMCs retroviral vector was kindly provided Dr. T. Kitamura (Tokyo Univ., Tokyo, Japan) and pBMN retroviral vector was from Addgene under a MTA with Stanford University (Stanford, CA). A lentivirus supernatant and retrovirus supernatants were produced as described previously [23]. Human embryonic kidney 293T cells (Clontech) were sequentially transduced with pSMPUW-(caga)12- Luc, pBMN-mouse CD32 (without IRES), pBMN-mouse CD86 (without IRES), pMCs-Serpinb9-IRES-Thy1.1, and pMCs-Ser- pinb9b-IRES-Thy1.2 vectors with cloning in each step. The resultant cells were termed 293T-caga-Luc-CD32-CD86 cells. Anti-TGF-b hybridoma 1D11 was from ATCC, and chicken anti- TGF-b (AF-101-NA) was from R&D Systems. Anti-mouse LAP mAbs TW7-16B4 and TW7-20B9, and anti-latent TGF-b/pro- TGF-b mAb TW7-28G11 were described previously [14]. Anti- FasL (clone MFL3) was from BioLegend. ALK5 inhibitor II was from EMD/Calbiochem. TGF-b ELISA TGF-b ELISA was performed using anti-TGF-b mAb 1D11 as a coating antibody and biotinylated chicken anti-TGF-b IgY (BAF240, R&D Systems) as a detection antibody. Recombinant human TGF-b (R&D Systems) was used as a standard (0– 2,000 pg/ml). Sample acidification was done by adding 1/10 volume of 1 N HCl, incubating at room temperature for 10 min, and neutralizing with 1/10 volume of 1 N NaOH/0.1 M Tris. The samples were then diluted twofold by adding 25 mM Tris buffered saline. Discussion Alternatively, disulfide bonding inside mature TGF-b may take irregular forms that make the TGF-b segment undetectable by ELISA even if the TGF-b segment is released by acidification. Whatever the case, it should be noted that one cannot detect the new form of TGF-b by ELISA even after acidification. Thus, this new form of TGF-b does not appear to be part of the ‘‘total’’ TGF-b detected by ELISA after acidification. PLoS ONE | www.plosone.org April 2011 | Volume 6 | Issue 4 | e18365 9 A New Form of T Cell Derived TGF-b T cell stimulation, 100 U/ml recombinant IL-2 was added both in CD4+CD25+ T cell cultures and in CD4+CD252 T cell cultures. The cells were split into non-coated wells and rested for 1 day. The cells were recovered, washed with the culture medium, counted, and used for the TGF-b bioassay, or re-stimulated with plate- bound anti-CD3/CD28 for 24 h hrs for culture supernatants. When indicated, TGF-b-depleted FBS [20] was used for the culture medium. At this time we do not know what cell properties and/or molecules are required to initiate TGF-b signaling by the new form of TGF-b we have identified. In preliminary experiments, we did not find that T cell-produced TGF-b induced Smad2 phosphorylation in CD4 T cells or in bone marrow-derived DCs. However, it is possible that sub-populations of T cells or DCs would respond T cell-produced TGF-b under special conditions. In conclusion, our work demonstrates that murine CD4 T cells produce an unconventional form of TGF-b which has biological activity as measured by 293T-caga-Luc-CD32-CD86 reporter cells but not by other assay systems and is not produced in significant amounts by conventional Treg cells. Our finding of a new form of T cell-produced TGF-b and the newly developed TGF-b bioassay system will provide a new avenue to investigate T cell function of the immune system. Materials and Methods Cell lines, Plasmids, and antibodies TGF-b bioassay 293T-caga-Luc-CD32-CD86 TGF-b reporter cells were seeded at 26104 cells/100 ml/well on collagen-coated 96-well plates 1 day before addition of T cells. On the day of assay, 10 ml of 1 mg/ml anti-CD3 (145-2C11) (BD Biosciences) was added to each well (final 0.5 mg/ml). When CD4+CD25+ T cells were tested, IL-2 was also added to final 100 U/ml. Pre-activated CD4 T cells or recombinant human TGF-b (R&D Systems) were added at 100 ml/well (final total volume 210 ml/well) and cultured for 16 hrs. Similarly, the TGF-b bioassay from culture supernatants was conducted by adding 100 ml of diluted T cell culture supernatants to 293T-caga-Luc-CD32-CD86 cell culture wells and the reporter cells were cultured for the indicated time. When neutralizing antibodies were tested, T cell culture supernatants were diluted to be equivalent to 200 pg/ml recombinant TGF-b activity and were then premixed with the antibodies at 100 mg/ml for 30 min at room temperature. 100 ml of the mixture was added to 100 ml of 293T-caga-Luc-CD32-CD86 reporter wells. 293T- caga-Luc-CD32-CD86 cells were lysed with Glo-Lysis buffer (Promega), and luciferase activity was measured by ONE-Glo luciferease assay reagent (Promega). References 13. Nakamura K, Kitani A, Strober W (2001) Cell contact-dependent immunosup- pression by CD4+CD25+ regulatory T cells is mediated by cell surface-bound transforming growth factor b. J Exp Med 194: 629–644. 1. Rubtsov YP, Rudensky AY (2007) TGFb signalling in control of T-cell-mediated self-reactivity. Nat Rev Immunol 7: 443–453. 1. Rubtsov YP, Rudensky AY (2007) TGFb signalling in control of T-cell-mediated self-reactivity. Nat Rev Immunol 7: 443–453. 2. Kulkarni AB, Huh CG, Becker D, Geiser A, Lyght M, et al. (1993) Transforming growth factor b1 null mutation in mice causes excessive inflammatory response and early death. Proc Natl Acad Sci U S A 90: 770–774. g g p 14. Oida T, Weiner HL (2010) TGF-b induces surface LAP expression on murine CD4 T cells independent of Foxp3 induction. PLoS ONE 5: e15523. y p y 3. Christ M, McCartney-Francis NL, Kulkarni AB, Ward JM, Mizel DE, et al. (1994) Immune dysregulation in TGF-b1-deficient mice. J Immunol 153: 1936–1946. 15. Tran DQ, Andersson J, Hardwick D, Bebris L, Illei GG, et al. (2009) Selective expression of latency-associated peptide (LAP) and IL-1 receptor type I/II (CD121a/CD121b) on activated human FOXP3+ regulatory T cells allows for their purification from expansion cultures. Blood 113: 5125–5133. 4. Veldhoen M, Hocking RJ, Atkins CJ, Locksley RM, Stockinger B (2006) TGFb in the context of an inflammatory cytokine milieu supports de novo differentiation of IL-17-producing T cells. Immunity 24: 179–189. 16. Tran DQ, Andersson J, Wang R, Ramsey H, Unutmaz D, et al. (2009) GARP (LRRC32) is essential for the surface expression of latent TGF-b on platelets and activated FOXP3+ regulatory T cells. Proc Natl Acad Sci U S A 106: 13445–13450. 5. Mangan PR, Harrington LE, O’Quinn DB, Helms WS, Bullard DC, et al. (2006) Transforming growth factor-b induces development of the TH17 lineage. Nature 441: 231–234. 17. Stockis J, Colau D, Coulie PG, Lucas S (2009) Membrane protein GARP is a receptor for latent TGF-b on the surface of activated human Treg. Eur J Immunol 39: 3315–3322. 6. Bettelli E, Carrier Y, Gao W, Korn T, Strom TB, et al. (2006) Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells. Nature 441: 235–238. 18. Dennler S, Itoh S, Vivien D, ten Dijke P, Huet S, et al. (1998) Direct binding of Smad3 and Smad4 to critical TGFb-inducible elements in the promoter of human plasminogen activator inhibitor-type 1 gene. Supporting Information Figure S1 Effect of blocking anti-Fas Ligand antibody to T cell-produced TGF- b. Pre-activated CD4 T cells were harvested on day 4, which is one day delayed compared with the regular stimulation (day 3 recovery), and the CD4 T cells were co- cultured with 293T-caga-Luc-CD32-CD86 reporter cells in presence of blocking anti-FasL mAb. Depletion of ‘‘total’’ TGF-b from culture supernatants with an anti-LAP Ab 400 ml of 1 mg/ml of anti-mouse IgG magnetic beads (BioMag Plus, Polysciences) was placed in a 1.5 ml microcentrifuge tube and the beads were washed with PBS three times. 400 ml PBS containing 20 mg of anti-mouse LAP mAb TW7-16B4 or isotype control MOPC21 was added to the beads and incubated with PLoS ONE | www.plosone.org April 2011 | Volume 6 | Issue 4 | e18365 10 A New Form of T Cell Derived TGF-b rotation for 4 hrs. After washing with PBS three times, 0.6 ml of the T cell culture supernatant from plate-bound anti-CD3/CD28 re-stimulated CD4+CD252 T cells in 10% TGF-b-depleted FBS IMDM was added to the bead pellets, and incubated at 4uC for overnight. The unbound supernatant was recovered by magnetic separation. The amount of TGF-b before and after separation was measured by TGF-b ELISA after acidification. Figure S2 Species specificity of TW7 antibodies. human TGFB1-transduced P3U1 cells (clone 32, without IRES-GFP) (GFP2 population) and mouse Tgfb1-transduced P3U1 cells (clone 11, containing IRES-GFP) (GFP+ population) were mixed and surface stained with TW7-16B4, TW7-20B9, or TW7-28G11 mAb. TW7-16B4 and TW7-20B9 stained only mouse Tgfb1- transduced cells while TW7-28G11 stained both human TGFB1- transduced cells and mouse Tgfb1-transduced cells. (TIF) Author Contributions Conceived and designed the experiments: TO HLW. Performed the experiments: TO. Analyzed the data: TO. Contributed reagents/ materials/analysis tools: TO. Wrote the paper: TO HLW. Conceived and designed the experiments: TO HLW. Performed the experiments: TO. Analyzed the data: TO. Contributed reagents/ materials/analysis tools: TO. Wrote the paper: TO HLW. Latent TGF-b Recombinant human latent TGF-b was purchased from R&D Systems. Recombinant mouse latent TGF-b was made as a culture supernatant of mouse Tgfb1-transduced P3U1 cells. The 16 culture supernatant contained 84 ng/ml total TGF-b (mostly latent TGF-b) and 142 pg/ml active TGF-b determined by TGF- b ELISA with, and without acidification, respectively. Figure S3 Production of TGF-b activity from naı¨ve CD4 T cells and memory CD4 T cells. CD62L+CD44lo naı¨ve CD4 T cells or CD62LloCD44hi memory CD4 T cells were stimulated with plate-bound anti-CD3/CD28 for 2 days, and rested for 1 day. The pre-activated CD4 T cells were recovered, and the indicated numbers of T cells were added to 293T-caga-Luc- CD32-CD86 cells with 0.5 mg/ml of anti-CD3 antibody. Recom- binant human TGF-b was also added as a standard. After 16 hr culture, the reporter cells were lysed and the luciferase activity was measured. Error bars represent mean 6 S.D. of duplicates. (TIF) Figure S3 Production of TGF-b activity from naı¨ve CD4 T cells and memory CD4 T cells. CD62L+CD44lo naı¨ve CD4 T cells or CD62LloCD44hi memory CD4 T cells were stimulated with plate-bound anti-CD3/CD28 for 2 days, and rested for 1 day. The pre-activated CD4 T cells were recovered, and the indicated numbers of T cells were added to 293T-caga-Luc- CD32-CD86 cells with 0.5 mg/ml of anti-CD3 antibody. Recom- binant human TGF-b was also added as a standard. After 16 hr culture, the reporter cells were lysed and the luciferase activity was measured. Error bars represent mean 6 S.D. of duplicates. (TIF) References EMBO J 17: 3091–3100. 7. Nurieva R, Yang XO, Martinez G, Zhang Y, Panopoulos AD, et al. (2007) Essential autocrine regulation by IL-21 in the generation of inflammatory T cells. Nature 448: 480–483. 19. Docagne F, Colloc’h N, Bougueret V, Page M, Paput J, et al. (2001) A soluble transforming growth factor-b (TGF-b) type I receptor mimics TGF-b responses. J Biol Chem 276: 46243–46250. 8. Korn T, Bettelli E, Gao W, Awasthi A, Ja¨ger A, et al. (2007) IL-21 initiates an alternative pathway to induce proinflammatory T(H)17 cells. Nature 448: 484–487. 20. Oida T, Weiner HL (2010) Depletion of TGF-b from fetal bovine serum. J Immunol Methods 362: 195–198. 9. Komiyama Y, Nakae S, Matsuki T, Nambu A, Ishigame H, et al. (2006) IL-17 plays an important role in the development of experimental autoimmune encephalomyelitis. J Immunol 177: 566–573. 21. Abe M, Harpel JG, Metz CN, Nunes I, Loskutoff DJ, et al. (1994) An assay for transforming growth factor-b using cells transfected with a plasminogen activator inhibitor-1 promoter-luciferase construct. Anal Biochem 216: 276–284. 10. Nakae S, Nambu A, Sudo K, Iwakura Y (2003) Suppression of immune induction of collagen-induced arthritis in IL-17-deficient mice. J Immunol 17: 6173–6177. 22. Oida T, Xu L, Weiner HL, Kitani A, Strober W (2006) TGF-b-mediated suppression by CD4+CD25+ T cells is facilitated by CTLA-4 signaling. J Immunol 177: 2331–2339. 11. Li MO, Wan YY, Flavell RA (2007) T cell-produced transforming growth factor-b1 controls T cell tolerance and regulates Th1- and Th17-cell differentiation. Immunity 26: 579–591. 23. Oida T, Weiner HL (2010) Overexpression of TGF-b1 gene induces cell surface localized Glucose-Regulated Protein 78-associated Latency-associated peptide/ TGF-b. J Immunol 185: 3529–3535. y 12. Miyazono K, Ichijo H, Heldin CH (1993) Transforming growth factor-b: latent forms, binding proteins and receptors. Growth Factors 8: 11–22. PLoS ONE | www.plosone.org April 2011 | Volume 6 | Issue 4 | e18365 11
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Наукові нотатки Наукові нотатки 1 Від травня 2022 року, згідно з п. 1 § 54 «Українського правопису» (Український правопис ; Ін-т мовознав. ім. О. О. Потебні НАН України, Ін-т укр. мови НАН України, Укр. мов.- інформ. фонд НАН України, НВП «Вид-во “Наук. думка”». Київ, 2019. С. 83), «в офіційних складених назвах органів влади, установ і  організацій, товариств і  об’єднань з  великої букви пишемо перше слово і всі власні назви, що входять до складу цих назв: <…> Збройні сили України <…>». Водночас у  законодавчих і  підзаконних актах залишилося старе написання — Збройні Сили України. Наталія Панченко * a, Ірина Гордієнко ** b, Ольга Грек *** c * Сумське відділення ННЦ «ІСЕ ім. Засл. проф. М. С. Бокаріуса», м. Суми, Україна, ORCID: https://orcid.org/0000-0002-8277-7731, e-mail: svhndise@meta.ua ** Сумське відділення ННЦ «ІСЕ ім. Засл. проф. М. С. Бокаріуса», м. Суми, Україна, ORCID: https://orcid.org/0000-0001-8703-5481 *** Сумське відділення ННЦ «ІСЕ ім. Засл. проф. М. С. Бокаріуса», м. Суми, Україна, ORCID: https://orcid.org/0000-0001-7080-2226 a Методологія, концепція, написання оригінального проєкту. a Методологія, концепція, написання оригінального проєкту. b Кураторство даними, формальний аналіз. c Адміністрування проєкту, ресурси, нагляд. c Адміністрування проєкту, ресурси, нагляд. DOI: 10.32353/khrife.2.2022.08 УДК 343.98:665.71:355/359(477) Надійшло 06.06.2022 / Рецензовано 15.06.2022 / Прийнято до друку 17.06.2022 / Доступно онлайн 30.06.2022 DOI: 10.32353/khrife.2.2022.08 УДК 343.98:665.71:355/359(477) Надійшло 06.06.2022 / Рецензовано 15.06.2022 / Прийнято до друку 17.06.2022 / Доступно онлайн 30.06.2022 Досліджено теоретичні напрацювання судових експертів щодо особливостей обліку пального в транспортній та обо- ронній сферах, наведено перелік законодавчих і нормативних актів, якими врегульовано порядок обліку, руху та списання пально-мастильних матеріалів у військових частинах. Ав- торки мали на меті висвітлити питання обліку пального в умовах військового стану й російської військової агресії, до- кументально обґрунтувати ефективне використання паль- ного військовими частинами Збройних сил України та те- риторіальної оборони у процесі виконання бойових завдань. Узагальнено об’єкти дослідження судових економічних експер- тиз, окреслено коло наданих експертам повноважень під час проведення таких експертиз. Зазначено особливості обліку й руху військового майна, характерні для правил прийому, об- ліку, видавання та списання матеріальних цінностей у Зброй- них силах України. Визначено питання й завдання, вирішувані експертами під час проведення судових економічних експертиз, пов’язаних з обліком і використанням пального військовими © 2022 Автор(и). Видано Національним науковим центром «Інститут судових експертиз ім. Засл. проф. М. С. Бокаріуса» та Національним юридичним університетом імені Ярослава Мудрого. Це стаття з відкритим доступом, розповсюджена на умовах Ліцензії атрибуції Creative Commons (CC_BY_4.0), що дає змогу необмежено використовувати, розповсюджувати й відтворювати на будь-якому носії за умови посилання на оригінального автора та джерела. Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal частинами Збройних сил України. Наведено перелік законо- давчих та нормативно-правових актів, якими мають керу- ватися у своїй професійній діяльності економісти-експерти, обліковуючи військове майно. Звернено увагу на неврегульо- ваність деяких питань такого обліку (наприклад, коли одні законодавчі акти втратили чинність, а нових натомість не ухвалено), що спричиняє певні складнощі. Постановка наукової проблеми кордони. Тому ефективне розв’язання питань використання пального військо- вими частинами Збройних сил України в обставинах російської агресії здатне безпосередньо вплинути на боєздат- ність нашої держави. В умовах військової агресії росії доволі важливими та актуальними стають пи- тання обліку й ефективного викорис­ тання пального військовими частинами Збройних сил України 1 (далі — ЗСУ) і те- риторіальної оборони. Водночас проведення судових еко- номічних експертиз із питань обліку та використання пального військови- ми частинами має деякі особливості порівняно із цивільними об’єктами. Від першого дня вторгнен- ня в  Україну російські загарбники цілеспрямовано знищують українську виробничу (зокрема, нафтоперероб- ну) і соціальну інфраструктури. Дефі- цит пального в  Україні, який відчули не тільки пересічні громадяни, виник унаслідок руйнування основного вироб- ника такого пального — Кременчуцько- го нафтопереробного заводу, низки ве- ликих нафтобаз, блокування морських шляхів і зупинки постачання з Білорусії. Фактично країні доводиться з нуля ви- будовувати нову інфраструктуру по- стачання нафтопродуктів через західні Наталія Панченко * a, Ірина Гордієнко ** b, Ольга Грек *** c Висвітлено й розкри- то основні види обліку військового майна (кількісний і якісний обліки; обліки військового майна в обліково-номерних і вартіс- них показниках). Ключові слова: військове майно; особливості обліку май- на; пально-мастильні матеріали; кількісний, якісний, обліко- во-номерний облік; облік військового майна у вартісних показ- никах. 8 Al Qubaisi M. A. Modern military expenditures and problems of sustainable development. Eco- nomic and Social Development : 55th International Scientific Conference on Economic and Social De- velopment (Baku, 18—19 June, 2020). 2020. Vol. 2/4. Pp. 483—488. URL: https://www.esd-confer- ence.com/upload/book_of_proceedings/Book_of_Proceedings_esdBaku2020_Vol2_Online.pdf (дата звернення: 31.05.2022). Аналіз основних досліджень і публікацій Як і будь-яка інша оборонна сфера, функціювання державних інститутів підлягає контролюванню й оцінюван- ню як з боку суспільства, так і з боку фахівців-економістів. Раціональне опе- рування видатками на оборону здатне не тільки забезпечити незалежність країни, а  й стимулювати розвиток її 104 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 економіки. Одними з перших висвіт- ленню взаємозв’язку витрат на оборону й економічного зростання присвятили дослідження S. Atesoglu та М. Mueller 2, а також C. Xuang та А. Mintz 3. економіки. Одними з перших висвіт- ленню взаємозв’язку витрат на оборону й економічного зростання присвятили дослідження S. Atesoglu та М. Mueller 2, а також C. Xuang та А. Mintz 3. тя та зазначено, що всупереч усталеній думці й  багатьом попереднім дослі­ дженням, він не зміг виявити жодного стійкого негативного впливу військо- вих витрат на економічне зростання. У роботі JiTian You, LinXi OuYang, XueYing Zhang, ShaoYi Du 6 зауважено, що на тлі інтеграції світового господарства й нової міжнародної ситуації, яка скла- лася на середину 2010-х років, оборонне законодавство стало важливою націо- нальною стратегією, а його аналізуван- ня засобами економіки відіграє важливу роль у розбудові й навіть зростанні кон- курентоспроможності країни та нації у міжнародному співтоваристві. J. S. Smith і M. H. Tuttle 4 ще 2008 року довели, що витрати на оборону можуть сприяти економічному зростанню, якщо їх використовують для покращен- ня соціальної сфери й інфраструкту- ри, що дає змогу бізнесу розвиватися усталено, спокійно та стабільно. Вони за­уважують, що військові витрати під час війни швидко зростають, прямо впливаючи на реальний внутрішній ва- ловий продукт упродовж перших двох кварталів, але втрачають свою прогно- зованість у цей період. J. S. Smith і M. H. Tuttle 4 ще 2008 року довели, що витрати на оборону можуть сприяти економічному зростанню, якщо їх використовують для покращен- ня соціальної сфери й інфраструкту- ри, що дає змогу бізнесу розвиватися усталено, спокійно та стабільно. Вони за­уважують, що військові витрати під час війни швидко зростають, прямо впливаючи на реальний внутрішній ва- ловий продукт упродовж перших двох кварталів, але втрачають свою прогно- зованість у цей період. Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 р 7 Kotov V., Drobaha V. Increase accuracy accounting and control of diesel fuel consumption. Collected scientific works of Ukrainian State University of Railway Transport. March 2019. DOI: 10.18664/1994-7852.183.2019.169648 (дата звернення: 31.05.2022). 2 Atesoglu H. S., Mueller J. M. Defense Spending and Economic Growth. Defence Economics. 1990. Vol. 2. Is. 1. Pp. 19—27. DOI: 10.1080/10430719008404675 (дата звернення: 31.05.2022). 3 X C Mi t A D f E dit d E i G th Th E t lit Eff t Ibid Аналіз основних досліджень і публікацій У роботі JiTian You, LinXi OuYang, XueYing Zhang, ShaoYi Du 6 зауважено, що на тлі інтеграції світового господарства й нової міжнародної ситуації, яка скла- лася на середину 2010-х років, оборонне законодавство стало важливою націо- нальною стратегією, а його аналізуван- ня засобами економіки відіграє важливу роль у розбудові й навіть зростанні кон- курентоспроможності країни та нації у міжнародному співтоваристві. З іншого боку, цілу низку робіт при- свячено економічним дослідженням у галузі обліку й контролю пально-мас­ тильних матеріалів. До останніх нале- жать, зокрема, дослідження М. Котова й В. Дробахи 7 та ін. У дослідженні А. Abu-Qarn 5 про­ аналізовано (за допомогою версії Тода — Ямамото причиново-наслідкового тесту Ґрейнджера) взаємозв’язок між витрата- ми на оборону й економічним зростан- ням суперників в арабо-ізраїльському конфлікті за останні чотири десятиліт- М. А. Al Qubaisi 8 запропонував таку класифікацію витрат на матеріально-­ технічне забезпечення військ: 4 Smith J. S., Tuttle M. H. Does Defense Spending Really Promote Aggregate Output in the United States? Defence and Peace Economics. 2008. Vol. 19. Is. 6. Pp. 435—447. DOI: 10.1080/10242690701701950 (дата звернення: 31.05.2022).l 5 Abu-Qarn A. The Defense-growth nexus: An application for the Israeli-Arab conflict. MPRA Pa- per. Ben Gurion University of the Negev, 2010. URL: https://mpra.ub.uni-muenchen.de/22275/1/ MPRA_paper_22275.pdf (дата звернення: 31.05.2022). 5 Abu-Qarn A. The Defense-growth nexus: An application for the Israeli-Arab conflict. MPRA Pa- per. Ben Gurion University of the Negev, 2010. URL: https://mpra.ub.uni-muenchen.de/22275/1/ MPRA_paper_22275.pdf (дата звернення: 31.05.2022). p p p р 6 JiTian You, LinXi OuYang, XueYing Zhang, ShaoYi Du. The Application of Economic Analysis in the Field of Military and National Defense Legislation. ICEBT 2018 : Proceedings of the 2nd In- ternational Conference on E-Education, E-Business and E-Technology. July 2018. Pp. 175—180. DOI: 10.1145/3241748.3241766 (дата звернення: 31.05.2022). р 7 Kotov V., Drobaha V. Increase accuracy accounting and control of diesel fuel consumption. Collected scientific works of Ukrainian State University of Railway Transport. March 2019. DOI: 10.18664/1994-7852.183.2019.169648 (дата звернення: 31.05.2022). 8 Al Qubaisi M. A. Modern military expenditures and problems of sustainable development. Eco- nomic and Social Development : 55th International Scientific Conference on Economic and Social De- velopment (Baku, 18—19 June, 2020). 2020. Vol. 2/4. Pp. 483—488. URL: https://www.esd-confer- ence.com/upload/book_of_proceedings/Book_of_Proceedings_esdBaku2020_Vol2_Online.pdf (дата звернення: 31.05.2022). 105 Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal на оборонних витратах. Аналіз основних досліджень і публікацій Але тільки 1999  року офіс заступника міністра оборони США з питань закупівель, технологій і матеріально-технічного забезпечення звернувся до Наукової ради з  питань оборони з проханням дослідити проблеми армії, пов’язані з пальним,— через збільшення кіль- кості подібних проблем. У звіті за цим запитом, оприлюдненому 2001 року,— «Ефективніше ведення війни завдяки зменшенню паливного тягаря» — зазна- чено, що поки Міністерство оборони не почне обчислювати справжню вартість пального та не розробить чіткі плани щодо зменшення споживання пального військовими транспортними засобами, збройні сили й надалі зазнаватимуть значних матеріально-технічних і фінан- сових труднощів, а також проблем із транспортуванням пального на поле бою. Міністерство оборони є  найбіль- шим споживачем пального у  США, ви- користовуючи приблизно 1,8 % загаль- ного обсягу транспортного пального в  країні  10. Це не дивно, зважаючи на типи транспортних засобів військ США. Цікаво, що з-поміж 10 найбільших ар- мійських споживачів пального лише танк М1 Abrams і гелікоптер McDonnell Douglas AH-64 Apache є бойовими маши- нами, решта — допоміжна техніка (для підвезення пального й інших припасів). а) закупівля озброєння та військової техніки (далі — ОВТ); а) закупівля озброєння та військової техніки (далі — ОВТ); а) закупівля озброєння та військової техніки (далі — ОВТ); а) закупівля озброєння та військової техніки (далі — ОВТ); б) експлуатація й утримання ОВТ; б) експлуатація й утримання ОВТ; в) утримання військових баз і трену- вальних майданчиків як усередині країни, так і за її межами; г) пально-мастильні матеріали г) пально-мастильні матеріали. г) пально-мастильні матеріали. За цілком зрозумілих причин дані обліку й ефективного використання пального в оборонній сфері є недо- ступними для широкого загалу. Якщо звернутися, наприклад, до організації обліку витрат пально-мастильних ма- теріалів у США, то ми з’ясували таке. За даними американського неурядового порталу GlobalSecurity.org 9, підрозділ, відповідальний за запаси армійського пального, зазвичай перебуває на рівні батальйону або вище: саме там відбу- ваються фактичні процеси обліку паль- но-мастильних матеріалів, відпуще- них і спожитих різними підрозділами. Дані про надходження й видачу нако- пичують і передають відповідальній особі, яка використовує їх для підго- товки й подання запитів на наступний період. Якщо якийсь підрозділ (напри- клад, рота) діє як окрема одиниця, то її командир несе відповідальність за за- мовлення пального для роботи транс- портних засобів. Для запланованих заходів розраховують потреби у паль- но-мастильних матеріалах на чотири місяці (поточний плюс три наступні). У цих службах проводять щоденну та щотижневу інвентаризації нафтопро- дуктів, які належать армії, окремо за кожним типом продуктів. 9 Chapter 8. Accounting / Petroleum Pipeline and Terminal Operating Units // GlobalSecurity.org. 12 May 1998. URL: https://www.globalsecurity.org/military/library/policy/army/fm/10-416/ch8. htm (дата звернення: 31.05.2022). 10 Book E. Pentagon Needs Accurate Accounting of Fuel / National Defense Magazine. 03/01/2002. URL: https://www.nationaldefensemagazine.org/articles/2002/2/28/2002march-penta- gon-needs-accurate-accounting-of-fuel (дата звернення: 31.05.2022). 11 Andrews A. Department of Defense Fuel Spending, Supply, Acquisition, and Policy. CRS Report for Congress. September  22, 2009. 27  p. URL: https://sgp.fas.org/crs/natsec/R40459.pdf (дата звернення: 31.05.2022). 12 Dachkovskyі V., Kondratiuk I. Technical and economic assessment of the weapons and military equipment exploitation. Political Science and Security Studies Journal. 2021. Vol. 2. № 4. Pp. 39— 47. DOI: 10.5281/zenodo.5810146 (дата звернення: 31.05.2022). Аналіз основних досліджень і публікацій Наукова рада також рекомендувала Міністерству оборони стандартизува- ти методи ціноутворення для оціню- вання вартості пального (до того часу воно встановлювало ціни на пальне, спираючись на оптову ціну нафтопере- робного заводу, не враховуючи вартості В армії США пальне обліковували завжди, хоча й не звикли економити 106 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 500 %. За тим самим звітом у США пра- цював 141 нафтопереробний завод. доставки, через що справжня вартість пального набагато перевищувала зазна- чену в системах військового обліку). Цікаво, що комп’ютерна програма, якою військові послуговувалися для розра- хунку паливної ефективності, написана мовою Fortran (комп’ютерна мова, яку зараз не використовують) ще 1972 року, яку відтоді не оновлювали. доставки, через що справжня вартість пального набагато перевищувала зазна- чену в системах військового обліку). Цікаво, що комп’ютерна програма, якою військові послуговувалися для розра- хунку паливної ефективності, написана мовою Fortran (комп’ютерна мова, яку зараз не використовують) ще 1972 року, яку відтоді не оновлювали. Водночас В. Дачковський та І. Кон- дратюк 12 зауважують, що нові або мо- дернізовані зразки озброєння та військо- вої техніки повинні бути ефективними у  виконанні військових завдань. Проте невід’ємною складовою прийняття на озброєння нових і модернізації старих зразків є не лише адекватна вартість їх придбання, а й витрати на їх експлуата- цію. Згадані дослідники запропонували методику техніко-економічного оціню- вання зразків ОВТ, прийнятих на озбро­ єння або допущених до експлуатації у ЗСУ, у якій структура загальних витрат на експлуатацію ОВТ має такі складові: витрати на зберігання, технічне обслу- говування, пально-мастильні матері­ али, ремонт зразків ОВТ і витрати на боєприпаси. Ще одна рекомендація Наукової ради (до якої, можливо, має сенс при- слухатися і нашим законотворцям) — стимулювати економію пального в усьо- му Міністерстві оборони: закуповуючи нові озброєння, обов’язково враховувати його паливну ефективність (зауважимо, що розподіл ресурсів і бухгалтерський облік у Міноборони на той час іще не заохочували за ефективність і не карали за непродуктивність). Надмірні витрати пального є не тільки бездумним витра- чанням бюджетних коштів: зрештою, це стає на заваді ефективному веденню війни. Існують також бойові переваги економії пального — у зростанні можли- востей до розгортання, маневреності, дальності, швидкості, надійності та ін. р 13 Ball H. Working in the Killing Fields: Forensic Science in Bosnia. University of Nebraska Press, 2015. 232 p. DOI: 10.2307/j.ctt1d9nj5c (дата звернення: 31.05.2022). 11 Andrews A. Department of Defense Fuel Spending, Supply, Acquisition, and Policy. CRS Report for Congress. September  22, 2009. 27  p. URL: https://sgp.fas.org/crs/natsec/R40459.pdf (дата звернення: 31.05.2022). 12 Dachkovskyі V., Kondratiuk I. Technical and economic assessment of the weapons and military equipment exploitation. Political Science and Security Studies Journal. 2021. Vol. 2. № 4. Pp. 39— 47. DOI: 10.5281/zenodo.5810146 (дата звернення: 31.05.2022). 13 Ball H. Working in the Killing Fields: Forensic Science in Bosnia. University of Nebraska Press, 2015. 232 p. DOI: 10.2307/j.ctt1d9nj5c (дата звернення: 31.05.2022). 14 Про правовий режим майна у Збройних Силах України : Закон України від 21.09.1999 р. №  1075-XIV (зі змін. та допов.). URL: https://zakon.rada.gov.ua/laws/show/1075-14 (дата звернення: 31.05.2022). Мета статті Військовим майном управляє Мініс­ терство оборони України шляхом його закріплення за військовими частинами (у разі їх формування або переформу- вання) і перерозподілу цього майна між військовими частинами (у разі їх роз- формування). Військове майно закріп­ люють за військовими частинами ЗСУ на праві оперативного управління. Висвітлення питань обліку пального в умовах військового стану та російської військової агресії, визначення докумен- тального обґрунтування ефективного використання пального військовими час­тинами ЗСУ та територіальної оборо- ни під час виконання бойових завдань. у Обліковувати необхідно все війсь- кове майно незалежно від його призна- чення та джерел надходження, водночас його слід проводити своєчасно, дос­ товірно й точно. Це необхідно для того, щоб отримувати фактичні дані про на- явність, утрату, нестачу, рух, вартість і  якісний (технічний) стан військового майна, що, зі свого боку, сприятиме пра- вильній організації матеріально-техніч- ного забезпечення військових частин, облаштуванню належного контролю за умовами зберігання, доцільністю й  ефективністю використання (витра- чання) військового майна, а також до- поможе підготувати дані для складання облікових документів і державної ста­ тистичної звітності. Аналіз основних досліджень і публікацій із вирішення питань щодо дослідження обліку військового майна». Як відомо, до військового майна належать, зокре- ма, пально-мастильні матеріали. В умо- вах бойових дій і дефіциту пального в Україні питання обліку й ефективного використання пального військовими частинами ЗСУ потребують більш пиль- ної уваги. лене за військовими частинами, закла- дами, установами й організаціями ЗСУ. До нього належать «будинки, споруди, передавальні пристрої, всі види озброєння, бойова та інша техніка, боєприпаси, паль- но-мастильні матеріали, продовольство, технічне, аеродромне, шкіперське, речове, культурно-просвітницьке, медичне, ве- теринарне, побутове, хімічне, інженерне майно, майно зв’язку тощо» 14. Аналіз основних досліджень і публікацій й б Ще одна рекомендація Наукової ради (до якої, можливо, має сенс при- слухатися і нашим законотворцям) — стимулювати економію пального в усьо- му Міністерстві оборони: закуповуючи нові озброєння, обов’язково враховувати його паливну ефективність (зауважимо, що розподіл ресурсів і бухгалтерський облік у Міноборони на той час іще не заохочували за ефективність і не карали за непродуктивність). Надмірні витрати пального є не тільки бездумним витра- чанням бюджетних коштів: зрештою, це стає на заваді ефективному веденню війни. Існують також бойові переваги економії пального — у зростанні можли- востей до розгортання, маневреності, дальності, швидкості, надійності та ін. Утім, такий перехід до більш енер- гоефективної зброї, на жаль, не може відбутися швидко. За даними A. Andrews (2009) 11, Міністерство оборони США спо- живало 145 млн барелів нафтопродуктів щороку. 2000 фінансового року витрати на пальне склали 1,2 % від загальних ви- трат Міноборони, а 2008-го — зросли до 3,0 %. За той самий час загальні витра- ти на оборону зросли більш аніж удвічі, але витрати на пальне зросли майже на Утім, більшість матеріалів розкри- вають ці питання станом на мирний час. Слід зазначити, що певний досвід функціювання судово-експертної систе- ми під час війни, що забезпечувала про- ведення необхідних досліджень у Юго­ славії (1991—2001), висвітлено у книзі H. Ball 13, яка вийшла друком набагато пізніше завершення югославських війн. Утім, такий перехід до більш енер- гоефективної зброї, на жаль, не може відбутися швидко. За даними A. Andrews (2009) 11, Міністерство оборони США спо- живало 145 млн барелів нафтопродуктів щороку. 2000 фінансового року витрати на пальне склали 1,2 % від загальних ви- трат Міноборони, а 2008-го — зросли до 3,0 %. За той самий час загальні витра- ти на оборону зросли більш аніж удвічі, але витрати на пальне зросли майже на Натомість особливості застосування експертиз протягом військового стану в цих роботах не розглянуто. Фахівці Сумського відділення ННЦ «ІСЕ ім. Засл. проф. М. С. Бокаріуса» протягом 2020 року розробили «Мето- дичні рекомендації з проведення судо- вих економічних експертиз у справах 107 Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal із вирішення питань щодо дослідження обліку військового майна». Як відомо, до військового майна належать, зокре- ма, пально-мастильні матеріали. В умо- вах бойових дій і дефіциту пального в Україні питання обліку й ефективного використання пального військовими частинами ЗСУ потребують більш пиль- ної уваги. Викладення основного матеріалу дослідження Питання збереження й ефективного ви- користання військового майна останні- ми роками набуло значної актуальності. Це пов’язано насамперед зі збройною агресією в Криму та на Сході України, розпочатою росією 2014 року, і бойови- ми діями на всій території України, що тривають із лютого 2022 року, а також складною економічною ситуацією, яка наразі склалася. Крім того, у військовій галузі існують проблеми недосконалого нормативного й законодавчого забез- печення обліку та поводження з вій- ськовим майном (зокрема, щодо його списання), усунення яких дасть змогу якнайшвидше убезпечити військове майно від розкрадання, псування, зни- щення та ін. Зважаючи на воєнний стан, що на- разі діє на території України, із метою недопущення зловживань і ефективно- го використання пально-мастильних матеріалів, на вирішення судовим екс- пертам-економістам ставлять питання Зважаючи на воєнний стан, що на- разі діє на території України, із метою недопущення зловживань і ефективно- го використання пально-мастильних матеріалів, на вирішення судовим екс- пертам-економістам ставлять питання Законодавство України визначає вій- ськове майно як державне майно, закріп­ 108 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 го обліку в державному секторі 121 «Основні засоби» 18; го обліку в державному секторі 121 «Основні засоби» 18; про документальну й нормативну обґрунтованість використання пально- го військовими частинами ЗСУ. • Положенням про інвентариза- цію військового майна у Зброй- них Силах 19; • Положенням про інвентариза- цію військового майна у Зброй- них Силах 19; Судові експерти мають право діяти лише в межах наданих їм повноважень. Саму ж судову економічну експертизу за встановленими фактами нестачі та по- наднормового списання пального про- водять на виконання відповідної ухвали слідчого судді або постанови слідчого. Викладення основного матеріалу дослідження • Порядком застосування Плану рахунків бухгалтерського об- ліку в державному секторі; Ти- повою кореспонденцією субра- хунків бухгалтерського обліку для відображення операцій з ак- тивами, капіталом та зобов’я- заннями розпорядниками бю­ джетних коштів та державними цільовими фондами; Типовою кореспонденцією субрахунків бухгалтерського обліку для відо- браження операцій з виконання державного бюджету; Типовою кореспонденцією субрахунків бухгалтерського обліку для відо- браження операцій з виконання місцевого бюджету; Змінами до деяких нормативно-право- вих актів Міністерства фінансів України з бухгалтерського об- ліку 20; Дослідження цих питань здійсню- ють з урахуванням особливостей обліку та руху військового майна, відповідно до прийнятих правил прийому, видачі та списання матеріальних цінностей у ЗСУ, що регламентовано відповідними нормативними актами, зокрема: нормативними актами, зокрема: • Законом України «Про право- вий режим майна Збройних Сил України» 15; • Інструкцією з обліку військового майна у Збройних Силах Укра­ їни 16; • Положенням про порядок об- ліку, зберігання, списання та ви- користання військового майна у Збройних Силах 17; • Національним положенням (стандартом) бухгалтерсько- • Порядком складання типових форм меморіальних ордерів та 15 Про правовий режим майна Збройних сил України … . URL: https://zakon.rada.gov.ua/laws/ show/1075-14 (дата звернення: 31.05.2022). 15 Про правовий режим майна Збройних сил України … . URL: https://zakon.rada. 16 Про затвердження Інструкції з обліку військового майна у  Збройних Силах України  : наказ Міноборони України від 17.08.2017 р. № 440 (зі змін. та допов.). URL: https://zakon. rada.gov.ua/laws/show/z1192-17 (дата звернення: 31.05.2022). 17 Про затвердження Положення про порядок обліку, зберігання, списання та використання військового майна у Збройних Силах : Постанова КМУ від 04.08.2000 р. № 1225 (зі змін. та допов.). URL: https://zakon.rada.gov.ua/laws/show/1225-2000-%D0%BF#Text (дата звернення: 31.05.2022). 18 Про затвердження національних положень (стандартів) бухгалтерського обліку в державному секторі : наказ Мінфіну України від 12.10.2010 р. № 1202 (зі змін. та допов.). URL: https://zakon.rada.gov.ua/laws/show/z1017-10 (дата звернення: 31.05.2022). 18 Про затвердження національних положень (стандартів) бухгалтерського обліку в державному секторі : наказ Мінфіну України від 12.10.2010 р. № 1202 (зі змін. та допов.). URL: https://zakon.rada.gov.ua/laws/show/z1017-10 (дата звернення: 31.05.2022). 18 Про затвердження національних положень (стандартів) бухгалтерського обліку в державному секторі : наказ Мінфіну України від 12.10.2010 р. № 1202 (зі змін. та допов.). URL: https://zakon.rada.gov.ua/laws/show/z1017-10 (дата звернення: 31.05.2022). 19 Про затвердження Положення про інвентаризацію військового майна у Збройних Силах : Постанова КМУ від 03.05.2000 р. № 748 (зі змін. та допов.). URL: https://zakon.rada.gov.ua/ laws/show/748-2000-%D0%BF#Text (дата звернення: 31.05.2022). 20 Про затвердження деяких нормативно-правових актів з бухгалтерського обліку в державному секторі : наказ Мінфіну України від 29.12.2015 р. № 1219 (зі змін. та допов.). 21 Про затвердження типових форм меморіальних ордерів, інших облікових регістрів суб’єктів державного сектору та порядку їх складання  : наказ Мінфіну України від 08.09.2017  р. №  755 (зі змін. та допов.). URL: https://zakon.rada.gov.ua/laws/show/z1416-17 (дата звернення: 31.05.2022). Викладення основного матеріалу дослідження URL: https://zakon.rada.gov.ua/laws/show/z0085-16 (дата звернення: 31.05.2022). 109 Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal інших облікових регістрів суб’єк- тів державного сектору; ме- моріальними ордерами № 1—17; книгою аналітичного обліку депонованої заробітної плати і стипендій; реєстром депонова- них сум; оборотною відомістю; бухгалтерською довідкою; кни- гою «Журнал-головна» 21; інших облікових регістрів суб’єк- тів державного сектору; ме- моріальними ордерами № 1—17; книгою аналітичного обліку депонованої заробітної плати і стипендій; реєстром депонова- них сум; оборотною відомістю; бухгалтерською довідкою; кни- гою «Журнал-головна» 21; перебуває на довгостроковому зберіган- ні у військових частинах), обліковують окремо від іншого. Військове майно на об’єктах війсь- кового (корабельного) господарства, у  службах забезпечення органів війсь- кового управління, службах військових частин і з’єднань, на складах, арсеналах і базах обліковують як у мирний час, так і в особливий період згідно з вимо- гами нормативно-правових актів Мініс­ терства оборони України та законодав- чих актів України. • Методичними рекомендаціями з організації та ведення бухгал- терського обліку у Збройних Си- лах України 22; У бухгалтерському обліку військо- вих частин забезпечено відображення повної й достовірної інформації про військове майно та кошти, доходи та ви- трати, а також про всі здійснені госпо- дарські операції за: • Планом рахунків бухгалтерсь- кого обліку в державному сек- торі 23; • Положенням з бухгалтерського обліку в Збройних Силах Укра­ їни 24; • Інструкцією про використання автомобільної техніки у Мініс­ терстві оборони та Збройних Си- лах України 25. • балансовими й позабалансови- ми рахунками, передбаченими Планом рахунків бухгалтерсько- го обліку бюджетних установ 26; • загальним і спеціальним фонда- ми державного бюджету Укра­ їни; Слід пам’ятати, що облік військового майна у випадках, передбачених зако- нодавством, ведуть із дотриманням ви- мог до збереження державної таємниці. Військове майно непорушних за- пасів, яке призначене для використання в особливий період (і яке в мирний час (д р ) 22 Методичні рекомендації з організації та ведення бухгалтерського обліку у  Збройних Силах України : наказ Міноборони України від 19.12.2014 р. № 905 (зі змін. та допов.). ( р ) 22 Методичні рекомендації з організації та ведення бухгалтерського обліку у  Збройних Силах України : наказ Міноборони України від 19.12.2014 р. № 905 (зі змін. та допов.). 23 Про затвердження Плану рахунків бухгалтерського обліку в державному секторі : наказ Мінфіну України від 31.12.2013 р. № 1203 (із змін. та допов.). URL: https://zakon.rada.gov.ua/ laws/show/z0161-14 (дата звернення 31.05.2022). р 22 Методичні рекомендації з організації та ведення бухгалтерського обліку у  Збройних Силах України : наказ Міноборони України від 19.12.2014 р. № 905 (зі змін. та допов.). Викладення основного матеріалу дослідження р 24 Положення з бухгалтерського обліку в  Збройних Силах України  : затв. наказом Міноборони України від 21.06.2007 р. № 363 (зі змін. та допов). URL: http://parusconsultant. com/?doc=06VHE9B9B8&abz=ARUA4 (дата звернення 31.05.2022). 25 Про затвердження Інструкції про використання автомобільної техніки у  Міністерстві оборони та Збройних Силах України : наказ Міноборони України від 12.12.2016 р. № 678. Київ, 2016. 25 Про затвердження Інструкції про використання автомобільної техніки у  Міністерстві оборони та Збройних Силах України : наказ Міноборони України від 12.12.2016 р. № 678. Київ, 2016. 26 Про затвердження деяких нормативно-правових актів … . URL: https://zakon.rada.gov.ua/ laws/show/z0085-16#n13 (дата звернення: 31.05.2022). 26 Про затвердження деяких нормативно-правових актів … . URL: https://zakon.rada.gov.ua/ laws/show/z0085-16#n13 (дата звернення: 31.05.2022). 110 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 класифікації доходів бюджету за спеціальним фондом; у  стандартних одиницях вимірювання й  обліку, визначених Державним кла- сифікатором України «Класифікатор сис­теми позначень одиниць вимірю- вання та обліку ДК 011-96» 27. За якісним (технічним) станом військове майно обліковують за категоріями (не більше п’яти), за ступенями придатності (при- датні чи непридатні) або за сортом від- повідно до державних стандартів. класифікації доходів бюджету за спеціальним фондом; • статтями видатків за коштори- сом Міністерства оборони або видами надходжень спеціально- го фонду; • службами забезпечення; • структурними підрозділами; • матеріально відповідальними особами; • військовими частинами, зарахо- ваними на забезпечення. Військове майно обліковують в об- ліково-номерних показниках згідно із заводськими номерами зразків війсь- кового майна. Вартісний облік військо- вого майна здійснюють у національній валюті України. Далі ми розглянемо види обліку вій- ськового майна, які ведуть відповідні служби (продовольча, речова, квартир- но-експлуатаційна, пально-мастильних матеріалів тощо), деякі особливості такого обліку, а також обсяг знань екс- пертів, необхідний для проведення судових економічних експертиз, пов’я- заних із обліком і використанням паль- ного військовими частинами ЗСУ. Вартість військового майна (станом на момент його надходження до сфе- ри управління Міністерства оборони) визначено його закупівельною ціною або вартістю (ціною), зазначеною в укла- дених на його виготовлення та поставку договорах. Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Викладення основного матеріалу дослідження По-перше, існують чотири основні види обліку військового майна, що ве- дуть відповідні служби (зокрема, служба пально-мастильних матеріалів): Вартість військового майна, що пе- ребуває у військових частинах і закріп­ лене за ними на праві оперативного управління, визначають за Методикою визначення залишкової вартості майна Збройних Сил України та інших війсь- кових формувань 28 (за винятком випад- ків, коли вартість військового майна визначають на підставі звіту про оцінку майна, складеного відповідно до Закону України «Про оцінку майна, майнових прав та професійну оціночну діяльність в Україні» 29). пально-мастильних матеріалів): • кількісний облік військового майна; • якісний облік військового май- на; • облік військового майна в об- ліково-номерних показниках; • облік військового майна у вартіс- них показниках. Кількісний облік військового май- на ведуть у натуральних показниках Кількісний облік військового май- на ведуть у натуральних показниках 27 Державний класифікатор України «Класифікатор системи позначень одиниць вимірювання та обліку ДК 011-96» : затв. наказом Держкомстандартизації, метрології та сертифікації України від 09.01.1997 р. № 8 ; чинний від 01.07.1997 р. URL: https://zakon.rada. gov.ua/rada/show/v0008217-97 (дата звернення: 31.05.2022). 28 Про затвердження Методики визначення залишкової вартості майна Збройних Сил України та інших військових формувань : Постанова КМУ від 29.05.1998 р. № 759 (зі змін. та допов.). URL: https://zakon.rada.gov.ua/laws/show/759-98-%D0%BF (дата звернення: 31.05.2022). 28 Про затвердження Методики визначення залишкової вартості майна Збройних Сил України та інших військових формувань : Постанова КМУ від 29.05.1998 р. № 759 (зі змін. та допов.). URL: https://zakon.rada.gov.ua/laws/show/759-98-%D0%BF (дата звернення: 31.05.2022). 29 Про оцінку майна, майнових прав та професійну оціночну діяльність в Україні : Закон України від 12.07.2001 р. № 2658-III (зі змін. та допов.). URL https://zakon.rada.gov.ua/laws/ show/2658-14 (дата звернення: 31.05.2022). 29 Про оцінку майна, майнових прав та професійну оціночну діяльність в Україні : Закон України від 12.07.2001 р. № 2658-III (зі змін. та допов.). URL https://zakon.rada.gov.ua/laws/ show/2658-14 (дата звернення: 31.05.2022). 111 Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal По-друге, облік військового майна ве- дуть матеріально відповідальні особи та відповідні служби. го сектору, у результаті чого бюджетні установи отримали оновлену форму акта списання запасів. Також за відсутності затверджених типових форм для оформлення окре- мих господарських операцій із запаса- ми суб’єктові держсектору дозволено са- мостійно розробляти й затверджувати в розпорядчому документі про органі- зацію бухгалтерського обліку відповід- ні форми необхідних первинних доку- ментів, які повинні містити обов’язкові реквізити. Раніше військове майно, що за його ха- рактеристиками кваліфікували як запаси (зокрема, пально-мастильні матеріали), згідно з вимогами наказу Держказначей- ства України «Про затвердження типових форм обліку та списання запасів бюджет- них установ та Інструкції про їх складан- ня» 30 (утратив чинність на підставі наказу Мінфіну України від 31.12.2020 р. № 838 31) обліковували за такими обліковими ре- гістрами: Існують два види обліку військового майна в органах військового управлін- ня: оперативний і за первинними об- ліковими документами. Оперативний облік військового майна є основним видом обліку, його ведуть на основі до- несень і звітів, періодичність надання яких визначено табелями термінових донесень. 30 Про затвердження типових форм обліку та списання запасів бюджетних установ та Інструкції про їх складання  : наказ Держказначейства України від 18.12.2000  р. №  130 (утрат. чин.). URL: https://zakon.rada.gov.ua/laws/show/z0962-00 (дата звернення: 31.05.2022). 31 Про визнання таким, що втратив чинність, наказу Державного казначейства України від 18 грудня 2000 року № 130 : наказ Мінфіну України від 31.12.2020 р. № 838. URL: https:// zakon.rada.gov.ua/laws/show/z0085-21#Text (дата звернення: 31.05.2022). пально-мастильних матеріалів): Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 В облікових регістрах відображе- но наявність, рух і якісний (технічний) стан військового майна (його вартість). • у підрозділі, розміщеному або ді­ ючому зі своєю військовою части- ною,— у літрах, за найменування- ми, марками та кількістю; • у підрозділі, розміщеному або ді­ ючому зі своєю військовою части- ною,— у літрах, за найменування- ми, марками та кількістю; • у підрозділі, розміщеному або ді­ ючому зі своєю військовою части- ною,— у літрах, за найменування- ми, марками та кількістю; Військове майно обліковують за міс- цем його відповідального зберігання (знаходження) і у фінансовій службі. • у фінансово-економічному органі військової частини, центру за- безпечення, а також на кораблі (судні) — у кілограмах за наймену- ваннями, марками, кількістю та вартістю. Бухгалтерський облік у військових частинах ведуть за меморіально-ордер- ною формою. Усі меморіальні ордери реєструють у регістрах синтетичного бухгалтерсь- кого обліку — книзі «Журнал-головна». Структурним підрозділом Міноборо- ни, який призначений для організації та проведення державних закупівель, укладан- ня і супроводження договорів на постачання військового майна за напрямом тилового забезпечення, ведеться облік пально-мас­ тильних матеріалів, які надходять від виробників (постачальників) за централі- зованими розрахунками, за найменуван- нями, марками, кількістю та вартістю, а також здійснюється контроль за вико- нанням умов договорів з постачання паль- но-мастильних матеріалів. кого обліку книзі Журнал головна . Порядок ведення обліку пального, мастильних матеріалів служби паль- но-мастильних матеріалів в підрозділі військової частини визначено у розд. ХVІІІ «Особливості обліку паль- но-мастильних матеріалів, спеціаль- них рідин, спирту та технічних засобів служби пально-мастильних матеріалів» Інструкції з обліку військового майна у Збройних Силах України 33 (далі — Ін- струкція № 440), де визначено: б Порядок ведення обліку пального, мастильних матеріалів служби паль- но-мастильних матеріалів в підрозділі військової частини визначено у розд. ХVІІІ «Особливості обліку паль- но-мастильних матеріалів, спеціаль- них рідин, спирту та технічних засобів служби пально-мастильних матеріалів» Інструкції з обліку військового майна у Збройних Силах України 33 (далі — Ін- струкція № 440), де визначено: «1. Облік пально-мастильних ма- теріалів, спеціальних рідин та спирту ведеться за такими стандартними оди- ницями виміру: 2. На заправлення техніки пально-ма- стильними матеріалами в службі війсь- кової частини на кожний підрозділ окре- мо складається роздавальна (здавальна) відомість, яка передається на виконання начальнику пункту заправлення тех- ніки пальним військової частини. 33 Про затвердження Інструкції з обліку військового майна … . URL: https://zakon.rada.gov. ua/laws/show/z1192-17 (дата звернення: 31.05.2022). пально-мастильних матеріалів): • книгами кількісно-сумового об- ліку (типова форма № 3-6); • книгами кількісно-сумового об- ліку (типова форма № 3-6а); • картками кількісно-сумового об- ліку (типова форма № 3-7); • оборотною відомістю (типова форма № 3-11). Обліку за первинними обліковими документами підлягає військове майно (зокрема, пально-мастильні матеріали), яке надходить від постачальника. Тобто облік військового майна від- бувався шляхом запису в картках, кни- гах обліку, інших матеріальних носіях спеціального (паперового або електрон- ного) формату у вигляді відомостей, ордерів, книг, журналів, машинограм, що містять інформацію про кількість облікованого майна, його якісний (тех- нічний) стан, облікові й заводські номе- ри, вартість (ціну), а також про його рух, утрату або нестачу. До первинних облікових документів належать: накладні, наряди, раху- нок-наряди, чекові вимоги, роздаваль- но-здавальні відомості, акти, квитанції, дорожні, робочі, виробничі й роздаваль- ні листи, атестати. Вони призначені для оформлення операцій, пов’язаних із рухом і зміною вартісного та якісного (технічного) стану військового майна, і є підставою для записів облікових да- них в облікових регістрах. Натомість Мінфін України (наказом від 28.12.2020 р. № 816 32) змінив норми Методичних рекомендацій з бухгалтер- ського обліку для суб’єктів державно- 30 Про затвердження типових форм обліку та списання запасів бюджетних установ та Інструкції про їх складання  : наказ Держказначейства України від 18.12.2000  р. №  130 (утрат. чин.). URL: https://zakon.rada.gov.ua/laws/show/z0962-00 (дата звернення: 31.05.2022). 31 Про визнання таким, що втратив чинність, наказу Державного казначейства України від 18 грудня 2000 року № 130 : наказ Мінфіну України від 31.12.2020 р. № 838. URL: https:// k d /l / h / 0085 21#T t ( 31 05 2022) 30 Про затвердження типових форм обліку та списання запасів бюджетних установ та Інструкції про їх складання  : наказ Держказначейства України від 18.12.2000  р. №  130 (утрат. чин.). URL: https://zakon.rada.gov.ua/laws/show/z0962-00 (дата звернення: 31.05.2022). 31 П і Д й У ї у 31 Про визнання таким, що втратив чинність, наказу Державного казначейства України від 18 грудня 2000 року № 130 : наказ Мінфіну України від 31.12.2020 р. № 838. URL: https:// zakon.rada.gov.ua/laws/show/z0085-21#Text (дата звернення: 31.05.2022). 32 Про затвердження Змін до деяких Методичних рекомендацій з бухгалтерського обліку для суб’єктів державного сектору : наказ Мінфіну України від 28.12.2020 р. № 816. URL: https://zakon.rada.gov.ua/rada/show/v0816201-20 (дата звернення: 31.05.2022). 32 Про затвердження Змін до деяких Методичних рекомендацій з бухгалтерського обліку для суб’єктів державного сектору : наказ Мінфіну України від 28.12.2020 р. № 816. URL: https://zakon.rada.gov.ua/rada/show/v0816201-20 (дата звернення: 31.05.2022). 112 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 пально-мастильних матеріалів): Після закінчення строку її дії (у кінці кожного робочого дня) начальник пункту заправ- лення техніки пальним військової части- ни у  відомості підбиває підсумки видачі пального (в літрах і кілограмах) і здає її у відповідну службу забезпечення військо- вої частини. 2. На заправлення техніки пально-ма- стильними матеріалами в службі війсь- кової частини на кожний підрозділ окре- мо складається роздавальна (здавальна) відомість, яка передається на виконання начальнику пункту заправлення тех- ніки пальним військової частини. Після закінчення строку її дії (у кінці кожного робочого дня) начальник пункту заправ- лення техніки пальним військової части- ни у  відомості підбиває підсумки видачі пального (в літрах і кілограмах) і здає її у відповідну службу забезпечення військо- вої частини. • у службах забезпечення органів військового управління та війсь- кових частин, в операційно-об- ліковому підрозділі, підрозділах зберігання та ПТЗВ центру за- безпечення, на складі пального та пункті заправлення техніки пальним військової частини, у  підрозділі авіаційної частини, а також у підрозділі, розміщеному або діючому окремо від своєї вій- ськової частини,— у  кілограмах за найменуваннями, марками та кількістю, а у складах (сховищах) центру забезпечення, на складі пального — у ціновому вираженні за одиницю обліку; Перерахунок виданого пального з літ­ рів у кілограми здійснюється начальни- ком складу військової частини або на- чальником пункту заправлення. Точність перерахунку — один кілограм (при цьому маса 0,5 кг і більше округлюється до 1 кг, а менше 0,5 кг — до нуля). 33 Про затвердження Інструкції з обліку військового майна … . URL: https://zakon.rada.gov. ua/laws/show/z1192-17 (дата звернення: 31.05.2022). 33 Про затвердження Інструкції з обліку військового майна … . URL: https://zakon.rada.gov. ua/laws/show/z1192-17 (дата звернення: 31.05.2022). 113 Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal 3. Відпуск пального зі складу військо- вої частини водію паливозаправника або автоцистерни для заправлення техніки здійснюється під підпис у книзі обліку вій- ськового майна, що видається в тимча- сове користування. Одночасно начальник служби забезпечення військової частини видає під підпис у книзі реєстрації обліко- вих документів водію паливозаправника (автоцистерни) роздавальну (здавальну) відомість, за якою водій паливозаправни- ка (автоцистерни) проводить заправлен- ня техніки пальним та приймання паль- ного, яке зливається з неї. Заправлення та приймання пального оформляються окремими роздавальними (здавальними) відомостями. відомостями з відповідними записами про кількість виданого пального в дорож- ніх листах (додаток 82) і робочих листах агрегатів (додаток 83)». Форма дорожнього листа та його оформлення визначено п. пально-мастильних матеріалів): 1 додатка 82 Інструкції № 440, згідно з яким «дорож- ній лист є розпорядчим документом, що видається командиру підрозділу та водію на виконання завдання і є підставою для обліку роботи машини, а також для спи- сання витрат і визначення економії (пере- витрат) пального». Інструкція про використання авто- мобільної техніки у Міністерстві оборо- ни та Збройних Силах України (далі  — Інструкція № 678) 34 визначає основні заходи щодо ефективного викорис­тання машин, економії моторесурсів, дизель- ного пального, автомобільного бензину, мастильних матеріалів та ін., а також порядок і особливості використання ма- шин у Міноборони та ЗСУ. У ній зазначе- но таке: Після закінчення заправлення (прий- мання) пального роздавальну (здавальну) відомість і пальне, яке залишилося (прий- няте), водій паливозаправника (автоцис­ терни) здає на склад військової частини. Начальник складу ставить свій підпис у книзі обліку військового майна, що ви- дається в тимчасове користування, про приймання від водія паливозаправника (автоцистерни) пального і роздавальних (здавальних) відомостей. У кінці кожного робочого дня начальник складу військової частини в роздавальній (здавальній) відо- мості підбиває підсумки видачі пального (у літрах і кілограмах) та здає її у  від- повідну службу забезпечення військової частини. «2.5. Основними заходами щодо еко- номії моторесурсів та пального є: дотримання норм і правил експлу­ атації автомобільної техніки, визначе- них у інструкціях з експлуатації зразків техніки; використання машин на найбільш економічних режимах роботи двигунів; <…> використання машин на найбільш економічних режимах роботи двигунів; <…> 4. Пальне, отримане на складі (пун- кті заправлення) військової частини підрозділом, який проводить самостійне заправлення техніки пальним штат- ними засобами, обліковується в цьому підрозділі в книзі обліку військового майна (склад, підрозділ). 3.2. Планування використання машин має забезпечити бойову готовність, бо­ йове чергування, виконання планів бойової підготовки та господарської діяльності військових частин, ефективне та без­ аварійне використання машин і економне використання пального. Видавання пального в підрозділі, який проводить самостійне заправлення тех- ніки пальним штатними засобами, здійс- нюється за роздавальними (здавальними) бі ї і 3.35. Облік використання машин та ви­конаної роботи проводиться: у дорож- ньому та маршрутному листах, робочому 34 Про затвердження Інструкції про використання автомобільної техніки … . 114 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 листі агрегату, у книзі обліку роботи ма- шин, витрат пального та мастильних матеріалів, у журналі обліку роботи ав- томобільної техніки (додаток 11), у Мі- сячному плані експлуатації, у паспорті (формулярі) на машину (спеціальну уста- новку, двигун). листі агрегату, у книзі обліку роботи ма- шин, витрат пального та мастильних матеріалів, у журналі обліку роботи ав- томобільної техніки (додаток 11), у Мі- сячному плані експлуатації, у паспорті (формулярі) на машину (спеціальну уста- новку, двигун). підрозділу (частини), видаються старшо- му, що прямує у парк з водіями. В окремих випадках (при наявності особливостей дислокації або виконанні завдань військовою частиною) порядок зберігання та видачі дорожніх листів установлюється командиром військової частини. 3.36. Машини військових частин вико- ристовуються за дорожнім листом <…>. 3.40. Робота машини у процесі викорис­ тання підтверджується записами у дорож- ньому листі. Після кожної поїздки або в день повернення машини водієм заповнюється розділ ІІ «Робота машини». Старший ма- шини (особа, у чиє розпорядження виділя- лася машина) у графі 14 дорожнього листа робить запис про показання спідометра, час і місце відпуску машин та ставить осо- бистий підпис. Якщо використання маши- ни доручалося водію, запис у дорожньому ли- сті про її роботу проводиться водієм. Після закінчення використання машини дорож- ній лист перевіряється, підписується ко- мандиром (старшим техніком) підрозділу або особою, призначеною командиром війсь- кової частини, і передається в автомобіль- ну службу (технічну частину) військової час­тини. Дорожній лист є розпорядженням командиру підрозділу та водію на ви- конання завдання. Він є підставою для списання та визначення економії (пере- витрачання) пального, а також обліку виконаної роботи. Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal установах (військових частинах, складах тощо); ордери, книги «Журнал-голов- на»). установах (військових частинах, складах тощо); ордери, книги «Журнал-голов- на»). • обов’язковим видом обліку, який ведуть на підприємстві, є бухгал- терський облік; Експерт досліджує поставлені йому на вирішення питання, а за результата- ми ретельного аналізування цих об’єк- тів надає обґрунтований висновок. • підставою для відображення за- пису в облікових регістрах є на- лежно оформлені первинні до- кументи; Утім, як свідчить експертна практи- ка, найчастіше представлені на дослі­ дження документи унеможливлюють на- дання категоричних відповідей, оскільки вони не мають повного й достатнього обсягу інформації, або є вибірковими та містять значну кількість необумовлених виправлень. Також відповідальні особи військових частин ЗСУ в умовах військо- вого стану складають документи з обліку пального несвоєчасно, що, зі свого боку, спричиняє несвоєчасне їх надання для проведення експертизи. • первинні документи повинні мати обов’язкові реквізити; • військове майно обліковують за місцем його відповідально- го зберігання (знаходження) та у фінансовій службі; • бухгалтерський облік у війсь- кових частинах здійснюють за меморіально-ордерною формою обліку; • усі меморіальні ордери реєстру- ють у регістрах синтетичного бухгалтерського обліку (книзі «Журнал-головна»); Отже, з одного боку, питання ефек- тивного використання пального вій- ськовими частинами ЗСУ є дуже важ- ливими й актуальними. З іншого боку, проведенню судових економічних екс- пертиз із питань обліку й використання пального військовими частинами ЗСУ супутні такі проблеми: • дорожній лист є розпорядчим документом, який видають ко- мандиру підрозділу та водію для виконання завдання, він є під- ставою для обліку роботи маши- ни, а також для списання витрат і визначення економії (переви- трат) пального. • надання неповного пакета доку- ментів, необхідних для розв’я- зання поставлених перед еко- номічною експертизою питань; • надання неповного пакета доку- ментів, необхідних для розв’я- зання поставлених перед еко- номічною експертизою питань; • надання документів, що містять значну кількість необумовлених виправлень; • надання документів, що містять значну кількість необумовлених виправлень; Тобто об’єктами дослідження під час проведення судової економічної експер- тизи з питань обліку та використання пального військовими частинами ЗСУ є: складність під час проведення розрахунку загальної суми вико- ристаного пального, яке у пов’я- заних між собою бухгалтерсь- ких документах обліковують або в кілограмах, або в літрах, що по- требує правильного перерахунку з однієї величини в іншу, беручи до уваги коливання температури повітря й густини пального (такі дані, які не завжди можна надати на дослідження експертові). використання машин на найбільш економічних режимах роботи двигунів; <…> Дорожній лист виписується у авто- мобільній службі (технічній частині) вій- ськової частини, підписується начальни- ком автомобільної служби, засвідчується гербовою печаткою та передається під підпис у підрозділ (в окремих випадках — черговому по частині). Дорожній лист виписується на одну добу, на чергові транспортні засо- би — черговий тягач, пожежний авто- мобіль, пожежні автомобілі пожежних підрозділів — до п’яти діб, а при відправ- ленні машини на бойове чергування, на- вчання та у тривале відрядження — на строк виконання завдання, але не більше 10 діб. При більш тривалому відряджен- ні старшому машини (начальнику коло- ни) видаються під звіт бланки дорожніх листів, що зареєстровані і підписані за- ступником командира військової частини з озброєння (начальником автомобільної служби) та засвідчені гербовою печаткою. Забороняється видавати водіям новий дорожній лист, якщо не оформлено і не здано дорожній лист за попередній вихід машини з парку, а у випадку втрати — до з’ясування причин та вжиття заходів. 3.41. Дані з дорожнього листа про ро- боту машини, витрати пального щоден- но записуються у Книгу обліку роботи ма- шини, витрати пального і масел». Дорожні листи вручаються під підпис командирові підрозділу, від якого призна- чені машини, з урахуванням забезпечення достатнього часу для підготовки водіїв і машин до рейсу, але не пізніше 16:00 на- передодні виїзду. Отже, вимоги наведених вище зако- нодавчих актів передбачають, що: • бухгалтерський облік у ЗСУ ве- дуть відповідно до норматив- но-правових актів Міноборони та Держказначейства України, якими визначено правила й  особ­ливості ведення бухгал- терського обліку в бюджетних • бухгалтерський облік у ЗСУ ве- дуть відповідно до норматив- но-правових актів Міноборони та Держказначейства України, якими визначено правила й  особ­ливості ведення бухгал- терського обліку в бюджетних На випадок виходу військової части- ни за тривогою дорожні листи готують- ся завчасно і зберігаються у чергового 115 Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal Висновки Автори проаналізували чинне законо- давство України, яким регламентовано експертну економічну діяльність щодо обліку витрат пального в ЗСУ, зазначив- ши, що воно не дає змоги однозначно відповісти на поставлені експертові пи- тання. З іншого боку, воно не враховує особливостей проведення таких екс- пертиз в умовах воєнного часу, що, на нашу думку, також потребує окремого врегулювання. 3) «Чи документально підтвердже- но нестачу пально-мастильних матеріалів (зазначити, яких саме) військової частини … за матеріаль- но-відповідальною особою …, зазна- ченою в інвентаризаційному описі від … на загальну суму … грн станом на (зазначити дату)?»; 4) «Чи документально підтвердже- но залишки пально-мастильних матеріалів (зазначити, яких саме) військової частини … за матеріаль- но-відповідальною особою …, зазна- ченою в інвентаризаційному описі від … на загальну суму … грн станом на (зазначити дату)?»; 4) «Чи документально підтвердже- но залишки пально-мастильних матеріалів (зазначити, яких саме) військової частини … за матеріаль- но-відповідальною особою …, зазна- ченою в інвентаризаційному описі від … на загальну суму … грн станом на (зазначити дату)?»; Наведені у статті теоретичні та практичні аспекти проведення судових економічних експертиз з питань обліку й використання пального військови- ми частинами ЗСУ можна застосувати в експертній практиці з метою оптимі- зації робочого часу судових експертів. 5) «Чи документально підтверджено висновки аудиторського звіту (пе- ревірки або іншого контрольного за- ходу) щодо спричинення матеріаль- ної шкоди військовій частині … (отже — державі) у вигляді нестачі пально-мастильних матеріалів (зазначити, яких саме) на загальну суму … грн, зазначених в інвентари- заційному описі від …?»; 5) «Чи документально підтверджено висновки аудиторського звіту (пе- ревірки або іншого контрольного за- ходу) щодо спричинення матеріаль- ної шкоди військовій частині … (отже — державі) у вигляді нестачі пально-мастильних матеріалів (зазначити, яких саме) на загальну суму … грн, зазначених в інвентари- заційному описі від …?»; Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal складність під час проведення розрахунку загальної суми вико- ристаного пального, яке у пов’я- заних між собою бухгалтерсь- ких документах обліковують або в кілограмах, або в літрах, що по- требує правильного перерахунку з однієї величини в іншу, беручи до уваги коливання температури повітря й густини пального (такі дані, які не завжди можна надати на дослідження експертові). • первинні облікові документи; • договори купівлі чи поставки майна; • матеріали проведених інвента- ризацій, • облікові бухгалтерські регістри аналітичного обліку військового майна (пального) щодо кількості, руху, нестачі або надлишку; • регістри синтетичного бухгал- терського обліку (меморіальні Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 6) «Чи документально підтвердже- но висновки спеціалістів щодо спричинення матеріальної шкоди військовій частині … (отже — дер- жаві) у  вигляді нестачі пально-мас­ тильних матеріалів (зазначити, яких саме) на загальну суму … грн, зазначених в інвентаризаційному описі від …, за умови неврахування первинних облікових документів, до яких (як установлено слідством) внесено завідомо неправдиві відо- мості щодо видачі пального на пун- кті бойового постачання військової частини … (або зазначити інші при- чини)?». Під час судових економічних екс- пертиз, пов’язаних з обліком і викорис­ танням пального військовими части- нами ЗСУ, експерти вирішують такі питання: 1) «Чи нормативно обґрунтовано списання пально-мастильних ма- теріалів (зазначити, яких саме) за даними первинних документів і  бухгалтерського обліку військової частини … за період … для роботи військової техніки (зазначити, якої саме)?»; 1) «Чи нормативно обґрунтовано списання пально-мастильних ма- теріалів (зазначити, яких саме) за даними первинних документів і  бухгалтерського обліку військової частини … за період … для роботи військової техніки (зазначити, якої саме)?»; 2) «У якій кількості та на яку суму за даними дорожніх листів військової частини … зазначено використан- ня пально-мастильних матеріалів (зазначити, яких саме) за період  … для роботи військової техніки (зазна- чити, якої саме)?»; Forensic Economics Regarding Fuel Accounting in Armed Forces of Ukraine Nataliya Panchenko, Irina Нordiіenko, Olga Grek Theoretical best practices of forensic experts on peculiarities of fuel accounting in transport and defense fields has been studied and a list of legislative and regulatory acts 117 Теорія та практика судової експертизи і криміналістики. 2022. Випуск 2 (27) ISSN 1993-0917 e-ISSN 2708-5171 https://khrife-journal.org/index.php/journal regulating the procedure for accounting, movement and write-off of fuel and lubricants in military units is given. The authors aimed to highlight the issue of fuel accounting in conditions of martial law and Russian military aggression, document effective use of fuel by military units of the Armed Forces of Ukraine and territorial defense while carrying out combat missions. Research objects of forensic economic examinations are summarized, range of powers granted to experts while conducting such examinations is outlined. Peculiarities of the accounting and movement of military property that are characteristic of the rules for receiving, accounting, issuing and writing off material assets in Armed Forces of Ukraine are indicated. The issues and tasks solved by forensic experts while forensic economic examinations related to accounting and use of fuel by military units of Armed Forces of Ukraine are defined. The list of legislative and normative legal acts that should be guided by forensic economists in their professional activities while accounting for military property, is presented. Attention has been drawn to the unsettledness of some issues of such accounting (for example when some legislative acts have lost their validity, and new ones have not been adopted instead) causing certain difficulties. The main types of accounting of military property (quantitative and qualitative accounting; accounting of military property in numerical and value indicators) are highlighted and disclosed. regulating the procedure for accounting, movement and write-off of fuel and lubricants in military units is given. The authors aimed to highlight the issue of fuel accounting in conditions of martial law and Russian military aggression, document effective use of fuel by military units of the Armed Forces of Ukraine and territorial defense while carrying out combat missions. Research objects of forensic economic examinations are summarized, range of powers granted to experts while conducting such examinations is outlined. Peculiarities of the accounting and movement of military property that are characteristic of the rules for receiving, accounting, issuing and writing off material assets in Armed Forces of Ukraine are indicated. Відмова від відповідальності Засновники не грали жодної ролі у роз­ робленні дослідження, добиранні й аналізуванні даних, рішенні про пуб­ лікацію чи підготовку руко­пису. Відмова від відповідальності Засновники не грали жодної ролі у роз­ робленні дослідження, добиранні й аналізуванні даних, рішенні про пуб­ лікацію чи підготовку руко­пису. Forensic Economics Regarding Fuel Accounting in Armed Forces of Ukraine Nataliya Panchenko, Irina Нordiіenko, Olga Grek The issues and tasks solved by forensic experts while forensic economic examinations related to accounting and use of fuel by military units of Armed Forces of Ukraine are defined. The list of legislative and normative legal acts that should be guided by forensic economists in their professional activities while accounting for military property, is presented. Attention has been drawn to the unsettledness of some issues of such accounting (for example when some legislative acts have lost their validity, and new ones have not been adopted instead) causing certain difficulties. The main types of accounting of military property (quantitative and qualitative accounting; accounting of military property in numerical and value indicators) are highlighted and disclosed. Keywords: military property; property accounting specifics; fuel and lubricants; References Abu-Qarn, A. (2010). The Defense-growth nexus: An application for the Israeli-Arab conflict. MPRA Paper. Ben Gurion University of the Negev. URL: https://mpra.ub.uni- muenchen.de/22275/1/MPRA_paper_22275. pdf. p Al Qubaisi, M. A. (2020). Modern military expenditures and problems of sustainable development. Economic and Social Deve­ lopment : 55th International Scientific Confe­ rence on Economic and Social Development (Baku, 18—19 June, 2020). Vol. 2/4. URL: https://www.esd-conference.com/ upload/book_of_proceedings/Book_of_ Proceedings_esdBaku2020_Vol2_Online.pdf. Andrews, A. (2009). Department of Defense Fuel Spending, Supply, Acquisition, and Policy. CRS Report for Congress. September 22, 2009. URL: https://sgp.fas.org/crs/natsec/R40459. pdf. Keywords: military property; property accounting specifics; fuel and lubricants; quantitative, qualitative, account number accounting; military property accounting in value indicators. Keywords: military property; property accounting specifics; fuel and lubricants; quantitative, qualitative, account number accounting; military property accounting in value indicators. Keywords: military property; property accounting specifics; fuel and lubricants; quantitative, qualitative, account number accounting; military property accounting in value indicators. p Atesoglu, H. S., Mueller, J. M. (1990). Defense Spending and Economic Growth. Defence Economics. Vol. 2. Is. 1. DOI: 10.1080/10430719008404675. Ball, H. (2015). Working in the Killing Fields: Forensic Science in Bosnia. University of Nebraska Press. DOI: 10.2307/j.ctt1d9nj5c. Учасники Авторки внесли свій внесок винятково в  інтелектуальну дискусію, що є  осно- вою цього документа, дослідження су- дової практики, написання та редагу- вання, і беруть на себе відповідальність за її зміст і тлумачення. Декларація щодо конфлікту інтересів Авторки заявляють, що у них відсутній конфлікт інтересів. Панченко, Н., Гордієнко, І., Грек, О. (2022). Судові економічні експертизи з питань обліку пального у Збройних силах України. Теорія та практика судової експертизи і  криміна­ лістики. Вип. 2 (27). С. 103—119. DOI: 10.32353/khrife.2.2022.08. Наталія Панченко, Ірина Гордієнко, Ольга Грек. Судові економічні експертизи з питань обліку пального у Збройних силах України. DOI: 10.32353/khrife.2.2022.08 Фінансування Це дослідження не отримало жодно- го спеціального гранту від фінансових установ у державному, комерційному чи некомерційному секторах. Book, E. (2002). Pentagon Needs Accurate Accounting of Fuel / National Defense Magazine. 03/01/2002. URL: https:// www.nationaldefensemagazine.org/ 118 articles/2002/2/28/2002march-pentagon- needs-accurate-accounting-of-fuel. articles/2002/2/28/2002march-pentagon- needs-accurate-accounting-of-fuel. Conference on E-Education, E-Business and E-Technology. DOI: 10.1145/3241748.3241766. Kotov, V., Drobaha, V. (2019). Increase accuracy accounting and control of diesel fuel consumption. Collected scientific works of Ukrainian State University of Railway Transport. DOI: 10.18664/1994- 7852.183.2019.169648. Chapter 8. Accounting / Petroleum Pipeline and Terminal Operating Units // GlobalSecurity. org. 12 May 1998. URL: https://www. globalsecurity.org/military/library/policy/ army/fm/10-416/ch8.htm. y Dachkovskyі, V., Kondratiuk, I. (2021). Technical and economic assessment of the weapons and military equipment exploitation. Political Science and Security Studies Journal. Vol. 2. № 4. DOI: 10.5281/zenodo.5810146. Smith, J. S., Tuttle, M. H. (2008). Does Defense Spending Really Promote Aggregate Output in the United States? Defence and Peace Economics. Vol. 19. Is. 6. DOI: 10.1080/10242690701701950. JiTian, You, LinXi, OuYang, XueYing, Zhang, Shao,Yi Du. (2018). The Application of Economic Analysis in the Field of Military and National Defense Legislation. ICEBT 2018 : Proceedings of the 2nd International Xuang, C., Mintz, A. (1991). Defence Expenditures and Economic Growth: The Externality Effect. Defence Economics. Vol. 3. Is. 1. DOI: 10.1080/10430719108404713. 119
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Exploiting the Potential of Bioactive Molecules Extracted by Ultrasounds from Avocado Peels—Food and Nutraceutical Applications
Antioxidants
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cc-by
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  Citation: Rodríguez-Martínez, B.; Ferreira-Santos, P.; Gullón, B.; Teixeira, J.A.; Botelho, C.M.; Yáñez, R. Exploiting the Potential of Bioactive Molecules Extracted by Ultrasounds from Avocado Peels—Food and Nutraceutical Applications. Antioxidants 2021, 10, 1475. https:// doi.org/10.3390/antiox10091475 Received: 24 August 2021 Accepted: 13 September 2021 Published: 16 September 2021 Keywords: agri-food by-products; bioactive compounds; ultrasound assisted extraction; optimization; biological properties Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Exploiting the Potential of Bioactive Molecules Extracted by Ultrasounds from Avocado Peels—Food and Nutraceutical Applications Beatriz Rodríguez-Martínez 1 , Pedro Ferreira-Santos 2 , Beatriz Gullón 1,*, José António Teixeira 2 , Cláudia M. Botelho 2 and Remedios Yáñez 1,3 1 Department of Chemical Engineering, Faculty of Science, University of Vigo (Campus Ourense), 1 Department of Chemical Engineering, Faculty of Science, University of Vigo (Campus Ourense) As Lagoas, 32004 Ourense, Spain; beatriz.rodriguez@uvigo.es (B.R.-M.); reme@uvigo.es (R.Y.) g p g g g 2 Centre of Biological Engineering, Universidade do Minho, 4710-057 Braga, Portugal; pedrosantos@ceb.uminho.pt (P.F.-S.); jateixeira@deb.uminho.pt (J.A.T.); claudiabotelho@deb.uminho.pt (C.M.B.) p ( ) 3 Biomedical Research Centre (CINBIO), University of Vigo, University Campus As Lagoas-Marcosende, 36310 Vigo, Spain 3 Biomedical Research Centre (CINBIO), University of Vigo, University Campus As Lagoas-Marcosende, 36310 Vigo, Spain g p * Correspondence: bgullon@uvigo.es Abstract: Natural bioactive compounds from food waste have fomented interest in food and pharma- ceutical industries for the past decade. In this work, it purposed the recovery of bioactive avocado peel extract using an environmentally friendly technique: the ultrasound assisted extraction. The response surface methodology was applied in order to optimize the conditions of the extraction, ethanol-water mixtures and time. The optimized extracts (ethanol 38.46%, 44.06 min, and 50 ◦C) were chemically characterized by HPLC-ESI-MS and FTIR. Its antioxidant ability, as well as, its effect on cell metabolic activity of normal (L929) and cancer (Caco-2, A549 and HeLa) cell lines were assessed. Aqueous ethanol extracts presented a high content in bioactive compounds with high antioxidant potential. The most representative class of the phenolic compounds found in the avocado peel extract were phenolic acids, such as hydroxybenzoic and hydroxycinnamic acids. Another important chemical group detected were the flavonoids, such as flavanols, flavanonols, flavones, flavanones and chalcone, phenylethanoids and lignans. In terms of its influence on the metabolic activity of normal and cancer cell lines, the extract does not significantly affect normal cells. On the other hand, it can negatively affect cancer cells, particularly HeLa cells. These results clearly demonstrated that ultrasound is a sustainable extraction technique, resulting in extracts with low toxicity in normal cells and with potential application in food, pharmaceutical or nutraceutical sectors. Citation: Rodríguez-Martínez, B.; Ferreira-Santos, P.; Gullón, B.; Teixeira, J.A.; Botelho, C.M.; Yáñez, R. Exploiting the Potential of Bioactive Molecules Extracted by Ultrasounds from Avocado Peels—Food and Nutraceutical Applications. Antioxidants 2021, 10, 1475. https:// doi.org/10.3390/antiox10091475  Citation: Rodríguez-Martínez, B.; Ferreira-Santos, P.; Gullón, B.; Teixeira, J.A.; Botelho, C.M.; Yáñez, R. Exploiting the Potential of Bioactive Molecules Extracted by Ultrasounds from Avocado Peels—Food and Nutraceutical Applications. Antioxidants 2021, 10, 1475. https:// doi.org/10.3390/antiox10091475 Academic Editor: Michał Swieca Received: 24 August 2021 Accepted: 13 September 2021 Published: 16 September 2021 antioxidants antioxidants antioxidants antioxidants 1. Introduction Avocado (Persea americana Mill.) is a dicotyledonous plant belonging to the Lauraceae family, native from Central America and Mexico. It is one of the most consumed fruits in the world, with a global production of approximately 6.3 million tonnes in 2018 [1]. Currently, it is cultivated in tropical and subtropical places all over the world, being Mexico as the leading producer with one third of the total worldwide production [2]. In Europe, Spain reached a production of about 90,000 tons in 2018, around 95% of the European output [3]. In recent years, the intensification of the global production and increased consumption of avocado are related to its nutritional value and health benefits [4,5]. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). p Among the avocado varieties within the P. americana species (Bacon, Fuerte, Hass, Gwen, etc.), Hass is the most industrialized [6]. The avocado industry is important for the guacamole or oils market, for example [7,8]. This industry generates significant amounts of https://www.mdpi.com/journal/antioxidants Antioxidants 2021, 10, 1475. https://doi.org/10.3390/antiox10091475 Antioxidants 2021, 10, 1475 2 of 18 under-utilized by-products, which, if not managed properly, can cause serious environmen- tal problems [9]. These by-products include peels, seeds, or exhausted pulp representing between 21% and 30% of the total weight of the fruit [10]. The use of avocado by-products as composting [11] or natural adsorbent for the removal of dies [12] has already reported. However, due to its chemical composition this material has great economic potential since its use in the food or medical industry is generating great expectations. Even though its composition will be affected by factors such as the cultivar, the growing conditions or the maturation degree, the literature has reported the presence of high contents of carbohydrates (44–84 wt%), and percentages of lipids (2–6 wt%), protein (3–8 wt%), and minerals (2–6 wt%) [13]. Moreover, avocado peels are a remarkable source of biomolecules including phenolic acids, flavonoids as catechins, procyanidins, flavanols, and hydroxycinnamic and hydroxybenzoic acids [14,15]. Recently, it was reported that avocado peel extracts, due to their chemical composition, have numerous biological activities, namely antioxidant, anti-inflammatory, anti-hypertensive and antiproliferative properties [2,15]. The renewable nature, biodegradability, abundance, and low cost associated with their chemical composition makes avocado peels an interesting sustainable raw material. 1. Introduction They can be used for the development of integrated biorefinery approaches, based on sequen- tial environmentally friendly processes, which will reinforce the industrial bio-economy promoting well-being and human health [16]. In this context, avocado peels should be reprocessed, in close association with the conception of circular economy and industrial symbiosis, for the production of chemical platforms or functional molecules, with novel industrial applications in the growing market for “natural products”. In addition, it should be taken into account the great interest of food, pharmaceutical, and cosmetic industries in replacing synthetic compounds, normally associated with harmful health effects, by innocuous natural bioactive compounds with beneficial potential in the management (pre- vention and treatment) of various medical conditions like cancer, cardiovascular diseases, high blood pressure, diabetes, and neurological disorders [9,17–20]. A key aspect for the isolation of biomolecules from agro-industrial residues is the selec- tion of the most appropriate technology to obtain a high extraction efficiency and maintain the bioactive characteristics of the recovered molecules. Traditionally, these biomolecules were obtained using extraction procedures such as Soxhlet, hydrodistillation, maceration, among others. However, these methods demand a long processing time and large amounts of toxic organic solvents. In the last decade, ultrasound-assisted extraction (UAE) was considered a safe and green technology for the extraction of bioactive compounds from several renewable raw materials, such as olive trees [21], grape pomace [22], pomegranate peels [23], among others [24]. In sonication, the cavitation bubbles on the plant cell walls’ surface causes their disruption, helping the solvent to penetrate within them, thus in- creasing the mass transfer and ending in better diffusion into the cell material [25,26]. Moreover, the observed structural modifications are beneficial in reducing the severity of the treatment (shorter reaction times and lower temperatures) [27,28]. Compared with other modern extraction techniques, UAE has several advantages like versatility, simplicity and mild temperature operation. These characteristics are attracting attention, as this technique is one of the most feasible and promising technologies to be implemented at an industrial level [29,30]. However, despite this, UAE was scarcely applied for the recovery of bioactives from avocado peels. Different operational variables, such as temperature, ultrasonication time, solvent type, solvent-sample ratio, power, and frequency affect the efficiency of UAE [31]. Therefore, precise control of these parameters is necessary for optimal extraction. 2.4. Experimental Design A two-factor and three-level central composite design (CCD) with three replicates at the central point (11 experiments) was built to optimize the extraction conditions. Table 1 displays the fixed, independent, and dependent variables selected as well as the nomen- clature and their value or range. A summary of the experimental conditions of the set of experiments proposed is also listed in Table 2. Experimental data were fitted applying the regression analysis function of Microsoft Excel’s Data Analysis Add-In, USA. The adequacy of the model was demonstrated by appraising the coefficient of determination (R2), the significance of the regression coefficients, and the F-test value obtained from the analysis of variance. 2.3. Ultrasound Assisted Extraction (UAE) The UAE assays were performed in an ultrasonic bath (Branson CPX 3800 H) at a constant temperature of 50 ◦C and running at a frequency of 37 kHz. This temperature was selected based on preliminary studies (data not shown) and other related research [21,32,33]. For this, AP was placed in a 100 mL beaker with a fixed liquid–solid ratio (LSR) of 8:1 mL/g. When the extraction is finished, the extracts were recovered by vacuum filtration and stored at −20 ◦C until further analysis. 2.2. Reagents and Chemicals All chemicals and reagents were of analytical grade. Ethanol, methanol, gallic acid, rutin, trolox (6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid), Folin-Ciocalteu reagent, ABTS (2,2′-azino-di(3-ethylbenzothiazoline-6-suslfonic acid), TPTZ (2,4,6-tri(2- pyridyl)-S-triazine), DPPH (2,2-diphenyl-1-picrylhydrazyl), sodium carbonate, sodium acetate 3-hydrate, potassium persulfate, acetic acid, hydrochloric acid, iron(III) chloride hexahydrate, sodium hydroxide and Dulbecco’s Modified Eagle Medium (DMEM), foetal bovine serum (FBS), penicillin-streptomycin solution, resazurin sodium salt, and dimethyl sulfoxide (DMSO, ≥99.9%) were obtained from Sigma-Aldrich (Barcelona, Spain). 2.1. Raw Material Avocado peels (AP) from the Hass variety were obtained in a local restaurant in Ourense (Spain). The AP were washed with tap water and subjected to drying at 50 ◦C for 24 h in a drying oven (JP Selecta Theroven) until at a constant moisture content (<6%). Then, the dried samples were ground to a particle size between 0.3–1 mm using a Polymix PX-MFC 90D. Finally, the ground AP was stored at −20 ◦C in plastic bags until use. 1. Introduction The response surface methodology (RSM) is a widely mathematical tool employed in the optimization of bioactive compounds extraction process from several by-product sources [21,32,33]. Thus, the objective of the present research was to optimize the UAE conditions, time, and solvent content (aqueous EtOH), for the isolation of phenolic compounds from avocado peels. For this purpose, RSM based on a central composite design (CCD) of two-factor Antioxidants 2021, 10, 1475 3 of 18 3 of 18 at three-levels was used. The total phenolic content (TPC), the total flavonoid content (TFC) and antioxidant activity, and ABTS, DPPH, and FRAP assays were evaluated. The extract recovered under optimal conditions was analyzed by HPLC ESI-MS and FTIR for the identification of functional compounds. Furthermore, in vitro cell metabolic activity of the avocado peels extracts was determined using normal and cancer cell lines (L929, Caco-2, A549, and HeLa). 2.6.2. Antioxidant Activity The antioxidant potential of obtained APE was established employing the following methods: DPPH radical scavenging ability assay, ABTS+ scavenging activity assay and ferric reducing antioxidant power (FRAP). The assays were performed employing the same protocols described in detail by Gullón et al. [32]. For the three methods, three replicates from each experiment were analyzed and the results were recorded in milligram of Trolox equivalents (TE)/g dried AP. 2.6. Analyses of the Avocado Peels Extracts (APE) 2.6. Analyses of the Avocado Peels Extracts (APE) y f 2.6.1. Determination of Total Phenolic (TPC) and Flavonoid Content (TFC) Assays for TPC were performed following the procedure of Folin-Ciocalteau and the TFC through the colorimetric method employed by Blasa et al. [34]. Both analyses were carried out in three replicates and the results were conveyed as milligrams of gallic acid equivalent (GAE) per g dry AP for TPC and milligrams of rutin equivalent (RE) per g dry AP for TFC. 2.5. Selection of Optimal UAE Conditions and Validation of the Model For the purpose of obtaining an extract rich in phytochemicals with high bioactivity (evaluated by DPPH, ABTS, and FRAP), a multi-response surface optimization was applied to determine the extraction conditions which maximize all response variables simultane- ously. This optimization was performed using the desirability function of the software Statgraphics Centurion version XVI (Statpoint Technologies Inc., Warrenton, VA, USA). The impact coefficient for all responses was the same. The validity of the model was confirmed experimentally by carrying out three assays under the optimal UAE conditions. Antioxidants 2021, 10, 1475 4 of 18 Table 1. Experimental variables used in this study. Variable Definition and Units Nomenclature Value or Range Fixed Liquid to solid ratio of extraction (v/w) LSR 8 mL/g Frequency Temperature 37 kHz 50 ◦C Independent Ethanol concentration (% v/v) EtOH 0–80% Extraction time (min) tE 10–60 min Dependent Total phenolic content (mg GAE/g dried AP) TPC or y1 Total flavonoid content (mg RE/g dried AP) TFC or y2 DPPH• radical scavenging activity (mg TE/g dried AP) DPPH or y3 ABTS cation radical scavenging activity (mg TE/g dried AP) ABTS or y4 Ferric reducing antioxidant power (mg TE/g dried AP) FRAP or y5 Table 1. Experimental variables used in this study. Table 2. Operational conditions assayed (expressed in terms of coded and uncoded independent variables) and experimental values obtained for response variables. Experiment 1 2 3 4 5 6 7 8 9 10 11 Independent Variables EtOH (%) or x1 0(−1) 0(−1) 0(−1) 80(1) 80(1) 80(1) 40(0) 40(0) 40(0) 40(0) 40(0) Et (min) or x2 10(−1) 35(0) 60(1) 10(−1) 35(0) 60(1) 10(−1) 60(1) 35(0) 35(0) 35(0) Dependent Variables TPC or y1 (mg GAE/g dried AP) 18.1 19.9 18.0 15.0 18.9 20.1 36.4 41.8 42.3 42.9 43.6 TFC or y2 (mg RE/g dried AP) 31.8 37.1 32.6 34.8 37.1 42.2 72.7 79.9 82.2 84.3 85.3 DPPH or y3 (mg TE/g dried AP) 11.1 13.0 11.9 24.8 26.2 31.0 64.2 74.9 73.4 75.3 76.1 ABTS or y4 (mg TE/g dried AP) 54.2 64.8 67.3 73.8 87.7 83.1 114.7 138.8 146.7 148.1 149.7 FRAP or y5 (mg TE/g dried AP) 18.7 23.5 22.4 19.3 19.6 24.4 34.2 41.8 40.2 42.8 39.7 2.7. Characterization of the Selected Extract In order to have a detailed chemical composition and structural profile of bioactive compounds present in APE obtained under the optimized conditions, different analytical techniques were used including HPLC-ESI-MS and FTIR. 5 of 18 Antioxidants 2021, 10, 1475 2.7.2. ATR-Fourier Transform Infrared Spectroscopy An ALPHA II-Bruker compact FTIR spectrometer (Ettlingen, Germany) was used for the determination of the functional groups and bonding arrangement of the dried APE. The spectrum was recorded over the wavelength range from 4000 to 400 cm−1, a resolution of 4 cm−1 and 64 scans. 2.7.1. HPLC-ESI-MS A tentative identification of APE phenolic compounds recovered under optimal ex- traction conditions was carried out by liquid chromatography coupled with trapped ion mobility spectrometry and TOF high-resolution mass spectrometry (HPLC TOF MS). The sample was injected into a ZORBAX Eclipse XDB-C18 rapid resolution HD (2.1 × 100 mm 1.8 Micron de Agilent) and LC separation were carried out on an Elute HPLC (Bruker Daltonics). The mobile phases employed were: 0.1% aqueous formic acid (solvent A) and 0.1% formic acid in acetonitrile (solvent B) at a flow rate of 0.4 mL/min. The linear gradient was: 2% solvent B over 2 min, from 2% to 30% solvent B over 13 min, 30% to 100% solvent B over 2 min, 100 % solvent B over 4 min, 100% to 2% solvent B over 1 min and then isocratically 2% solvent B for 2 min. Ions were generated by an ESI source in negative ion mode. The working conditions were the following: 3000 V capillary voltage, 500 V end plate offset, 8.0 L/min dry gas, 2 bar nebulizer pressure, 220 ◦C dry heater. Identification of metabolites was based on the accurate mass data, isotopic pattern matching (mSigma value), retention time (when the standard was available) and the compounds reported in the literature. 2.8. Cell Viability In vitro cell metabolic activity of the APE was evaluated using four cell lines: normal mouse fibroblast (L929, ATCC® CCL-1), human colorectal adenocarcinoma (Caco-2, ATCC® HTB-37), human lung cancer (A549, ATCC® CCL-185) and human cervix epithelioid carcinoma (HeLa, ATCC® CCL-2). Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (1% non-essential amino acids were added to Caco-2 culture medium), at 37 ◦C in a 5% CO2 humidified atmosphere. Upon confluence, cells were trypsinized and seeded in a 96-well plate at a density of 1 × 105 cells per well. Different concentrations of the APE (8, 16, 32, 63, 125, 250, 500 and 1000 µg/mL) were prepared in supplemented culture medium and the viability activity was assessed using the resazurin reduction assay [35,36]. Cell viability was carried out using the procedure described in detail by Ferreira-Santos et al. [35]. The % cell viability was computed based on the values of the cell-free medium (blank) and the negative controls (0.5% DMSO). Only a viable cell has the capability to convert the resazurin into the fluorescent resorufin. 3.1. Experimental Design Proposed by Studying the Recovery of Bioactive Molecules 3.1. Experimental Design Proposed by Studying the Recovery of Bioactive Molecules In this study, with the purpose of recovering liquid fractions enriched in bioactive compounds from AP, the application of ultrasonic technology in ethanol-water media was selected. Ultrasonic assisted technology has been previously employed in obtaining valuable biomolecules from agri-food by-products [24]. This technique helps to reduce time, solvent and energy spend and can, therefore, contribute to the development of environmentally friendly applications [9]. Moreover, the use of ethanol as the solvent is another advantage, it is cheap, non-toxicity [37], and generally recognized as safe (GRAS) [9]. ( ) Preliminary experiments were carried out to identify the most influential variables and their range of action. These assays were used to determine the values for the fixed variables (data not show). Afterwards, an experimental design of 11 experiments was performed, where the chosen independent variables were: ethanol percentage (EtOH, % v/v or x1) and Antioxidants 2021, 10, 1475 6 of 18 time (t, min or x2). The variable ranges considered were 0–80% and 10–60 min, respectively (see Table 1). ( ) So, with the aim to optimize the recovery of the key compounds, TPC, TFC, and antioxidant activities (analyzed by DPPH, ABTS, and FRAP assays) were selected as dependent variables. Table 2 shows the main experimental results obtained for these parameters in the set of experiments proposed in the design. From these results, it should be noted that the ethanol concentration was more influential than time. As a general trend, increasing time had a positive effect in the recovery of phenolic and flavonoid compounds, whereas intermediate concentrations of ethanol allowed reaching high TPC and TFC, both decreasing considerably thereafter. Interestingly, the highest experimental TPC and TFC (with average values of 42.9 mg GAE/g dried AP and 83.9 mg RE/g dried AP, respectively) were obtained in the central point of the design, at intermediate EtOH concentration and reaction times (40% EtOH and 35 min). As can be seen in Table 2, these experimental conditions also resulted in very high experimental antioxidant activities, established by DPPH, ABTS, and FRAP assays, with average values of 74.9, 148.2 and 40.9 mg TE/g dried AP, respectively. 3.1. Experimental Design Proposed by Studying the Recovery of Bioactive Molecules p y Good correlations between TPC, TFC, and antioxidant activities were previously re- ported for several substrates using different extraction methods: (i) conventional treatment with ethanol-water of yerba mate [38], coffee silverskin [39], and spent yerba mate [33]; (ii) in acetone extracts of peach fruit [40]; (iii) after ultrasonic ethanol-water treatment of olive tree by-products [21] and grapefruit wastes [41]; (iv) or even in hydrothermal treatment liquors of melon by-products [42]. The effects of the extraction variables depend mostly on the raw material used. For example, a negative effect on variable time on TPC was reported by Segovia et al. [43] using UAE with avocado seeds at different temperatures and powers. On the other hand, Ilaiyaraja et al. [44] and Dahmoune et al. [45] showed a great influence of the percentage of ethanol during the extraction of phytochemicals from Feronia limonia fruit, and Citrus limon residues, reaching higher yields at medium EtOH contents. García-Castelló et al. [41] have reported the same trend in the recovery of flavonoids from grapefruit wastes by UAE and 0.4 g/g of ethanol-water. However, the influence of this parameter on TPC and TFC was not evaluated in previous studies performed with avocado by-products [2,6,9]. In this context, in the study by Trujillo-Mayol et al. [9] optimization of UAE was proposed for polyphenols recovery, but only the effect of time (15–60 min) and temperature (40–60 ◦C) was evaluated. On the other hand, our work adds another important variable into the process (ethanol concentration) that has a great impact on the recovery process of phenolic compounds. 3.2.1. Effect of the Ultrasonic Pre-Treatment on the Total Phenolic Content (TPC) ratic term of the EtOH concentration was the most influential variab ) f ll d b th d ti d li l t f th ti Th d 3.2.1. Effect of the Ultrasonic Pre-Treatment on the Total Phenolic Content (TPC) ratic term of the EtOH concentration was the most influential variab ) f ll d b th d ti d li l t f th ti Th d 3.2.1. Effect of the Ultrasonic Pre-Treatment on the Total Phenolic Content (TPC) ratic term of the EtOH concentration was the most influential variab ) f ll d b th d ti d li l t f th ti Th d In agreement with the absolute value of the coefficients shown in Table 3, the quadratic term of the EtOH concentration was the most influential variable on TPC (denoted y1), followed by the quadratic and lineal terms of the time. The quadratic terms exercised a negative effect on the isolation of the phenolic compounds, whereas the linear effect of the extraction time was positive. Figure 1 shows the relation between the EtOH concentration and extraction time on TPC. This response variable increased with the extraction time up to times close to 42 min; afterward, the model predicted a slight decrease of the TPC. However, EtOH concentrations higher than 40% had a negative impact on the content of phenolic compounds. Therefore, the higher TPC predicted by the model (42.7 mg GAE/g dried AP) was reached at 40–45 min and EtOH concentrations about 40%. y1), followed by the quadratic and lineal terms of the time. The quadratic ter a negative effect on the isolation of the phenolic compounds, whereas the lin the extraction time was positive. Figure 1 shows the relation between the E tration and extraction time on TPC. This response variable increased with th time up to times close to 42 min; afterward, the model predicted a slight de TPC. However, EtOH concentrations higher than 40% had a negative impac tent of phenolic compounds. Therefore, the higher TPC predicted by the mo GAE/g dried AP) was reached at 40–45 min and EtOH concentrations about Figure 1. Response surface of total phenolic content (TPC) for AP as a function of et tration and ultrasonication time. Figure 1. Response surface of total phenolic content (TPC) for AP as a function of ethanol concentra- tion and ultrasonication time. Figure 1. Response surface of total phenolic content (TPC) for AP as a function of et tration and ultrasonication time Figure 1. 3.2. Response Surface Methodology Assessment for the Optimization of Bioactive Compounds Recovery from Avocado For an easier elucidation of the results obtained, response surface methodology (RSM) was employed. For that purpose, dependent variables (listed in Table 3) were correlated with independent variables (EtOH and extraction time) by empirical models, as follows: yj = b0j + 2 ∑ i=1 bijxi + 2 ∑ i=1 2 ∑ k=1 bikjxixk (1) (1) where yj (j = 1 to 5) reflects the dependent variables; xi or xk (i or k: 1 to 2, k ≥i) the normalized, independent variables (defined in Table 1), and b0j . . . bikj represent the regression coefficients calculated by multiple regression using the least-squares method from experimental results. The regression coefficients, statistical significance (based on the Students t-test) and the statistical significance of model (Fischer’s F parameter) were collected in Table 3. The high R2 values (>0.985) and the values of the other statistical parameters stated a close correlation between the experimental and the predicted data, as well as a good significance of the model. 7 of 18 45.07 9.71 b Antioxidants 2021, 10, 1475 Table 3. Analysis of the variance (ANOVA) of the fitted second-order polynomial models. Coefficient y1 y2 y3 y4 y5 b0 42.45 a 82.71 a 73.77 a 145.07 a 40.37 a b1 −0.31 2.09 7.68 a 9.71 b −0.20 b2 1.71 b 2.56 c 2.95 c 7.76 b 2.73 b b12 1.32 c 1.67 1.36 −0.96 0.37 b11 −22.36 a −43.72 a −52.43 a −64.15 a −18.02 a b22 −2.64 b −4.57 c −2.50 −13.67 b −1.54 R2 0.995 0.992 0.994 0.985 0.978 F-exp 222.6 130.3 182.9 66.9 44.96 Significance level (%) 99.999 99.997 99.998 99.986 99.963 a Significant coefficient at the 99% confidence level. b Significant coefficient at the 95% confidence level. c Signifi- cant coefficient at the 90% confidence level. b12 1.32 c 1.67 1.36 −0.96 b11 −22.36 a −43.72 a −52.43 a −64.15 a b22 −2.64 b −4.57 c −2.50 −13.67 b R2 0.995 0.992 0.994 0.985 F-exp 222.6 130.3 182.9 66.9 Significance level (%) 99.999 99.997 99.998 99.986 a Significant coefficient at the 99% confidence level. b Significant coefficient at the 95% level. c Significant coefficient at the 90% confidence level. 3.2.1. Effect of the Ultrasonic Pre-Treatment on the Total Phenolic Content (T In agreement with the absolute value of the coefficients shown in Table Table 3. Analysis of the variance (ANOVA) of the fitted second-order polynomial models. 3.2. Response Surface Methodology Assessment for the Optimization of Bioactive Compounds Recovery from Avocado b12 1.32 c 1.67 1.36 b11 22 36 a 43 72 a 52 43 a 3.2.1. Effect of the Ultrasonic Pre-Treatment on the Total Phenolic Content (TPC) ratic term of the EtOH concentration was the most influential variab ) f ll d b th d ti d li l t f th ti Th d Response surface of total phenolic content (TPC) for AP as a function of ethanol concentra- tion and ultrasonication time. Previous studies also reported similar behavior for the surface responses of TPC with EtOH concentration, reaching the optimum phenolic contents at intermediate ethanol concentrations and then decreasing [14,21,44,45]. This fact would be associated with the negative influence of the quadratic term of EtOH on the phenolic recovery, also observed in other studies previously cited [21,41,44]. Moreover, certain authors highlight the important role of the solvent polarity in the solubilization of phenolic compounds, since these com- pounds present a wide spectrum of solubilization and, therefore, mixtures of ethanol-water Antioxidants 2021, 10, 1475 8 of 18 lowing ration 8 of 18 lowing ration may be more efficient than single solvents [32,44]. In this sense, certain authors emphasize the importance of the similarity of the polarity of solvents and solutes [37] and the decreas- ing of the solvent dielectric constant caused by ethanol, in enhancing phenolic compounds solubilization and diffusion [41]. lineal term of extraction time had a positive effect on the TFC. Conversely, th was negatively affected by the quadratic terms of both factors. Figure 2 dep bined influence of the percentage of EtOH and extraction time on the TFC. A the calculated TFC ranged from 31.4 to 83.1 mg RE/g dried AP, values pre 3.2.2. Effect of the Ultrasonic Treatment on the Total Flavonoid Content (TFC) extraction without ethanol at the lowest time evaluated (10 min) and about 40 42 min respectively Therefore maximum TFC we Similarly, to the variation pattern observed for the TPC, the quadratic term of the EtOH concentration was the most influential variable on TFC, also following by the quadratic and lineal terms of the time; but in this case, the EtOH concentration had a higher influence. From the regression parameters shown in Table 3, it should be noted that the lineal term of extraction time had a positive effect on the TFC. Conversely, this parameter was negatively affected by the quadratic terms of both factors. Figure 2 depicts the combined influence of the percentage of EtOH and extraction time on the TFC. As can be seen, the calculated TFC ranged from 31.4 to 83.1 mg RE/g dried AP, values predicted in the extraction without ethanol at the lowest time evaluated (10 min) and with 40% ethanol and about 40–42 min, respectively. 3.2.1. Effect of the Ultrasonic Pre-Treatment on the Total Phenolic Content (TPC) ratic term of the EtOH concentration was the most influential variab ) f ll d b th d ti d li l t f th ti Th d Therefore, maximum TFC were obtained in similar experimental conditions to the ones previously discussed for the maximum TPC. and about 40–42 min, respectively. Therefore, maximum TFC were obtain experimental conditions to the ones previously discussed for the maximum Other studies also reported a similar behavior for TFC and a positive e nol:water mixtures in their recovery. In this context, Martínez-Patiño et al. maximum TFC at intermediate ethanol concentrations (closed to 50%). Ho crease observed at extraction times higher than 12 min, evidence a possible of thermo-sensitive compounds. The same trend of flavonoids extraction w ethanol concentrations was also described by Xu et al. [37] in Limonium sinu or by García-Castelló et al. [41] with grapefruit solid residues. Figure 2. Response surface of total flavonoid content (TFC) for AP as a function of e tration and ultrasonication time. Figure 2. Response surface of total flavonoid content (TFC) for AP as a function of ethanol concentra- tion and ultrasonication time. Figure 2. Response surface of total flavonoid content (TFC) for AP as a function of e tration and ultrasonication time. Figure 2. Response surface of total flavonoid content (TFC) for AP as a function of ethanol concentra- tion and ultrasonication time. 3.2.3. Effect of the Ultrasonic Treatment on Antioxidant Capacity To assess the impact of the UAE on the antioxidant potential of the extr from AP, data from DPPH, ABTS, and FRAP assays were included as depend Other studies also reported a similar behavior for TFC and a positive effect of ethanol:water mixtures in their recovery. In this context, Martínez-Patiño et al. [21] re- ported maximum TFC at intermediate ethanol concentrations (closed to 50%). However, a decrease observed at extraction times higher than 12 min, evidence a possible degradation of thermo-sensitive compounds. The same trend of flavonoids extraction with different ethanol concentrations was also described by Xu et al. [37] in Limonium sinuatum extracts or by García-Castelló et al. [41] with grapefruit solid residues. 3.2.3. Effect of the Ultrasonic Treatment on Antioxidant Capacity To assess the impact of the UAE on the antioxidant potential of the extracts obtained from AP, data from DPPH, ABTS, and FRAP assays were included as dependent variables and modelled. As can be deduced for the regression coefficients showed in Table 3, the quadratic term of the EtOH concentration was the most influence variable and had a negative impact in the three response variables. Moreover, the antioxidant capacity measured by ABTS was also negatively influenced by the quadratic term of the extraction Antioxidants 2021, 10, 1475 9 of 18 9 of 18 time. However, a positive effect of the linear terms of the EtOH concentration and time was obtained in the DPPH and ABTS regression analysis, being higher in both cases for EtOH. On the contrary, this last dependence variable had no influence on the polynomial model obtained for FRAP. The response surfaces obtained for the antioxidant potential determined by DPPH, ABTS and FRAP tests are collected in Figure 3 (a, b and c respectively). The values predicted by the model for these parameters ranged from 9.6 and 74.9 for DPPH, between 48.8 and 146.5 for ABTS and 17.5 to 41.6 for FRAP, all expressed in mg TE/g dried AP. These maximum antioxidant activities were obtained at intermediate ethanol concentration (40–44%) and prolonged reaction times, about 50, 45, and 57 min for FRAP, DPPH and ABTS modelling, respectively. As with TPC and TFC, ethanol concentrations higher than 40–44% had a marked negative impact on antioxidant capacity, which would indicate a good correlation between these parameters. The higher values for ABTS were obtained at extraction times close to predicted for maximum TPC and TFC (40–44 min), being necessary to prolong the duration of the treatment up to 50–57 min to reach the highest values of DPPH and FRAP. García-Castelló et al. [41] also described the same trend of DPPH with ethanol content in grapefruit solid wastes extracts. Xu et al. [37], in a previous study dealing with the UAE of the flower of Limonium sinuatum, displayed that the linear and quadratic coefficients of ethanol content were significant on ABTS modelling, whereas the influence of the ultrasound time was not significant. In this case, the negative effect of the quadratic term on the percentage of ethanol was also reported. Araújo et al. 3.2.3. Effect of the Ultrasonic Treatment on Antioxidant Capacity [46] also noted a significant effect of the quadratic term of the ethanol content on the isolation of antioxidant compounds in MAE of avocado seeds. In this study, the highest content of phenolic compounds and antioxidant activities were also identified at intermediate percentages of ethanol (close to 50%). Establishing comparisons between the antioxidant activities collected in literature for avocado by-products is not easy, due to the large number of analytical methods available for their determination and the different extraction conditions. 3.3. Process Optimization and Validation of the Model In this work, for the purpose of achieving an extract with high content of phytochemi- cals and with high bioactivity, a multiple response optimization applying the desirability function was used to determine the UAE conditions that enabled simultaneous maximiza- tion of the five studied responses. The selected conditions resulting in an extract with these characteristics were: ethanol concentration of 38.46% (v/v) and 44.06 min. Using microwave-assisted extraction, Araújo et al. [19] estimated an optimal ethanol concentra- tion similar to that found here to obtain bioactive compounds from this same residue. In another work, Martínez-Patiño et al. [21] reported a shorter extraction time (15 min) and a higher ethanol percentage (51.3%) as optimal conditions for the ultrasonic treatment of olive mill leaves. With the purpose to confirm the validity and the adequacy of the model, three trials under optimal conditions were performed. Table 4 collects the predicted and experimental results for all responses analyzed in this study. As can be seen, the experimental data were similar to the predicted response values (the error varied between 3 and 5.6%), which indicates the suitability of the experimental design to optimize the recovery of antioxidants from AP. Under these optimum conditions, the TPC and TFC were of 45.34 mg GAE/g dried AP and 87.56 mg RE/g dried AP, respectively, with DPPH of 73.25 mg TE/g dried AP, ABTS of 160.34 mg TE/g dried AP and FRAP of 44.65 mg TE/g dried AP. Comparing the experimental results, the TPC observed by Tremocoldi et al. [2] after ultrasonic treatment (80% ethanol, 40 KHz, 15 min at 25 ◦C, LSR of 10 mL/g) of AP of the Hass variety was 63.5 mg GAE/g lyophilized AP. Trujillo-Mayol et al. [9] using the same conditions but increasing the temperature at 60 ◦C and the LSR at 25 mL/g found a TPC value of around 2.9 times higher than that obtained in our research. Regarding antioxidant activity, in Antioxidants 2021, 10, 1475 10 of 18 10 of 18 the cited studies, Trujillo-Mayol et al. [9] reported for UAE extracts, values of DPPH and FRAP of 772.2 and 161.7 µgTE/g dried extract, respectively; whereas Tremocoldi et al.’s [2] values of DPPH and ABTS of 310 and 791.5 µmol TE/g of AP lyophilized, respectively, and FRAP of 1175.1 µmol Fe2+ g of AP lyophilized. 3.3. Process Optimization and Validation of the Model It is important to take into account that the differences detected by different authors in the antioxidant potential of the extracts recovered from AP is affected by different variables, such as the type of cultivar, ripeness stage, and environmental and nutritional growth conditions [10]. VIEW 10 of 19 Figure 3. Response surface of DPPH (a) ABTS (b) and FRAP (c) for avocado peel (AP) as a function of ethanol concentration and ultrasonication time. Figure 3. Response surface of DPPH (a) ABTS (b) and FRAP (c) for avocado peel (AP) as a function of ethanol concentration and ultrasonication time. igure 3. Response surface of DPPH (a) ABTS (b) and FRAP (c) for avocado peel (AP) as a function of ethanol concentration nd ultrasonication time. Figure 3. Response surface of DPPH (a) ABTS (b) and FRAP (c) for avocado peel (AP) as a function of ethanol concentration and ultrasonication time. 3.3. Process Optimization and Validation of the Model In this work, for the purpose of achieving an extract with high content of phytochem- icals and with high bioactivity, a multiple response optimization applying the desirability function was used to determine the UAE conditions that enabled simultaneous maximi- zation of the five studied responses. The selected conditions resulting in an extract with these characteristics were: ethanol concentration of 38.46% (v/v) and 44.06 min. Using mi- crowave-assisted extraction, Araújo et al. [19] estimated an optimal ethanol concentration i il t th t f d h t bt i bi ti d f thi id I Table 4. Validation of the predicted values at optimal conditions of UAE. TPC (mg GAE/g dried AP) TFC (mg RE/g dried AP) DPPH (mg TE/g dried AP) ABTS (mg TE/g dried AP) FRAP (mg TE/g dried AP) Predicted value 43.65 84.87 76.61 150.21 42.26 Experimental value a 45.34 ± 1.7 87.56 ± 1.2 73.25 ± 3.4 160.34 ± 65.7 44.65 ± 2.7 a Mean ± standard deviation (SD) of three determinations (n = 3) from three extract replications. 3 3 Process Optimization and Validation of the Model Table 4. Validation of the predicted values at optimal conditions of UAE. ( / ) crowave-assisted extraction, Araújo et al. [19] estimated an optimal ethan a Mean ± standard deviation (SD) of three determinations (n = 3) from three extract replications. 3.4. Characterization of the Extract Obtained under the Optimum Conditions 3.4.1. HPLC-TOF-MS Analysis The identification of compounds present in the APE was based on the following criteria: (i) the measurement of the accurate mass of pseudomolecular ion [M-H]- compared to the theoretical mass (the mass error among the theoretical and the measured mass was <10 ppm), (ii) the mSigma value lower than 50, (iii) retention time (when the standard was available) and (iv) the information reported in previous reports [17,19,47]. Table 5 collects the main identified compounds in AP extracts. HPLC-TOF MS analysis allowed to identify different families of compounds in the extracts including phenolic acids, organic acids, and lignans that are associated with the in vitro antioxidant activity previously determined in the APE. Table 5. Tentative identification of phenolic compounds in AP extracts. Table 5. Tentative identification of phenolic compounds in AP extracts. Proposed Compounds Class/Subclass Molecular Formula m/z Meas. RT (min) mSigma Quinic acid Organic acid C7H12O6 191.0560 4.54 10.6 Tyrosol-hexoside-pentoside Phenylethanoids C19H28O11 431.1557 4.8 17.7 4-Hydroxybenzoic acid PA/HB C7H6O3 137.0241 5.04 10 Chlorogenic acid/caffeoyl-quinic acid PA/HC C16H18O9 353.0879 6.62 20.6 Benzoic acid PA/HB C7H6O2 121.0293 6.79 1.7 Procyanidin trimer B FL/flavanol oligomer C45H38O18 865.1973 6.86 48.2 Procyanidin dimer B FL/flavanol oligomer C30H26O12 577.1338 7.01 4.7 Catechin FL/flavanol C15H14O6 289.0717 7.99 4.1 Quercetin—dihexose FL/flavanol C27H30O17 625.1405 9.44 21.7 Quercetin O-arabinosyl-glucoside FL/flavanol C26H28O16 595.1300 10.46 7.9 Rutin FL/flavanol C27H30O16 609.1457 10.76 9.8 Nudiposide Lignan C27H36O12 551.2130 11.34 5.6 Epigallocatechin 3-coumarate FL/flavanol C24H20O9 451.1031 11.61 8.6 Taxifolin FL/flavanonol C15H12O7 303.0507 11.64 3.9 Quercetin FL/flavanol C15H10O7 301.0352 11.82 25.6 Quercetin 3-glucoside FL/flavanol C21H20O12 463.0881 11.85 4.3 Quercetin 3-glucuronide FL/flavanol C21H18O13 477.0674 11.94 12.7 Procyanidin dimer A FL/flavanol oligomer C30H24O12 575.1189 12.45 12 Kaempferol-hexose FL/flavanol C21H20O11 447.0931 13.14 22.9 Luteolin 7-O-(2”-O-pentosyl) hexoside FL/flavone C26H28O15 579.1354 13.49 9.1 Procyanidin trimer A FL/flavanol oligomer C45H36O18 863.1812 14.03 58.5 Kaempferol O-glucosyl-rhamnoside FL/flavanol C27H30O15 593.1505 14.49 12.5 Neosakuranetin FL/chalcone C22H24O10 44731298 14.62 11.9 p-coumaric acid PA/HC C9H8O3 163.0399 16.32 6.5 (±)-Naringenin FL/flavanone C15H12O5 271.0611 16.69 14.1 * Abbreviations: PA: phenolic acid; HB: hydroxybenzoic acid; HC: hydroxycinnamic acid; FL: flavonoids. * Abbreviations: PA: phenolic acid; HB: hydroxybenzoic acid; HC: hydroxycinnamic acid; FL: flavonoids. The main phenolic acids identified in this work were 4-hydroxybenzoic acid, chloro- genic acid, benzoic acid, and p-coumaric acid. According to the literature, these compounds were previously reported in avocado peels [17,48,49]. For example, Figueroa et al. 3.3. Process Optimization and Validation of the Model Antioxidants 2021, 10, 1475 11 of 18 In order to have detailed information of the recovered extracts under optimal condi- tions (ethanol concentration of 38.46% (v/v) and 44.06 min), these were analyzed to identify the main phenolic compounds, their structural characteristics, and their cytotoxic potential. 3.4. Characterization of the Extract Obtained under the Optimum Conditions 3.4.1. HPLC-TOF-MS Analysis 3.4. Characterization of the Extract Obtained under the Optimum Conditions 3.4.1. HPLC-TOF-MS Analysis [14] used HPLC-Q-TOF MS/MS to detect caffeic acid, p-coumaric acid and different isomers of caffeoylquinic acids derivatives in extracts from avocado fruit peel obtained by acceler- ated water–ethanol extraction. These compounds present bioactive properties that make avocado by-products suitable sources for the formulation of functional ingredients. In this Antioxidants 2021, 10, 1475 12 of 18 12 of 18 sense, it has been described that chlorogenic acid presents hypoglycemic, hypolipidemic, and antioxidant properties [50] and p-coumaric acid exhibits antimicrobial activity. Regarding flavonoids, compounds belonging to different subclasses were identified: flavanols (catechin, epigallocatechin 3-coumarate) flavonols (quercetin-dihexose, quercetin O-arabinosyl-glucoside, rutin, quercetin, quercetin 3-glucoside, quercetin 3-glucuronide, kaempferol-hexose, kaempferol O-glucosyl-rhamnoside), flavones (luteolin 7-O-(2”-O- pentosyl) hexoside), flavanones (naringenin) and flavanonols (taxifolin). The identification of these compounds in our extract is in agreement with the flavonoids found by other authors in avocado peel extracts [15,17,46,47]. Multiple works have confirmed the ben- eficial health properties of flavonoids consumption including their role as antioxidant, hypolipidemic and anti-obesity, antimicrobial, neuroprotective, among others [51]. For example, Tremocoldi et al. [2] demonstrated that different flavonoids, such as epicatechin, trans-5-O-caffeoyl-D-quinic acid, catechin and epicatechin, exhibited anti-inflammatory and cytotoxic properties. Quercetin improves insulin-stimulated glucose uptake in mature adipocytes, and rutin presents hypoglycemic and hypolipidemic properties [50]. Different procyanidins were also identified in the extracts obtained by ultrasonication of avocado peels. Several reports have shown the presence of these condensed flavonoids in avocado by-products. For instance, Rosero et al. [47] studied the procyanidins in the seeds and peels of ‘Nariño’ avocado, providing the identification of types A (1 dimer and 1 trimer) and 7 of types B (four dimers and three trimers). Kosi´nska et al. [48] found in the Hass variety two type B procyanidin dimers and another type A. Various studies have reported that procyanidins present interesting bioactivities, such as modulate antioxidant enzymatic activities [52], exhibit chemoprotective properties against cancer [53,54], and prevent urinary tract infections [54], among other bioactivities. The presence of the lignan nudiposide and neosakuranetin is in consonance with previous research on avocado peel [17]. Other families of compounds such as organic acids (quinic acid), phenolic alcohol derivatives (tyrosol-hexoside-pentoside) were tenta- tively identified. g p ll b l 3.4.3. Cell Viability mention that the re o resorufin [67]. T 3.4.3. Cell Viability Some natural molecules from plants and by-products can be considered harmful consumers’ health. So, cytotoxic studies are necessary to evaluate the potential toxic effe of plant extracts [35,57]. In this study, the effect of APE was evaluated on normal mous fibroblast cells (L929). As can be seen in Figure 5, the data shows that APE induces a lo y Some natural molecules from plants and by-products can be considered harmful to consumers’ health. So, cytotoxic studies are necessary to evaluate the potential toxic effect of plant extracts [35,57]. In this study, the effect of APE was evaluated on normal mouse fibroblast cells (L929). As can be seen in Figure 5, the data shows that APE induces a low cytotoxic effect in normal fibroblasts, reporting IC50 values of 908.6 µg/mL. o resorufin [67]. This ability is correlated with cell viability and cell number/p The basis for this understanding is that the higher the conversion of the dye, he cell number. So, taking into consideration this fact, it is possible to interpr observed as the extracts’ influence on cellular proliferation. 3.4.3. Cell Viability Some natural molecules from plants and by-products can be considered harmful t consumers’ health. So, cytotoxic studies are necessary to evaluate the potential toxic effe of plant extracts [35,57]. In this study, the effect of APE was evaluated on normal mous fibroblast cells (L929). As can be seen in Figure 5, the data shows that APE induces a low Some natural molecules from plants and by-products can be considered harmful to consumers’ health. So, cytotoxic studies are necessary to evaluate the potential toxic effect of plant extracts [35,57]. In this study, the effect of APE was evaluated on normal mouse fibroblast cells (L929). As can be seen in Figure 5, the data shows that APE induces a low cytotoxic effect in normal fibroblasts, reporting IC50 values of 908.6 µg/mL. o resorufin [67]. This ability is correlated with cell viability and cell number/p The basis for this understanding is that the higher the conversion of the dye, he cell number. So, taking into consideration this fact, it is possible to interpre observed as the extracts’ influence on cellular proliferation. cytotoxic effect in normal fibroblasts, reporting IC50 values of 908.6 µg/mL. Similar results were described by other authors, which showed that avocado etha nolic extract by-products did not have a toxic effect on mouse macrophage RAW 264. cells. 3.4.2. ATR-FTIR Spectra Analysis It is mention that the resazurin test is based on the ability of living cells to transfo EVIEW with traditional narcotics is becoming a priority in anticancer research [58]. ucts or their derivatives are promising alternatives for anti-cancer thera studies have confirmed that polyphenol-rich extracts from natural reso health benefits by delaying tumor onset [59]. The anticarcinogenic propertie ecules are related with their capacity to inhibit cancer cell proliferation, ang tastasis, apoptosis, and inflammation [60]. In vitro cytotoxic characteristics against different tumor cell lines such as breast, colon, liver, lungs, leukem and prostate, were largely studied by other authors [58,61–66]. In the pre metabolic activity was quantified by the conversion of resazurin to resor / with ucts tud ional narco eir derivati Figure 4 ATR-FTIR spectra of freeze-dried APE Figure 4. ATR-FTIR spectra of freeze-dried APE. contact with various concentrations of ti th t th i t t i b d 3.4.2. ATR-FTIR Spectra Analysis Figure 4 displays the FTIR spectra of the optimized freeze-dried APE at a wavelength ranging from 400–4000 cm−1. The broad peak in the region of 3600–3000 cm−1 (3273 cm−1) can be accredited to the O–H stretching of phenolic and aliphatic structures. The hydropho- bic phenolic compounds signature is represented by the peaks at 2917 and 2849 cm–1 [35]. The band at 1735 cm−1 is attributed to the carbonyl C–O from the ester group related to esterified pectins. The peaks at 1605 and 1323 cm−1 are originated by the vibration of the aromatic skeletal, while the peak at 1232 cm−1 is due to the skeletal vibrations of the aromatic ring with C–O stretching. According to the literature the bands at 1440 and 1017 cm−1 are associated to polysaccharides, pectins, and sugars [55]. The chemical charac- terization of the avocado extract demonstrated the presence of phenolic compounds, which were detected by the FTIR spectra due to the stretching and bending vibrations of –CH from aromatic rings assigned to the peaks between 864 to 775 cm−1. Similarly, the presence of flavonoids and polyphenols were also observed due to the presence of vibrational bands assigned to the bonds O–H, C–H, C=C ring, C–OH, and C–C [56]. The FTIR spectra results are supported by the data previously described, as well as by the literature which refers the presence of pectins, starch, sugars, lignin, and phenolic compounds in avocado by-products resulting extracts [5,15]. 13 of 18 n avocad Antioxidants 2021, 10, 1475 13 of 18 n avocad Figure 4. ATR-FTIR spectra of freeze-dried APE. Figure 4. ATR-FTIR spectra of freeze-dried APE. EVIEW with traditional narcotics is becoming a priority in anticancer research [58]. N ucts or their derivatives are promising alternatives for anti-cancer therap studies have confirmed that polyphenol-rich extracts from natural resou health benefits by delaying tumor onset [59]. The anticarcinogenic properties ecules are related with their capacity to inhibit cancer cell proliferation, angio tastasis, apoptosis, and inflammation [60]. In vitro cytotoxic characteristics o against different tumor cell lines such as breast, colon, liver, lungs, leukemia and prostate, were largely studied by other authors [58,61–66]. In the prese metabolic activity was quantified by the conversion of resazurin to resoru contact with various concentrations of APE (0 to 1000 µg/mL) for 24 h. g p ll b l 3.4.3. Cell Viability mention that the re o resorufin [67]. T This Antioxidants 2021, 10, 1475 14 of 18 14 of 18 result corroborates those obtained in this study, in which even at higher doses, APE show low toxicity. These results indicate that these extracts are safe for human consumption [2]. y p [ ] To this day, cancer remains one of the leading causes of death worldwide. In this sense, the quest for safer strategies to be applied either as mono or adjunctive therapy with traditional narcotics is becoming a priority in anticancer research [58]. Natural products or their derivatives are promising alternatives for anti-cancer therapeutics. Some studies have confirmed that polyphenol-rich extracts from natural resources possess health benefits by delaying tumor onset [59]. The anticarcinogenic properties of these molecules are related with their capacity to inhibit cancer cell proliferation, angiogenesis, metastasis, apoptosis, and inflammation [60]. In vitro cytotoxic characteristics of AP extracts against different tumor cell lines such as breast, colon, liver, lungs, leukemia, oral, ovary, and prostate, were largely studied by other authors [58,61–66]. In the present work, the metabolic activity was quantified by the conversion of resazurin to resorufin upon the contact with various concentrations of APE (0 to 1000 µg/mL) for 24 h. It is important to mention that the resazurin test is based on the ability of living cells to transform resazurin to resorufin [67]. This ability is correlated with cell viability and cell number/proliferation. The basis for this understanding is that the higher the conversion of the dye, the higher is the cell number. So, taking into consideration this fact, it is possible to interpret the results observed as the extracts’ influence on cellular proliferation. The four cell lines showed a dose-response dependent effect (Figure 5). Nonetheless, the behavior of non-cancer L929 cells was different from that of tumour cells (A549, HeLa and Caco-2). Extracts at low concentration (8 to 73 µg/mL) favored L929 metabolic activity, while, for the same concentration, the tumour cells exhibited a reduction on their metabolic activity, which may be an indication of low proliferation. The most important finding was the ability of the extract to act differently on can- cer cells, as these were negatively influenced and the non-tumour cells were not. These facts are confirmed by the lower IC50 values for tumour cells (HeLa 169.2 µg/mL; A549 635.9 µg/mL; Caco-2 670.1 µg/mL) while the non-tumour cells present a higher IC50 (L929 908.6 µg/mL). g p ll b l 3.4.3. Cell Viability mention that the re o resorufin [67]. T This result corroborates those obtained in this study, in which even at higher doses APE show low toxicity. These results indicate that these extracts are safe for human con sumption [2]. To this day, cancer remains one of the leading causes of death worldwide. In thi sense, the quest for safer strategies to be applied either as mono or adjunctive therapy Figure 5. Cellular viability (%) of APE against normal mouse fibroblast (L929), hum adenocarcinoma (Caco-2), human lung cancer (A549), and human cervix epithelioi (HeLa). The four cell lines showed a dose response dependent effect (Figure 5) N Figure 5. Cellular viability (%) of APE against normal mouse fibroblast (L929), human colorectal ade- nocarcinoma (Caco-2), human lung cancer (A549), and human cervix epithelioid carcinoma (HeLa). Similar results were described by other authors, which showed that avocado ethanolic extract by-products did not have a toxic effect on mouse macrophage RAW 264.7 cells. This cytotoxic effect in normal fibroblasts, reporting IC50 values of 908.6 µg/mL. Similar results were described by other authors, which showed that avocado e nolic extract by-products did not have a toxic effect on mouse macrophage RAW 2 cells. This result corroborates those obtained in this study, in which even at higher d APE show low toxicity. These results indicate that these extracts are safe for human sumption [2]. To this day, cancer remains one of the leading causes of death worldwide. In sense, the quest for safer strategies to be applied either as mono or adjunctive the Figure 5. Cellular viability (%) of APE against normal mouse fibroblast (L929), hum d i (C 2) h l (A549) d h i ith li Figure 5. Cellular viability (%) of APE against normal mouse fibroblast (L929), human colorectal ade- nocarcinoma (Caco-2), human lung cancer (A549), and human cervix epithelioid carcinoma (HeLa). Figure 5. Cellular viability (%) of APE against normal mouse fibroblast (L929), hu d i (C 2) h l (A549) d h i ith l Figure 5. Cellular viability (%) of APE against normal mouse fibroblast (L929), human colorectal ade nocarcinoma (Caco-2), human lung cancer (A549), and human cervix epithelioid carcinoma (HeLa) denocarcinoma (Caco-2), human lung cancer (A549), and human cervix epithelio HeLa). Similar results were described by other authors, which showed that avocado ethanolic extract by-products did not have a toxic effect on mouse macrophage RAW 264.7 cells. g p ll b l 3.4.3. Cell Viability mention that the re o resorufin [67]. T As it is possible to see, these extracts show to be highly effective against cells of cervix epitheloid carcinoma (HeLa). Moreover, based on the results col- lected, it is hypothesized that the selectivity of APE is attributed to a synergistic effect of several molecules. When analyzing the extracts’ composition, it was possible to observe that they are rich in antioxidant phenolic compounds such as catechins, quercetins, kaempferol, phenolic acids, etc. (see Table 5). Most of these compounds have a negative effect in various types of cells. For example, the findings of a study conducted by Sun et al. [68] stated that catechins can adequately inhibit growth of A549 cells via regulating its cell cycle arrest or indirectly through the p21 signaling pathway. g p g g p y In another study, epigallocatechin gallate inhibited the proliferation and activation of the epidermal growth factor receptor and human epidermal growth factor receptor-2 signalling pathways in human colon cancer cells (Caco-2, HCT116, HT29, SW480 and SW837) [69]. Some studies have indicated that extracts rich in kaempferol are associated with a decreased risk of developing some types of cancer, in particular, skin, liver, and colon. Sev- eral mechanisms of action were described for this phenolic compound including apoptosis, cell-cycle arrest at the G2/M phase, downregulation of epithelial-mesenchymal transi- tion (EMT)-related markers, and phosphoinositide 3-kinase/protein kinase B signaling pathways [69]. p y Quercetin, is a distinctive antioxidant flavonoid that has a well-documented role in management of different human cancers. Quercetin exhibits direct apoptotic effects on tumour cells and thus can prevent the development of many human cancers. The anticancer properties of quercetin were described in many in vitro and in vivo studies that involved some cell lines and animal models. Moreover, the highly toxic effect of quercetin against cancer cells is accompanied with little or no side effects or harm to normal Antioxidants 2021, 10, 1475 15 of 18 15 of 18 cells [70]. Overall, these results open the path to the potential use of APE in the medical or nutraceutical sectors. cells [70]. Overall, these results open the path to the potential use of APE in the medical or nutraceutical sectors. Data Availability Statement: Data is contained within the article. Conflicts of Interest: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. 4. Conclusions The work clearly demonstrates that UAE is a good technique for the extraction of biomolecules from by-products of the agroindustry. Upon the variables involved in this extraction method, it is possible to obtain extracts with content in phenolic and flavonoid compounds. Moreover, this technique does not result in the loss of bioactivity of the recover compounds. As it was demonstrated the APE presents high antioxidant activity and low cellular toxicity in normal cells, on the other hand this extract can negatively affect cancer cells, particularly HeLa cells. The results presented in this work confirm that APE is safe for human consumption, and can be used as a food preservative, antioxidant, or as a bioactive/functional ingredient. Furthermore, the selectivity demonstrated by APE regarding normal and cancer cells opens the opportunity for its use in the pharmaceutical area. Author Contributions: Conceptualization: B.G.; methodology, B.G. and P.F.-S.; software, B.G.; validation, B.G., P.F.-S. and B.R.-M.; formal analysis, B.G.; investigation, B.G.; resources, B.G.; data curation, B.G. and R.Y.; writing—original draft preparation, R.Y., B.G. and P.F.-S.; writing—review and editing, B.G., P.F.-S., R.Y., J.A.T. and C.M.B.; visualization, B.G. and B.R.-M.; supervision, B.G. and R.Y.; project administration, B.G.; funding acquisition, B.G. and J.A.T. All authors have read and agreed to the published version of the manuscript. Funding: The authors acknowledge the financial support received from “Xunta de Galicia” (GRC ED431C 2017/62-GRC, and Project ED431F 2020/03). These projects are partially funded by the FEDER Program of the European Union (“Unha maneira de facer Europa”). This research was also funded by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. Beatriz Gullón would like to express her gratitude to the Spanish Ministry of Economy and Competitiveness for her postdoctoral grant (Reference RYC2018-026177-I). Institutional Review Board Statement: Not applicable. Institutional Review Board Statement: Not applicable. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. Informed Consent Statement: Not applicable. Data Availability Statement: Data is contained within the article. Data Availability Statement: Data is contained within the article. g oolf, A.B.; Wibisono, R.; Farr, J.; Hallett, I.; Richter, L.; Oey, I.; Wohlers, M.; Zhou, J.; Fletcher, G.C.; Requejo-Jac igh Pressure Processing on Avocado Slices. Innov. Food Sci. Emerg. Technol. 2013, 18, 65–73. [CrossRef] References [CrossRef] Ž Š R.E.; Dhewa, T.; Moreno-Rojas, J.M. Potential Health Benefits of Plant Food-Derived Bioactive Components 2021, 10, 839. [CrossRef] Ž Š 21. 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https://openalex.org/W3123294778
https://link.springer.com/content/pdf/10.1007/s00396-020-04629-0.pdf
English
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Recent advances in stimuli-responsive core-shell microgel particles: synthesis, characterisation, and applications
Colloid and polymer science/Colloid & polymer science
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ERROR: type should be string, got "https://doi.org/10.1007/s00396-020-04629-0\nColloid and Polymer Science (2020) 298:921–935 https://doi.org/10.1007/s00396-020-04629-0\nColloid and Polymer Science (2020) 298:921–935 INVITED ARTICLE Abstract Inspired by the path followed by Matthias Ballauff over the past 20 years, the development of thermosensitive core-shell microgel\nstructures is reviewed. Different chemical structures, from hard nanoparticle cores to double stimuli-responsive microgels have\nbeen devised and successfully implemented by many different groups. Some of the rich variety of these systems is presented, as\nwell as some recent progress in structural analysis of such microstructures by small-angle scattering of neutrons or X-rays,\nincluding modelling approaches. In the last part, again following early work by the group of Matthias Ballauff, applications with\nparticular emphasis on incorporation of catalytic nanoparticles inside core-shell structures—stabilising the nanoparticles and\ngranting external control over activity—will be discussed, as well as core-shell microgels at interfaces. Keywords Microgel . Small-angle scattering . SANS . Catalysis . Responsive interfaces Introduction emulsions [11–14], nanoreactors, or smart carriers for catalyt-\nically active nanoparticles [15, 16]. Since their first synthesis in 1986 by Pelton and Chibante [1],\nso-called smart microgels are subject of a steadily increasing\nnumber of studies, and in the period from 2018 to 2019, only\non the topic of N-isopropylacrylamide (NIPAM), which is still\nthe most studied responsive polymer, about 1600 publications\ncan be found in the web of science. A lot of these publications\ndeal with smart microgels. Microgels are fascinating materials\nbecause they are able to respond to changes of external pa-\nrameters like temperature, pH, ionic strength, or external fields\nby changing their state of swelling [2–4]. This makes them\ninteresting for applications in sensors [5], optics, and colloidal\ncrystals [6–8]. Moreover, they are also potentially useful in\ndrug delivery [9], as smart surface coatings, actuators in bio-\nmedical devices [10], stabilisers in switchable Pickering Besides NIPAM, other acrylamide monomers can be used to\nmake microgels which also exhibit a so-called volume phase\ntransition temperature (VPTT). The most prominent ones are\nN-vinylcaprolactam (VCL), N-isopropylmethacrylamide\n(NIPMAM), and N,n-propylacrylamide (NNPAM) [17, 18]. However, also some other monomers appear in the literature\nfrom time to time. The main difference between the respective\nmicrogels is their different VPTT. More details about copoly-\nmer microgels can be found in a review by one of us [19]. Copolymerisation of these monomers can be used to systemat-\nically vary the transition temperature. Moreover,\ncopolymerisation with acrylic or other organic acids can be\nused to tune and enhance the properties of these colloidal gels\n[20–22]. In this area, Matthias Ballauff’s group started to con-\ntribute at the end of the 1990s of the last century [23]. At about\nthe same time, Matthias’ group also started to work on core-\nshell microgels [24]. Increasingly complex microgel architec-\ntures like core-shell structures are of growing relevance, since\nthey allow to create improved properties and additional func-\ntions like, e.g. response to several stimuli, or a particular swell-\ning behaviour. Starting from pioneering works by M. Ballauff\net al. [25–27], this approach gave rise to increased interest in\nmaking nanoparticle-microgel (NP-MG) hybrids for different\napplications in optics [28, 29] and catalysis [27]. Recent advances in stimuli-responsive core-shell microgel particles:\nsynthesis, characterisation, and applications Julian Oberdisse1 & Thomas Hellweg2 Received: 15 January 2020 /Revised: 25 February 2020 /Accepted: 25 February 2020\n# The Author(s) 2020\n/ Published online: 26 March 2020 * Thomas Hellweg\nthomas.hellweg@uni-bielefeld.de 1\nLaboratoire Charles Coulomb (L2C), University of Montpellier,\nCNRS, 34095 Montpellier, France 2\nDepartment of Physical and Biophysical Chemistry, Bielefeld\nUniversity, Universitätsstr. 25, 33615 Bielefeld, Germany Introduction At the\nend, we will conclude and give perspectives for possible fu-\nture developments. While M. Ballauff’s group continued exploiting the particu-\nlar PS core/microgel shell system as tunable carrier for catalytic\napplications as discussed in “Applications of core-shell\nmicrogels in catalysis”, many other nanoparticle core/\nthermosensitive shell systems have been created since then. The common approach is usually to introduce a surface modi-\nfication of the NPs, typically by hydrophobising silane cou-\npling agents like methacryloxypropyl-trimethoxysilane (MPS)\noffering the possibility to start the polymerisation of NIPAM or\nsimilar monomers from the surface [39]. This technique is also\nsuitable for silica or silica-coated metallic nanoparticles [39]. For example, Nun et al. studied the hydrodynamic radius of a\nsilica core/p(NIPAM) shell particle in a recent article [40], with\na focus on the cross-linking density. Their surprising finding is\nthat the size evolution of the NP hybrid with temperature may\nbe non-monotonic, presumably due to anisotropic heterogene-\nities in cross-linking. A similar silane-grafting technology has\nbeen used to formulate temperature-sensitive carbon core/\nmicrogel shell particles [41]. When direct polymer-grafting\nfrom the particles was not feasible, in some cases, silica layers\nwere formed first, followed by silane surface modification and\npolymerisation. This has been the case, e.g. for magnetic nano-\nparticles. Haematite [42] or maghemite [43] particles have been\ncovered by silica, the surface of which was then used to grow\nthe cross-linked p(NIPAM) layer. Due to the anisotropy of these\nparticles, the alignment of such systems has been studied in\nexternal fields [42]. Moreover, the aspect ratio of the particles\nis then found to be temperature-dependent, due to the isotropic\nswelling of the p(NIPAM) layer. The same pathway of grafting\non a silica layer was followed with non-NIPAM polymers and\nother magnetic particles, like, e.g. manganite [44]. Back in M. Ballauff’s group, a yolk-type encapsulation of gold NPs was\ngenerated by first growing a silica layer on gold cores, then\npolymerising the cross-linked p(NIPAM) layer, before finally\netching the silica layer. This technique thus led to individual\ngold cores freely “swimming” inside a microgel shell, without\nbeing covalently connected to it. The consequence is great col-\nloidal stability of the latter, with tuning of optical and catalytic\nproperties by the microgel swelling [45, 46]. A thorough scat-\ntering study of amine surface-modified gold cores with a\np(NIPAM) shell was proposed by Dulle et al. [28]. Introduction At about the\nsame time at the beginning of the century, doubly This manuscript is dedicated to Matthias Ballauff on the occasion of his\ntransition to the state of a very active and busy senior-professor in 2019. * Thomas Hellweg\nthomas.hellweg@uni-bielefeld.de * Thomas Hellweg\nthomas.hellweg@uni-bielefeld.de 922 Colloid Polym Sci (2020) 298:921–935 thermosensitive core-shell microgels (MG-MG) have also been\ndeveloped [30, 31]. Both NP-MG and MG-MG particles will\nbe reviewed in this article, with a particular emphasis on their\nstructural properties as seen by small-angle scattering. dependent thickness of the grafted p(NIPAM) layer both di-\nrectly in the TEM pictures, and its effect via the resulting\nrepulsion between PS cores [35]. In an earlier article, the scat-\ntering model describing such core-shell structures, based on a\nhomogeneous core surrounded by a homogeneous shell, with\nadditional terms for network fluctuations and heterogeneities,\nhas been used to compare the thermal swelling properties of\nsuch core-shell particles to the ones of macrogels [24]. This\nmodel system continuously attracted interest of scientists in\nthe field, including variations of the chemical protocol deter-\nmining the type of core-shell morphology [36–38]. A recent review has reported on the evolution of the last\n3 years, in the field of microgel synthesis, topology, biologi-\ncal applications, drug delivery, microgel packing, and theo-\nretical approaches [4]. Another review focusing specifically\noncore-shellmicrogelsdatesbackto2013[32],whileSuzuki\nand colleagues have proposed a focus review of their many\ncontributions, including heterogeneous structures like Janus\nmicrogels and microgel nanocomposites, which may have a\ncore-shell structure and will be further discussed below [33]. Here, we adopt a different point of view, starting with the\npioneeringcontributionsatthebeginningofthecentury,more\norlessfollowingtheguidanceofM.Ballauff’swork.Wethen\npropose a special focus on recent progress in understanding\npolymer-based core-shell structures stemming from scatter-\ning methods. The article is thus organised as follows. In “The\nroute to stimuli-responsive multi-domain structures”, we\nsummarise different approaches to system developments of\ncore-shell and multi-domain structures, with various organic\nor inorganic nanoparticles, up to pure polymer core-shell\nmicrogels. The section “Internal architecture of core-shell\nmicrogels” is devoted to novel insights into the structure\nandpropertiesofcore-shellmicrogels,withthedifferentscat-\ntering models developed to describe isotropic but non homo-\ngeneous structures. This is followed by “Applications of\ncore-shell microgels in catalysis” dealing with potential ap-\nplications, in particular catalysis with embedded nanoparti-\ncles, of controllable activity via the swelling state of the\nmicrogel. “Core-shell microgels at surfaces and interfaces”\ndeals briefly with core-shell microgels at interfaces. Introduction By using\na combination of approaches, these authors characterised both The route to stimuli-responsive multi-domain\nstructures With relevance to the discussion in “Internal architecture of\ncore-shell microgels”, it is noteworthy that they have used a\ndeconvolution technique for spherical symmetries of the corre-\nlation function determined by indirect Fourier transform. y\nThe technique of removing the silica at high NaOH con-\ncentrations was also used to produce hollow microgel particles\n[47], which have more recently triggered quite some interest\nin their physical properties, in terms of individual structure,\nand compression in dense assemblies. Dubbert et al. have\nreported on a detailed small-angle neutron scattering\n(SANS) modelling study of the hollow cavity [48]. The void\nis found to be smaller than the original sacrificial silica core,\nand it is big for highly cross-linked, stiff shells (but then less\nthermosensitive), whereas it becomes rather small (albeit more\nthermosensitive) in the opposite case. The authors conclude\nthat a compromise has to be sought between both properties. In further studies, they added a second outer layer, and thus\nreach multilayer particles, either core-shell-shell, or hollow-\nshell-shell (after etching) [49, 50]. Silica-p(NIPAM)-\np(NIPMAM) and void-p(NIPAM)-p(NIPMAM) are thus dou-\nble thermoresponsive. In the presence of the core particle,\nswelling is restricted by the grafting via MPS onto the silica. After etching of the core, both shells can adapt more freely to\ntemperature changes, and a clear two-step variation is found. These authors underline the interest of the shell-shell geome-\ntry: while the outer shell governs the interaction with other\nparticles and stability, the state of the inner one may influence\nthe material encapsulated in the centre of the microgel. The\nstudy of the compression of hollow microgel particles embed-\nded in dense suspensions of homogeneous microgels has been\nproposed by Scotti et al. [51]. Using SANS and contrast\nmatching of the regular microgel particles, they managed to\nspecifically observe the response of the hollow ones to pres-\nsure by the neighbouring regular particles of same elastic\nproperties. The intriguing linear swelling curves motivated structural\nstudies in our groups [59–61]. In the framework of the PhD\nthesis of Marian Cors, the detailed temperature-dependent\nstructure of the core and the shell polymers has been studied\nby SANS using isotopic labelling. The corresponding model\nand the main results will be outlined in “Internal architecture\nof core-shell microgels”. The route to stimuli-responsive multi-domain\nstructures One of the early pioneers in this field was Matthias Ballauff. In absence of photoinitiators, the seeded precipitation poly-\nmerisation of NIPAM on a non-thermosensitive nanoparticle\n(NP) surface allowed growing and cross-linking the NIPAM\nchains, with however imperfections in the grafting of the\nmicrogel on the NP [24, 34]. He and his colleagues then trans-\nferred a well-established method for the photochemical syn-\nthesis of spherical polyelectrolyte brushes to the synthesis of\ncore-shell microgels predominantly with a polystyrene (PS)\ncore and a responsive and cross-linked poly(NIPAM) shell\n[26]. This method guaranteed grafting from the core particle. The resulting dense PS core is highly visible in electron mi-\ncroscopy, and the authors could see the temperature- 923 Colloid Polym Sci (2020) 298:921–935 peculiarities of such a system was pointed out early by Lyon\net al. [54]: the shell and the core exert forces on each other, and\nunequal volume phase transition temperatures imply the trans-\nmission of stresses at the interface, and thus impact of the\nswelling of the core on the shell and vice versa. By aiming\nat a higher difference in swelling temperature combining\np(NIPMAM) with p(NNPAM), Zeiser et al. opened the road\nto an unexpected phenomenon, linear swelling [55]. Indeed,\nthe swelling curves measured through the hydrodynamic ra-\ndius show a peculiar linear domain, where the radius does not\nchange abruptly, but continuously, over a large temperature\nrange located between the two transition temperatures, of the\ncore and of the shell. As shown in Fig. 1a, this behaviour is\nrobust: normalising the hydrodynamic radius in suspension or\nthe ellipsometric thickness when adsorbed to a surface repro-\nduces the same linear swelling at intermediate temperatures\n(see also “Core-shell microgels at surfaces and interfaces”). One may note that this is only the case when the transition\ntemperature of the shell is below the one of the core—in the\ninverse case, a two-step transition is found [30]. Incidentally,\nthis remains true in other solvents, as shown by Lee and Bae\nfor a p(MMA-HEMA) in 1-propanol [56]. For comparison,\nwe have also reproduced in Fig. 1b the more classical two-step\nbehaviour observed in a system where the VPTTof the shell is\nabove the one of the core. the density profile and the internal network structure as a func-\ntion of different shelling steps increasing the shell thickness. The route to stimuli-responsive multi-domain\nstructures Besides being a force of proposition of general core-shell\nstructures, Matthias’ group also pioneered the use of NP core/\nMG shell particles as carriers for nanoparticles, in particular of\npalladium, platinum, silver, and gold [25, 62–65]. His group\naccomplished to show that core-shell particles are able not\nonly to stabilise the catalytically active particles but also to\nallow to control their catalytic activity—this will be reviewed\nin “Applications of core-shell microgels in catalysis” below. However, it is worth noting in the present section on synthesis\nthat a variety of systems has been designed where nanoparti-\ncles are generated within the pre-existing core-shell microgel\ncarrier system serving also as a nanoreactor and template. The\nmicrogel is thus created beforehand, and NPs are embedded—\non the contrary to the above discussion the NPs do not form\nthe core, and depending on the chemistry, their exact\nlocalisation may be tuned. With respect to NP-MG particles, core-shell microgels\nconsisting of both a microgel core and microgel shell [52]\nintroduce a new functionality to core-shell systems: now the\ncore also undergoes a volume phase transition, and by con-\nveying different thermal properties to the core and the shell,\ne.g. by introducing acrylic acid monomers, tunable swelling\nproperties have been achieved [53]. The step to combinations\nof acrylamides in the core and the shell was quickly mastered\nby Berndt and Richtering, who studied the swelling curves of\np(NIPAM) and p(NIPMAM) with LCSTs of 34 and 44 °C,\nused either as cores or as shells [30]. Of course, the difference\nin transition temperatures triggers new effects, the presence\nand magnitude of which however depends on the relative\nthickness of the core and shell, as well as on their strength,\ni.e. the degree of cross-linking. Berndt et al. have presented a\nSANS study of these effects in 2006 [31]. One of the Early work by Suzuki [66, 67] reported on gold NPs being\ngenerated in situ close to the core surface and eventually\nforming a gold layer of AuNPs using modified p(NIPAM-\nglycidyl methacrylate) copolymer microgels. These microgels\ncomprise epoxy groups in the core which can be subsequently Colloid Polym Sci (2020) 298:921–935 924 presence of hydrophobic domains of SDS, the particles lost\nthermosensitivity. When performing the polymerisation of\nstyrene in the swollen state (under appropriate pH conditions),\nthe PS particles are found to form a non-compact surface layer. Internal architecture of core-shell microgels The tuning of the localisation of in-microgel generated\nnanoparticles has been promoted by Suzuki’s group in the past\nyears to design new types of thermoresponsive particles, with\nthermoresponsive microgels of poly(N-isopropylacrylamide)\ncross-linked with N,N′-methylene-bis-acrylamide as cores or\nseeds for the polymerisation which are surrounded by a hard\npolystyrene shell [72–74]. Following a seeded emulsion pro-\ntocol in the presence of p(NIPAM) microgel particles, the PS\nparticles where found to form raspberry-like structures under\nhigh temperature, surfactant-free polymerisation, with howev-\ner some remaining thermosensitivity, presumably due to in-\ncomplete coverage by PS [72]. An example of TEM pictures\nillustrating such a MG particle core-shell structure is shown in\nFig. 2, for different mole percentages of styrene in the feed,\nand the SDS concentration given in the sample codes. In In a first approximation, most microgel particles are globular,\nand are conveniently described as spheres. Photon correlation\nspectroscopy (PCS) gives the hydrodynamic radius of these\nspheres, whereas small-angle scattering measures the radius\nof gyration, or the corresponding equivalent hard sphere radius. Comparison of both immediately shows that the microgel par-\nticles are in general not homogeneous hard spheres, but possess\na temperature-dependent gradient profile, with, e.g. dangling\nchains at the surface. In scattering, this is immediately visible\nin the high-q range, where deviations from a Porod q−4-law are\neasily measured. Indeed, a progressive radial decrease of den-\nsity may be caused by different monomer and cross-linker re-\nactivities: microgels are thus spatially inhomogeneous and pos-\nsess a fuzzy surface [75], unless cross-linker is added Fig. 1 Swelling curves of core-shell microgel particles. (a) p(NIPMAM) core\nwith p(NNPAM) shell in H2O. Comparison between particles in bulk (PCS)\nand on surfaces (ellipsometry), normalised to the high-temperature average of\neither the hydrodynamic radius or the ellipsometric thickness, for core cross-\nlinker contents of 10%mol. (b) p(NIPAM) core with p(NIPMAM) shell in\nD2O. Panel (a) reprinted with permission from reference [57]. Copyright\n2017 American Chemical Society. Panel (b) reprinted with permission from\nreference [58]. Copyright 2005 American Chemical Society linker contents of 10%mol. (b) p(NIPAM) core with p(NIPMAM) shell in\nD2O. Panel (a) reprinted with permission from reference [57]. Copyright\n2017 American Chemical Society. Panel (b) reprinted with permission from\nreference [58]. Copyright 2005 American Chemical Society Fig. 1 Swelling curves of core-shell microgel particles. (a) p(NIPMAM) core\nwith p(NNPAM) shell in H2O. The route to stimuli-responsive multi-domain\nstructures Under pH-induced deswelling, this layer does not become\nmore compact, but NPs seem to diffuse inside the microgel\n[73]. Finally, in a very recent contribution on the same subject,\nthe Suzuki group presented seeded polymerisation of styrene\nin presence of microgels below the volume phase transition\ntemperature [74]. While raspberry-like structures are again\nfound, the authors point out issues of colloidal stability of\nthe microgels which are related to electrostatic repulsion,\nwhich in turn also governs the location of the polystyrene\nseeds. Last but not least, noteworthy cryo-electron tomogra-\nphy images (and movies) allow understanding of the three-\ndimensional arrangement of the polystyrene particles inside\nthe microgels. modified by reaction with 2-aminoethane thiol to introduce\nSH and also NH2 groups [66, 67]. Brändel et al. optimised\ncatalytic response of silver NPs also located around the core in\ncore-shell microgels with linear thermoresponse, the structure\nof which will be further discussed below [68]. Suzuki and\nKawaguchi also achieved high loadings of in situ synthesised\nmagnetic particles in the spherical microgel core using again\ncopolymerisation of glycidyl methacrylate to introduce\nimmobilising functions [69], whereas Xu et al. provided an\nexample of a cylindrical core-shell structure loaded with mag-\nnetite particles stabilised by the shell. They thus gained an-\nisotropy on the mesoscale, which can moreover be oriented\nwith low magnetic fields [70]. By localising beta-diketone groups capable of complexing\nand reducing aureate ions in the core of core-shell microgel\nparticles, Thies et al. managed to grow individual gold NPs in\neach core [71]. Moreover, they used these particles as a seed for\nfurther growth, with anisotropic rod-like shapes at high ionic\nconcentrations, and avoiding the formation of secondary gold\nnuclei. Internal architecture of core-shell microgels Comparison between particles in bulk (PCS)\nand on surfaces (ellipsometry), normalised to the high-temperature average of\neither the hydrodynamic radius or the ellipsometric thickness, for core cross- linker contents of 10%mol. (b) p(NIPAM) core with p(NIPMAM) shell in\nD2O. Panel (a) reprinted with permission from reference [57]. Copyright\n2017 American Chemical Society. Panel (b) reprinted with permission from\nreference [58]. Copyright 2005 American Chemical Society Colloid Polym Sci (2020) 298:921–935 925 Fig. 2 Electron micrographs. a, b\nNIPAM-styrene composites\nNS200 (0.5), c, d NS200 (6.5),\nand dried on solid substrates at\n25 °C. The first number\nrepresents the styrene\nconcentration in mmol in the feed,\nthe second one the SDS\nconcentration. (a, c) FE-SEM\nimages. Scale bars are 1 μm. (b,\nd) TEM images, scale bars\nrepresent 300 nm. Reprinted with\npermission from reference [72]. Copyright 2014 American\nChemical Society continuously to reach a more even distribution [76]. In the first\npart of this article, “multi-domain” thermosensitive microgel\nstructures have been reviewed following the original pathway\nof Matthias Ballauff. Some of them are well described by a\ncore-shell structure, or, more general, a non-monotonous den-\nsity profile. As described in “The route to stimuli-responsive\nmulti-domain structures”, a particular class of core-shell\nmicrogels was obtained by the combination of largely different\nVPTTs, where the core swells first when decreasing the tem-\nperature [55]. The outstanding property of such core-shell to-\npologies [32] is the linear evolution of their radius as a function\nof temperature between the two polymer phase transition tem-\nperatures as shown in Fig. 1a [55, 57, 77]. This linear response\nmay be favourable in particular for sensors and actuators, but it\nremains unclear how this property is related to the structure of\nthe shell. A possible explanation of the limited core swelling\nbetween the two VPTTs has been proposed and has been called\nthe “corset effect” [55]. This concept claims that the shell em-\nbedding the core is not swollen at the same temperature, thus\nrestricting the volume phase transition of the core. It is unclear,\nhowever, how well this structural picture of a well-defined shell\nrestricting the core is appropriate. It is the aim of the present\nsection to review the corresponding small-angle scattering and\nmodelling approach. suited, and it is particularly useful for particles suspended in\nsolvent at various temperatures. Internal architecture of core-shell microgels This technique is capable of\nsimultaneously measuring both average particle sizes and poly-\ndispersity, as well as the local structure of macromolecules. SANS and isotopic substitution may reveal the distribution of\nmonomers within particles, as for example in core-shell\nmicrogels having one monomer deuterated, which is the ultimate\ngoal of our approach extracting radial density profiles based on a\nform-free model. In this section, we will discuss modelling\napproaches to small-angle scattering from such systems. Contrast matching through the solvent and employing isotopic\nsubstitution of either shell or core monomers enables studying\nthe monomers selectively in SANS, and thereby gives\naccess to independent measurements of their monomer\ndensity profiles. One should note that deuteration causes small\ndifferences in swelling, as published by us for p(NIPMAM) [60],\nbut its impact remains negligible far from the VPTT. We add that\nalthough small-angle scattering is not the only technique to ob-\nserve microgels [78–80], it is indeed very powerful due to the\npossibilities of deuteration allowing differentiating core and shell\npolymer, in bulk suspensions, without fluorescence labelling. Core-shell models for small-angle scattering The common point of the various fuzzy sphere models\nproposed in the literature discussed above is that predefined\nparameters fix and limit the possibilities for unexpected struc-\ntures. For example, a given number of shells may be used as a\nstarting point, with possible variation of thickness and posi-\ntion of the interfaces. In some cases, unforeseen fit results may\nmotivate an extension of the model, e.g. by adding a shell. In\nsome occasions, the choice of a given model has been guided\nby a first form-free modelling [85]. In others, the form-free\nmethod proved to be essential to discover an unusual density\ndistribution—microgels less dense in the centre—with\nultralowly cross-linked particles [86]. “Form-free” modelling\nis obtained by the construction of any general profile based on\nthe densities in (thin) concentric shells. The intensity can thus\nbe calculated easily by analytical Fourier transformation. Such\nmodels have also been applied to copolymer micelles [87]. In\nVirtanen et al. and also in our approach outlined below, the\nmethod has further been extended to include particle polydis-\npersity [86]. In the past, such approaches have been applied successfully\nto describe the structure of core-shell microgel particles inves-\ntigated by small-angle neutron scattering. The resulting scat-\ntering curves were analysed with different core-shell models\nbased on the above-mentioned concepts [30, 31, 58, 82]. In\nthese experiments, the absence of isotopic substitution did not\nallow differentiation of the core and shell monomers. Such\nmeasurements and analyses showed the presence of both\nmonomers, and appeared to endorse the intuition that the shell\nis located just outside the core—we will see below that de-\npending on the system, this is not necessarily the complete\npicture. The strength of these core-shell models is that they\nare given by analytical formulas of the radial density profiles. It is thus straightforward to Fourier transform them and com-\npare the result with the experimental intensities, and proceed\nwith fitting, needing to fix only a small number of parameters:\nthe location/radii and densities of the core and the shell, and\npossibly interfacial fuzziness [31, 82, 83]. As already\ndiscussed, by adding additional layers, core-shell-shell parti-\ncles have been synthesised. After silica core etching, hollow-\nshell-shell structures have been observed [49, 50]. Core-shell models for small-angle scattering The scattering of isotropic particles is usually described as a\nsum of terms, the first of which is linked to the density profile, The synthesis of complex architectures of microgels thus trig-\ngers the necessity of structural characterisation. SANS is well Colloid Polym Sci (2020) 298:921–935 926 while the others account for chain scattering, as well as for\nheterogeneities and dynamic fluctuations [81]. Usually, a\nLorentzian term is used to describe the internal polymer mesh,\nwith a mesh size extracted from fitting the correlation length,\nbut other polymer scattering terms like Debye functions or\ngeneralized Gaussian coils may be applied empirically [59]. Single compartment microgels (“core-only”) can be modelled\nin a first approximation by sphere scattering—one of the char-\nacteristics of which is the steep high-q Porod law, which can\nbe masked by internal and chain contributions, or by fuzziness\nof the interface, which also smears oscillations, just like poly-\ndispersity. For more complicated geometries, the density\nprofile may be defined piecewise, and constant but\ndistinct densities in the core and in the shell are an obvious\nstarting point to describe core-shell particles. Again, introduc-\ning fuzziness allows a more realistic description of the inter-\nface, and most differences between such fixed-form models\nactually stem from the type of decay describing the interfaces. Often, the decays are described by Gaussians or piecewise\npolynomials, like parabolic decays. By combining piecewise\nparabolic functions, different geometries can be constructed,\nand namely an empty shell can be described easily [31, 82,\n83]. For completeness, let us mention another model based on\nFlory-Rehner theory recently developed by Boon and\nSchurtenberger. In p(NIPAM) microgels, this model gave ac-\ncess to the non-homogeneity of the spatial distribution of\ncross-linker within microgel particles [84]. unravel the structure of hollow microgels and their precursors,\nsilica-microgel core-shell particles. By varying the isotopic\ncomposition of the solvent between light and heavy water,\nthe contributions of the silica core and of the protonated poly-\nmer layer to scattering could be varied via their respective\ncontrast. In particular, Dubbert et al. have succeeded in fitting\na single model discriminating the inorganic silica core from\nthe shell under all contrast situations [48]. Finally, by compar-\ning this result to the one of hollow microgels, the evolution of\nthe shell with the etching of the core could be followed in\ndetail [48]. Core-shell models for small-angle scattering Light scat-\ntering has been discussed qualitatively—these authors conjec-\nture that a generalisation of core-shell models with different\nshells might have been able to quantitatively account for the\nobserved intensity features, in particular for the shift in first\nminima [49]. SANS and detailed modelling has been used to Form-free density profiles of spherically symmetric\nmicrostructures In recent contributions, we have implemented a reverse Monte\nCarlo (RMC) optimisation of general, form-free density pro-\nfiles Φ(r) [59]. Such arbitrary profiles allow the description of\nSANS intensities without a priori parametrisation. The mono-\nmer density profiles evolve stochastically, driven by a χ-square\nminimisation. The aim is to reach agreement between the ex-\nperimental and theoretical scattering functions. The resulting\ndensities have been demonstrated to be robust with respect to\nstarting conditions or other simulation parameters. In a first\narticle, we have confronted the density profiles of the most\nsimple “core-only” microgels to the models of the literature,\nand a performance equivalent to the well-established\n(parabolic) fuzzy sphere model was evidenced. In this ap-\nproach, it was supposed that the microgels are polydisperse as\nmeasured by AFM, and spherically symmetric. The contribu-\ntion of polymer chains is visible in the mid- to high-q range, and\nis successfully described by the generalised coil model [88]. Our aim of understanding the outstanding linear swelling\nproperties of core-shell microgels motivated an in-depth form- 927 Colloid Polym Sci (2020) 298:921–935 free modelling of their internal microstructure. This could be\nachieved with contrast-variation SANS combined with the\ndetermination of the core and shell density profiles. Due to\nthe unexpected geometries, it was important to be able to\nanalyse the data without any a priori assumptions on the shape\nof the density profiles. Our approach combined several mea-\nsurements: at first, a pure p(NIPMAM) core (“core-only”),\nonto which either deuterated or hydrogenated p(NNPAM)\nshells have been grown. It is stressed that all cores are the\nsame in our studies [57, 59, 61, 89], i.e. the second synthesis\nstep of the shell has been performed with pre-existing cores,\nenabling thus direct comparisons. free modelling of their internal microstructure. This could be\nachieved with contrast-variation SANS combined with the\ndetermination of the core and shell density profiles. Due to\nthe unexpected geometries, it was important to be able to\nanalyse the data without any a priori assumptions on the shape\nof the density profiles. Our approach combined several mea-\nsurements: at first, a pure p(NIPMAM) core (“core-only”),\nonto which either deuterated or hydrogenated p(NNPAM)\nshells have been grown. It is stressed that all cores are the\nsame in our studies [57, 59, 61, 89], i.e. the second synthesis\nstep of the shell has been performed with pre-existing cores,\nenabling thus direct comparisons. Form-free density profiles of spherically symmetric\nmicrostructures and experimental intensity is measured by χi\n2. In the inset, the\ninitial guess and the final fit are compared to the experimental\nintensity. In order to find a physically acceptable solution to\nthis ill-posed problem, a compromise based on the L-shaped\n“stability plot” with smoothing term χr\n2 (see [86]) was sought\nby systematically varying the relative importance of fit quality\nand profile smoothness. These functions are also shown in\nFig. 3b, χT\n2 representing the virtual annealing temperature\nallowing progressive freezing of a solution. The result of our\nsimulation is a smooth volume fraction profile of monomers\nleading by Fourier transformation to an intensity prediction\ncompatible with the experimental intensity. We have first investigated the density profiles of the “core-\nonly” system synthesised using NIPMAM with a LCST of\nabout 44 °C [59], and which has been used as the core of\nthe deuterated core-shell particles later [61, 89]. We have first\nperformed PCS and direct imaging providing details on poly-\ndispersity and shape which are necessary to set parameters for\nthe SANS analysis. An example of this analysis showing the\npolymer chain and density profile parts of the scattered inten-\nsity is shown in Fig. 4a. The resulting profiles describe the\n“core-only” microgels as a function of cross-linking and tem-\nperature (shown in Fig. 4b), for subsequent comparison with\ncores within added shells. This representation of the particle\nmorphology gives direct access both to the internal density\n(which is directly linked to the amount of water) in the centre,\nand to the details of the particle interface, which is shown to\nbecome smoother with decreasing temperature. In our studies, the monomer density profile Φ(r) is defined\non Np = 30 homogeneous shells of fixed thickness set to ΔR =\n2 nm as building units. The profile Φ(r) is then transformed\ninto the scattering length density ρ(r), and ultimately into the\nscattered intensity I(q). Through the low-angle intensity and\nparticle concentration, the total number of monomers in a\nmicrogel particle is known. In some cases, interactions be-\ntween particles generate a very weak structure factor\nappearing in the low-q domain, in particular below the\nVPTT where microgels are swollen. For this reason, usually\nvery low volume fractions are measured; moreover, it has\nbeen checked that the results are virtually identical when cut-\nting off the low-q oscillations [61]. Form-free density profiles of spherically symmetric\nmicrostructures synthesized the shell with\np(NIPAM) and its VPTT of ca. 33 °C [60, 90, 91, 93, 94];\nthus, the linear region is larger in our case, extending from ca. 20 to 45 °C. These microgels are similar to the ones investi-\ngated by Zeiser [55], but they are smaller and possess H-D\ncontrast. The smaller size with respect to Zeiser et al. allows\nmeasuring the entire form factor in a standard small-angle\nscattering experiment, and thus gives access to a more detailed\nanalysis of the measured intensities as described below. It\nbecomes thus thinkable that the underlying nature of the corset\neffect may be understood on a structural basis. For the H core/\nD shell microgels, measurements in 12 v%/88 v% H2O/D2O\nare of particular interest. They have been designed to contrast-\nmatch the deuterated shell polymers and investigate the core\nstructure in presence of the invisible shell chains. Recent data\nfrom IR-spectroscopy indicated interpenetration of the core with the shell polymers [77], further motivating a detailed\nlook into the spatial extension of both monomers. It is again\nunderlined that the “core-only” microgel particles investigated\nin our previous paper are identical to the ones studied here, i.e. the shell synthesis has been performed with the same samples\nas in [59], and otherwise identical conditions as in the article\nby Zeiser et al. [55]. We have measured a series with various\ncore cross-linker contents (CCC), for several temperatures\nranging from 15, 30, 35, 40, and finally 55 °C, encompassing\nthe VPTT of core and shell polymers. As illustrated in Fig. 5a, the unexpected result of our anal-\nysis is that the cores embedded in core-shell microgels occupy\na larger space than the original “core-only” microgels [61]. Due to conservation of monomer numbers—this is exactly\nthe advantage of using the same cores—the cores possess\nthe same mass and thus the same low-q intensity in absence\nof interaction. They are thus characterised by a lower volume\nfraction, which contradicts the prediction of core compression\nby the (hypothetical) corset effect. This unexpected experi-\nmental result could only be rationalised by swelling of the\ncore by the shell monomers. Fig. 4 a Fitted chain and profile contributions to scattered intensity of a\nmicrogel (CC = 10 mol%) at 55 °C. b Density profiles of the H-\np(NIPMAM) core with a CCC of 10 mol% in D2O. Adapted with\npermission from reference [59]. Form-free density profiles of spherically symmetric\nmicrostructures The physical model and the elementary RMC steps of the\nalgorithm are illustrated in Fig. 3a. Several different initial\nconditions in terms of distributions of monomers across the\nshells have been produced in order to verify the robustness of\nour approach. The progression of the algorithm is shown in\nFig. 3b. Monte Carlo steps are performed by random moves of\ngroups of Nmove monomers from any shell to another, respect-\ning maximum packing of 100%. This quantity is seen to be\ndecreased to one with simulation time, progressively fine-\ntuning the profile. The deviation between the theoretical curve In a following paper, we have reported on the synthesis and\nscattering analysis of particles made of a p(NIPMAM) core\nand a p(NNPAM) shell [61]. These experiments have been set\nup to verify the spatial structure of the core embedded in a\nshell. We have based these measurements on the NIPMAM\ncore monomer used by Berndt et al. (VPTT ≈45 °C) [18, 60,\n83, 90–92], but have taken NNPAM monomer (VPTT ≈ Fig. 3 a Shell model of average microgel particle indicating moves of\ngroups of monomers between shells. b Simulation parameters as a\nfunction of the number of MC steps (χi\n2, χT\n2, Nmove, the number\nmonomers moved in one step, as indicated in the legend. The lowest\nvalue is (1). Once χ2 falls below 1 the profiles and fits are averaged\nover the next 100,000 steps. In the inset, the initial guess for the\nintensity (in red) and the final simulation result (in green) are compared\nto the experimental intensity (black). Reprinted with permission from\nreference [59]. Copyright 2018 American Chemical Society Fig. 3 a Shell model of average microgel particle indicating moves of\ngroups of monomers between shells. b Simulation parameters as a\nfunction of the number of MC steps (χi\n2, χT\n2, Nmove, the number\nmonomers moved in one step, as indicated in the legend. The lowest\nvalue is (1). Once χ2 falls below 1 the profiles and fits are averaged over the next 100,000 steps. In the inset, the initial guess for the\nintensity (in red) and the final simulation result (in green) are compared\nto the experimental intensity (black). Reprinted with permission from\nreference [59]. Copyright 2018 American Chemical Society 928 Colloid Polym Sci (2020) 298:921–935 23 °C) [60] for the shell synthesis, thereby generating the\nlinear swelling. Berndt et al. Form-free density profiles of spherically symmetric\nmicrostructures Copyright 2018 American Chemical\nSociety In the same paper, we have estimated the shell profiles\nwithout having the corresponding measurements with core-\nmatching [61]. This was achieved by comparing the H-H with\nthe H-D monomer density profiles, which by subtraction pro-\nvide the D-profile. Based on the assumption that H-H and D-D\nsyntheses gave rigorously identical particle size distributions,\nthe location of the monomers of the shell and thus their radial\ndensity profile could be estimated indirectly. In a third article,\nwe have then directly measured the radial density profile of\nthe shell monomers by contrast matching the hydrogenated\ncore monomers in 77 v%/23 v% H2O/D2O solvent mixtures. The resulting SANS curves have been analysed by applying\nour form-free multi-shell RMC procedure to the data, and the\nresult is shown in Fig. 5b [89]. From the comparison of Fig. 5a and b, which have been\nobtained on the same microgels for different solvent mixtures\n(different scattering contrast), it results that the core mono-\nmers are diluted in the centre and therefore extend further\ntowards the outside. This is caused by the presence of the\n(so-called) shell monomers, which are seen in Fig. 5b to reach\ndeeply into the core. The shell monomers form both a small\nexternal shell and an internal insoluble skeleton with a density\ngradient which restricts the swelling of the core once its VPTT\nis reached. For comparison, a homogeneous blend of core and\nshell monomers within the microgel particle would generate a\nsingle swelling step, whereas regions of varying monomer\nratio would respond at different temperatures. It would be\ninteresting to conceive a mechanical model describing the\nswelling and shrinking of such heterogeneous microgel parti-\ncles. Indeed, one may conjecture that it is this gradient struc-\nture which causes the linear swelling between the VPTTs of\nthe monomers involved. Moreover, it can be guessed that the Fig. 4 a Fitted chain and profile contributions to scattered intensity of a\nmicrogel (CC = 10 mol%) at 55 °C. b Density profiles of the H-\np(NIPMAM) core with a CCC of 10 mol% in D2O. Adapted with\npermission from reference [59]. Copyright 2018 American Chemical\nSociety Fig. 4 a Fitted chain and profile contributions to scattered intensity of a\nmicrogel (CC = 10 mol%) at 55 °C. b Density profiles of the H-\np(NIPMAM) core with a CCC of 10 mol% in D2O. Applications of core-shell microgels\nin catalysis One of these systems, shown in Fig. 6, exhibits excellent\nre-usability and even after the fifth catalytic cycle there is\nnearly no loss in activity observable. In between the catalytic\nreactions, the hybrids are separated from the reaction mixture\nusing centrifugation steps. The use of core-shell microgels in catalysis was pioneered by\nthe Ballauff group [15, 16, 25, 27, 62, 95, 96] and still repre-\nsents an active area of research which is close to potential\napplications. Especially in catalysis based on metal\nnanocrystals, core-shell microgels are very useful, since they\nstabilise the nanoparticles and prevent aggregation. This al-\nlows for an easy separation of the hybrid particles from the\nreaction mixture which enhances largely the re-usability of the\ncatalysts and leads to a straightforward work-up of the reac-\ntion mixture. This topic was addressed by Suzuki and co-\nworkers [97]. Shuli Dong and co-workers [98] have prepared another\ncore-shell system which can be used for catalysis. The hard\ncore of this system consists of silica-coated Au nanorods\nwhich are used as seeds in the microgel synthesis. As in some\nof our old works, MPS is used to enhance the incorporation of\nthe inorganic core into the shell [39, 99]. In addition to\nNIPAM, the authors use 1-vinlyimidazole as comonomer. This enhances the binding of spherical gold NPs which the\nauthors generate from HAuCl4 by reduction using NaBH4 in\npresence of the core-shell microgels. These particles present a\nhierarchically organised functional structure and the nanorod\ncore provides the possibility to shrink the particles by irradia-\ntion in the near-infrared (see also related works by\nKumacheva et al. [100, 101]). Hence, light can be used to\nexternally control the degree of shrinking of the shell of these\nparticles and hence, to control the activity of the spherical Au\nNPs embedded in the shell. Shuli Dong et al. also use the\nreduction of p-nitrophenol to measure the catalytic activity. Moreover, as also already shown by Matthias Ballauff and\nco-workers, the responsive hydrogel part of such hybrid ma-\nterials can be used to produce non-Arrhenius behaviour which\nis a sign for the control of the catalytic activity [25, 27, 63, 95]. Meanwhile, several authors tried to improve the carrier parti-\ncles, and the recent publications in this context will be pre-\nsented in the following. As already mentioned, Suzuki et al. Form-free density profiles of spherically symmetric\nmicrostructures Adapted with\npermission from reference [59]. Copyright 2018 American Chemical\nSociety Colloid Polym Sci (2020) 298:921–935 929 Fig. 5 Results of SANS analysis (CCC = 10%mol). a Density profiles of\nthe core monomers of the H-p(NIPMAM) core D7-p(NNPAM) shell\nsystem with an index-matched shell (H2O/D2O = 12 v%/88v%). The\nfigure was reproduced from [61]. b Density profile of the D7-\np(NNPAM) shell monomers of same system with contrast matched core\n(H2O/D2O = 77 v%/23v%). Figure 5 b was reproduced from [89] with\npermission from the The Royal Society of Chemistry p(NNPAM) shell monomers of same system with contrast matched core\n(H2O/D2O = 77 v%/23v%). Figure 5 b was reproduced from [89] with\npermission from the The Royal Society of Chemistry p(NNPAM) shell monomers of same system with contrast matched core\n(H2O/D2O = 77 v%/23v%). Figure 5 b was reproduced from [89] with\npermission from the The Royal Society of Chemistry Fig. 5 Results of SANS analysis (CCC = 10%mol). a Density profiles of\nthe core monomers of the H-p(NIPMAM) core D7-p(NNPAM) shell\nsystem with an index-matched shell (H2O/D2O = 12 v%/88v%). The\nfigure was reproduced from [61]. b Density profile of the D7- p(NNPAM) shell monomers of same system with contrast matched core\n(H2O/D2O = 77 v%/23v%). Figure 5 b was reproduced from [89] with\npermission from the The Royal Society of Chemistry linear swelling and shrinking property is intimately related to\nthe exact shape of the density gradient. five different hybrid systems with Au NPs were made. Also,\nSuzuki et al. use the reduction of p-nitrophenol as model re-\naction to follow the activity of the catalyst. Hence, the results\nare nicely comparable to the works by Ballauff et al. Applications of core-shell microgels\nin catalysis have prepared core-\nshell poly (NIPAM-co-glycidylmethacrylate) microgels with a\nrigid core mainly consisting of the glycidyl methacrylate\n(GMA) comomer [97]. The core-shell structure is obtained\nin a simple one-pot precipitation polymerisation due the faster\npolymerisation of GMA. In some cases, in a different reaction\nstep, the authors added 2-amino-ethanol to the reaction mix-\nture leading to a localisation of positive charges at the inter-\nface between GAM core and p(NIPAM) shell. This is after-\nwards helpful to generate catalytically active nanoparticles\n(NPs) which are localised at this internal interface. In total, Another article which also uses the same model reaction\nwas published in 2019 by Tzounis and co-workers [102]. In\nthis work, the authors describe the formation of a hierarchi-\ncally ordered core-shell microgel with a core made of silver\nand gold covered by a cross-linked p(NIPAM-co-allylamine)\nshell. In this thermoresponsive shell, silver nanoparticles are\ngenerated by reduction and prevented from bleeding by the\nallylamine. Hence, the particles have the following structure:\nAuAg@p(NIPAM-co-allylamine)@Ag. The distribution of 930 Colloid Polym Sci (2020) 298:921–935 Fig. 7 High-resolution TEM (a) and STEM (b) image of the particles\nprepared by Yang et al. The STEM-EDS image nicely reveals the\ndistribution of the silver nanoparticles in the hybrid core-shell\nmicrogels. Reproduced with permission by Springer Nature from\nRef. [96] the Ag particles inside the polymer shell is described by the\nterm “satellites” by the authors. The AuAg cores are obtained by first making a\nAu@p(NIPAM-co-allylamine) system and subsequently over-\ngrowing the gold cores with silver. In the reduction of p-nitro-\nphenol, this new structure seems to have superior turnover\ncompared to other microgel nanoparticle hybrids and very\nhigh-rate constants are achieved. Another way to achieve stronger persistence of the nano-\nparticles in the microgel network is the use of carboxylic acid\ngroups. Based on this idea, Yang et al. have prepared core-\nshell microgels with carboxylic acid groups in the shell [103]. The microgel particles have thus a p(styrene-co-NIPAM) @\np(NIPAM-co-methacrylic acid) structure and are made in a\ntwo-step synthesis. The shell has a remarkably high nominal\nmethacrylic acid content of 30 mol% with respect to NIPAM. Following the synthesis, the core-shell microgels were dried\nand redispersed in ethanol. In this medium, the authors re-\nduced [Ag(NH3)2]+ to generate the Ag NPs. The obtained\nhybrid particles were characterised by TEM and Fig. 7a shows\na typical image. In Fig. 7b, a STEM-EDS image is shown. Applications of core-shell microgels\nin catalysis Here, the silver particles appear as red dots. The silver parti-\ncles are mainly formed in the shell indicating that the\nmethacrylic acid has an influence on the Ag localisation. Also, Yang et al. have used the reduction of p-nitrophenol to\nstudy the catalytic activity of the new core-shell hybrid\nmicrogels, and the observed behaviour is similar compared\nto the findings presented in Matthias Ballauff’s pioneering\nworks on this topic. However, the swelling curves of these\nparticles seem to exhibit a two-step transition which is differ-\nent compared to the PS@p(NIPAM) particles used by\nMatthias. Fig. 7 High-resolution TEM (a) and STEM (b) image of the particles\nprepared by Yang et al. The STEM-EDS image nicely reveals the\ndistribution of the silver nanoparticles in the hybrid core-shell\nmicrogels. Reproduced with permission by Springer Nature from\nRef. [96] were used: p(NIPAM-co-AAc)@p(NNPAM), p(NIPMAM-\nc o - A A c ) @ p ( N N PA M ) , a n d p ( N N PA M - c o -\nAAc)@p(NNPAM). In all cases, the core contained acrylic\nacid as comonomer to improve the binding of the metal\nNPs. In this context, the swelling behaviour of the carriers\nand the stability of silver NPs inside the polymer network\nwas investigated by photon correlation spectroscopy, trans-\nmission electron microscopy, and by following the surface\nplasmon resonance of the NPs. Depending on the cross- were used: p(NIPAM-co-AAc)@p(NNPAM), p(NIPMAM-\nc o - A A c ) @ p ( N N PA M ) , a n d p ( N N PA M - c o -\nAAc)@p(NNPAM). In all cases, the core contained acrylic\nacid as comonomer to improve the binding of the metal\nNPs. In this context, the swelling behaviour of the carriers\nand the stability of silver NPs inside the polymer network\nwas investigated by photon correlation spectroscopy, trans-\nmission electron microscopy, and by following the surface\nplasmon resonance of the NPs. Depending on the cross- Also, one of us has recently started to work on catalytically\nactive core-shell microgels [68] using carboxylic acid groups\nto achieve better fixation of the metal NPs as well. In this\nwork, acrylamide-based, thermoresponsive core-shell\nmicrogels with a linear phase transition region are exploited\nas improved carriers for catalytically active silver nanoparti-\ncles. The particles are slightly different compared to those\ndescribed in [57]. The following general microgel structures Fig. Applications of core-shell microgels\nin catalysis 6 Image of the successful system from the work of Suzuki et al. This core-shell system shows excellent re-usability as catalyst. Reproduced from\nRef. [97] (Open Access Publication in ACS Omega) Fig. 6 Image of the successful system from the work of Suzuki et al. This core-shell system shows excellent re-usability as catalyst. Reproduced from\nRef. [97] (Open Access Publication in ACS Omega) 931 Colloid Polym Sci (2020) 298:921–935 linker content of the microgel core, very good stability of the\nNPs inside the microgel network was observed, with nearly no\nbleeding or aggregation of the NPs over several weeks for\ncore cross-linker contents of 5 and 10 mol%. The architecture\nof the hybrid particles in the swollen state was investigated\nwith cryogenic transmission electron microscopy. The parti-\ncles exhibit a core-shell structure, with the silver NPs located\nmainly at the interface between the core and shell. Such a\nhybrid architecture was not yet used before and leads to im-\nproved stability of the Ag nanocrystals inside the microgels. Also, in this work, reduction of p-nitrophenol was used as\nmodel reaction. By studying the reaction at different temper-\natures, a good switchability of the catalytic activity was re-\nvealed as shown in Fig. 8. in catalysis. In addition to these topics, core-shell microgels\ndeposited on surfaces, e.g. as actuators or at interfaces to make\nsmart emulsions are of growing relevance. This is of course\nrelated to the growing interest in adsorbed microgels and smart\nPickering emulsions in general [105]. In this context, recent\nwork was published by Yi Gong and co-workers [106]. These\nauthors studied the interfacial rheology of core-shell microgels\nat the decane-water interface. The particles were p(NIPAM-co-\nAAc)@poly-2,2,2-trifluoroethyl methacrylate (PTFMA) core-\nshell systems and the authors measured the interfacial pressure\nin a Langmuir trough. The microgel monolayers at the oil-water\ninterface were exposed to compression expansion cycles. The\nwork shows that the elastic behaviour of the monolayer is dom-\ninated by the properties of the shell. Also, Vasudevan and co-workers have studied core-shell\nmicrogels in this case with silica cores of variable diameter\nand p(NIPAM) shells of variable thickness with respect to\ntheir behaviour at the oil-water interface [107]. First, the au-\nthors presented a theoretical model for the wetting behaviour\nof this type of inorganic-organic core-shell microgel as a func-\ntion of the specific geometrical and compositional features of\nthe different particles. Applications of core-shell microgels\nin catalysis The model is in line with experimental\nfindings showing that the occupied area per core-shell\nmicrogel is strongly dependent on both varied parameters,\nnamely the core size and shell thickness. Below a critical shell\nthickness, the cores are found to be located in a position where\nthey just touch the oil-water interface. Beyond a critical shell\nthickness, the core detaches from the interface. Compared to\nhard sphere particles at the oil-water interface such hard-soft\nhybrids exhibit a subtle interplay between position at the in-\nterface, interfacial dynamics, and might have interesting ap-\nplications in interfacial rheology. This is in line with the ob-\nservations by Yi Gong et al. [106]. Similar to previous works, the obtained Arrhenius plots\nshow that the swelling of the core and shell can influence\nthe catalytic activity of the silver nanoparticles. As mentioned\nbefore, the cross-linker content of the core seems to be a very\nimportant parameter for the switchability of the catalytic ac-\ntivity. A higher cross-linker content of the core appears to be\nconnected to a stronger influence of the carrier swelling/\nshrinking degree on the catalytic activity of the silver NPs. Besides the often used reduction of p-nitrophenol, also\nCongo red was used in a recent example of silver NPs in PS\ncore/MG shell particles, where the NPs can be located only in\nthe shell. Dyes are a major problem in regions with intense\ntextile production due to release in the environment. Especially, Congo red is problematic since it is harmful for\nmammals. Hence, it would be desirable to have an efficient\nprocedure to decompose this dye. The work by Naseem et al. reveals an enhanced reduction efficiency of Congo red by this\nparticular core-shell microgel dispersion type [104]. Besides the behaviour of core-shell microgels at liquid-\nliquid interfaces, their behaviour at solid surfaces has also\nbeen studied. This topic is of great relevance when applica-\ntions as sensors or actuators are envisaged. In a work on par-\nticles made of a p(NIPMAM) core and a p(NNPAM) shell, we\nhave shown that these core-shell microgels still exhibit a linear Core-shell microgels at surfaces\nand interfaces In the previous sections, we have already discussed structure\nand properties of core-shell microgels and also their application PNN10@PNN (right). Especially the last system shows a drastic change\nof the reaction rate. Reproduced from reference [68], American Chemical\nSociety ACS Omega Fig. 8 Arrhenius plots for the different synthesised microgels showing\nthe enormous influence of the swelling/shrinking state of the core-shell\nparticles on the activity of the Ag NPs. The figure presents the hybrid\nsystems based on PNI10@PNN (left), PMAM10@PNN (middle), and\nPNN10@PNN (right). Especially the last system shows a drastic change\nof the reaction rate. Reproduced from reference [68], American Chemical\nSociety ACS Omega PNN10@PNN (right). Especially the last system shows a drastic change\nof the reaction rate. Reproduced from reference [68], American Chemical\nSociety ACS Omega Fig. 8 Arrhenius plots for the different synthesised microgels showing\nthe enormous influence of the swelling/shrinking state of the core-shell\nparticles on the activity of the Ag NPs. The figure presents the hybrid\nsystems based on PNI10@PNN (left), PMAM10@PNN (middle), and 932 Colloid Polym Sci (2020) 298:921–935 swelling behaviour even if confined to a solid interface (Si-\nwafer) [57]. In this work, we have used ellipsometry to mea-\nsure the film thickness as a function of temperature while the\nwafers were immersed in water. Such surface coatings might\nbe suitable actuating units in, e.g. etalons [108] giving rise to a\nlinear piezo-like response. Related to this, it is of course inter-\nesting to study adsorbed core-shell microgels with respect to\ntheir mechanical properties and changes. According to\nSchulte el al., this can be done by nano-indentation experi-\nments [109]. For sensing applications, adsorbed core-shell\nmicrogels can be used as templates for making composite\nfilms for surface enhanced Raman scattering (SERS). This\nwas shown by Sen Yan and co-workers using poly(styrene-\nco-N-isopropylacrylamide)@polyacrylic acid microgels\nwhich were deposited in an ordered array and subsequently\nsputtered with an Au film [110]. Such a process yields very\nnice highly ordered surface coatings. This is shown in Fig. 9. scattering techniques and in particular small-angle scattering\nwith simulation-aided structural analysis coincides with our\nown research interests over the past years. Core-shell microgels at surfaces\nand interfaces Other topics which\nmay be looked at as related, like protein or enzyme adsorption\nonto microgels also studied by Matthias Ballauff [16, 111,\n112] have not been included in this review for lack of space,\nalthough other pioneering studies have been recently pub-\nlished by other groups active in this field [50, 113]. Due to our inclination towards scattering techniques, a trait\nof character we share with Matthias, we have mostly restricted\nourselves to core-shell particles of spherical symmetry. Naturally, nanorod structures as studied by Dong et al. [114], the groups of Dietsch and Schurtenberger [42, 43],\nand the ones of Ballauff and Müller [70] can also be\napprehended in detail by scattering due to the high degree of\nsymmetry. Computer simulations have certainly not been\ntreated here at the level they deserve, as they now allow to\nfollow the formation of complex topologies in detail\n[115–118]. Finally, self-assembly of microgels, as well as their\ninterfacial activity and their possible application as switchable\ncell culture substrates for vertebrate cells have also been omit-\nted [119]. Fig. 9 The upper row (images a,\nb) shows SEM micrographs of a\nPSN@PAA monolayered\nfilm. Images c, d show a\nPSN@PAA/Au composite film.\nThe insets show the macroscopic\noptical appearance of the prepared\nfilms. The obtained hybrid film\nexhibits excellent SERS\nenhancement factors and are\nshown to be re-usable several\ntimes for sensing without any loss\nof performance. Reproduced with\npermission from reference [110].\nCopyright 2020 Elsevier Conclusion and perspectives On the occasion of this special issue in honour of the contri-\nbutions of Matthias Ballauff and his group to the field of\ncolloid and polymer science, we have organised this review\non core-shell thermosensitive microgel particles taking contri-\nbutions by Matthias and co-workers as starting point and guid-\nance. We have deliberately focused our article on either soft\ncopolymer microgel core-shell structures, or microgel shells\ngrown onto hard nanoparticle cores, as recent progress using If one looks at recent progress in the field of microgels, one\ncan only be surprised by the liveliness of the subject, several\ndecades after their discovery, and at least 20 years of in-depth\nstudies. Current directions of research seem to develop to-\nwards more complex topologies, like multi-shell or hollow\nstructures with multi-responsiveness. Obviously, the main\ndriving force comes from chemical synthesis, which can Fig. 9 The upper row (images a,\nb) shows SEM micrographs of a\nPSN@PAA monolayered\nfilm. Images c, d show a\nPSN@PAA/Au composite film. The insets show the macroscopic\noptical appearance of the prepared\nfilms. The obtained hybrid film\nexhibits excellent SERS\nenhancement factors and are\nshown to be re-usable several\ntimes for sensing without any loss\nof performance. 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Electronic Health Lifestyle Coaching Among Diabetes Patients in a Real-Life Municipality Setting: Observational Study
JMIR diabetes
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Corresponding Author: Corresponding Author: Anastasija Komkova, MSc Institute of Applied Economics and Health Research Aps Ewaldsgade 3 Copenhagen, 2200 Denmark Phone: 45 28817307 Email: akom@appliedeconomics.dk KEYWORDS eHealth; diabetes mellitus; healthy lifestyles; weight reduction; obesity eHealth; diabetes mellitus; healthy lifestyles; weight reduction; obesity “...available weight loss interventions suitable to the real-world PC setting, with most research and guideline formulation conducted inside academic silos...” [5] as well as there is a “...need for long-term interventions to evaluate sustainability” [4]. The authors have previously found that eHealth lifestyle coaching providing various behavior change techniques (BCTs) such as tailored information, self-monitoring, lifestyle coaching, in-person feedback, reminders, and person-to-person support based on a strong personal relationship led to a significant Abstract Background: Internet and mobile interventions aiming to promote healthy lifestyle have attracted much attention because of their scalability and accessibility, low costs, privacy and user control, potential for use in real-life settings, as well as opportunities for real-time modifications and interactive advices. A real-life electronic health (eHealth) lifestyle coaching intervention was implemented in 8 Danish municipalities between summer 2016 and summer 2018. Objective: The aim of this study was to assess the effects associated with the eHealth intervention among diabetes patients in a real-life municipal setting. The eHealth intervention is based on an initial meeting, establishing a strong empathic relationship, followed by digital lifestyle coaching and collaboration supported by a Web-based community among patients. Methods: We conducted an observational study examining the effect of an eHealth intervention on self-reported weight change among 103 obese diabetes patients in a real-life municipal setting. The patients in the study participated in the eHealth intervention between 3 and 12 months. A weight change was observed at 6, 9, and 12 months. We used regression methods to estimate the impacts of the intervention on weight change. Results: We found that the eHealth intervention significantly reduced weight among diabetes patients, on average 4.3% of the initial body mass, which corresponds to 4.8 kg over a mean period of 7.3 months. Patients who were in intervention for more than 9 months achieved a weight reduction of 6.3% or 6.8 kg. Results: We found that the eHealth intervention significantly reduced weight among diabetes patients, on average 4.3% of the initial body mass, which corresponds to 4.8 kg over a mean period of 7.3 months. Patients who were in intervention for more than 9 months achieved a weight reduction of 6.3% or 6.8 kg. Conclusions: This study brings forward evidence of a positive effect of a real-life eHealth lifestyle intervention on diabetes patients’lifestyle in a municipal setting. Future research is needed to show if the effect is sustainable from a long-term perspective. Conclusions: This study brings forward evidence of a positive effect of a real-life eHealth lifestyle intervention on diabetes patients’lifestyle in a municipal setting. Future research is needed to show if the effect is sustainable from a long-term perspective. Electronic Health Lifestyle Coaching Among Diabetes Patients in a Real-Life Municipality Setting: Observational Study Anastasija Komkova1, MSc; Carl Joakim Brandt2, MD, PhD; Daniel Hansen Pedersen3, MSc; Martha Emneus1, MSc; Camilla Sortsø1, PhD 1Institute of Applied Economics and Health Research Aps, Copenhagen, Denmark 2Research Unit of General Practice, Department of Public Health, University of Southern Denmark, Odense, Denmark 3The Maersk Mc-Kinney Moller Institute, University of Southern Denmark, Odense, Denmark JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 1 (page number not for citation purposes) Original Paper Electronic Health Lifestyle Coaching Among Diabetes Patients in a Real-Life Municipality Setting: Observational Study Anastasija Komkova1, MSc; Carl Joakim Brandt2, MD, PhD; Daniel Hansen Pedersen3, MSc; Martha Emneus1, MSc; Camilla Sortsø1, PhD 1Institute of Applied Economics and Health Research Aps, Copenhagen, Denmark 2Research Unit of General Practice, Department of Public Health, University of Southern Denmark, Odense, Denmark 3The Maersk Mc-Kinney Moller Institute, University of Southern Denmark, Odense, Denmark Komkova et al JMIR DIABETES JMIR DIABETES Komkova et al Original Paper http://diabetes.jmir.org/2019/1/e12140/ Research Design This is an observational study examining the effect of an eHealth lifestyle intervention on self-reported weight change among diabetes patients in a real-life municipality setting. Background A majority of premature deaths from noncommunicable diseases are preventable by facilitating healthier lifestyles [1,2]. Recent systematic reviews conclude that Web-based and mobile digital electronic health (eHealth) solutions can improve lifestyle behaviors [3-8]; however, they also stress that there is a lack of http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX XSL•FO RenderX JMIR DIABETES Komkova et al and May 2, 2018, (2) had registered to use the platform because of their diabetes, (3) had at least 90 days and maximum 365 days between their first and the last weight measurement registration, and (4) had no registrations of unrealistic rapid weight change (>0.5 kg/day). All data on patients were collected from the intervention database based on patients’ own and their HCPs’ registrations. weight loss of 7.0 kg during a 20-month period [9]. A refinement of this eHealth intervention (LIVA) [10] was implemented in 8 Danish municipalities between summer 2016 and summer 2018 on the basis of a number of qualitative studies [11,12]. Municipalities invest in preventive programs with the ambition of reducing health care professional (HCP) input and time per patient while still enabling tailored and effective care [2,4,13-15]. eHealth lifestyle coaching is markedly more efficient than traditional in-person meetings [16]. Intervention In this study, we applied an observational design to investigate the first outcome data on self-reported weight change among diabetes patients participating in an eHealth intervention with municipality HCPs for at least 3 months. We combine these results with literature findings regarding the impact of weight change on diabetes patients’costs in a municipality perspective to estimate the potential savings related to societal costs of diabetes. An eHealth lifestyle coaching intervention has been developed by applying the experiences from previously developed Web-based eHealth solutions used by approximately 140,000 individuals for more than 15 years on which extensive research has been conducted [6,11,16,17]. The key concepts in the eHealth intervention are listed in Textbox 1, and an overview is given in Figure 1. The aim of this study was to evaluate data regarding self-reported weight change of eHealth lifestyle coaching among diabetes patients and assess impacts associated with offering the program as tertiary prevention among diabetes patients in Danish municipalities. The intervention provides various BCT’s evidenced to be effective for changing lifestyle such as tailored information, self-monitoring, lifestyle coaching, in-person feedback, reminders, and peer-to-peer support [18]. By establishing a personal relationship initially in a face-to-face meeting, which is then continued digitally through the eHealth intervention, the intervention enables tailored care and sustained patient engagement over time with a minimal of HCP input in the process of successfully changing lifestyle and sustaining this change [6,9,16]. JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 2 (page number not for citation purposes) Setting and Study Population Participants in the intervention were introduced to the eHealth intervention by a municipal HCP during a first face-to-face meeting of approximately 45 min to 60 min. Together, the participant and the municipal HCP established a relationship and agreed on goals for diet, physical exercise, sleep, and other life areas if relevant. Goal setting is based on the specific, measurable, attainable, relevant, and timely (SMART) model according to a predefined guideline structure, described in Table 1. All advices are based on recommendations from the Danish National Board of Health. The eHealth intervention was implemented in an ongoing process in 8 Danish municipalities between summer 2016 and summer 2018. Each municipality offered the eHealth intervention within their own organizational framework with local HCPs such as dieticians, nurses, physiotherapists, and occupational therapists, with wide decision discretion resulting in a heterogeneous program setting. The study population consisted of 103 diabetes patients obese at baseline, with body mass index (BMI) ≥30, who (1) had used the eHealth platform at any time point between June 7, 2016, Textbox 1. Key concepts of the electronic health intervention. Textbox 1. Key concepts of the electronic health intervention. 1. Establishment of an empathic relationship with a health care professional (HCP) in an initial face-to-face meeting. 2. Integration of main stakeholders (HCPs in the municipalities and the patients’ personal profile through smartphone or Web-based), allowing for HCPs to look over the shoulder of the patient. 3. Intuitive design enables ease of use for both the user (<1 min for registration a day) and HCPs (5-10 min per consultation) developed through ongoing extensive and systematic user involvement. 4. Different modes of communication channels allow for active communication at all levels of prerequisites among users, creating peer-to-peer support. 5. The backend control panel, including a content library and communication templates, enables optimizing of tailored quality advices asynchronously and via short message service text messaging and video. JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 2 http://diabetes.jmir.org/2019/1/e12140/ (page number not for citation purposes) L•FO derX Establishment of an empathic relationship with a health care professional (HCP) in an initial face-to-face meeting. 2. Integration of main stakeholders (HCPs in the municipalities and the patients’ personal profile through smartphone or Web-based), allowing for HCPs to look over the shoulder of the patient. 3. Setting and Study Population Intuitive design enables ease of use for both the user (<1 min for registration a day) and HCPs (5-10 min per consultation) developed through ongoing extensive and systematic user involvement. 4. Different modes of communication channels allow for active communication at all levels of prerequisites among users, creating peer-to-peer support. 5. The backend control panel, including a content library and communication templates, enables optimizing of tailored quality advices asynchronously and via short message service text messaging and video. JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 2 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX JMIR DIABETES Komkova et al Figure 1. Overview of the eHealth intervention. The patients registered their data on a smartphone or logged into a personal profile using the internet (see Figure 2). to summarize characteristics of the study population. We reported means and SDs. We estimated weight change among diabetes patients in the periods of up to 6, 9, and 12 months. To examine the intervention impact on weight change, we used ordinary least square regression, including age, gender, and initial BMI as confounders. We investigated the effect of potential explanatory variables: number of messages sent by the patient, number of posts written in the forum, and engagement rate, which is the percentage of weeks where a patient actively uses the app out of the total weeks in the intervention. Applying t test and analysis of variance (ANOVA) tests, we compared weight change between male and female patients as well as across 3 age groups: <40 years, 40-59 years, and ≥60 years. Statistical significance was inferred at a 2-tailed P<.05. All analyses were completed using Stata version 14.1 (Stata, College Station, TX, USA). The patients filled in a daily record as well as their comments, concerns, and questions to the municipal HCP, who had access to the participant profiles through a control panel. The municipal HCP provided individual asynchronous online consultation according to the patient’s needs based on the patient’s own registrations. The municipal HCP encouraged and praised goal attainment and sought to maintain the patient motivation. Within the first 3 months, patients were guided by the municipal HCP once every week. In the following 2 months, consultations were provided every second week. After this, guidance took place monthly until 12 months. The following year, the patient proceeded to the retention phase, receiving quarterly consultations described in Figure 3. JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 3 (page number not for citation purposes) Data Analysis Every patient received personal eHealth coaching sessions from their designated health coach. The feedback given was based on the patient’s inputs on LIVA. Tailoring aTIDieR: template for intervention description and replication. bOn the basis of the study by Hoffmann et al [19]. c Komkova et al JMIR DIABETES The health care professionals (HCPs) received training in setting SMARTc goals and digital coaching. Patients receive 1 or 2 personal meetings (face-to-face or digital) with the HCP, followed by asynchronous Web-based consultations based on dialog by means of short message service text message or video. The consultations addressed the patient’s registrations, goal setting, and questions regarding diet, exercise, and lifestyle plan and took chronic diseases into consideration. The LIVA app is set up with short explanations on different functions and notifications and reminders to the patients to register and give feedback on the health coaching. The sessions provide the user with information in relation to their status, specific focus on goals, and recommendations on how to improve their behaviors. Included BCTd from CALO-REe taxonomy (hereafter referred to as BCT): provide information on consequences of the behavior in general and to the individual, goal setting: behavior and outcome, action planning, barrier iden- tification or problem solving, set graded tasks, prompt review of behavioral goals, prompt review of outcome goals, prompt rewards contingent on effort or progress toward behavior, prompting generalization of a target behavior, and provide feedback on performance. The goals and inputs described underneath are available to the patient, who can choose his or her focus area, set specific concrete goals, and keep record of specified behaviors by reporting on them on a daily, weekly, or monthly basis. This allows the user and the HCP to follow progress or setbacks as the numbers and registrations get visualized with graphs and curves. All advices from the HCP follow national guidelines from the Danish Na- tional Board of Health. Dietary goals and plans can be set at many different levels from simple changes aiming at changing 1 meal a day to more complex changes aiming at a completely new diet composition to remedy digestion problems. Goal setting and recording of type and time for executing any given physical activity. Data Analysis Outcome data were pooled across municipalities, and average findings were reported. We used a descriptive statistics approach JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 3 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX Komkova et al JMIR DIABETES Table 1. Template for intervention description and replication checklist for the electronic health lifestyle intervention. Description TIDieRa,b checklist item The health care professionals (HCPs) received training in setting SMARTc goals and digital coaching. Patients receive 1 or 2 personal meetings (face-to-face or digital) with the HCP, followed by asynchronous Web-based consultations based on dialog by means of short message service text message or video. The consultations addressed the patient’s registrations, goal setting, and questions regarding diet, exercise, and lifestyle plan and took chronic diseases into consideration. The LIVA app is set up with short explanations on different functions and notifications and reminders to the patients to register and give feedback on the health coaching. The sessions provide the user with information in relation to their status, specific focus on goals, and recommendations on how to improve their behaviors. What? Included BCTd from CALO-REe taxonomy (hereafter referred to as BCT): provide information on consequences of the behavior in general and to the individual, goal setting: behavior and outcome, action planning, barrier iden- tification or problem solving, set graded tasks, prompt review of behavioral goals, prompt review of outcome goals, prompt rewards contingent on effort or progress toward behavior, prompting generalization of a target behavior, and provide feedback on performance. eHealth coaching sessions The goals and inputs described underneath are available to the patient, who can choose his or her focus area, set specific concrete goals, and keep record of specified behaviors by reporting on them on a daily, weekly, or monthly basis. This allows the user and the HCP to follow progress or setbacks as the numbers and registrations get visualized with graphs and curves. All advices from the HCP follow national guidelines from the Danish Na- tional Board of Health. Goals and inputs Dietary goals and plans can be set at many different levels from simple changes aiming at changing 1 meal a day to more complex changes aiming at a completely new diet composition to remedy digestion problems. Dietary goals and plans Goal setting and recording of type and time for executing any given physical activity. Data Analysis The user receives advice and/or video on activities in a variety of contexts to foster physical activity as a more integrated part of the person’s life (BCT: provide instruction on how to perform the behavior, prompting generalization of a target behavior, and relapse prevention or coping planning). Physical activity goals and plans Goals on a healthy, joyful life as the patient sees it, for example, daily life with less stress, stronger social bonds with friends and family, and coping skills for diseases. Life goals Set current weight and goal for a lower or higher weight and register new measurements on a daily, weekly, or monthly basis. Weight-input When downloading the app, the user can accept that their information on steps recorded on a smartphone are im- ported directly, and tailored messages on progress toward a set goal appear simultaneously (BCT: teach to use prompts or cues). Steps-input Give daily feedback on pain, sleep, and mood, which can affect the ability to perform a given behavior (BCT: relapse prevention or coping planning). Pain, sleep, and mood-input Set goals to bring down the number of cigarettes smoked on a daily basis, leading to cessation. Smoking-input Keeping a record of specified measures expected to be influenced by the different behavior changes addressed. In LIVA, this includes blood glucose, cholesterol, and lung capacity. (BCT: prompt self-monitoring of behavioral outcome and provide information on consequences of the behavior in general and to the individual). Blood glucose, cholesterol, and lung capacity-input Online forum where the users can exchange knowledge, gain social support, and build new relationships; the health coach can add advices to the forum users (BCT: plan social support or social change). Forum Health professionals with basic training as nurses, physiotherapist, dieticians, and occupational therapists were performing the health coaching. Who provided? Individually delivered via the app or Web. How? Initial personal meeting in the health centers or digital. Then solely Web-based delivery. Where? The initial consultations with a health coach is estimated to last approximately 45 to 60 min. The following asyn- chronous eHealth coaching sessions were carried out once weekly in the first 3 months and then for maintenance every third week for the last 9 months. Hereafter, the patient can receive 2 eHealth coaching sessions and use LIVA as a personal behavioral change tool. (BCT: use of follow up prompts). When and how much? Data Analysis The user receives advice and/or video on activities in a variety of contexts to foster physical activity as a more integrated part of the person’s life (BCT: provide instruction on how to perform the behavior, prompting generalization of a target behavior, and relapse prevention or coping planning). Goals on a healthy, joyful life as the patient sees it, for example, daily life with less stress, stronger social bonds with friends and family, and coping skills for diseases. Set current weight and goal for a lower or higher weight and register new measurements on a daily, weekly, or monthly basis. When downloading the app, the user can accept that their information on steps recorded on a smartphone are im- ported directly, and tailored messages on progress toward a set goal appear simultaneously (BCT: teach to use prompts or cues). Give daily feedback on pain, sleep, and mood, which can affect the ability to perform a given behavior (BCT: relapse prevention or coping planning). mood-input Set goals to bring down the number of cigarettes smoked on a daily basis, leading to cessation. Keeping a record of specified measures expected to be influenced by the different behavior changes addressed. In LIVA, this includes blood glucose, cholesterol, and lung capacity. (BCT: prompt self-monitoring of behavioral outcome and provide information on consequences of the behavior in general and to the individual). Online forum where the users can exchange knowledge, gain social support, and build new relationships; the health coach can add advices to the forum users (BCT: plan social support or social change). Health professionals with basic training as nurses, physiotherapist, dieticians, and occupational therapists were performing the health coaching. Initial personal meeting in the health centers or digital. Then solely Web-based delivery. The initial consultations with a health coach is estimated to last approximately 45 to 60 min. The following asyn- chronous eHealth coaching sessions were carried out once weekly in the first 3 months and then for maintenance every third week for the last 9 months. Hereafter, the patient can receive 2 eHealth coaching sessions and use LIVA as a personal behavioral change tool. (BCT: use of follow up prompts). Every patient received personal eHealth coaching sessions from their designated health coach. The feedback given was based on the patient’s inputs on LIVA. aTIDieR: template for intervention description and replication. bOn the basis of the study by Hoffmann et al [19]. http://diabetes.jmir.org/2019/1/e12140/ Figure 2. Patient experience using the eHealth intervention. Figure 3. Healthcare professionals experience using the eHealth intervention. Observed Weight Change Results Majority of the study population, 88 out of 103 participants (85.4%), lost weight, whereas 15 patients (15/103, 14.6%) maintained or gained weight (Figure 4). Data Analysis cSMART: specific, measurable, agreed upon, realistic, and time-based goals. dBCT: behavior change technique. eCALO-RE: Coventry, Aberdeen, and London-Refined taxonomy [20]. JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 4 (page number not for citation purposes) JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 4 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX Figure 2. Patient experience using the eHealth intervention. Figure 3. Healthcare professionals experience using the eHealth intervention. Results Patients at Baseline On average, diabetes patients who participated in the program for 90 days or longer were obese at baseline, with 57 out of 103 (55.3%) being females. The study population has on average b i h i i f 220 d (7 3 h T bl 2) Observed Weight Change Majority of the study population, 88 out of 103 particip (85.4%), lost weight, whereas 15 patients (15/103, 14 maintained or gained weight (Figure 4). According to the examined data, on average, individuals diabetes reduced their weight by 4.78 kg or 4.3% of their in Komkova JMIR DIABETES JMIR DIABETES Komkova et al Figure 2. Patient experience using the eHealth intervention. Figure 2. Patient experience using the eHealth intervention. Patients at Baseline On average, diabetes patients who participated in the program for 90 days or longer were obese at baseline, with 57 out of 103 (55.3%) being females. The study population has on average been in the intervention for 220 days (7.3 months; Table 2). On average, diabetes patients who participated in the program for 90 days or longer were obese at baseline, with 57 out of 103 (55.3%) being females. The study population has on average been in the intervention for 220 days (7.3 months; Table 2). According to the examined data, on average, individuals with diabetes reduced their weight by 4.78 kg or 4.3% of their initial body mass, which corresponds to a 1.58-point change in BMI. Female patients lost 4.22% of the initial body mass, whereas male patients reduced their weight by 4.41% (Table 3). JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 5 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX JMIR DIABETES Komkova et al Table 2. Baseline characteristics of the study population. Statistics Characteristics 103 Individuals (n) 55.6 (10.8) Age (years), mean (SD) 57 (55.3) Female, n (%) 106.8 (18.8) Weight (kg), mean (SD) 36.0 (5.2) Body mass index (kg/m2), mean (SD) 219.9 (92, 365) Duration (days), mean (min, max) Figure 4. Observed weight change among the diabetes patients. Table 3. Weight change during the intervention according to the observation period (duration). Duration (270-365 days) Duration (180-269 days) Duration (90-179 days) Duration (90-365 days) Characteristics 39 54 97 103 Individuals (n) 21 (54) 31 (57) 53 (55) 57 (55.3) Female, n (%) 330.5 (273, 365) 240.5 (182, 269) 148.8 (92, 179) 219.9 (92, 365) Duration (days), mean (min, max) −6.78 (8.1) −6.14 (7.92) −4.31 (5.9) −4.78 (6.67) Weight change (kg), mean (SD) −6.27 (7.64) −5.56 (6.93) −3.9 (5.34) −4.3 (5.93) Weight change (% of initial weight), mean (SD) −6.78 (9.12) −5.96 (8.03) −0.91 (6.09) −4.22 (6.83) Weight change in female −5.68 (5.67) −5.02 (5.23) −3.9 (4.33) −4.41 (4.63) Weight change in male −2.24 (2.67) −2.05 (2.67) −1.43 (2.0) −1.58 (2.24) Body mass index change (kg/m2), mean (SD) Figure 5 illustrates the distribution of percentage weight change among the diabetes patients, where negative numbers indicate weight loss and positive numbers indicate weight gain. JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 6 (page number not for citation purposes) Patients at Baseline The weight change of those individuals who have registered their parameters up to 180 days was −3.9%, for those up to 270 days was −5.56%, and for those up to 365 days was −6.27% (Table 3). Figure 6 illustrates the weight change in kilos per person per day. Table 3. Weight change during the intervention according to the observation period (duration). Duration (270-365 days) Duration (180-269 days) Duration (90-179 days) Duration (90-365 days) The weight change of those individuals who have registered their parameters up to 180 days was −3.9%, for those up to 270 days was −5.56%, and for those up to 365 days was −6.27% (Table 3). Figure 6 illustrates the weight change in kilos per person per day. Figure 5 illustrates the distribution of percentage weight change among the diabetes patients, where negative numbers indicate weight loss and positive numbers indicate weight gain. http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX XSL•FO RenderX JMIR DIABETES Komkova et al Figure 5. Distribution of percentage weight change among the diabetes patients. Figure 6. Weight change among the diabetes patients in intervention. Each dot represents a weight change estimated from the weight parameters registered by each diabetes patient. The red line with grey area illustrates prediction from a linear regression of weight change on days in intervention, including the CIs. Figure 5. Distribution of percentage weight change among the diabetes patients. Figure 6. Weight change among the diabetes patients in intervention. Each dot represents a weight change estimated from the weight parameters registered by each diabetes patient. The red line with grey area illustrates prediction from a linear regression of weight change on days in intervention, including the CIs. Difference Between Patient Groups The mean weight change among male patients was –5.04 kg and among female patients was –4.56 kg; the difference of 0.48 kg between the gender groups was not significant (P=.72). The observed mean weight change among patients older than 40 years (N=9) was −4.7 kg, 40 years to 59 years (N=56) was 4 9k d 60 ld (N 38) 4 6 k W li d Impact of Intervention on Weight Change The results of regression analysis indicate that participation in intervention has a significant impact on weight change, where time in intervention is associated with weight loss, implying that an extra day in intervention corresponds to 16 g weight loss (P=.02) or about 480 g per month (Table 4). Patients at Baseline Th ddi i l l i bl i i d i h Figure 5. Distribution of percentage weight change among the diabetes patients. Figure 5. Distribution of percentage weight change among the diabetes patients. Figure 5. Distribution of percentage weight change among the diabetes patients. Figure 6. Weight change among the diabetes patients in intervention. Each dot represents a weight change estimated from the weight parameters registered by each diabetes patient. The red line with grey area illustrates prediction from a linear regression of weight change on days in intervention, including the CIs. Figure 6. Weight change among the diabetes patients in intervention. Each dot represents a weight change estimated from the weight parameters registered by each diabetes patient. The red line with grey area illustrates prediction from a linear regression of weight change on days in intervention, including the CIs. Difference Between Patient Groups Impact of Intervention on Weight Change Figure 6. Weight change among the diabetes patients in intervention. Each dot represents a weight change estimated from the weight parameters registered by each diabetes patient. The red line with grey area illustrates prediction from a linear regression of weight change on days in intervention, including the CIs. Difference Between Patient Groups The mean weight change among male patients was –5.04 kg and among female patients was –4.56 kg; the difference of 0.48 kg between the gender groups was not significant (P=.72). The observed mean weight change among patients older than 40 years (N=9) was −4.7 kg, 40 years to 59 years (N=56) was −4.9kg, and 60 years or older (N=38) was −4.6 kg. We applied 1-way ANOVA to examine mean weight change between the 3 age groups and found that the difference observed between the age groups was insignificant (P=.99). Impact of Intervention on Weight Change The results of regression analysis indicate that participation in intervention has a significant impact on weight change, where time in intervention is associated with weight loss, implying that an extra day in intervention corresponds to 16 g weight loss (P=.02) or about 480 g per month (Table 4). The additional explanatory variables were investigated with regard to the impact on weight change (kg). Table 5 presents the outcomes of the linear regression, where number of forum posts and engagement rate (%) are associated with weight loss, but results are statistically insignificant (P>.10). Figure 6. Weight change among the diabetes patients in intervention. Principal Findings Results show an average weight loss of 4.8 kg corresponding to 4.3% of initial body weight over a mean period of approximately 7 months. According to regression analysis, the weight loss is significant over time (P<.05). We found that time spent in intervention was the main driver for weight loss. Gender and age did not significantly influence the outcomes, indicating that the intervention effect is not dependent on traditional demographic characteristics, as often anticipated in lifestyle interventions [21]. Within the scope of this study, we conducted an extensive review of available literature that observes the impacts of weight reduction among the obese diabetes patients on the costs of diabetes [26-31]. Following the literature review, we expect that a 1% reduction in weight among diabetes patients corresponds to 3.1% decrease in societal costs of diabetes in Denmark, which were previously estimated by Sortsø et al [32]. The average weight loss of 4.3% among the diabetes patients within the cohort has a potential to reduce the annual diabetes costs of a single diabetes patient by 13.33%, corresponding to Euro 2676 savings per diabetes patient per year, compared with the no-intervention scenario (the costs of intervention were not included). Subtracting the implementation and running costs of the intervention, the implementation was found to be cost-effective in a municipal perspective already after 1 year of implementation [33]. Despite the anticipated impact of engagement in the app along with forum activity and messaging frequency on weight loss, the insignificant results indicate that motivation within the intervention is not equal to activity and engagement in the digital device. Further research based on a larger sample size would improve the results. Haste et al found an average weight loss of 5.4 kg for the ones who completed a 12-month Web-based weight loss intervention for men with type 2 diabetes in a previous Web-based version of the collaborative eHealth intervention in a pilot randomized controlled trial in a municipality setting [6]. Other eHealth coaching programs among diabetes patients have found weight reductions of 6.8% to 7.5% of body weight among completers after 6 to 12 months [22-24]. A review concluded a mean reduction in body weight of 3.73 kg after 12 months among 13 studies, analyzing the effect of BCTs on diet and physical activity in type 2 diabetes [25]. Patients at Baseline P value Regression coefficient Explanatory variable .03 −0.013 Time .06 −0.252 Baseline body mass index .78 −0.018 Age .43 1.079 Gender .69 0.017 Sent messages .29 −0.131 Forum posts .50 −0.024 Engagement .29 8.503 Constant Discussion This study evaluates the effects associated with a real-life eHealth lifestyle coaching intervention (LIVA) in 8 Danish ssion analyses for prediction of weight change (kg). Regression model summary: N=103; R2=.120; adjusted R2=.055. P value Regression coefficient This study evaluates the effects associated with a real-life eHealth lifestyle coaching intervention (LIVA) in 8 Danish municipalities. The observational design allows for data to reflect a real-life setting based on a substantial number of observations; results show clear tendencies of significant self-reported weight reduction among diabetes patients. This study evaluates the effects associated with a real-life eHealth lifestyle coaching intervention (LIVA) in 8 Danish municipalities. The observational design allows for data to reflect a real-life setting based on a substantial number of observations; results show clear tendencies of significant self-reported weight reduction among diabetes patients. JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 8 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ Patients at Baseline Each dot represents a weight change estimated from the weight parameters registered by each diabetes patient. The red line with grey area illustrates prediction from a linear regression of weight change on days in intervention, including the CIs. Impact of Intervention on Weight Change Difference Between Patient Groups The results of regression analysis indicate that participation in intervention has a significant impact on weight change, where time in intervention is associated with weight loss, implying that an extra day in intervention corresponds to 16 g weight loss (P=.02) or about 480 g per month (Table 4). The mean weight change among male patients was –5.04 kg and among female patients was –4.56 kg; the difference of 0.48 kg between the gender groups was not significant (P=.72). The observed mean weight change among patients older than 40 years (N=9) was −4.7 kg, 40 years to 59 years (N=56) was −4.9kg, and 60 years or older (N=38) was −4.6 kg. We applied 1-way ANOVA to examine mean weight change between the 3 age groups and found that the difference observed between the age groups was insignificant (P=.99). The additional explanatory variables were investigated with regard to the impact on weight change (kg). Table 5 presents the outcomes of the linear regression, where number of forum posts and engagement rate (%) are associated with weight loss, but results are statistically insignificant (P>.10). JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 7 (page number not for citation purposes) JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 7 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX XSL•FO RenderX JMIR DIABETES JMIR DIABETES Komkova et al Komkova et al Table 4. Results from regression analyses for prediction of weight change (kg). Regression model summary: N=103; R2=.108; adjusted R2=.071. P value Regression coefficient Explanatory variable .02 −0.016 Time .03 −0.280 Baseline body mass index .90 −0.008 Age .69 0.519 Gender .29 8.503 Constant Table 5. Results from regression analyses for prediction of weight change (kg). Regression model summary: N=103; R2=.120; adjusted R2=.055. Conclusions We found that the collaborative eHealth tool significantly reduced weight among diabetes patients, on average 4.3% of the initial body mass with potential substantial cost savings. This study is based on a study population consisting of 103 individuals with diabetes, and it brings forward evidence of a positive effect of a running municipal secondary preventive offer that targets diabetes patients. Our study establishes a framework for further evaluation of eHealth tools where new data from longer follow-up can be examined to strengthen conclusions from this study. Principal Findings This indicates that the validity of the trends observed is promising, especially given the modest investment compared with traditional lifestyle change or exercise interventions. Preventive strategies within diabetes have gained ground the past decade, for example, the Diabetes Prevention Program in the United States [22,24,34]. The National Health Service also launched a National Diabetes Prevention Program (NDPP) in 2016, which covered 75% of the nation in April 2017 [35,36]. These programs were initiated based on the expectation that lifestyle change among people at risk of or early in their diabetes will be effective in reducing the incidence of diabetes as well as late complications, thereby reducing costs. The economic assessment of the NDPP is undertaken from a 20-year perspective because of the disease structure of diabetes with http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX JMIR DIABETES Komkova et al Komkova et al risk of complications, and hence costs, increasing over time [37]. Perspectives and Implications This study reflects a natural experiment in the sense that we observe a running program implemented in a real-life municipal setting. This is a strength as well as a limitation in relation to disentangling the effect of the program. In a longer follow-up, analysis with more observations within municipalities would provide valuable insights. The findings in this study are of relevance for all HCPs working with primary and secondary prevention of diabetes. Collaborative eHealth lifestyle coaching tools offer promising new opportunities for successfully changing diabetes patients’ lifestyles. However, much remains unknown in this new era of eHealth possibilities. The results presented in this study are of importance, stressing that with a relatively modest personal resource investment, a collaborative eHealth lifestyle coaching tool can enable tailored coaching, resulting in significant weight losses among diabetes patients. We believe that these preliminary results show promising tendencies; however, there is a way yet to demonstrate sustainability of the weight loss attained as well as specific cost savings. We will investigate these issues along with long-term data arriving. Long-term evidence on sustainability of results is needed within this area. Hence, a register-based study with observation of actual costs of participants over a longer follow-up period and subsequent comparison with control population would provide important new knowledge. Furthermore, as we observe different effects of the program across municipalities, there is a need for in-depth analysis within each municipality to investigate what is decisive for the effect. Acknowledgments The study is funded by LIVA Healthcare A/S, the University of Southern Denmark, and the Region for Southern Denmark. The study is funded by LIVA Healthcare A/S, the University of Southern Denmark, and the Region for Southern Denmark. Limitations of the Study Self-reported data are always subject for reporting bias. Other studies have, however, shown that self-reported data in Web-based eHealth solutions are valid [38]. 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Clinical and economic impact of a digital, remotely-delivered intensive behavioral counseling program on medicare beneficiaries at risk for diabetes and cardiovascular disease. PLoS One 2016;11(10):e0163627 [FREE Full text] [doi: 10.1371/journal.pone.0163627] [Medline: 27706216] 23. Castro SC, Chiguluri V, Gumpina R, Abbott P, Madero EN, Payne M, et al. Outcomes of a digital health program with 22. Chen F, Su W, Becker SH, Payne M, Castro SC, Peters AL, et al. Clinical and economic impact of a digital, remotely-delivered intensive behavioral counseling program on medicare beneficiaries at risk for diabetes and cardiovascular disease. PLoS One 2016;11(10):e0163627 [FREE Full text] [doi: 10.1371/journal.pone.0163627] [Medline: 27706216] 22. Chen F, Su W, Becker SH, Payne M, Castro SC, Peters AL, et al. Clinical and economic impact of a digital, remotely-delivered intensive behavioral counseling program on medicare beneficiaries at risk for diabetes and cardiovascular disease. 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Burke LE, Wang J, Sevick MA. Self-monitoring in weight loss: a systematic review of the literature. J Am Diet Assoc 2011 Jan;111(1):92-102 [FREE Full text] [doi: 10 1016/j jada 2010 10 008] [Medline: 21185970] 37. Briggs A, Claxton K, Sculpher M. Decision Modelling For Health Economic Evaluation (Handbooks In Health Economic Evaluation). New York: Oxford University Press; 2006. 38 B k LE W J S i k MA S lf i i i i h l i i f h li J A Di A 2011 References Am J Manag Care 2014 Aug 01;20(8):e320-e329 [FREE Full text] [Medline: 25295795] JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 10 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 11 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ Abbreviations ANOVA: analysis of variance ApHER: Institute of Applied Economics and Health Research Aps BCT: behavior change technique BMI: body mass index eHealth: electronic health HCP: health care professional Edited by G Eysenbach; submitted 07.09.18; peer-reviewed by T Toro-Ramos, S Zheng; comments to author 08.10.18; r received 03.12.18; accepted 29.12.18; published 12.03.19 Please cite as: Komkova A, Brandt CJ, Hansen Pedersen D, Emneus M, Sortsø C Electronic Health Lifestyle Coaching Among Diabetes Patients in a Real-Life Municipality Setting: Observational Study JMIR Diabetes 2019;4(1):e12140 URL: http://diabetes.jmir.org/2019/1/e12140/ doi: 10.2196/12140 PMID: 30860486 ©Anastasija Komkova, Carl Joakim Brandt, Daniel Hansen Pedersen, Martha Emneus, Camilla Sortsø. Originally published in JMIR Diabetes (http://diabetes.jmir.org), 12.03.2019. This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in JMIR Diabetes, is properly cited. The complete bibliographic information, a link to the original publication on http://diabetes.jmir.org/, as well as this copyright and license information must be included. JMIR Diabetes 2019 | vol. 4 | iss. 1 | e12140 | p. 11 (page number not for citation purposes) http://diabetes.jmir.org/2019/1/e12140/ XSL•FO RenderX
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Optimizing the Load Curve of Electric Vehicle Battery Swapping Station
Elektronika ir elektrotechnika
2,017
cc-by
6,565
A. EV Charging Modes Index Terms—Battery swapping station; electric vehicle; load characteristics; optimal charge/discharge strategy. As it is mentioned above, there are mainly three charging modes for EVs at present. Their characteristics are briefly introduced as below: Wei-Qing Sun1, Yi-Ming Tan1, Lei Ye1, Shun-Feng Chen1 1Department of Electrical Engineering, University of Shanghai for Science & Technology, Jungong Rd. 516, Shanghai, China sunwq@usst.edu.cn Wei-Qing Sun1, Yi-Ming Tan1, Lei Ye1, Shun-Feng Chen1 1Department of Electrical Engineering, University of Shanghai for Science & Technology, Jungong Rd. 516, Shanghai, China sunwq@usst.edu.cn 1Abstract—To develop electric vehicle (EV) is an efficient method to deal with energy shortage and environment pollution. Based on the comparison among three battery charging modes, this paper first clarifies the advantage of battery swapping mode. Compared with normal charging mode and fast charging mode, battery swapping mode is much easier to control the charging and discharging behaviour of EVs. Reflect on the load curve, the load curve of EV battery swapping stations (EVBSS) have more potential to be optimized. Then, the profit pattern, load characteristics and effects to grid of the mode is analysed in detail. After that, an optimal charge/discharge strategy for an EVBSS is established and studied. And the optimized load curve of an EVBSS can be obtained. Furthermore, sensitivity analysis is made to improve the profit of the EVBSS. Finally, some conclusions are made, and some suggestions for electric vehicle development are prospected. charging behaviours, but also control the electricity discharging behaviours by EV battery swapping station (EVBSS). The EVBSSs can be regarded as energy storage systems, and bring benefit to power systems both in security and economy. This paper first makes a detailed comparison among the three charging modes for EVs, and focuses on an analysis of the advantage of BSM. Then, the profit pattern and load characteristics of EVBSSs are analyse, and their effects to power systems can be concluded. After that, a linear optimization model for EVBSS operation is established, and simulated on the IEEE 14-bus test system. Finally, some conclusions and perspectives are made. This research was funded by a grant (No. 51407117) from the National Natural Science Foundation of China, a grant (No. 14YF1410100) from the Yang-fan Program of Shanghai, China. Manuscript received 4 November, 2016; accepted 11 June, 2017. This research was funded by a grant (No. 51407117) from the National Natural Science Foundation of China, a grant (No. 14YF1410100) from the Yang-fan Program of Shanghai, China. I. INTRODUCTION 1. NCM, or slow charging mode. In this mode, EVs are linked and charged from normal AC power sources. This charging mode is comparatively simple, and the charging current is comparatively small. But EVs need a comparatively longer time to be fully charged. Thus, this charging mode is mainly used in residential districts or parking garages. However, as the wide distribution of charging-piles, the arbitrariness of charging behaviours are large. Power grid operators can hardly manage or forecast the charging behaviours. The development of electric vehicles (EVs) has been a consensus in response to energy shortage and environment pollution worldwide. In China, it is predicted that the retain number of automobile will be over 200 million in 2020. They will consume more than 55 % of the total petroleum consumption in the country, namely about 400 million tons every year. The energy consumption is huge, while a mass of pollution is also ineluctable. In this context, EV industry is faced with a unprecedented development opportunity. However, with the rapid incensement of EVs, if their charging behaviours are unordered, they will bring potential threats to the security and reliability of power system operation [1]. Conversely, if their charging even discharging behaviours are well ordered, EVs can safely access to power systems in a large scale, and bring benefits in the meanwhile [2]. In other words, well ordered EVs can be regarded as flexible loads in the grid, which can participate in the optimal operation of power systems [3]. 2. FCM, or emergency charging mode. In this mode, EVs are linked and charged from large-current cables of AC charging-piles. About 70 %~80 % of the full battery capacity can be charged in a fast time. This charging mode is suitable for traffic flow populated areas or in emergency. Similar with NCM, charging behaviours can also hardly be managed or forecasted in FCM. Meanwhile, due to the large charging current, the battery life will be shortened. 2. FCM, or emergency charging mode. In this mode, EVs are linked and charged from large-current cables of AC charging-piles. About 70 %~80 % of the full battery capacity can be charged in a fast time. This charging mode is suitable for traffic flow populated areas or in emergency. Similar with NCM, charging behaviours can also hardly be managed or forecasted in FCM. Meanwhile, due to the large charging current, the battery life will be shortened. 2. Manuscript received 4 November, 2016; accepted 11 June, 2017. http://dx.doi.org/10.5755/j01.eie.23.4.18715 http://dx.doi.org/10.5755/j01.eie.23.4.18715 http://dx.doi.org/10.5755/j01.eie.23.4.18715 ELEKTRONIKA IR ELEKTROTECHNIKA, ISSN 1392-1215, VOL. 23, NO. 4, 2017 B. Advantage of Battery Swapping Mode B. Advantage of Battery Swapping Mode 1 1 1 1 2 0 1 ( ) ( / ). N sell i c i f f f C a N C                (2) (2) Compared with NCM and FCM, BSM is easy to operate and maintain, and easy to manage centrally. Thus, it has been regarded as an important battery charging mode, and has a wide application prospects. On the other hand, as for the grid, EVBSS charges (buy electricity from the grid) during light-load periods in low prices and discharges (sell electricity to the grid) during heavy-load periods in high prices. Such profits can be expressed as In BSM, on one hand, BSS can charge batteries (buy electricity from the grid) during light-load periods with a comparatively low electricity price, which will help to reduce the operation cost. On the other hand, BSS can discharge batteries (sell electricity to the grid) during heavy-load periods with a comparatively high electricity price. This undoubtedly increases the BSS's revenue. Besides, such a profitable behaviour objectively realize peak load shifting, which means it also benefits the grid. 2 , , 0 1 ( / ) , M d i d c i c i i f C a TC             (3) (3) where TC refers to the charge/discharge times; d  refers to the discharging efficiency; , d i  and ,c i  refer to the average discharging and charging electricity price for the ith charge/discharge. Obviously, only when the difference between the buying and selling is larger than the battery depreciation, such a charge/discharge behavior is profitable. To the grid, EV charging/discharging management based on vehicle to grid (V2G) technology has to depend on vehicle-mounted smart chargers on the EVs to realize intelligent energy storage [4]. However, such smart chargers are difficult and complex to realized, and will increase the battery management costs. Besides, as the distribution of EVs is uncertain, intelligent energy management on single units can still not be well utilized by the grid [5]. Thus, the total profits gained of the EVBSS in the research period is 1 2 = f f + f . B. Load Characteristics of EVBSS Based on the profit pattern analysis of EVBSS above, it can be concluded that: 1. When the battery swapping demand and price are fixed, the profits from the EV owners are fixed. If the EVBSS wills to gain a larger profit, to reduce its own operation costs is the only way. That means EVBSS should reduce its battery charging costs to the greatest extent. Thus, on the promise of satisfying battery swapping demands, EVBSS should charge its battery during light-load periods in low electricity prices as far as possible. In conclusion, EVBSS can gain profits both from EV owners and grid. Meanwhile, its electricity charge/discharge behaviours objectively realize peak load shifting. Thus, EVBSS increase its profit while also improve the security and economy of grid operation. III. PROFIT PATTERN AND LOAD CHARACTERISTICS OF EVBSS 2. Under the time-of-use (TOU) or step tariff electricity price mechanisms, if the difference of electricity price between heavy-load and light-load is large enough, EVBSS can increase its profit by charging during light-load periods and discharging during heavy-load periods. The precondition is that the EVBSS has enough batteries to guarantee that such a behaviour will not affect the basic battery changing demands. The boundary condition is that the profit gained from every charge/discharge cycle is larger than the depreciation cost. Further, the load characteristics of EVBSS appear clear: 1. The load of EVBSS is ordered and controllable, and its time distribution mainly depends on the charge/discharge strategy of the EVBSS. Thus, the load of EVBSS can be regarded as a kind of flexible load. 2. Under the time-of-use (TOU) or step tariff electricity price mechanisms, if the difference of electricity price between heavy-load and light-load is large enough, EVBSS can increase its profit by charging during light-load periods and discharging during heavy-load periods. The precondition is that the EVBSS has enough batteries to guarantee that such a behaviour will not affect the basic battery changing demands. The boundary condition is that the profit gained from every charge/discharge cycle is larger than the depreciation cost. 2. Under the time-of-use (TOU) or step tariff electricity price mechanisms, if the difference of electricity price between heavy-load and light-load is large enough, EVBSS can increase its profit by charging during light-load periods and discharging during heavy-load periods. The precondition is that the EVBSS has enough batteries to guarantee that such a behaviour will not affect the basic battery changing demands. The boundary condition is that the profit gained from every charge/discharge cycle is larger than the depreciation cost. B. Advantage of Battery Swapping Mode For the above reasons, if V2G can be transfer to B2G (battery to grid), the managed and controlled objective can be transfer from single EV to EVBSS. And then, centralized management and control of EV batteries can be realized. I. INTRODUCTION FCM, or emergency charging mode. In this mode, EVs are linked and charged from large-current cables of AC charging-piles. About 70 %~80 % of the full battery capacity can be charged in a fast time. This charging mode is suitable for traffic flow populated areas or in emergency. Similar with NCM, charging behaviours can also hardly be managed or forecasted in FCM. Meanwhile, due to the large charging current, the battery life will be shortened. 3. BSM, or mechanical charging mode. In this mode, EVs swap their empty batteries in EVBSSs, and EVBSSs charges the empty batteries in other times. Usually, the charging time is arranged during the light-load periods. Thus, peak load shifting can be realized, and EVBSSs can pay a comparatively low electricity price to the grid. However, BSM puts forward comparatively high standardization requirements to battery charging technology, battery specification, interface standard, etc. At present, there are mainly three charging modes for EVs, namely normal charging mode (NCM), fast charging mode (FSM), and battery swapping mode (BSM). Different from NCM and FCM, BSM can not only control the electricity 3. BSM, or mechanical charging mode. In this mode, EVs swap their empty batteries in EVBSSs, and EVBSSs charges the empty batteries in other times. Usually, the charging time is arranged during the light-load periods. Thus, peak load shifting can be realized, and EVBSSs can pay a comparatively low electricity price to the grid. However, BSM puts forward comparatively high standardization requirements to battery charging technology, battery specification, interface standard, etc. 3 ELEKTRONIKA IR ELEKTROTECHNIKA, ISSN 1392-1215, VOL. 23, NO. 4, 2017 costs, 1 2 1 = ( / ) i c i f C      refers to the variable costs. 2) Transmission Lines p g p Then, the model established can be as: Then, the model established can be as: As for transmission lines, the total power loss during a certain period can be expressed as 24 ( ) 1 max 1 1 24 ( ) 0 1 1 ( ) ( ) 1 1 ( ) (1) 1 1 1 1 ( ) (1) 1 1 ( ) ( 1) 1 max ( ), . . , , , , w m m w m w T i d sell t t t i T i t c t t i T T i i t t t t t t i i T t t t t t t t T t t t t t i i t t F C N P W P M a N TC s t N X J K M W Z X M J N X W J N W K M K M M                                                      ( ) ( 1) 1 ( ) max 1 24 max 1 , , ( ) / , m i i t t T i t i t t W W M M TC P W C             (10) 2 2 2 2 ( ) / ( cos ), loss H H L L E R P h P h V       (7) (7) 24 ( ) 0 1 1 ( ), m T i t c t t i P M a N TC          where V refers to the node voltage amplitude; R refers to the transmission line resistance; refers to the power factor angle; H P and L P refer to the average active power during heavy-load period and light-load period respectively; H h and L h refer to the duration of heavy-load period and light-load period respectively. 1) Transformers 1) Transformers Taking the power loss calculation of double winding transformer as an example to clarify the loss reduction of peak load shifting. Assume that the apparent power of the transformer is H S and L S respectively, the short-circuit loss is k P , and the nominal capacity is N S . Then, the total power loss of the transformer during a certain period is as 2 2 2 2 2 ( ) ( ) / ( cos ) 0. loss loss E E R h k k P V           (9) (9) ELEKTRONIKA IR ELEKTROTECHNIKA, ISSN 1392-1215, VOL. 23, NO. 4, 2017 ELEKTRONIKA IR ELEKTROTECHNIKA, ISSN 1392-1215, VOL. 23, NO. 4, 2017 operators, as well as be an important basis for grid operators to analyse EVBSS loads. 2 2 cos loss R E V      IV. OPTIMAL MODEL The charging or discharging is continues, namely it will not be paused once started. The difference between , T loss E  and , T loss E  is the transformer loss reduction after peak load shifting, which should always be positive 5. The number of full-charged batteries should always satisfy the demand forecast at the beginning of a period, which means the arrival distribution will not affect the charge/discharge strategy of the EVBSS. 2 2 2 , , 2 ( ) ( ) / 0. T loss T loss k N E E P h k k S S         (6) (6) 6. The empty batteries swapped for the EVs during the ith period will be arranged at the next period. IV. OPTIMAL MODEL     2 2 , / / , T loss H N k H L N k L E S S P h S S P h        (4) Taking maximum benefits of the EVBSS as the objective 1 2 = f f + f , an optimal charge/discharge strategy model for an EVBSS in 24 hours can be established. To simplify the model, it is established under such assumptions: where H h and L h are the duration of heavy-load period and light-load period respectively. Assume that the difference between heavy-load power and light-load power is S  , namely H L S S S   ; and the heavy-load period and the light-load period is equal, namely . H L h h h   Then, if (0 1) k S k    is shifted from heavy-load period to the light-load period, the total power loss of the transformer is as 1. The research period, namely 24 hours, is divided into 24 periods, corresponds to 0:00~1:00, 1:00~2:00, … , 23:00~0:00 every day. 2. Assume that the battery capacity is C, and it need time T to be fully charged. Then, the charging power is / , cP C T  and / c c c P P   when the charging efficiency is considered. 2. Assume that the battery capacity is C, and it need time T to be fully charged. Then, the charging power is / , cP C T  and / c c c P P   when the charging efficiency is considered.       2 , 2 2 2 2 2 (1 ) / ( ) / [2 2 (1 2 2 ) ( ) ] / . T loss L N k L N k L L k N E S k S S P h S k S S P h S S S k k S P h S                        (5) 3. Assume that the batteries discharge power at their maximum power max P when sell electricity to the grid, and the actual discharging power is max max = d P P    if the discharging efficiency is considered. 4. A. Profit Pattern of EVBSS As it is mentioned above, EVBSS mainly benefits from two respects, namely the EV owners and the grid. As for the EV owners, EVBSS charges batteries during light-load periods from the grid with a comparatively low electricity price, and sells the full-charged batteries to the EV owners in a high price. The profits owned can be expressed as 1 0 1 [ / ], N sell i c i f C C a           (1) (1) 1. The load of EVBSS is ordered and controllable, and its time distribution mainly depends on the charge/discharge strategy of the EVBSS. Thus, the load of EVBSS can be regarded as a kind of flexible load. where N refers to the battery swapping demands in the research period; C (kWh) refers to the battery capacity; sell  ($/kWh) refers to the electricity sold to EV owners; i($/kWh) refers to the average charging electricity price for the ith battery; c  refers to the charging efficiency; 0 a ($) refers to the battery depreciation for a charge/discharge cycle. 2. As the electricity price under TOU or step tariff mechanisms usually has a positive relationship with load level, namely heavy load corresponds to high electricity price while light load corresponds to low electricity price, EVBSS will try its best to charge during light-load periods and discharge during heavy-load periods. Thus, EVSS can realize peak load shifting, which facilitate the security and economy of power system operation. Equation (1) can be divided into two parts as (2), where 1 1 0 =( ) sell f C a N      refers to the fixed incomes and costs, 1 2 =1 = ( / ) N i c i f C      refers to the variable costs. 3. Taking the maximum profits as the operation strategy of EVBSS, can meet the interest requirements of EVBSS 4 C. Effects to Grid 2 2 2 2 {[ (1 ) ] ( ) } cos L L P k P h P k P h R h V               As it is analysed above, EVBSS can realize peak load shifting, which can benefit the grid both in security and economy. As for the economy, peak load shifting can reduce power losses efficiently. The power loss reduction will be analysed from transformers and transmission lines respectively. 2 2 2 [2 2 (1 2 2 ) ( ) ]. L L P P P k k P       (8) (8) The difference between loss E  and loss E  is the transmission line loss reduction after peak load shifting, which should always be positive, too V. SENSITIVITY ANALYSIS The optimal solution of a mathematical model is meaningful when the mathematical model can reflect the real problem. Actually, the analysis is not finished when using the model in this manuscript yield the optimal solution, because parameters in the linear programming problem are always changing. The parameters in the model are just forecast to the future and the initial data to estimate the parameter are also changeable. From Table II, it can be found that the total batter swapping demand during the day is N = 2000. The battery swapping peaks are a bit earlier than the grid load peaks, because morning battery peak usually appears before people start their work (morning grid peak), and afternoon battery swapping peak usually appears before people get home (afternoon grid peak). Besides, EV owners should pay $6 every time for battery swapping, which includes $3.6 for the electricity price, $1.8 for the battery depreciation, and $0.6 for the EVBSS's profit. That means, the fixed income for one battery swapping is $4.2 if the electricity charging cost is not considered. The most important part of the sensitivity analysis is getting the sensitive parameters. These sensitive parameters have a great influence to the final income and the charge/discharge strategy. A standard form of the linear programming model is: max , . . , 0, Z C X s t A X B X           (11) (11) Then, case study is made under two cases. Case 1: 1100 Z  , max 400 M  ; Case 2: 1200 Z  , max 450 M  . TABLE III. EVBSS MAXIMUM DAILY PROFITS. TABLE III. EVBSS MAXIMUM DAILY PROFITS. Income and expense Case 1 Case 2 Fixed incomes / ×103$ 8.400 8.400 Profits from selling electricity / ×103$ 0.154 0.666 Total charging costs/ ×103$ 4.784 4.938 Battery depreciationa / ×103$ 0.054 0.234 Total profits F1d / ×103$ 3.716 3.894 Note: a only refers to the battery depreciation that battery buy electricity during light-load periods and sell electricity during heavy-load periods. where Z, X, C, A, B refer to the maximizes of the linear programming model, variables, coefficients of the variables in the objective function, coefficients of the variables in the constraints, constants on right-hand side of the constraints. V. SENSITIVITY ANALYSIS If the constant on the right-hand side of the constraints is changed, assumed that only one constant br is changed, from br to br’, ' r r r b = b +Δb , b is changed to b .The optimal solution is b* after b is changed, * -1 b = B b , the most favourable value of objective function is Z*, * * Z = y b , B-1 is the matrix of the decision variables in the simplex tableau, y* is the coefficient of the slack variables after b is changed. Note: a only refers to the battery depreciation that battery buy electricity during light-load periods and sell electricity during heavy-load periods. From Table III, it can be seen that both in case 1 and 2, the EVBSS gains profits from the grid by low-price-charge and high-price-discharge. The difference is that in case 2, as the EVBSS has more batteries and charging-piles, it has more opportunity to gain profits from the grid. Table IV shows the operation data of the EVBSS during 24 hours in case 2. ELEKTRONIKA IR ELEKTROTECHNIKA, ISSN 1392-1215, VOL. 23, NO. 4, 2017 ELEKTRONIKA IR ELEKTROTECHNIKA, ISSN 1392-1215, VOL. 23, NO. 4, 2017 TABLE I. OPERATION PARAMETERS OF EV BATTERIES. Index Parameter Battery capacity C/(kWh) 30 Charging power Pc/(kW) 15 Max charging power Pmax/(kW) 30 Charge/discharge efficiency/(%) 95 Battery cost/($·(kWh)-1) 240 Cycle life/(time) 4000 TABLE I. OPERATION PARAMETERS OF EV BATTERIES. , , , , t t t t t N X J K  refer to the battery swapping where where , , , , t t t t t N X J K  refer to the battery swapping demand quantity, backup battery quantity, keep-full battery quantity, keep-empty battery quantity, and electricity price during the tth period respectively; Z and max M refer to the total battery quantity and charger-pile quantity in the EVBSS respectively; N refers to the total battery swapping demands during the day. As for charging, if a battery needs Tm periods to be fully charged, then its charging process can be divided into Tm parts. ( ) t ( 1,2,..., ) i m M i = T refers to the battery quantity that at the ith charging part during the tth period. Similarly, as for discharging, if a battery needs Tw periods to be fully discharged, then its discharging process can be divided into Tw parts. ( ) t ( 1,2,..., ) i w W i = T refers to the battery quantity that at the ith discharging part during the tth period. TABLE II. ELECTRICITY PRICE, BATTERY SWAPPING DEMANDS, AND BACKUP QUANTITY IN 24 HOURS. TABLE II. ELECTRICITY PRICE, BATTERY SWAPPING DEMANDS, AND BACKUP QUANTITY IN 24 HOURS. t t λ t N t X t t λ t N t X 1 0.06 50 10 13 0.08 80 15 2 0.05 30 5 14 0.09 60 10 3 0.05 30 5 15 0.10 50 10 4 0.06 50 10 16 0.12 140 20 5 0.08 60 10 17 0.13 200 25 6 0.12 100 15 18 0.15 150 20 7 0.14 150 20 19 0.17 100 15 8 0.15 130 20 20 0.18 60 10 9 0.14 100 15 21 0.17 80 10 10 0.13 60 10 22 0.15 100 15 11 0.10 50 10 23 0.10 70 10 12 0.09 50 10 24 0.08 50 10 The optimal model established is actually a linear optimal model, and it is solved using LINGO in this manuscript. 2) Transmission Lines (10) Similarly, assume that the difference between heavy-load period and light-load period is P , namely H L P P P   ; and the heavy-load period and the light-load period is equal, namely H L h h h   . If (0 1) k P k    is shifted from heavy-load period to the light-load period, the total power loss of the transmission line is as ( ) max 1 , m T i t i M M    24 max 1 ( ) / , t t TC P W C     5 VI. CASE STUDY Assume that there an imaginary EVBSS, its battery parameters are as Table I. Load power of the EVBSS during 24 hours is shown in Fig. 1, where positive power refers to charging from the grid and negative power refers to discharging to the grid. And the TOU reflects the grid load. Usually, high electricity price corresponds to a heavy grid load, while low electricity price corresponds to a light grid load. From Table I, it can be easily found that 0 240 30 / 4000 1.8 a    $, 2 m T  h, and 1 w T h. The electricity price, battery swapping demands, backup quantity during the day are listed in Table II. 6 ELEKTRONIKA IR ELEKTROTECHNIKA, ISSN 1392-1215, VOL. 23, NO. 4, 2017 refers to the active power output of the ith generator. TABLE IV. EVBSS OPERATION DATA DURING 24 HOURS. t (1) t M (2) t M (1) t W tJ t K t (1) t M (2) t M (1) t W tJ t K 1 100 350 0 0 690 13 70 380 0 355 320 2 350 100 0 325 390 14 380 70 0 680 0 3 100 350 0 395 320 15 0 380 0 700 60 4 350 100 0 690 0 16 0 0 0 930 110 5 0 350 0 730 50 17 0 0 0 725 250 6 0 0 0 975 110 18 0 0 0 580 450 7 0 0 0 820 210 19 0 0 0 485 600 8 0 0 0 690 360 20 0 0 130 300 700 9 0 0 0 595 490 21 0 0 0 220 890 10 0 0 0 540 590 22 0 0 0 115 970 11 0 0 0 490 650 23 50 0 0 50 1020 12 380 0 0 440 320 24 350 50 0 0 740 TABLE IV. EVBSS OPERATION DATA DURING 24 HOURS. VI. CASE STUDY t (1) t M (2) t M (1) t W tJ t K t (1) t M (2) t M (1) t W tJ t K 1 100 350 0 0 690 13 70 380 0 355 320 2 350 100 0 325 390 14 380 70 0 680 0 3 100 350 0 395 320 15 0 380 0 700 60 4 350 100 0 690 0 16 0 0 0 930 110 5 0 350 0 730 50 17 0 0 0 725 250 6 0 0 0 975 110 18 0 0 0 580 450 7 0 0 0 820 210 19 0 0 0 485 600 8 0 0 0 690 360 20 0 0 130 300 700 9 0 0 0 595 490 21 0 0 0 220 890 10 0 0 0 540 590 22 0 0 0 115 970 11 0 0 0 490 650 23 50 0 0 50 1020 12 380 0 0 440 320 24 350 50 0 0 740 Fig. 1. EVBSS load power during 24 hours. TABLE IV. EVBSS OPERATION DATA DURING 24 HOURS. t (1) t M (2) t M (1) t W tJ t K t (1) t M (2) t M (1) t W tJ t K 1 100 350 0 0 690 13 70 380 0 355 320 2 350 100 0 325 390 14 380 70 0 680 0 3 100 350 0 395 320 15 0 380 0 700 60 4 350 100 0 690 0 16 0 0 0 930 110 5 0 350 0 730 50 17 0 0 0 725 250 6 0 0 0 975 110 18 0 0 0 580 450 7 0 0 0 820 210 19 0 0 0 485 600 8 0 0 0 690 360 20 0 0 130 300 700 9 0 0 0 595 490 21 0 0 0 220 890 10 0 0 0 540 590 22 0 0 0 115 970 11 0 0 0 490 650 23 50 0 0 50 1020 12 380 0 0 440 320 24 350 50 0 0 740 refers to the active power output of the ith generator. Fig. 2. Flow chart for forming the optimal simplex tableau. Fig. 1. EVBSS load power during 24 hours. Fig. 1. EVBSS load power during 24 hours. Fig. 1. EVBSS load power during 24 hours. VI. CASE STUDY From Fig. 2, it can be clearly seen that the EVBSS charges during the light-load periods and discharges or does not charge during the heavy-load periods, which realizes peak load shifting. Further, assume that the above EVBSS is accessed to the IEEE 14-bus test system [6] on bus 2. And the load multiples k in 24 hours is as shown in Table V. Fig. 2. Flow chart for forming the optimal simplex tableau. TABLE VI. COMPARISON OF SYSTEM OPERATION ECONOMY. Orderly charge Disorderly charge Total operation costs / $ 279,250.95 279,797.03 Total energy losses / MWh 230.67 231.78 TABLE VI. COMPARISON OF SYSTEM OPERATION ECONOMY. Orderly charge Disorderly charge Total operation costs / $ 279,250.95 279,797.03 Total energy losses / MWh 230.67 231.78 TABLE V. LOAD MULTIPLES IN 24 HOURS. t k t k t k 1 1.05 9 1.45 17 1.40 2 1.00 10 1.40 18 1.50 3 1.00 11 1.25 19 1.65 4 1.05 12 1.20 20 1.7 5 1.15 13 1.15 21 1.65 6 1.35 14 1.20 22 1.55 7 1.45 15 1.25 23 1.25 8 1.50 16 1.35 24 1.15 Table VI shows that whatever the total operation costs or the energy losses, the grid shows a better performance when the EVBSS charges orderly using the strategy proposed. In case 2, making the sensitivity analysis, the increased value of the EVBSS benefits will be yielded after the battery depreciation cost or battery number is increased one unit, the increased value is as show in Table VII. Taking the minimum grid operation costs in 24 hours as the objective function, namely (12), two cases are compared. One is that the EVBSS charges using the optimal strategy proposed above, while the other is that the EVBSS charges disorderly (fitting according to the disordered charging load in [7]–[10], the power factor of EVBSS is always 0.95, and its discharging to grid is not considered) TABLE VII. SENSITIVITY ANALYSIS. Changed parameter Increased EVBSS benefits Battery depreciation cost -4.11 Battery number 0.81 In case 2, the changed EVBSS benefits will be yielded after changing the battery depreciation cost from -40 %~40 % or the electricity price which following the rule that both increased 10 %~40 % the electricity cost during the heavy-load periods, such as period in 7, 8, 9, 19, 20, 21 and decreased 10 %~40 % the electricity cost during the light-load periods, such as period in 1, 2, 3, 4.The value is as show in Table VIII. 24 2 cost 1 1 ( ), Ng i Gi i Gi i t i f a P b P c       (12) (12) where Ng refers to the generator number in the system; ai, bi, ci refer to the economy coefficient of the ith generator; PGi 7 ELEKTRONIKA IR ELEKTROTECHNIKA, ISSN 1392-1215, VOL. 23, NO. 4, 2017 TABLE VIII. COMPARISON OF EVBSS BENEFITS WHEN EACH PARAMETER CHANGED. REFERENCES It is more clearly that transferring the data in the Table VIII into a diagram which is shown as Fig. 3. It is more clearly that transferring the data in the Table VIII into a diagram which is shown as Fig. 3. [1] K. Clement-Nyns, E. Haesen, J. Driesen, “The impact of charging plug-in hybrid electric vehicles on a residential distribution grid”, IEEE Trans. Power Systems, vol. 25, no. 1, pp. 371–380, 2010. [Online]. Available: http://dx.doi.org/10.1109/TPWRS.2009.2036481 [1] K. Clement-Nyns, E. Haesen, J. Driesen, “The impact of charging plug-in hybrid electric vehicles on a residential distribution grid”, IEEE Trans. Power Systems, vol. 25, no. 1, pp. 371–380, 2010. [Online]. Available: http://dx.doi.org/10.1109/TPWRS.2009.2036481 Fig. 3. EVBSS Tendency of EVBSS benefits when each parameter changed. y pp Available: http://dx.doi.org/10.1109/TPWRS.2009.2036481 [2] L. Pieltain Fernandez, T. G. S. Roman, R. Cossent, C. M. Domingo, P. Frias, “Assessment of the impact of plug-in electric vehicles on distribution networks”, IEEE Trans. Power Systems, vol. 26, no. 1, pp. 206–213, 2011. [Online]. Available: http://dx.doi.org/ 10.1109/TPWRS.2010.2049133 [3] M. P. Moghaddam, P. T. Baboli, E. Alishahi, F. Lotfifard, “Flexible load following the wind power generation”, IEEE Int. Energy Conf. and Exhibition (EnergyCon), 2010, pp. 802–807. [Online]. Available: http://dx.doi.org/10.1109/ENERGYCON.2010.5771792 [4] Y. Ota, H. Taniguchi, T. Nakajima, K. M. Liyanage, A. Yokoyama, “An autonomous distributed vehicle-to-grid control of grid-connected electric vehicle”, Industrial and Information Systems (ICIIS), 2009, pp. 414–418. [Online]. Available: http://dx.doi.org/10.1109/ ICIINFS.2009.5429826 Fig. 3. EVBSS Tendency of EVBSS benefits when each parameter changed. [5] A. Y. Saber, G. K. Venayagamoorthy, “Unit commitment with vehicle-to-grid using particle swarm optimization”, IEEE Bucharest Power Tech: Innovative Ideas Toward the Electrical Grid of the Future, 2009, pp. 1–8. [Online]. Available: http://dx.doi.org/10.1109/ PTC.2009.5282201 From Fig. 3, it can be clearly seen that the EVBSS benefits increased slowly when the battery number is increased, it will be saturation when the battery number increased more than 10 %. The battery number is not a sensitivity parameter. On the other side, the EVBSS benefits decreased deeply when the battery depreciation cost is increased, the sensitivity of this parameter is much higher than the battery number. Battery number is a sensitivity parameter. [6] R. D. Zimmerman, C. E. Murillo-Sanchez, D. Q. Gan. MATPOWER. [Online]. Available: http://www.pserc.cornell.edu/matpower/ [7] . W. Xu, Z. C. Hu, Y. H. Song, Z. W. Luo, K. Q. Zhan, H. Shi, “Coordinated charging of plug-in electric vehicles in charging stations”, Automation of Electric Power Systems, vol. 36, pp. REFERENCES 38–43, 2012. (in Chinese) ) [1] Li Zhiwei, Zhao Shuqiang, Liu Yingmei, “Control strategy and application of distributed electric vehicle energy storage”, Dianwang Jishu/Power System Technology, vol. 40, no. 2, pp. 442–450, 2016. TABLE VI. COMPARISON OF SYSTEM OPERATION ECONOMY. Orderly charge Disorderly charge Total operation costs / $ 279,250.95 279,797.03 Total energy losses / MWh 230.67 231.78 Electricity price changed degree/% EVBSS benefits/$ Battery depreciation cost /$ EVBSS benefits/$ -40 3305.66 1.08 5483.41 -30 3385.72 1.26 5067.26 -20 3542.35 1.44 4673.02 -10 3698.98 1.62 4279.83 0 3894.28 1.81 3895.28 10 4135.81 1.98 3512.92 20 4457.67 2.16 3134.16 30 4869.62 2.34 2773.44 40 5568.05 2.53 2412.72 TABLE VIII. COMPARISON OF EVBSS BENEFITS WHEN EACH PARAMETER CHANGED. profits, but also realize peak load shifting for the grid, which creates a win-win business between EVBSS and the grid. What’s more, in the same setting background, whatever the total operation costs or the energy losses, the grid shows a better performance when the EVBSS charges orderly using the strategy proposed. As the energy storage function, EVBSS loads affect the energy consumption distribution of the grid in different time. As the energy storage function, EVBSS loads affect the energy consumption distribution of the grid in different time. With the larger scale of EV application, EVBSS can bring more benefits to power systems, such as balancing the uncertainties of renewable energy power, participating system backup, etc. VII. CONCLUSIONS [2] R. Mkahl, A. Nait-Sidi-Moh, J. Gaber, M. Wack, “An optimal solution for charging management of electric vehicles fleets”, Electric Power Systems Research, vol. 146, pp. 177–188, 2017. [Online]. Available: https://doi.org/10.1016/j.epsr.2016.11.008 Based on the analysis on profit pattern and load characteristics of EVBSS, this paper established an optimal charge/discharge model for EVBSS by considering the effects to grid. Taking the minimum grid operation costs in 24 hours as the objective function, case study shows that the optimal strategy can not only help the EVBSS gain more [3] Luo Yugong, Zhu Tao, Wan Shuang, Zhang Shuwei, Li Keqiang, “Optimal charging scheduling for large-scale EV (electric vehicle) deployment based on the interaction of the smart-grid and intelligent-transport systems”, Energy, vol. 97, pp. 359–368, 2016. [Online]. Available: https://doi.org/10.1016/j.energy.2015.12.140 8
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Factors associated with development of opportunistic infections among patients on ART at a Ugandan Program-MJAP
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Background Early identification of HIV-infected individuals and linkage to HIV care and treatment is likely to minimize the incidence of Opportunistic Infections. To establish the factors associated with development of opportunistic infections among patients on ART at an HIV/AIDS Program in Uganda. Published: 11 May 2010 Published: 11 May 2010 Results Data of 4,878 patients on ART was analyzed. 3,247 (67.2%) were females. Median age 33 years (SD 8.5) and Median weight 53 kg (SD 10.0). Incidence of OIs 329 (6.7%); Oral candidiasis 106 (32%), Vaginal candidiasis 80 (24%), Kaposi’s sarcoma 40 (12%), Herpes simplex 28 (9%), Oesophageal candidiasis 25 (8%), Tuberculosis 15 (5%), others 38 (10%). WHO stage 3&4 (OR 2.64, CI 2.04-3.43, P < 0.001), CD4 count <100 cells/mm3 (OR 1.92, CI 1.52-2.42, P < 0.001), not being married (OR 1.69, CI 1.33-2.14, P < 0.001) and having no formal edu- cation (OR 1.61 CI 1.09-2.36, P = .0015) were signifi- cantly associated with development of OIs among patients on ART. Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Ltd Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Ltd Submit your next manuscript to BioMed Central and take full advantage of: Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit l Ltd Sex, age, body weight, ART regimen and Karnofsky score were not associated with development of OIs. Muhumuza et al. Retrovirology 2010, 7(Suppl 1):P77 http://www.retrovirology.com/content/7/S1/P77 Open Access Factors associated with development of opportunistic infections among patients on ART at a Ugandan Program-MJAP Simon Muhumuza* Joseph Ouma Fred Semitala Simon Muhumuza*, Joseph Ouma, Fred Semitala From 16th International Symposium on HIV and Emerging Infectious Diseases Marseille, France. 24-26 March 2010 Methods Retrospective cohort analysis on adult patients initiated on ART between November 2005 and November 2007. The socio demographics, clinical and laboratory charac- teristics of patients that developed OIs were studied. doi:10.1186/1742-4690-7-S1-P77 Cite this article as: Muhumuza et al.: Factors associated with development of opportunistic infections among patients on ART at a Ugandan Program-MJAP. Retrovirology 2010 7(Suppl 1):P77. * Correspondence: simonmhmz@yahoo.com Mulago-Mbarara Teaching Hospitals Joint AIDS Program (MJAP), Kampala, Uganda Discussion The risk of OIs is higher among patients with a low CD4 count, high WHO clinical stage, no formal educa- tion and in those that are not married. * Correspondence: simonmhmz@yahoo.com Mulago-Mbarara Teaching Hospitals Joint AIDS Program (MJAP), Kampala, Uganda © 2010 Muhumuza et al; licensee BioMed Central Ltd. © 2010 Muhumuza et al; licensee BioMed Central Ltd.
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Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation
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Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation Nick Powell,1,2,3 Jonathan W. Lo,1,3 Paolo Biancheri,4 Anna Vossenkämper,4 Eirini Pantazi,1,3 Alan W. Walker,5,6 Emilie Stolarczyk,1,3,7 Francesca Ammoscato,4 Rimma Goldberg,1,2 Paul Scott,5 James B. Canavan,1,3 Esperanza Perucha,1,3 Natividad Garrido-Mesa,1,3 Peter M. Irving,2 Jeremy D. Sanderson,2 Bu Hayee,8 Jane K. Howard,1,3,7 Julian Parkhill,5 Thomas T. MacDonald,4 and Graham M. Lord1,3 Nick Powell,1,2,3 Jonathan W. Lo,1,3 Paolo Biancheri,4 Anna Vossenkämper,4 Eirini Pantazi,1,3 Alan W. Walker,5,6 Emilie Stolarczyk,1,3,7 Francesca Ammoscato,4 Rimma Goldberg,1,2 Paul Scott,5 James B. Canavan,1,3 Esperanza Perucha,1,3 Natividad Garrido-Mesa,1,3 Peter M. Irving,2 Jeremy D. Sanderson,2 Bu Hayee,8 Jane K. Howard,1,3,7 Julian Parkhill,5 Thomas T. MacDonald,4 and Graham M. Lord1,3 1Department of Experimental Immunobiology, Division of Transplantation Immunology and Mucosal Biology, 7Division of Diabetes and Nutritional Sciences, King’s College London, London, United Kingdom; 2Gastroenterology Department, 3National Institute for Health Research Biomedical Research Centre, Guy’s and St Thomas’ National Health Service Foundation Trust, London, United Kingdom; 4Centre for Immunology and Infectious Disease, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom; 5Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, United Kingdom; 6Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom; 8Gastroenterology Department, Kings College Hospital, London, United Kingdom I I BACKGROUND & AIMS: Innate lymphoid cells (ILCs) are a heterogeneous group of mucosal inflammatory cells that participate in chronic intestinal inflammation. We investigated the role of interleukin 6 (IL6) in inducing activation of ILCs in mice and in human beings with chronic intestinal inflammation. METHODS: ILCs were isolated from colons of Tbx21-/-  Rag2-/- mice (TRUC), which develop colitis; patients with in- flammatory bowel disease (IBD); and patients without colon inflammation (controls). ILCs were characterized by flow cytometry; cytokine production was measured by enzyme- linked immunosorbent assay and cytokine bead arrays. Mice were given intraperitoneal injections of depleting (CD4, CD90), neutralizing (IL6), or control antibodies. Isolated colon tissues were analyzed by histology, explant organ culture, and cell culture. Bacterial DNA was extracted from mouse fecal samples to assess the intestinal microbiota. RESULTS: IL17A- and IL22- producing, natural cytotoxicity receptor–negative, ILC3 were the major subset of ILCs detected in colons of TRUC mice. Combinations of IL23 and IL1a induced production of cyto- kines by these cells, which increased further after administra- tion of IL6. Antibodies against IL6 reduced colitis in TRUC mice without significantly affecting the structure of their intestinal microbiota. Gastroenterology 2015;149:456–467 Gastroenterology 2015;149:456–467 Abbreviations used in this paper: CD, Crohn’s disease; cLPMC, colonic lamina propria mononuclear cell; ELISA, enzyme-linked immunosorbent assay; IBD, inflammatory bowel disease; IL, interleukin; ILC, innate lymphoid cell; IL7RD, IL7R-receptor–positive; mLN, mesenteric lymph node; NCR, natural cytotoxicity receptor; OTU, operational taxonomic unit; PCR, polymerase chain reaction; PMA, phorbol 12-myristate 13-acetate; sIL6Ra, soluble interleukin 6Ra; Th, T-helper cell; TRUC, Tbx21-/- Rag2-/- ulcerative colitis; UC, ulcerative colitis. Keywords: UC; CD; Innate Immunity; Immune Regulation. Human Studies Cytokine concentrations were measured in culture super- natants by ELISA or T-helper cell (Th)1, Th2, or Th17 CBA (BD Biosciences). Studies in human tissues received ethical approval from the City and Hackney Local Research Ethics Committee (REC reference: 10/H0704/74 and 10/H0804/65). Colonic lamina propria mononuclear cells (cLPMCs) were isolated as described previously18 from colectomy specimens and endoscopically acquired biopsy specimens. Normal colonic mucosal samples were collected from macroscopically unaffected areas of pa- tients undergoing intestinal resection for colon cancer or polyps. Informed written consent was obtained in all cases. Ex Vivo Organ Culture Colon explants cultures from murine experiments were performed as described previously.7 Three biopsy punches from the distal colon were cultured in 500 mL of complete medium for 24 hours at 37C. In human studies explant cul- tures were set up as described previously.18 Cytokine produc- tion in culture supernatants was measured by enzyme-linked immunosorbent assay (ELISA). Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation Addition of IL6 increased production of IL17A, IL22, and interferon-g by human intestinal CD3-negative, IL7- receptor–positive cells, in a dose-dependent manner. CON- CLUSIONS: IL6 contributes to activation of colonic natural cytotoxicity receptor–negative, CD4-negative, ILC3s in mice with chronic intestinal inflammation (TRUC mice) by increasing IL23- and IL1a-induced production of IL17A and IL22. This pathway might be targeted to treat patients with IBD because IL6, which is highly produced in colonic tissue by some IBD patients, also increased the production of IL17A, IL22, and interferon-g by cultured human colon CD3-negative, IL7- receptor–positive cells. I nflammatory bowel disease (IBD), comprising Crohn’s disease (CD) and ulcerative colitis (UC), is an increasingly common immune-mediated disease of the gut of unknown cause.1,2 The genetic architecture of IBD is complex, with more than 130 significantly associated sus- ceptibility loci identified to date,3 indicating that multiple mechanisms of disease may exist. Nevertheless, prominent roles for innate immunity and particular immune response pathways, including the interleukin (IL) 23/IL17 axis, strongly are implicated. BASIC AND TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT Innate lymphoid cells (ILCs) are emerging as important players in mucosal immunity. Although recognized to perform protective roles against mucosal pathogens,4,5 they also contribute to chronic intestinal inflammation, which is particularly apparent in mice lacking conventional T and B cells.6,7 This is in part dependent on their capacity to pro- duce inflammatory cytokines, including interferon-g, IL17A, and IL22.4–8 ILCs can be subdivided into discrete pop- ulations, which accumulate in mucosal tissues in different pathologic settings.9 At least 3 subsets exist, including ILC1s, which produce interferon-g; ILC2s, which produce IL5/ IL13; and ILC3, which can be subdivided further based on differential expression of natural cytotoxicity receptors (NCRs), CD4, and production of IL17 and/or IL22.9 Abbreviations used in this paper: CD, Crohn’s disease; cLPMC, colonic lamina propria mononuclear cell; ELISA, enzyme-linked immunosorbent assay; IBD, inflammatory bowel disease; IL, interleukin; ILC, innate lymphoid cell; IL7RD, IL7R-receptor–positive; mLN, mesenteric lymph node; NCR, natural cytotoxicity receptor; OTU, operational taxonomic unit; PCR, polymerase chain reaction; PMA, phorbol 12-myristate 13-acetate; sIL6Ra, soluble interleukin 6Ra; Th, T-helper cell; TRUC, Tbx21-/- Rag2-/- ulcerative colitis; UC, ulcerative colitis. © 2015 by the AGA Institute 0016-5085/$36.00 http://dx.doi.org/10.1053/j.gastro.2015.04.017 Keywords: UC; CD; Innate Immunity; Immune Regulation. Keywords: UC; CD; Innate Immunity; Immune Regulation. Mice Balb/C Rag2-/- and wild-type mice were sourced commer- cially (Jackson Laboratories; Bar Harbor, ME). TRUC mice were a gift from Laurie Glimcher. Animal experiments were per- formed in accredited facilities in accordance with the UK Ani- mals (Scientific Procedures) Act 1986 (Home Office License Number PPL: 70/6792 and PPL: 70/7869 from November 2013). Cell Culture Unfractionated murine splenocytes (2  106/mL) and mesenteric lymph node (mLN) cells (1  106/mL) or cLPMCs (1  106/mL) were cultured in complete medium for 24 hours at 37C as described previously.7 cLPMCs from IBD and noninflammatory control patients were cultured with recom- binant human IL6 (R&D) (0–100 ng/mL) overnight at 37C, 5% CO2, and then restimulated with PMA (50 ng/mL) and ion- omycin (1 mmol/L). In some experiments, cLPMCs were cultured with IL6 (100 ng/mL) for 6 hours in the presence of monensin (3 mmol/L). Fluorescence-activated cell sorter–puri- fied NCR- ILC3s (CD45þ CD90þ IL7Rþ NKp46-) from TRUC mice were cultured at 5  104/mL for 24 hours. Cytokine concen- trations in culture supernatants were measured by ELISA (R&D Systems and eBioscience). IL6 Increases Cytokines by ILCs 457 Tbx21-/- Rag2-/- ulcerative colitis (TRUC) mice sponta- neously develop severe colitis with striking similarities to some aspects of human UC.10 Colon lesions histologically resemble UC with goblet cell depletion, crypt abscess for- mation, epithelial hyperplasia, and infiltration of colonic lamina propria with neutrophils and mononuclear cells.7,10 TRUC mice develop inflammation-associated epithelial dysplasia, which frequently progresses to frank adenocar- cinoma,11 one of the most severe complications in human forms of IBD. TRUC disease is dependent on interactions between intestinal CD11cþ mononuclear phagocytes and CD90þ IL7R-receptor–positive (IL7Rþ) ILCs.7 Depletion of ILCs or genetic deficiency of the common g-chain cytokine receptor, which is necessary for ILC survival, prevents dis- ease.7 Similarly, blockade of IL23 or IL17A significantly at- tenuates disease.7 ILCs accumulate in gut lesions from IBD patients12–14 and it has been speculated that targeting these cells might represent a viable therapeutic approach in IBD.15 IL236,7 and IL1b16 contribute to ILC activation, although curiously TRUC mice that additionally are deficient for either IL23R or IL1R are not fully protected from colitis,17 consistent with a possible role for alternative ILC activa- tion pathways contributing to disease. The purpose of this study was to investigate the proximal signals responsible for driving intestinal ILC activation and to determine whether similar pathways might exist in human disease. Tbx21-/- Rag2-/- ulcerative colitis (TRUC) mice sponta- neously develop severe colitis with striking similarities to some aspects of human UC.10 Colon lesions histologically resemble UC with goblet cell depletion, crypt abscess for- mation, epithelial hyperplasia, and infiltration of colonic lamina propria with neutrophils and mononuclear cells.7,10 TRUC mice develop inflammation-associated epithelial dysplasia, which frequently progresses to frank adenocar- cinoma,11 one of the most severe complications in human forms of IBD. TRUC disease is dependent on interactions between intestinal CD11cþ mononuclear phagocytes and CD90þ IL7R-receptor–positive (IL7Rþ) ILCs.7 Depletion of ILCs or genetic deficiency of the common g-chain cytokine receptor, which is necessary for ILC survival, prevents dis- ease.7 Similarly, blockade of IL23 or IL17A significantly at- tenuates disease.7 ILCs accumulate in gut lesions from IBD patients12–14 and it has been speculated that targeting these cells might represent a viable therapeutic approach in IBD.15 ILCs, CD45þ cells first were sorted immunomagnetically from unfractionated cLPMCs using anti-CD45 beads (Miltenyi) and LS columns (Miltenyi). CD45þ cells were stained with CD90, NKp46, and IL7R. Antibodies used in flow cytometry experi- ments are listed in Supplementary Table 1. Histology Colon histology was processed, stained (H&E), and colitis scores were calculated as described previously.7 Proximal and distal colitis scores from individual mice were averaged, unless otherwise stated. Microarray and Real-Time Polymerase Chain Reaction RNA was extracted from 3 Rag2-/- and 3 TRUC mice, aged 10 weeks, using TRIzol reagent (Invitrogen Carlsbad, CA). Transcript expression was analyzed with Mouse Genome 430 2.0 Affymetrix Expression Array. For real-time polymerase chain reaction (PCR) experiments cells were lysed in TRIzol reagent (Invitrogen) and RNA was extracted. Complementary DNA was generated with the complementary DNA synthesis kit (Bioline, Taunton, MA). Quantitative PCR was used to quantify messenger RNA transcripts using TaqMan gene expression as- says (Applied Biosystems). Gene expression was normalized to the expression of b-actin to generate DCT values and relative abundance was quantified using the 2-DCT method. Human RORC (Hs01076112_m1) and b-actin (4326315E) TaqMan quantitative PCR primer sets were used. Materials and Methods BASIC AND TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT NCR- CD4- ILC3 Cells Are the Predominant Colonic ILC Subset in Chronic Intestinal Inflammation in TRUC Mice NCR- CD4- ILC3 Cells Are the Predominant Colonic ILC Subset in Chronic Intestinal Inflammation in TRUC Mice We validated the phenotype of ILCs in TRUC mice, confirming excessive accumulation of IL17A- and IL22- producing CD90þ IL7Rþ NCR- ILC3 in diseased colons (Figure 1A and 1B, Supplementary Figure 1A–D). CD4- expressing NCR- ILC3s resembling lymphoid tissue inducer cells participate in mucosal immune responses in the gut,5 therefore, we considered the possibility that CD4þ ILCs might be the NCR- ILC3 subset responsible for medi- ating chronic inflammation in TRUC mice. CD4þ cells were present in mLNs of TRUC mice (many of which co-expressed CD90); however, very few CD4þ cells were present in the colon (Figure 1C). Given the low frequency of intestinal CD4þ ILCs in TRUC mice we considered it unlikely that these cells would play a major role in disease. To test this assumption we depleted CD4-expressing cells in vivo. The administration of anti-CD4 antibodies suc- cessfully depleted CD4-expressing cells in mLNs and colon of TRUC mice (Figure 1C). However, many CD90þ cells still remained in the colon and there was no reduction in the number of IL17A- or IL22-producing cells (Figure 1D). Depleting anti-CD4 treatment did not alter the severity of TRUC disease significantly (Figure 1E). In contrast, anti- CD90 treatment depleted both CD90- and CD4-expressing ILCs, reduced the number of IL17- and IL22-producing cells in the colon, and significantly attenuated disease (Figure 1C–E). Taken together, these data indicate IL17A/IL22 producing CD90þ IL7Rþ NCR- CD4- ILC3 are the key ILC population in the colon responsible for causing disease in TRUC mice. To determine whether IL6 might trigger ILC-derived cyto- kines we stimulated unfractionated cLPMCs and mLN cells fromTRUCmicewithrecombinantIL6.Strikingly,IL6triggered IL17A production by both cLPMCs and mLN cells (Figure 2B). We also performed flow cytometry with intracellular cytokine staining after IL6 stimulation of unfractionated mLN cells. Although less potent than IL23, IL6 induced expression of IL17A in NCR- ILC3s (Figure 2C). To determine whether this was a cell-intrinsic phenomenon we purified CD90þ IL7Rþ NCR- ILC3s from TRUC colons by fluorescence-activated cell sorting (Supplementary Figure 3A). To our surprise, neither IL6, IL23, nor IL1a by themselves induced significant cytokine production by purified colonic NCR- ILC3s (Figure 2D). How- ever, the combination of IL23 and IL1a was a potent trigger for ILC production of IL17A and IL22. The addition of IL6 together with IL23 and IL1a was the most potent trigger of all. In Vivo Antibody Treatment up-regulated, and, indeed in most instances were down- regulated in the colon of TRUC mice in comparison with Rag2-/- controls. Intraperitoneal injections of anti-CD4 (1 mg, GK1.5), anti- CD90 (1 mg, 30H12), anti-IL6 (750 mg, MP5-20F3), or isotype-matched control antibodies (LTF-2 or HRPN) (Bio X Cell, West Lebanon, NH) were administered on days 0, 7, 14, 21, and 28 (anti-CD4, anti-CD90) or days 0, 4, 9, 14, 18, 23, and 27 (anti-IL6). g IL23 and IL1 have been described to play an important role triggering ILCs in TRUC disease, therefore, in this study we focussed our attention on IL6. In addition to increased Il6 transcripts in the colon, there were very high concen- trations of IL6 in serum and significantly increased pro- duction of IL6 in colon explant cultures from TRUC mice (Supplementary Figure 2A). Transcripts of genes known to be regulated by IL619 were up-regulated in the colon of TRUC mice in comparison with Rag2-/- controls (Supplementary Figure 2B), including well-recognized im- mune genes (Socs1, Socs3, and Icam1), IL6 signaling com- ponents (Stat1 and Stat3), and anti-apoptotic genes (Bcl3, Bcl6, and Bcl-x1). The most highly expressed IL6-regulated gene in the colon of TRUC mice (12-fold enrichment) was Pou2af1, which encodes a transcriptional co-activator responsible for IL6-mediated regulation of IL17 responses in T cells.20 458 Powell et al 458 Powell et al Gastroenterology Vol. 149, No. 2 Microbiota Analysis See the Supplementary Materials and Methods section for more detail. Flow Cytometry and Cell Sorting Intracellular cytokine expression was measured as described previously.7 Cells were stimulated with IL23 (10–20 ng/mL), IL6 (10–100 ng/mL), or phorbol 12-myristate 13- acetate (PMA) (50 ng/mL) and ionomycin (1 mmol/L) for 4–6 hours at 37C with monensin (3 mmol/L) added for the last 2 hours. In human work, antibodies used to stain cell surface antigens were incubated with unstimulated cells for 25 minutes and then fixed in 2% paraformaldehyde pending analysis. For fluorescence-activated cell sorter purification of murine NCR- CD4- ILC3 Cells Are the Predominant Colonic ILC Subset in Chronic Intestinal Inflammation in TRUC Mice Purified intestinal NCR- ILCs from TRUC mice produced little tumor necrosis factor a or interferon-g under these conditions (Supplementary Figure3B). IL23andIL1awereweakinducers of IL6 by colonic NCR- ILCs (Supplementary Figure 3B). Taken together, these data showed that IL6 augments IL23/IL1a- induced pathogenic cytokine production by intestinal ILCs in TRUC mice in a cell-intrinsic manner. IL6 signals through a heterodimeric receptor comprising ubiquitously expressed gp130 and selectively expressed IL6Ra. However, IL6Ra also exists as a soluble form, which can complex with IL6 in solution and then bind to cells expressing gp130, enabling cells, which do not usually ex- press IL6Ra, to respond to IL6 stimulation. Therefore, we investigated IL6Ra and soluble IL6Ra (sIL6Ra) expression in TRUC mice. IL6Ra expression by ILCs was highly variable in the colon of TRUC mice, but typically was less than 10% (Supplementary Figure 4A, and data not shown). However, sIL6Ra was abundant in the serum of TRUC mice and was detected in supernatants from cultured colon explants and unfractionated splenocytes (Supplementary Figure 4B). Therefore, it is likely that ILCs respond to IL6 stimulation directly, but also potentially through trans-signaling given the abundance of sIL6R in TRUC mice. IL6 Is Expressed Highly and Augments Pathogenic Cytokine Production in TRUC Mice IL6 Is Expressed Highly and Augments Pathogenic Cytokine Production in TRUC Mice We sought to define the proximal immune signals responsible for triggering effector function of colonic NCR- ILC3 in TRUC mice. IL1b and IL6 were among the most highly expressed (>2-fold induction) cytokine transcripts in the colon of TRUC mice in comparison with Rag2-/- mice (Figure 2A). The other IL1 family member, Il1a, and the IL23 subunit transcripts (Il23a and Il12b) also were increased. Proximal cytokines responsible for driving ILC1 (IL12, IL15, and IL18) or ILC2 (IL25 and IL33) responses were not /IL22- NCR- is in Flow of live, ng to 0 and ns of mice, mbers D90þ ons of mice. repre- ouse. edian. flow (left) alysis on of cells cells) ns of with ontrol anti- CD90 Statis- per- cells ion of after **P < tative plots anal- opor- IL22þ D45þ TRUC otype- anti- -CD4 0 (n ¼ were A and racel- g *P < tative (H&E atisti- colitis TRUC otype- anti- anti- *P < 90 vs anti- Each ts an Lines IL6 Increases Cytokines by ILCs 459 BASIC AND IL6 Increases Cytokines by ILCs 459 August 2015 2- R- in w e, to nd of e, rs 0þ of e. e- e. n. w ft) sis of ls s) of th ol ti- 90 s- er- ls f of e. e- e. n. ow ft) sis of lls s) of th ol ti- 90 s- er- lls of er < ve ts al- or- 2þ 5þ C e- ti- D4 ¼ re nd el- < ve &E ti- tis C e- ti- ti- < vs ti- ch an es flow (left) ysis n of cells cells) s of with ntrol anti- D90 atis- per- cells on of after *P < ative plots anal- por- L22þ D45þ RUC ype- anti- CD4 (n ¼ were and acel- *P < ative H&E tisti- olitis RUC ype- anti- anti- P < 0 vs anti- Each an ines Figure 2. IL6 promotes cytokine production by NCR- ILC3s in a cell-intrinsic manner. (A) Microarray analysis showing an abundance of cytokine tran- scripts in the colon of TRUC mice relative to Rag2-/- mice. Blue dotted line depicts 2-fold induction. (B) IL17A production by unfractionated cLPMCs and mLN cells isolated from TRUC mice in medium alone (-) or after supplementation with recombinant IL6 or IL23. Columns represent mean cytokines and error bars depict SEM. Analysis of cLPMCs comprised 4 biological replicates. IL6 Is Expressed Highly and Augments Pathogenic Cytokine Production in TRUC Mice Analysis of mLN included 9 biological replicates for the unstimulated condition and 7 biological replicates for each of the stimulated conditions. *P < .02; **P < .003. (C) Flow 460 Powell et al Gastroenterology Vol. 149, No. 2 BASIC AND TRANSLATIONAL AT Gastroenterology Vol. 149, No. 2 IL6 Blockade Attenuated TRUC Disease Independently of Changes to Intestinal Microbiota Community Profiles IL6 Blockade Attenuated TRUC Disease Independently of Changes to Intestinal Microbiota Community Profiles (CD3-) fraction, particularly in IBD patients. Within the non–T-cell fraction (CD3-), we could identify a population of IL7R-expressing cells in the colon of patients with CD, UC, and noninflammatory control patients (Figure 5B). Although the frequency of these cells was variable, their proportional abundance within the lymphocyte population was increased in IBD patients in comparison with noninflammatory con- trols (Figure 5B). Consistent with ILC3s being present among the CD3- IL7Rþ population, there was enriched expression of RORgt and c-kit (CD117) (Figure 5C and Supplementary Figure 6C). RORC transcripts also were enriched in fluorescence-activated cell sorter–purified CD3- IL7Rþ cells analyzed by real-time PCR (Supplementary Figure 6B), corroborating the likelihood of ILCs being pre- sent in the CD3- IL7Rþ population. Analysis of the CD3- IL7Rþ population according to NCR expression showed the presence of 3 discrete populations, comprising NKp46þ NKp44- cells, NKp44þ NKp46- cells, and NCR- (NKp44- NKp46-) cells (Figure 5D and Supplementary Figure 6C), indicating that NCRþ and NCR- ILCs are present within this CD3- IL7Rþ population. In most patients, including IBD and noninflammatory control patients, CD3- IL7Rþ NKp44þ NKp46- cells were the predominant subset present (Figure 5D and Supplementary Figure 6C). To determine whether IL6-mediated activation of innate immunity was functionally important in TRUC disease, mice were treated with monoclonal antibodies that neutralize the biological activity of IL6. Treatment with anti-IL6 resulted in loss of IL6 bioavailability (Supplementary Figure 5A). IL17A production by unfractionated cLPMCs and splenocytes was reduced significantly in anti-IL6–treated TRUC mice, although was not abolished completely (Figure 3A). IL6 neutralization significantly attenuated TRUC disease, including reduced colitis scores and reduced splenomegaly (Figure 3B and C). ( g ) Similar to the situation in human IBD, TRUC disease is associated with perturbation of intestinal microbial com- munities. Because IL6 directly influences the success of mucosal colonization by some intestinal bacteria,21 we considered the possibility that attenuation of chronic TRUC disease after IL6 blockade might have occurred secondarily to changes in key components in the composition of the intestinal microbiota. To address this question we sequenced 16S ribosomal RNA genes that were PCR- amplified from fecal samples from anti-IL6 or control anti- body–treated TRUC mice. Overall, we identified 2642 different operational taxonomic units (OTUs). Treatment with anti-IL6 antibody appeared to have a relatively minor impact on the microbiota (Figure 4A). IL6 Augments Pathogenic Cytokine Production by Colonic CD3- IL7Rþ Cells From IBD Patients Our preclinical data support the possibility that targeting IL6 may be therapeutically tractable in chronic gut inflam- mation. Therefore, we aimed to verify whether this pathway was relevant in human disease. As expected, stimulation of unfractionated intestinal immune cells with PMA and ion- omycin resulted in production of pathogenic cytokines, including IL17A, IL22, and interferon-g by CD3þ T cells (Figure 5A and Supplementary Figure 6A). However, we also observed production of these cytokines in the non–T-cell 460 Powell et al 460 Powell et al Figure 2 NCR- ILC analysis scripts in mice. Blu IL17A pro mLN cel alone (-) o IL6 or IL2 error ba comprise included condition 460 Powell et al BASIC AND TRANSLATIONAL AT Figure 2. IL6 NCR- ILC3s in analysis show scripts in the c mice. Blue dot IL17A product mLN cells iso alone (-) or afte IL6 or IL23. Co error bars de comprised 4 b included 9 biol condition and 7 stimulated con cytometry plot CD90þ NKp46 nated mLN cel (-), which wer Data are repre (D) Cytokine p cell sorted C purified from t strategy for Supplementary stimulated with as depicted. Af were measured CBA. Data are periments with Bars show the bars depict SE BASIC AND BASIC AND TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT Figure 2. IL6 promotes cytokine production by NCR- ILC3s in a cell-intrinsic manner. (A) Microarray analysis showing an abundance of cytokine tran- scripts in the colon of TRUC mice relative to Rag2-/- mice. Blue dotted line depicts 2-fold induction. (B) IL17A production by unfractionated cLPMCs and mLN cells isolated from TRUC mice in medium alone (-) or after supplementation with recombinant IL6 or IL23. Columns represent mean cytokines and error bars depict SEM. Analysis of cLPMCs comprised 4 biological replicates. Analysis of mLN included 9 biological replicates for the unstimulated condition and 7 biological replicates for each of the stimulated conditions. *P < .02; **P < .003. (C) Flow cytometry plots of intracellular IL17A expression by CD90þ NKp46- cells after stimulation of unfractio- nated mLN cells with IL6, IL23, or unstimulated cells (-), which were incubated with monensin alone. Data are representative of 3 separate experiments. (D) Cytokine production by fluorescence-activated cell sorted CD45þ CD90þ IL7Rþ NKp46- ILCs purified from the colons of TRUC mice (the gating strategy for cell sorting is illustrated in Supplementary Figure 3A). Purified NCR- ILCs were stimulated with combinations of IL1a, IL6, and IL23 as depicted. After 24 hours cytokine concentrations were measured in culture supernatant by ELISA or CBA. Data are representative of 2 individual ex- periments with ILCs pooled from 10–15 colons. Bars show the mean cytokine production and error bars depict SEM. IL6 Blockade Attenuated TRUC Disease Independently of Changes to Intestinal Microbiota Community Profiles At the phylum level, Firmicutes were reduced slightly in proportional abundance in anti-IL6–treated mice (P ¼ .035) (Figure 4A) but, at finer taxonomic levels, anti-IL6 treatment did not impact the proportional abundance of the most common 150 OTUs significantly, which cumulatively accounted for more than 96% of the total amount of sequence data generated (Supplementary Table 2). Cluster analysis, using the Bray Curtis calculator, confirmed that there was no signature microbiota profile associated with anti-IL6 treatment (Supplementary Figure 5B). Helicobacter typhlonius was ubiquitously present in anti-IL6– or isotype control–treated mice, however, the proportional abundance did not differ significantly between the 2 groups either before or after treatment (Figure 4B). There was a tendency for increased bacterial diversity in the gut of anti-IL6–treated mice in comparison with control antibody–treated mice, although this did not achieve statistical significance (P < .095) (Supplementary Figure 5C). To determine whether CD3- IL7Rþ cells present in diseased mucosa of IBD patients were responsive to IL6, cLPMCs were incubated overnight with recombinant human IL6 before being restimulated with PMA and ionomycin. Production of IL17A, IL22, and interferon-g by CD3- IL7Rþ cells was increased significantly when cLPMCs were cultured in the presence of IL6 (Figure 6A and B). In addi- tion, some samples were stimulated with IL6 directly without mitogen, which showed induction of IL17A by CD3- IL7Rþ cells in a dose-dependent manner (Figure 6C). Finally, we analyzed IL6 production by diseased mucosa from IBD patients to see whether blocking IL6 might be a reasonable therapeutic strategy in some or all IBD patients. IL6 was produced by colon explant cultures in CD, UC, and noninflammatory control patients (Supplementary Figure 6D). However, IL6 production was variable, espe- cially in IBD patients, ranging from 72.2 to 8426.4 pg/mg colonic tissue. IBD patients could be stratified according to mucosal production of IL6, with half of IBD patients pro- ducing relatively low levels comparable with noninflam- matory control patients and the other half producing high amounts (>1000 pg/mg tissue). Taken together, these data indicate that IL6, which is produced in very high quantities in approximately 50% of CD and UC patients drives patho- logically relevant immune pathways in chronic intestinal inflammation. August 2015 August 2015 August 2015 461 IL6 Increases Cytokines by ILCs 46 IL6 Increases Cytokines by ILCs 463 August 2015 colon of TRUC mice, consistent with data from other groups reporting a requirement for T-bet in NKp46þ ILC develop- ment and differentiation.22 Intestinal CD4þ ILCs are important in host resistance to intestinal pathogens, such as Citrobacter rodentium.5 Here, we show that CD4þ ILCs, which are abundant in mLN, but infrequent in the colon, do not play a major role in TRUC disease. Depletion of CD4þ ILCs had no impact on pathogenic cytokine production or disease outcome. In TRUC mice, highly purified colonic NCR- ILC3 did not respond to IL23 or IL1a in isolation. Instead, combinations of IL23 together with IL1a were required for production of effector cytokines by ILC3. Furthermore, additional expo- sure to IL6 was required for optimal IL17A and IL22 pro- duction, showing a novel role for IL6 in the innate immune system in chronic intestinal inflammation. Figure 4. IL6 blockade does not significantly impact the composition of the intestinal microbiota in TRUC mice. (A) The mean percentage of sequences of particular phyla pre- sent in the intestinal microbiota of TRUC mice before (top panel) and after (bottom panel) treatment with anti-IL6 (red bars) or isotype-matched control antibodies (white bars). (B) The mean proportional abundance of H typhlonius in the in- testinal microbiota of TRUC mice before and after treatment with anti-IL6 (red bars) or isotype-matched control antibodies (white bars). Error bars depict the SEM. IL17A-, IL22-, and interferon-g–producing CD3- IL7Rþ cells also were identified in the colonic lamina propria of patients with IBD. Although this population is heteroge- neous, there was enrichment of RORgt and c-kit, confirming the likelihood that ILC3 were present within this compart- ment. Most CD3- IL7Rþ cells were NKp44þ, although NKp46þ and NCR- (NKp44- NKp46-) cells also were present. These data are broadly consistent with previous reports of ILC populations in human gut.12–14 Crucially, IL6 increased pathogenic cytokine production by CD3- IL7Rþ cLPMCs from IBD patients in a dose-dependent manner, consistent with our preclinical data showing IL6-responsive colonic ILC3s. IL6 is a pleiotropic cytokine that may be important in IBD. Discussion CD4- NCR- ILC3s are the predominant CD90þ IL7Rþ ILC population in the colon of TRUC mice responsible for causing disease. Purified intestinal NCR- ILC3 from TRUC mice produced IL17A and IL22, but were poor producers of interferon-g and tumor necrosis factor a. They were also a modest source of IL6. Few NCRþ ILCs were present in the Figure 3. IL6 blockade reduces IL17A production and attenu- ates TRUC disease. (A) IL17A concentration in culture super- natants of unfractionated cLPMCs and splenocytes from TRUC mice treated with anti-IL6 (n ¼ 8) or isotype-matched control antibodies (n ¼ 8). (B) Representative colon micro- graphs (H&E stained) (left panel) and statistical analysis (right panel) of colitis scores of distal colons of TRUC mice treated with anti-IL6 or isotype- matched control antibodies. (C) Spleen and colon mass of TRUC i t t d ith ti IL6 462 Powell et al Gastroenterology Vol. 149, No. 2 BASIC AND TRANSLATIONAL AT Gastroenterology Vol. 149, No. 2 462 Powell et al TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT Figure 3. IL6 blockade reduces IL17A production and attenu- ates TRUC disease. (A) IL17A concentration in culture super- natants of unfractionated cLPMCs and splenocytes from TRUC mice treated with anti-IL6 (n ¼ 8) or isotype-matched control antibodies (n ¼ 8). (B) Representative colon micro- graphs (H&E stained) (left panel) and statistical analysis (right panel) of colitis scores of distal colons of TRUC mice treated with anti-IL6 or isotype- matched control antibodies. (C) Spleen and colon mass of TRUC mice treated with anti-IL6 or isotype-matched control an- tibodies. Each dot/square rep- resents an individual mouse. Lines represent medians. Re- sults from 2 separate antibody blockade experiments con- ducted under the same experi- mental conditions were pooled. IL6 Increases Cytokines by ILCs 46 Peripheral blood and cLPMCs produce excess IL6 in IBD,23,24 often at levels correlating with disease activity.25 Genetic variation at the IL6 locus is linked with early onset IBD26 and polymorphisms at loci encoding IL6R signaling components are associated with increased IBD risk.3 IL6 blockade is therapeutic in some preclinical models of IBD, although it has been assumed that the therapeutic mechanism likely was attributable to limitation of T-cell–mediated pathology27–30 because IL6 contributes to intestinal Th17 differentiation.31 We show a novel role of IL6 in innate immune-mediated chronic intestinal pathol- ogy. It is interesting that cytokines contributing to CD4þ Th17 differentiation, including IL1, IL23, and IL6, have conserved roles promoting innate IL17 production. Our data build on other work implicating ILCs as potentially important mediators in IBD,12–14 and confirm NCR- ILC3 as a source of pathogenic cytokines in IBD. Polymorphisms at multiple susceptibility loci in IBD that previously were considered to impact adaptive immunity, similarly could impact ILC phenotype, including RORC, IL23R, IL12RB2, IL12B, IL22, IFNG, STAT1, STAT3, STAT4, CCR6, IL1R1, IL15RA, and IL6ST.3 Accordingly, it is possible that genetic variation at these loci in IBD could impact disease sus- ceptibility by altering the activation and effector function of mucosal ILCs. However, the relative contribution of ILC to the initiation and propagation of chronic intestinal inflammation in IBD remains to be determined. Polyclonal stimulus of unfractionated cLPMCs from IBD patients showed that most cytokine-expressing cells reside within Figure 4. IL6 blockade does not significantly impact the composition of the intestinal microbiota in TRUC mice. (A) The mean percentage of sequences of particular phyla pre- sent in the intestinal microbiota of TRUC mice before (top panel) and after (bottom panel) treatment with anti-IL6 (red bars) or isotype-matched control antibodies (white bars). (B) The mean proportional abundance of H typhlonius in the in- testinal microbiota of TRUC mice before and after treatment with anti-IL6 (red bars) or isotype-matched control antibodies (white bars). Error bars depict the SEM. Figure 4. IL6 blockade does not significantly impact the composition of the intestinal microbiota in TRUC mice. (A) The mean percentage of sequences of particular phyla pre- sent in the intestinal microbiota of TRUC mice before (top panel) and after (bottom panel) treatment with anti-IL6 (red bars) or isotype-matched control antibodies (white bars). IL6 Increases Cytokines by ILCs 46 (B) The mean proportional abundance of H typhlonius in the in- testinal microbiota of TRUC mice before and after treatment with anti-IL6 (red bars) or isotype-matched control antibodies (white bars). Error bars depict the SEM. Figure 4. IL6 blockade does not significantly impact the composition of the intestinal microbiota in TRUC mice. (A) The mean percentage of sequences of particular phyla pre- sent in the intestinal microbiota of TRUC mice before (top panel) and after (bottom panel) treatment with anti-IL6 (red bars) or isotype-matched control antibodies (white bars). (B) The mean proportional abundance of H typhlonius in the in- testinal microbiota of TRUC mice before and after treatment with anti-IL6 (red bars) or isotype-matched control antibodies (white bars). Error bars depict the SEM. Gastroenterology Vol. 149, No. 2 464 Powell et al 464 Powell et al Figure 5. CD3- IL7Rþ cells are expanded in IBD patients. (A) Flow cytometry plots showing CD3 and intracellular IL17A expression in unfractionated cLPMCs after stimu- lation with PMA and ionomycin Additional representative flow cytometry plots are illustrated in Supplementary Figure 6A. (B) Representative flow cytometry plots (left panel) and statistical analysis (right panel) of CD3 and IL7R stain- ing by LPMCs in the colon of noninflammatory control and IBD patients. Individual dots represent individual patients. *P < .04. (C) Flow cytometric analysis of the phenotype of colonic CD3- IL7Rþ cells. Grey histograms show isotype control antibody staining. White histograms show staining with spe- cific antibody. Data are representa- tive of more than 3 independent experiments in IBD patients. (D) Flow cytometry dot plots showing expression of NKp46 and NKp44 by colonic CD3- IL7Rþ cells in nonin- flammatory control and IBD pa- i F h l f ddi i 464 Powell et al Gastroenterology Vol. 149, No. 2 BASIC AND TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT BASIC AND RANSLATIONAL AT Figure 5. CD3- IL7Rþ cells are expanded in IBD patients. (A) Flow cytometry plots showing CD3 and intracellular IL17A expression in unfractionated cLPMCs after stimu- lation with PMA and ionomycin. Additional representative flow cytometry plots are illustrated in Supplementary Figure 6A. (B) Representative flow cytometry plots (left panel) and statistical analysis (right panel) of CD3 and IL7R stain- ing by LPMCs in the colon of noninflammatory control and IBD patients. Individual dots represent individual patients. *P < .04. (C) Flow cytometric analysis of the phenotype of colonic CD3- IL7Rþ cells. IL6 Increases Cytokines by ILCs 4 IL6 Increases Cytokines by ILCs 465 August 2015 August 2015 August 2015 Figure 6. IL6-responsive CD3- IL7Rþ cells are present in the colon of IBD patients. (A) Flow cytometry histograms and (B) statistical analyses of intracellular cytokine expression by CD3- IL7Rþ cells after overnight culture in the presence or absence of IL6 (100 ng/mL). Cells were restimulated with PMA and ionomycin before staining. (B) Each connected pair of dots represents an individual patient. (C) Flow cytometry histograms showing the number of CD3- IL7Rþ IL17Aþ cells after culture with increasing doses of IL6 induced stimulation of ILC effector function may prove to be especially pertinent in UC because IL23, the canon- ical ILC-activating cytokine, is produced at low levels in UC in comparison with CD.32 In this study, IL6 neutralization reduced innate pro- duction of IL17A in TRUC mice and significantly attenuated disease severity, although the magnitude of impact was less than seen with ILC depletion or IL23 blockade.7 This is in keeping with our observation that although IL6 is required for optimal activation of ILC effector function, other prox- imal cytokine signals, including IL23 and/or IL1 stimulation, additionally are required. IL6 blockade had a minimal impact on the intestinal microbiota, other than a minor shift in the proportional abundance of Firmicutes and a tendency for increased intestinal bacterial diversity. It is possible that this latter change occurred secondary to reduced intestinal inflammation in anti-IL6–treated mice. Indeed, IBD activity/ severity is recognized to correlate inversely with bacterial diversity in the gut.33,34 Our data support extending biological therapies targeting IL6 in IBD. The IL6R blocking antibody tocilizumab is effica- cious in other inflammatory diseases, including arthritis35,36 and lupus,37 and a pilot study in CD showed promising initial results.38 In this study mucosal IL6 production was highly variable, however, only half of IBD patients produced more IL6 than non-IBD control patients. Similarly, the fre- quency of CD3- IL7Rþ cells, and the magnitude of IL6-induced cytokine responses by these cells also markedly was variable. With the promise of personalized medicine on the horizon,39 it is tempting to speculate that treatment strategies targeting IL6 might be favored in patient subsets defined by high mucosal expression of IL6 and/or high frequencies of IL6 responsive effector cells in diseased tissue. Supplementary Material Figure 6. IL6-responsive CD3- IL7Rþ cells are present in the colon of IBD patients. (A) Flow cytometry histograms and (B) statistical analyses of intracellular cytokine expression by CD3- IL7Rþ cells after overnight culture in the presence or absence of IL6 (100 ng/mL). Cells were restimulated with PMA and ionomycin before staining. (B) Each connected pair of dots represents an individual patient. (C) Flow cytometry histograms showing the number of CD3- IL7Rþ IL17Aþ cells after culture with increasing doses of IL6. Note: To access the supplementary material accompanying this article, visit the online version of Gastroenterology at www.gastrojournal.org, and at http://dx.doi.org/10.1053/ j.gastro.2015.04.017. IL6 Increases Cytokines by ILCs 4 In summary, we have shown that IL6 augments patho- genic cytokine production by intestinal ILCs in chronic in- testinal inflammation and that this pathway may be operational in human IBD. Novel therapeutic strategies targeting ILC or their proximal cytokine signals may offer a new treatment paradigm in IBD. Figure 6. IL6-responsive CD3- IL7Rþ cells are present in the colon of IBD patients. (A) Flow cytometry histograms and (B) statistical analyses of intracellular cytokine expression by CD3- IL7Rþ cells after overnight culture in the presence or absence of IL6 (100 ng/mL). Cells were restimulated with PMA and ionomycin before staining. (B) Each connected pair of dots represents an individual patient. (C) Flow cytometry histograms showing the number of CD3- IL7Rþ IL17Aþ cells after culture with increasing doses of IL6. IL6 Increases Cytokines by ILCs 46 Grey histograms show isotype control antibody staining. White histograms show staining with spe- cific antibody. Data are representa- tive of more than 3 independent experiments in IBD patients. (D) Flow cytometry dot plots showing expression of NKp46 and NKp44 by colonic CD3- IL7Rþ cells in nonin- flammatory control and IBD pa- tients. Further analyses of additional patient replicates are shown in Supplementary Figure 6C and D. 466 Powell et al IL- 23-responsive innate lymphoid cells are increased in in- flammatory bowel disease. J Exp Med 2011; 208:1127–1133. 28. Naito Y, Takagi T, Uchiyama K, et al. Reduced intestinal inflammation induced by dextran sodium sulfate in interleukin-6-deficient mice. Int J Mol Med 2004; 14:191–196. 13. Bernink JH, Peters CP, Munneke M, et al. 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Conflicts of interest These authors disclose the following: Nick Powell has received honoraria for acting in an advisory capacity or speaking on behalf of Actavis UK, Ferring and AstraZeneca; Peter Irving has received honoraria for acting in an advisory capacity or speaking on behalf of AbbVie, MSD, Actavis UK, Shire, Ferring, Falk, Genentech, Tillotts, Takeda, Vifor Pharma, Pharmacosmos, and Symprove; Thomas MacDonald receives support from Glaxo Smith Kline, Janssen Pharmaceuticals, Grunenthal, VH2, and Topivert; and Bu Hayee has received honoraria for acting in an advisory capacity or speaking on behalf of AbbVie, Takeda, and Actavis UK. The remaining authors disclose no conflicts. 38. Ito H, Takazoe M, Fukuda Y, et al. A pilot randomized trial of a human anti-interleukin-6 receptor monoclonal anti- body in active Crohn’s disease. Gastroenterology 2004; 126:989–996; discussion 947. 39. Biancheri P, Powell N, Monteleone G, et al. The chal- lenges of stratifying patients for trials in inflammatory bowel disease. Trends Immunol 2013;34:564–571. Acknowledgments The authors are grateful to the Wellcome Trust Sanger Institute’s core sequencing team for performing 16S ribosomal RNA gene sequencing, and to Chris Evagora and support staff at the Pathology Core at Queen Mary University of London. 37. Illei GG, Shirota Y, Yarboro CH, et al. Tocilizumab in systemic lupus erythematosus: data on safety, pre- liminary efficacy, and impact on circulating plasma cells from an open-label phase I dosage-escalation study. Arthritis Rheum 2010;62:542–552. y Microbiota sequence data were deposited in the European Nucleotide Archive under Study Accession Number ERP005850 and Sample Accession Numbers ERS459682–ERS459702. Reprint requests Address requests for reprints to: Graham M. Lord, MD, Department of Experimental Immunobiology, Division of Transplantation Immunology and Mucosal Biology, King’s College London, United Kingdom, SE1 9RT. e-mail: graham.lord@kcl.ac.uk; fax: (44) 207-188-3638. Funding S t Supported by grants awarded from the Wellcome Trust (WT101159AIA to N.P.; WT088747MA to N.P., G.M.L., and T.T.M.; 091009 to G.M.L.; and 098051 to A.W.W., P.S., and J.P.), and the Medical Research Council (G0802068 to G.M.L. and T.T.M., and MR/K002996/1 to G.M.L. and J.K.H.), by the Scottish Government Rural and Environmental Science and Analysis Service (A.W.W.), and by the National Institute for Health Research Biomedical Research Centre at Guy’s and St Thomas’ and King’s College London. The views expressed are those of the author(s) and not necessarily those of the National Health Service, the National Institute for Health Research, or the Department of Health. Reprint requests Address requests for reprints to: Graham M. Lord, MD, Department of Experimental Immunobiology, Division of Transplantation Immunology and Mucosal Biology, King’s College London, United Kingdom, SE1 9RT. e-mail: graham.lord@kcl.ac.uk; fax: (44) 207-188-3638. BASIC AND TRANSLATIONAL AT BASIC AND TRANSLATIONAL AT BASIC AND 467.e1 Powell et al Gastroenterology Vol. 149, No. 2 removed. After these steps, more than 486,000 sequences were left in the final data set (range, 447–51,571 sequences per sample). Next, after a preclustering step (diffs, 3), 97% similarity OTUs were generated. Taxonomic classifications for each of these OTUs were created using the RDP taxon- omy provided at the mothur web page. Metastats,3 as implemented in mothur, was used to test for significant differences in the proportional abundance of each of the phyla present, and the 150 most abundant OTUs between anti-IL6 and control mice. Bacterial diversity was measured by generating Shannon and inverse Simpson indices in mothur. Before these calculations each sample was sub- sampled randomly down to 447 reads to ensure equal sequencing depth for each. Kruskall–Wallis and Mann– Whitney U tests, implemented in Minitab v16, were used to test for significant differences in diversity measures be- tween the anti-IL6 and control mouse groups. A cluster dendrogram, using the Bray Curtis calculator, also was generated in mothur from the subsampled data set, and subsequently was visualized using the iTOL online software resource.4 Microbiota Analysis Sequence data have been deposited in the European Nucleotide Archive under Study Accession Number ERP005850 and Sample Accession numbers ERS459682–ERS459702. Microbiota Analysis y DNA was extracted from mouse fecal samples using the FastDNA SPIN Kit for Soil and a FastPrep 24 machine (MP Biomedicals Santa Ana, CA) according to the protocol provided by the manufacturer. Bacterial 16S ribosomal RNA genes were PCR-amplified using barcoded primers MiSeq 27F (5’AAT GATACGGCGACCACCGAGATCTACACTATGGTAATTCCAGMGT TYGATYMTGGCTCAG-3’) and MiSeq-338R (5’-CAAGCAGAA GACGGCATACGAGAT-barcode-AGTCAGTCAGAAGCTGCCTCCC GTAGGAGT-3’), which target variable regions V1–V2 of the 16S ribosomal RNA gene. Q5 Taq polymerase (New England Biolabs, Ipswich, MA) was used for the PCR step, and 4 PCR reactions were performed per sample. Cycling conditions were as follows: 98C for 2 minutes, followed by 20 cycles of 98C for 30 seconds, 50C for 30 seconds, 72C for 90 sec- onds, and then a final extension step at 72C for 5 minutes. The 4 PCR reactions from each DNA extraction then were pooled and concentrated down to 25 mL volumes per sample. PCR amplicons then were quantified using a Qubit 2.0 Fluorometer (Life Technologies, Ltd, Carlsbad, CA) and equimolar concentrations of each were added to a final mastermix for sequencing, using an Illumina MiSeq (San Diego, CA) machine with 2  250 bp read length. Sequence data have been deposited in the European Nucleotide Archive under Study Accession Number ERP005850 and Sample Accession numbers ERS459682–ERS459702. DNA was extracted from mouse fecal samples using the FastDNA SPIN Kit for Soil and a FastPrep 24 machine (MP Biomedicals Santa Ana, CA) according to the protocol provided by the manufacturer. Bacterial 16S ribosomal RNA genes were PCR-amplified using barcoded primers MiSeq 27F (5’AAT GATACGGCGACCACCGAGATCTACACTATGGTAATTCCAGMGT TYGATYMTGGCTCAG-3’) and MiSeq-338R (5’-CAAGCAGAA GACGGCATACGAGAT-barcode-AGTCAGTCAGAAGCTGCCTCCC GTAGGAGT-3’), which target variable regions V1–V2 of the 16S ribosomal RNA gene. Q5 Taq polymerase (New England Biolabs, Ipswich, MA) was used for the PCR step, and 4 PCR reactions were performed per sample. Cycling conditions were as follows: 98C for 2 minutes, followed by 20 cycles of 98C for 30 seconds, 50C for 30 seconds, 72C for 90 sec- onds, and then a final extension step at 72C for 5 minutes. The 4 PCR reactions from each DNA extraction then were pooled and concentrated down to 25 mL volumes per sample. PCR amplicons then were quantified using a Qubit 2.0 Fluorometer (Life Technologies, Ltd, Carlsbad, CA) and equimolar concentrations of each were added to a final mastermix for sequencing, using an Illumina MiSeq (San Diego, CA) machine with 2  250 bp read length. References 1. Kozich JJ, Westcott SL, Baxter NT, et al. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013;79:5112–5120. 1. Kozich JJ, Westcott SL, Baxter NT, et al. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013;79:5112–5120. The sequence data were processed by following the MiSeq SOP of the mothur software package (Available at: http://www.mothur.org/wiki/MiSeq_SOP).1 Paired-read contigs were created from the forward and reverse read sequence data, and preliminary quality processing was performed by removing all contigs that were shorter than 260 bp, longer than 450 bp, or those that contained any ambiguous bases or homopolymeric stretches longer than 7 bases. Perseus,2 as implemented in mothur, was used to remove putative chimeras, and any reads mapping to chlo- roplasts, mitochondria, eukarya, or archaea also were 2. Quince C, Lanzen A, Davenport RJ, et al. Removing noise from pyrosequenced amplicons. BMC Bioinform 2011;12:38. 2. Quince C, Lanzen A, Davenport RJ, et al. Removing noise from pyrosequenced amplicons. BMC Bioinform 2011;12:38. 3. White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comp Biol 2009; 5:e1000352. 4. Letunic I, Bork P. Interactive tree of life v2: online anno- tation and display of phylogenetic trees made easy. Nucleic Acids Res 2011;39:W475–W478. References IL6 Increases Cytokines by ILCs 467.e2 IL6 Increases Cytokines by ILCs 467.e2 August 2015 August 2015 Supplementary Table 1.Flow Cytometry Antibodies Used Supplementary Table 1.Flow Cytometry Antibodies Used Antigen Clone Supplier Anti-mouse antibodies CD45 30-F11 eBioscience CD90.2 53-2.1 eBioscience CD127 A7R34 eBioscience NKp46 29A1.4 eBioscience CD126 D7715A7 Biolegend CCR6 140706 R&D Systems ICOS 7E.17G9 eBioscience CD4 RM4.5 eBioscience Hematopoietic lineage cocktail (CD3, CD45R, B220, CD11b, TER-119, Gr-1) 17A2, RA3-6B2, M1/70, TER-119 eBioscience CD62L MEL-14 eBioscience IL17RB 752101 R&D Systems CD69 H1.2F3 eBioscience RORgt AFKJS-9 eBioscience IL17A eBio17B7 eBioscience IL22 1H8PWSR eBioscience Interferon-g XMG1.2 eBioscience IL4 11B11 eBioscience Anti-human antibodies CD3 UCHT-1 Biolegend CD127 A019D5 (eBioRDR5) Biolegend (eBioscience) CD117 104D2 eBioscience NKp46 9E2 eBioscience NKp44 44.189 eBioscience IL17RB I170220 R&D Systems RORgt AFKJS-9 eBioscience IL17A eBio64DEC17 eBioscience IL22 22URTI eBioscience Interferon-g 4S.B3 eBioscience RDP taxonomic classifications NCBI MegaBLAST ID P value Q value Order Family Genus Lactobacillales(100) Lactobacillaceae(100) Lactobacillus(100) Lactobacillus animalis/murinus .287595 1 Clostridiales(100) Lachnospiraceae(100) unclassified(100) Butyrivibrio species P79 (86% similarity) .022376 1 Lactobacillales(100) Lactobacillaceae(100) Lactobacillus(100) Lactobacillus taiwanensis/ johnsonii/acidophilus .947484 1 Clostridiales(100) Lachnospiraceae(100) Clostridium_XlVb(100) Clostridium lactatifermentans (90% similarity) .15343 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Eubacterium plexicaudatum (92% similarity) .82004 1 Bacteroidales(100) Unclassified(100) Unclassified(100) Butyricimonas species JCM 18677 (80% similarity) .012182 1 00) Campylobacterales(100) Helicobacteraceae(100) Helicobacter(100) Helicobacter typhlonius .173889 1 Deferribacterales(100) Deferribacteraceae(100) Mucispirillum(100) Mucispirillum colimuris .063365 1 Bacteroidales(100) Rikenellaceae(100) Alistipes(100) Alistipes onderdonkii (90% similarity) .874014 1 Bacteroidales(100) Rikenellaceae(100) Alistipes(100) Alistipes senegalensis (91% similarity) .800781 1 Clostridiales(100) Unclassified(100) Unclassified(100) Clostridium scindens (88% similarity) .766219 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Coprococcus catus (88% similarity) .571687 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) Oscillibacter valericigenes (91% similarity) .03155 1 Bacteroidales(100) Bacteroidaceae(100) Bacteroides(100) Bacteroides acidofaciens/ uniformis .082054 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) Anaerotruncus colihominis (92% similarity) .489023 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Clostridium hathewayi (92% similarity) .861923 1 Lactobacillales(100) Lactobacillaceae(100) Lactobacillus(100) Lactobacillus reuteri .644746 1 ) Unclassified(100) Unclassified(100) Unclassified(100) Desulfocurvus vexinensis (87% similarity) .44467 1 Deferribacterales(100) Deferribacteraceae(100) Mucispirillum(100) Mucispirillum colimuris (97% similarity) .039672 1 Bacteroidales(100) Unclassified(99) Unclassified(99) Tannerella forsythensis (82% similarity) .262652 1 Bacteroidales(100) Bacteroidaceae(100) Bacteroides(100) Bacteroides acidifaciens .733786 1 Bacteroidales(100) Prevotellaceae(100) Paraprevotella(100) Prevotella species (87% similarity) .137208 1 Clostridiales(100) Lachnospiraceae(52) Unclassified(52) Coprococcus catus (84% similarity) .501202 1 3 Powell et al Gastroenterology Vol. 149, No. References 2 Between the Proportional Abundance of the Top 150 Most Abundant OTUs in the Microbiota Data Set Between Anti-IL6 ps RDP taxonomic classifications NCBI MegaBLAST ID P value Q value Order Family Genus Lactobacillales(100) Lactobacillaceae(100) Lactobacillus(100) Lactobacillus animalis/murinus .287595 1 Clostridiales(100) Lachnospiraceae(100) unclassified(100) Butyrivibrio species P79 (86% similarity) .022376 1 Lactobacillales(100) Lactobacillaceae(100) Lactobacillus(100) Lactobacillus taiwanensis/ johnsonii/acidophilus .947484 1 Clostridiales(100) Lachnospiraceae(100) Clostridium_XlVb(100) Clostridium lactatifermentans (90% similarity) .15343 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Eubacterium plexicaudatum (92% similarity) .82004 1 Bacteroidales(100) Unclassified(100) Unclassified(100) Butyricimonas species JCM 18677 (80% similarity) .012182 1 00) Campylobacterales(100) Helicobacteraceae(100) Helicobacter(100) Helicobacter typhlonius .173889 1 Deferribacterales(100) Deferribacteraceae(100) Mucispirillum(100) Mucispirillum colimuris .063365 1 Bacteroidales(100) Rikenellaceae(100) Alistipes(100) Alistipes onderdonkii (90% similarity) .874014 1 Bacteroidales(100) Rikenellaceae(100) Alistipes(100) Alistipes senegalensis (91% similarity) .800781 1 Clostridiales(100) Unclassified(100) Unclassified(100) Clostridium scindens (88% similarity) .766219 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Coprococcus catus (88% similarity) .571687 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) Oscillibacter valericigenes (91% similarity) .03155 1 Bacteroidales(100) Bacteroidaceae(100) Bacteroides(100) Bacteroides acidofaciens/ uniformis .082054 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) Anaerotruncus colihominis (92% similarity) .489023 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Clostridium hathewayi (92% similarity) .861923 1 Lactobacillales(100) Lactobacillaceae(100) Lactobacillus(100) Lactobacillus reuteri .644746 1 ) Unclassified(100) Unclassified(100) Unclassified(100) Desulfocurvus vexinensis (87% similarity) .44467 1 Deferribacterales(100) Deferribacteraceae(100) Mucispirillum(100) Mucispirillum colimuris (97% similarity) .039672 1 Bacteroidales(100) Unclassified(99) Unclassified(99) Tannerella forsythensis (82% similarity) .262652 1 Bacteroidales(100) Bacteroidaceae(100) Bacteroides(100) Bacteroides acidifaciens .733786 1 Bacteroidales(100) Prevotellaceae(100) Paraprevotella(100) Prevotella species (87% similarity) .137208 1 Clostridiales(100) Lachnospiraceae(52) Unclassified(52) Coprococcus catus (84% similarity) .501202 1 467.e3 Powell et al Gastroenterology Vol. 149, No. 2 6 e 467.e3 Powell et al Gastroenterology Vol. 149, No. References 2 August 2015 RDP taxonomic classifications NCBI MegaBLAST ID P value Q value Order Family Genus Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Pseudobutyrivibrio ruminis (88% similarity) .510185 1 Bacteroidales(100) Porphyromonadaceae(100) Paludibacter(77) Prevotella dentalis (81% similarity) .162484 1 Bacteroidales(100) Bacteroidaceae(100) Bacteroides(100) Bacteroides uniformis (96% similarity) .195279 1 Erysipelotrichales(99) Erysipelotrichaceae(99) Erysipelotrichaceae_ incertae_sedis(99) Eubacterium cylindroides (88% similarity) .605205 1 Clostridiales(100) Unclassified(100) Unclassified(100) Clostridium aminophilum (86% similarity) .246769 1 TM7_order_incertae_ sedis(100) TM7_family_incertae_ sedis(100) TM7_genus_incertae_ sedis(100) TM7 phylum species (93% similarity) .222701 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Clostridium phytofermentans (90% similarity) .574396 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Clostridium celerecrescens (93% similarity) .664006 1 Clostridiales(100) Unclassified(100) Unclassified(100) Clostridium scindens (84% similarity) .737231 1 0) Enterobacteriales(100) Enterobacteriaceae(100) Unclassified Escherichia/Enterobacter/ Citrobacter/Shigella species .497501 1 Bacteroidales(100) Rikenellaceae(100) Alistipes(100) Alistipes senegalensis (92% similarity) .127302 1 Unclassified(100) Unclassified(100) Unclassified(100) Segmented filamentous bacterium .798342 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) Eubacterium oxidoreducens (87%) .334068 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .263709 1 Bacteroidales(100) Unclassified(100) Unclassified(100) .951701 1 Bacteroidales(100) Bacteroidaceae(100) Bacteroides(100) .178105 1 Clostridiales(100) Lachnospiraceae(100) Lachnospiracea_incertae_ sedis(79) .987598 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .948299 1 Bacteroidales(100) Bacteroidaceae(100) Bacteroides(100) .334148 1 Clostridiales(100) Lachnospiraceae(100) Dorea(93) .850598 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) .622208 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .948849 1 Bacteroidales(100) Rikenellaceae(100) Alistipes(100) .211071 1 Clostridiales(100) Lachnospiraceae(100) Clostridium_XlVb(100) .449205 1 Clostridiales(100) Unclassified(100) Unclassified(100) .101219 1 Clostridiales(100) Ruminococcaceae(100) Butyricicoccus(100) .597761 1 Bacteroidales(100) Porphyromonadaceae(100) Odoribacter(100) .824846 1 467.e5 Powell et al Clostridiales(100) Lachnospiraceae(100) Unclassified(72) .889006 1 Unclassified(99) Unclassified(99) Unclassified(99) .352835 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .420749 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .807154 1 Clostridiales(100) Lachnospiraceae(100) Roseburia(100) .549208 1 Clostridiales(100) Lachnospiraceae(100) unclassified(100) .795695 1 Clostridiales(100) Ruminococcaceae(100) Acetanaerobacterium(100) .795544 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .594923 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .319484 1 Unclassified(100) Unclassified(100) Unclassified(100) .815476 1 Clostridiales(100) Unclassified(100) Unclassified(100) .245678 1 Clostridiales(100) Lachnospiraceae(100) Roseburia(100) .642752 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .866248 1 Clostridiales(100) Unclassified(100) Unclassified(100) .684305 1 Coriobacteriales(100) Coriobacteriaceae(100) Enterorhabdus(100) .470026 1 Unclassified(100) Unclassified(100) Unclassified(100) .781442 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .075425 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .23604 1 0) Desulfovibrionales(100) Desulfovibrionaceae(100) Desulfovibrio(93) .122282 1 Clostridiales(100) Lachnospiraceae(100) Dorea(100) .335755 1 Unclassified(100) Unclassified(100) Unclassified(100) .275564 1 Bacteroidales(100) Porphyromonadaceae(100) Unclassified(100) .6759 1 Clostridiales(100) Ruminococcaceae(98) Unclassified(98) .739009 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .099638 1 Bacteroidales(100) Porphyromonadaceae(100) Unclassified(100) .142259 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .446379 1 Clostridiales(100) Lachnospiraceae(100) Butyrivibrio(91) .048125 1 Coriobacteriales(100) Coriobacteriaceae(100) Unclassified(100) .020051 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .995336 1 Clostridiales(100) Lachnospiraceae(100) Dorea(100) .580909 1 Clostridiales(100) Lachnospiraceae(100) Butyrivibrio(96) .231131 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .144752 1 Coriobacteriales(100) Coriobacteriaceae(100) Asaccharobacter(100) .683732 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .059598 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) .557724 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) .829296 1 Clostridiales(100) Ruminococcaceae(100) Unclassified(100) .147604 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .325188 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .270353 1 Clostridiales(100) Lachnospiraceae(100) Clostridium_XlVa(98) .893607 1 Bacteroidales(100) Unclassified(97) Unclassified(97) .064746 1 Clostridiales(100) Lachnospiraceae(100) Syntrophococcus(100) .465783 1 August 2015 RDP taxonomic classifications NCBI MegaBLAST ID P value Q value Order Family Genus 0) Desulfovibrionales(100) Desulfovibrionaceae(100) Desulfocurvus(73) .719197 1 Clostridiales(100) Ruminococcaceae(100) Pseudoflavonifractor(100) .223923 1 Clostridiales(100) Ruminococcaceae(100) Pseudoflavonifractor(65) .323615 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .220402 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .755524 1 Erysipelotrichales(100) Erysipelotrichaceae(100) Clostridium_XVIII(100) .167966 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .658952 1 Lactobacillales(100) Streptococcaceae(100) Streptococcus(100) .271556 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .529912 1 Clostridiales(100) Ruminococcaceae(100) Unclassified(98) .239692 1 Coriobacteriales(100) Coriobacteriaceae(100) Unclassified(100) .438692 1 Clostridiales(100) Ruminococcaceae(100) Flavonifractor(97) .884299 1 Bacteroidales(100) Porphyromonadaceae(100) Parabacteroides(100) .604151 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .052835 1 Clostridiales(100) Lachnospiraceae(100) Lactonifactor(100) .688385 1 Unclassified(100) Unclassified(100) Unclassified(100) .808444 1 Unclassified(100) Unclassified(100) Unclassified(100) .580963 1 Bacteroidales(100) Rikenellaceae(100) Alistipes(100) .590556 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .70702 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) .629385 1 Clostridiales(100) Lachnospiraceae(100) Clostridium_XlVa(97) .690915 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .659852 1 Clostridiales(100) Unclassified(100) Unclassified(100) .052071 1 Clostridiales(100) Ruminococcaceae(100) Clostridium_IV(100) .496749 1 Clostridiales(100) Lachnospiraceae(100) Lachnospiracea_incertae_ sedis(64) .783083 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .450217 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) .474766 1 Clostridiales(100) Lachnospiraceae(100) Roseburia(100) .677578 1 Clostridiales(100) Ruminococcaceae(100) Pseudoflavonifractor(100) .764818 1 Clostridiales(100) Lachnospiraceae(100) Roseburia(71) .221575 1 0) Desulfovibrionales(100) Desulfovibrionaceae(100) Bilophila(100) .759601 1 Clostridiales(100) Ruminococcaceae(100) Hydrogenoanaero- bacterium(100) .641479 1 Clostridiales(100) Ruminococcaceae(100) Pseudoflavonifractor(100) .015658 1 Clostridiales(100) Ruminococcaceae(100) Flavonifractor(100) .017547 1 Clostridiales(100) Lachnospiraceae(100) Butyrivibrio(100) .106234 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .090769 1 Erysipelotrichales(100) Erysipelotrichaceae(100) Erysipelotrichaceae_ incertae_sedis(100) .304972 1 Clostridiales(100) Lachnospiraceae(100) Syntrophococcus(100) .351336 1 Clostridiales(100) Ruminococcaceae(100) Flavonifractor(100) .733134 1 RDP taxonomic classifications NCBI MegaBLAST ID P value Q value Order Family Genus 0) Desulfovibrionales(100) Desulfovibrionaceae(100) Desulfocurvus(73) .719197 1 Clostridiales(100) Ruminococcaceae(100) Pseudoflavonifractor(100) .223923 1 Clostridiales(100) Ruminococcaceae(100) Pseudoflavonifractor(65) .323615 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .220402 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .755524 1 Erysipelotrichales(100) Erysipelotrichaceae(100) Clostridium_XVIII(100) .167966 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .658952 1 Lactobacillales(100) Streptococcaceae(100) Streptococcus(100) .271556 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .529912 1 Clostridiales(100) Ruminococcaceae(100) Unclassified(98) .239692 1 Coriobacteriales(100) Coriobacteriaceae(100) Unclassified(100) .438692 1 Clostridiales(100) Ruminococcaceae(100) Flavonifractor(97) .884299 1 Bacteroidales(100) Porphyromonadaceae(100) Parabacteroides(100) .604151 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .052835 1 Clostridiales(100) Lachnospiraceae(100) Lactonifactor(100) .688385 1 Unclassified(100) Unclassified(100) Unclassified(100) .808444 1 Unclassified(100) Unclassified(100) Unclassified(100) .580963 1 Bacteroidales(100) Rikenellaceae(100) Alistipes(100) .590556 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .70702 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) .629385 1 Clostridiales(100) Lachnospiraceae(100) Clostridium_XlVa(97) .690915 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .659852 1 Clostridiales(100) Unclassified(100) Unclassified(100) .052071 1 Clostridiales(100) Ruminococcaceae(100) Clostridium_IV(100) .496749 1 Clostridiales(100) Lachnospiraceae(100) Lachnospiracea_incertae_ sedis(64) .783083 1 Clostridiales(100) Lachnospiraceae(100) Unclassified(100) .450217 1 Clostridiales(100) Ruminococcaceae(100) Anaerotruncus(100) .474766 1 Clostridiales(100) Lachnospiraceae(100) Roseburia(100) .677578 1 Clostridiales(100) Ruminococcaceae(100) Pseudoflavonifractor(100) .764818 1 Clostridiales(100) Lachnospiraceae(100) Roseburia(71) .221575 1 0) Desulfovibrionales(100) Desulfovibrionaceae(100) Bilophila(100) .759601 1 Clostridiales(100) Ruminococcaceae(100) Hydrogenoanaero- bacterium(100) .641479 1 Clostridiales(100) Ruminococcaceae(100) Pseudoflavonifractor(100) .015658 1 Clostridiales(100) Ruminococcaceae(100) Flavonifractor(100) .017547 1 Clostridiales(100) Lachnospiraceae(100) Butyrivibrio(100) .106234 1 Clostridiales(100) Ruminococcaceae(100) Oscillibacter(100) .090769 1 Erysipelotrichales(100) Erysipelotrichaceae(100) Erysipelotrichaceae_ incertae_sedis(100) .304972 1 Clostridiales(100) Lachnospiraceae(100) Syntrophococcus(100) .351336 1 Clostridiales(100) Ruminococcaceae(100) Flavonifractor(100) .733134 1 467.e7 Powell et al NCBI MegaBLAST ID P value Q value Genus 0) Pseudoflavonifractor(100) .651459 1 0) Oscillibacter(100) .336219 1 Alistipes(100) .364453 1 Unclassified(100) .297057 1 0) Anaerotruncus(100) .255234 1 Unclassified(66) .06594 1 Clostridium_XlVa(100) .934883 1 e(100) Unclassified(100) .364453 1 Unclassified(100) .019222 1 Unclassified(100) .486003 1 Unclassified(100) .714399 1 Unclassified(100) .641689 1 e(69) Unclassified(69) .511826 1 Unclassified(97) .718342 1 Alistipes(100) .977493 1 0) Oscillibacter(100) .345778 1 Unclassified(100) .08833 1 Clostridium_XlVb(100) .548781 1 Unclassified(100) .633538 1 atabase from the Ribosomal Database Project. References The numbers in parenthesis t) for all of the sequence reads within a given OTU. p values and q values g Metastats software (White JR et al. PLoS Comput Biol. 2009:e1000352). IL6 Increases Cytokines by ILCs 467.e8 August 2015 August 2015 ementary Figure 1. (A) Representative flow cytometry plot and statistical analysis (B) showing differential expression of and CCR6 in live CD45þ CD90þ IL7Rþ cells in the colon of Rag2-/- (n ¼ 6, white bar) and TRUC (n ¼ 5, red bar) mice. ars depict SEM. *P < .01, **P < .005. (C) Flow cytometric analysis of the phenotype of CD90þ IL7Rþ ILCs in the colons C mice. Grey histograms show staining with isotype-matched control antibody in comparison with staining with specific dy (white histograms with black lines). Data are representative of more than 3 individual experiments. (D) Proportion of ne-expressing CD45þ CD90þ IL7Rþ ILCs in the colons of Rag2-/- and TRUC mice after stimulation of unfractionated Cs with PMA and ionomycin. Each dot/square represents an individual mouse. Supplementary Figure 1. (A) Representative flow cytometry plot and statistical analysis (B) showing differential expression of NKp46 and CCR6 in live CD45þ CD90þ IL7Rþ cells in the colon of Rag2-/- (n ¼ 6, white bar) and TRUC (n ¼ 5, red bar) mice. Error bars depict SEM. *P < .01, **P < .005. (C) Flow cytometric analysis of the phenotype of CD90þ IL7Rþ ILCs in the colons of TRUC mice. Grey histograms show staining with isotype-matched control antibody in comparison with staining with specific antibody (white histograms with black lines). Data are representative of more than 3 individual experiments. (D) Proportion of cytokine-expressing CD45þ CD90þ IL7Rþ ILCs in the colons of Rag2-/- and TRUC mice after stimulation of unfractionated cLPMCs with PMA and ionomycin. Each dot/square represents an individual mouse. Gastroenterology Vol. 149, No. 2 467.e9 Powell et al 467.e9 Powell et al Gastroenterology Vol. 149, No. 2 467.e9 Powell et al Gastroenterology Vol. Supplementary Figure 2. (A) IL6 concentration in serum (left panel) and colon explant culture (right panel) of Rag2-/- and TRUC mice measured by ELISA. Dots/squares represent individual mice. Line depicts the median. (B) Microarray analysis showing abundance of transcripts encoded by genes known to be regulated by IL6 in the colon of TRUC mice relative to Rag2-/- mice. References Blue bars represent transcripts up-regulated in the colons of TRUC mice and red bars represent down-regulated genes (in comparison with Rag2-/- mice). Supplementary Figure 2. (A) IL6 concentration in serum (left panel) and colon explant culture (right panel) of Rag2-/- and TRUC mice measured by ELISA. Dots/squares represent individual mice. Line depicts the median. (B) Microarray analysis showing abundance of transcripts encoded by genes known to be regulated by IL6 in the colon of TRUC mice relative to Rag2-/- mice. Blue bars represent transcripts up-regulated in the colons of TRUC mice and red bars represent down-regulated genes (in comparison with Rag2-/- mice). Supplementary Figure 2. (A) IL6 concentration in serum (left panel) and colon explant culture (right panel) of Rag2-/- and TRUC mice measured by ELISA. Dots/squares represent individual mice. Line depicts the median. (B) Microarray analysis showing abundance of transcripts encoded by genes known to be regulated by IL6 in the colon of TRUC mice relative to Rag2-/- mice. Blue bars represent transcripts up-regulated in the colons of TRUC mice and red bars represent down-regulated genes (in comparison with Rag2-/- mice). upplementary Figure 3. (A) FACs gating strategy used to purify ILCs from the colon of TRUC mice. CD45þ cells were first riched from cLPMCs using anti-CD45 immunomagnetic beads. ILCs were FACs purified more than 98%. (B) Cytokine oduction by FACs purified CD90þ IL7Rþ NKp46- colonic ILCs from TRUC mice. Cells were cultured in the presence of ombinations of IL1a, IL23, IL6 (as depicted), or medium alone (unstimulated). IL6 was measured in culture supernatant by BA. Bars show the mean cytokine production and error bars depict the SEM. Data are from 2 independent experiments. gust 2015 IL6 Increases Cytokines by ILCs 467.e10 IL6 Increases Cytokines by ILCs 467.e10 August 2015 Supplementary Figure 3. (A) FACs gating strategy used to purify ILCs from the colon of TRUC mice. CD45þ cells were first enriched from cLPMCs using anti-CD45 immunomagnetic beads. ILCs were FACs purified more than 98%. (B) Cytokine production by FACs purified CD90þ IL7Rþ NKp46- colonic ILCs from TRUC mice. Cells were cultured in the presence of combinations of IL1a, IL23, IL6 (as depicted), or medium alone (unstimulated). IL6 was measured in culture supernatant by CBA. Bars show the mean cytokine production and error bars depict the SEM. Data are from 2 independent experiments. Supplementary Figure 3. = Supplementary Figure 5. (A) Concentration of IL6 in serum of TRUC mice treated with anti-IL6 or control isotype antibody. Dots/squares represent individual mice. Line depicts median. (B) Bray Curtis cluster dendrogram showing that anti-IL6 treatment is not associated with a distinct microbiota profile. “Pre” indicates samples before anti-IL6 treatment and “Post” indicates samples after treatment. Bacterial families colored in shades of green belong to the Firmicutes phylum, blue belong to the Bacteroidetes phylum, yellow belong to the Deferribacteres phylum (Mucispirillum genus), and maroon/red belong to the Proteobacteria phylum. (C) Box and whisker plots of Simpson diversity index of the intestinal microbiota from TRUC mice treated with anti-IL6 or isotype-matched control antibodies. Diversity indices are highly sensitive to differential sequencing depth. Therefore, analyses were confined to 477 reads per sample. References (A) FACs gating strategy used to purify ILCs from the colon of TRUC mice. CD45þ cells were first enriched from cLPMCs using anti-CD45 immunomagnetic beads. ILCs were FACs purified more than 98%. (B) Cytokine production by FACs purified CD90þ IL7Rþ NKp46- colonic ILCs from TRUC mice. Cells were cultured in the presence of combinations of IL1a, IL23, IL6 (as depicted), or medium alone (unstimulated). IL6 was measured in culture supernatant by CBA. Bars show the mean cytokine production and error bars depict the SEM. Data are from 2 independent experiments. Supplementary Figure 4. (A) Flow cytometry plots showing IL6R expression by CD4þ T cells, ILCs (lineage- IL7Rþ) in the colons of wild-type (WT) and TRUC mice. Data are representative of 3 independent experiments. (B) Concentration of sIL6R in serum (n ¼ 6) and supernatants of cultured colon explants (n ¼ 5) and unfractionated splenocytes (n ¼ 3) measured by ELISA. Bars represent the mean sIL6R concentration and error bars depict the SEM. 467.e11 Powell et al Gastroenterology Vol. 149, No. 2 Gastroenterology Vol. 149, No. 2 467.e11 Powell et al Supplementary Figure 4 (A) Flow cytometry plots showing IL6R expression by CD4þ T cells ILCs (lineage- IL7Rþ) in the Supplementary Figure 4. (A) Flow cytometry plots showing IL6R expression by CD4þ T cells, ILCs (lineage- IL7Rþ) in the colons of wild-type (WT) and TRUC mice. Data are representative of 3 independent experiments. (B) Concentration of sIL6R in serum (n ¼ 6) and supernatants of cultured colon explants (n ¼ 5) and unfractionated splenocytes (n ¼ 3) measured by ELISA. Bars represent the mean sIL6R concentration and error bars depict the SEM. Supplementary Figure 4. (A) Flow cytometry plots showing IL6R expression by CD4þ T cells, ILCs (lineage- IL7Rþ) in the colons of wild-type (WT) and TRUC mice. Data are representative of 3 independent experiments. (B) Concentration of sIL6R in serum (n ¼ 6) and supernatants of cultured colon explants (n ¼ 5) and unfractionated splenocytes (n ¼ 3) measured by ELISA. Bars represent the mean sIL6R concentration and error bars depict the SEM. August 2015 IL6 Increases Cytokines by ILCs 467.e12 IL6 Increases Cytokines by ILCs 467.e12 August 2015 467.e13 Powell et al Gastroenterology Vol. 149, No. 2 lementary Figure 6. (A) Representative flow cytometry plots of intracellular cytokine and surface CD3 expr flammatory control, CD, and UC patients. Cells were stimulated with PMA and ionomycin. References (B) Real-time PCR a C expression in sorted colonic CD3- IL7Rþ cells in comparison with CD14þ monocytes (immunomagnetically peripheral blood monocytes). Histogram shows the mean expression of RORC in purified colonic CD3- IL7Rþ ce patients) relative to monocytes. (C) Proportion of colonic CD3- IL7Rþ cells expressing c-kit (CD117) in noninfla ol, CD, and UC patients. (D) Proportion of colonic CD3- IL7Rþ cells expressing NKp46, NKp44, or double-nega 46- NKp44-) in noninflammatory control, CD, and UC patients. (E) IL6 production in colon explant cultures nts. In graphs, each dot represents an individual patient and a line depicts the median. st 2015 IL6 Increases Cytokines by ILCs IL6 Increases Cytokines by ILCs 467.e14 August 2015 August 2015 ugust 2015 IL6 Increases Cytokines by ILC August 2015 Supplementary Figure 6. (A) Representative flow cytometry plots of intracellular cytokine and surface CD3 expression in noninflammatory control, CD, and UC patients. Cells were stimulated with PMA and ionomycin. (B) Real-time PCR analysis of RORC expression in sorted colonic CD3- IL7Rþ cells in comparison with CD14þ monocytes (immunomagnetically selected from peripheral blood monocytes). Histogram shows the mean expression of RORC in purified colonic CD3- IL7Rþ cells (n ¼ 2 IBD patients) relative to monocytes. (C) Proportion of colonic CD3- IL7Rþ cells expressing c-kit (CD117) in noninflammatory control, CD, and UC patients. (D) Proportion of colonic CD3- IL7Rþ cells expressing NKp46, NKp44, or double-negative cells (NKp46- NKp44-) in noninflammatory control, CD, and UC patients. (E) IL6 production in colon explant cultures from IBD patients. In graphs, each dot represents an individual patient and a line depicts the median. Supplementary Figure 6. (A) Representative flow cytometry plots of intracellular cytokine and surface CD3 expression in noninflammatory control, CD, and UC patients. Cells were stimulated with PMA and ionomycin. (B) Real-time PCR analysis of RORC expression in sorted colonic CD3- IL7Rþ cells in comparison with CD14þ monocytes (immunomagnetically selected from peripheral blood monocytes). Histogram shows the mean expression of RORC in purified colonic CD3- IL7Rþ cells (n ¼ 2 IBD patients) relative to monocytes. (C) Proportion of colonic CD3- IL7Rþ cells expressing c-kit (CD117) in noninflammatory control, CD, and UC patients. (D) Proportion of colonic CD3- IL7Rþ cells expressing NKp46, NKp44, or double-negative cells (NKp46- NKp44-) in noninflammatory control, CD, and UC patients. (E) IL6 production in colon explant cultures from IBD patients. In graphs, each dot represents an individual patient and a line depicts the median. References Supplementary Figure 6. (Continued) 467.e15 Powell et al Gastroenterology Vol. 149, No. 2 467.e15 Powell et al Supplementary Figure 6. (Continued) Supplementary Figure 6. (Continued)
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Review of: "The Imperative of a Comprehensive One Health Approach for Mosquito-Borne Disease Control in Indonesia"
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Qeios, CC-BY 4.0 · Review, February 3, 2024 Qeios ID: 4NYPME · https://doi.org/10.32388/4NYPME Review of: "The Imperative of a Comprehensive One Health Approach for Mosquito-Borne Disease Control in Indonesia" Vivek Kumar Singh Potential competing interests: No potential competing interests to declare. Topic is interesting. Language editing is recommended. Please see comments below: 1. Use some other word for “such as” in the first sentence of the introduction. 2. Use a better word instead of “make” in the second sentence of the introduction. 3. Rephrase the sentence, “Therefore, it is important to explore the factors that need to be considered when developing a single health concept for mosquito-borne disease control, especially in Indonesia.” 4. Words like “hopefully” are not preferred in scientific writing. 3. Rephrase the sentence, “Therefore, it is important to explore the factors that need to be considered when developing a single health concept for mosquito-borne disease control, especially in Indonesia.” Community engagement and health education 1. Use some other word instead of “educators” in the last sentence. Key focus areas for mosquito-borne disease control in Indonesia 1. Rephrase “Increasing public awareness of minimizing breeding sites, teaching the basics of vectors, and presenting a clean and healthy environment are the smallest habit-forming efforts to realize the concept of one’s health at the household level.” 1. Rephrase “Increasing public awareness of minimizing breeding sites, teaching the basics of vectors, and presenting a clean and healthy environment are the smallest habit-forming efforts to realize the concept of one’s health at the household level.” Qeios ID: 4NYPME · https://doi.org/10.32388/4NYPME 1/1
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The association between breast arterial calcification and atherosclerotic cardiovascular disease in an Australian population-based breast cancer case–control study
˜La œRadiologia medica
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La radiologia medica (2023) 128:426–433 https://doi.org/10.1007/s11547-023-01611-y La radiologia medica (2023) 128:426–433 https://doi.org/10.1007/s11547-023-01611-y BREAST RADIOLOGY Abstract Purpose  Atherosclerotic cardiovascular disease (ASCVD) is a major cause of morbidity and mortality. Breast arterial calci- fication (BAC) on mammograms is not associated with breast cancer risk. However, there is increasing evidence supporting its association with cardiovascular disease (CVD). This study examines the association between BAC and ASCVD and their risk factors within an Australian population-based breast cancer study. Materials and methods  Data from the controls who participated in the breast cancer environment and employment study (BCEES) were linked with the Western Australian Department of Health Hospital Morbidity database and Mortality Registry to obtain ASCVD outcomes and related risk factor data. Mammograms from participants with no prior history of ASCVD were assessed for BAC by a radiologist. Cox proportional hazards regression was used to examine the association between BAC and later occurrence of an ASCVD event. Logistic regression was used to investigate the factors associated with BAC. Results  A total of 1020 women with a mean age of 60 (sd = 7.0 years) were included and BAC found in 184 (18.0%). Eighty (7.8%) of the 1020 participants developed ASCVD, with an average time to event of 6.2 years (sd = 4.6) from baseline. In univariate analysis, participants with BAC were more likely to have an ASCVD event (HR = 1.96 95% CI 1.29–2.99). However, after adjusting for other risk factors, this association attenuated (HR = 1.37 95% CI 0.88–2.14). Increasing age (OR = 1.15, 95% CI 1.12–1.19) and parity (pLRT < 0.001) were associated with BAC. LRT Conclusion  BAC is associated with increased ASCVD risk, but this is not independent of cardiovascular risk factors. Conclusion  BAC is associated with increased ASCVD risk, but this is not independent of cardiovas Keywords  Atherosclerotic cardiovascular disease · ASCVD · Breast arterial calcification · BAC · Mammogram · Cardiovascular disease Keywords  Atherosclerotic cardiovascular disease · ASCVD · Breast arterial calcification · BAC · Mammogram · Cardiovascular disease * Sing Ching Lee sing.lee@research.uwa.edu.au The association between breast arterial calcification and atherosclerotic cardiovascular disease in an Australian population‑based breast cancer case–control study Sing Ching Lee1,2   · Sarah Pirikahu3 · Lin Fritschi4 · Terry Boyle5 · Carl Schultz1,2 · Elizabeth Wyl Received: 18 August 2022 / Accepted: 16 February 2023 / Published online: 6 March 2023 © Crown 2023 Joint first authors: Sing Ching Lee and Sarah Pirikahu. Introduction Joint first authors: Sing Ching Lee and Sarah Pirikahu. Joint first authors: Sing Ching Lee and Sarah Pirikahu. Atherosclerotic cardiovascular disease (ASCVD), which includes myocardial infarction, stroke and peripheral artery disease, remains a major cause of death, and women are more likely than men to die from an ASCVD event [1, 2]. This disparity between women and men is partially due to women being more likely to have delayed presentations or diagnoses [3]. In addition, the underestimation of cardio- vascular risk in women from standard screening methods contributes to under-prescription of preventative therapies [4]. A female-specific screening tool that simultaneously increases ASCVD awareness and reduces risk factors could reduce these inequalities, especially if it was widely avail- able at a minimal cost.i * Sing Ching Lee sing.lee@research.uwa.edu.au * Sing Ching Lee sing.lee@research.uwa.edu.au 1 Department of Cardiology, Royal Perth Hospital, Perth, Australia 1 Department of Cardiology, Royal Perth Hospital, Perth, Australia 2 Medical School, University of Western Australia, Perth, Australia 3 Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, Australia 4 School of Population Health, Curtin University, Perth, Australia 5 Australian Centre for Precision Health, Allied Health and Human Performance, University of South Australia, Adelaide, Australia Breast arterial calcification (BAC) is a common incidental finding in screening mammograms (Fig. 1). It is not known 6 BreastScreen Western Australia, Perth, Australia :.(123456789 3 427 La radiologia medica (2023) 128:426–433 Fig. 1   Breast arterial calcification on a mammogram (highlighted by the arrows) Employment Study (BCEES) were selected for this ret- rospective study [6]. In brief, controls were women aged between 18 and 80 years with an age distribution matched to the expected distribution of breast cancer in the population. Of the participating controls, those who had a mammogram between May 2009 and January 2011 were potentially eli- gible for this study. Employment Study (BCEES) were selected for this ret- rospective study [6]. In brief, controls were women aged between 18 and 80 years with an age distribution matched to Women with a prior history of ASCVD were excluded. These data were obtained through data linkage with Breast- Screen Western Australia [7] and hospital morbidity and mortality databases from the Western Australian Depart- ment of Health Data Linkage Branch. ASCVD was defined as ischemic heart disease, stroke or peripheral artery dis- ease, as described by Weng et al. Data collection of outcome and covariates Incident ASCVD, as defined above, was ascertained through to the 11 October 2018, when follow-up ended, using the linkage to the hospital morbidity and mortality databases from the Western Australian Department of Health. Covari- ate data were obtained using the baseline epidemiologi- cal questionnaire data collected upon recruitment into the BCEES. This included information on age (years), body mass index (BMI, kg/m2), smoking (current, former and never), parity (number of births), breastfeeding (yes/no), hormone replacement therapy (HRT) use (yes/no) and con- traceptive use (combined, other hormonal, unknown hor- monal and no contraception). Other covariate data such as hypertension, dyslipidemia and diabetes mellitus were collected using data linkage. Hypertension, dyslipidemia and diabetes were defined as positive if a woman was ever diagnosed with ICD-9 and ICD-10 codes detailed in Online Resource 1. Utilizing data from an existing population-based breast cancer study, we selected a subset of women with no prior history of ASCVD to examine whether the presence of BAC was associated with the development of ASCVD. We also examined potential predictors of BAC, investigating if ASCVD risk factors were associated with the presence of BAC. Introduction [8], and the ICD-9 and -10 codes are detailed in Online Resource 1. Women were considered to have had an ASCVD event if they had a hos- pital admission for any of the relevant codes, or if they did not present to hospital but their cause of death was either one of the specified ICD codes, or was specified as cardiac arrest, myocardial infarction, cerebrovascular accident or a complication due to ischemic heart disease. Mammographic data An expert radiologist (EW) blinded to ASCVD status visually assessed BAC as present or absent for each breast from medio-lateral oblique and cranio-caudal film screen- ing mammograms. If BAC was present on either breast, a woman was classified as having BAC. Absolute dense area was obtained using the Cumulus software (Sunnybrook Health Sciences Centre, Toronto, Canada). Dense breast was defined as those whose absolute dense area was above the mean absolute dense area of the study population. Fig. 1   Breast arterial calcification on a mammogram (highlighted by the arrows) to be associated with breast cancer and is therefore, often not routinely mentioned in mammogram reports. A recent systematic review has shown that BAC may be a poten- tial marker of coronary artery disease, diabetes mellitus and hypertension [5], which suggests that mammographic screening may help to identify women at increased risk of chronic diseases other than breast cancer. However, many of the previously published studies were cross sectional and did not specifically select a population of women with no prior history of ASCVD. Statistical analysis 1789 BCEES study control par cipants eligible for par cipa on in this study 1108 study par cipants had linked morbidity/mortality data from the Western Australia Department of Health and BAC was assessed 57 women were excluded as they were diagnosed with ASCVD before their mammogram (N=1051) 31 women were excluded due to missing epidemiological data, 30 of which were missing BMI or age (N=1020) Fig. 2   Flowchart of study subjects Descriptive statistics were used to characterize the study population. Univariable and multivariable logistic regres- sion models were used to estimate odds ratios (OR) and 95% confidence intervals (CI) to describe the association between BAC and potential risk factors. The group with the greatest number of cases was selected as the reference group. Inclu- sion of covariates in the final multivariable model was deter- mined using stepwise regression and a threshold of p = 0.05. 1108 study par cipants had linked morbidity/mortality data from the Western Australia Department of Health and BAC was assessed Hazards ratios (HR) and 95% CI were estimated using univariable and multivariable Cox proportional hazards model to describe the association between each factor and occurrence of a ASCVD event over time. Time to event was calculated in years from the date of screening mammogram until either the date of an ASCVD event, death (due to any cause) or the end of the study period. Women were right censored in the model if they died due to a cause other than ASCVD. The reference group was defined as the group with the greatest number of cases. Proportional hazard assump- tions for the Cox models were assessed by Schoenfeld test and linearity of continuous variables via visualization of the Martingale residuals. Multivariable models were adjusted for age, BMI, hypertension, dyslipidemia, diabetes, smok- ing status, parity, breastfeeding, HRT use and contraceptive use. Inclusion of covariates in the final multivariable model was determined using stepwise regression and a threshold of p = 0.05. Factors considered important to ASCVD etiol- ogy (i.e., age, BMI) were retained in the model even if the p values were greater than the 0.05 level of significance. Interactions between BAC and hypertension or dyslipidemia were hypothesized a-priori, and evidence of interaction was assessed using likelihood ratio tests. Subset analyses were also carried out for women who had breast density measure- ments available. Fig. 2   Flowchart of study subjects likely to be older (mean age: 65.1 vs. Statistical analysis 59.3 years), have been diagnosed with hypertension (21.7 vs. 15.7%), diabetes (4.4 vs. 2.8%), never smoked (73.4 vs. 58.7%) and have previ- ously breastfed (87.0 vs. 76.7%) (Table 1). Univariable logistic regression (Table 1) showed that BAC was associated with increasing age (OR = 1.15 per year, 95% CI:1.12–1.19) and increased parity (OR = 0.06, 95% CI: 0.02–0.27, OR = 0.21, 95% CI: 0.08–0.53, OR = 0.44, 95% CI: 0.31–0.63 for none, one and two births, respec- tively, compared to three or more births). Women who had never breastfed were significantly less likely to have BAC (OR = 0.49, 95% CI: 0.31–0.78). Smoking was inversely associated with BAC (OR = 0.29, 95% CI: 0.12–0.76 and OR = 0.56, 95% CI: 0.39–0.82 for current and former smok- ers, respectively). In the multivariable analysis, only increas- ing age and parity showed evidence of association with BAC (Table 1). A total of 80 women (7.8%) developed ASCVD with the majority (77.5%) having ischemic heart disease, and the average time to event (i.e., time between mammo- gram and ASCVD hospitalization or death) was 6.2 years (sd = 4.6 years). Table 2 shows the characteristics of women who did and did not develop ASCVD. Overall, the preva- lence of cardiovascular risk factors was low, but, on aver- age, women who developed ASCVD were older at baseline than those without ASCVD (64.2 vs. 60.0 years) and had a greater BMI (28.0 vs. 26.8 kg/m2). At baseline, ASCVD cases were more likely than those without ASCVD to have hypertension (55.0 vs. 13.5%) or dyslipidemia (8.8 vs. 1.2%) and were more likely to have taken hormone replacement therapy (70.0 vs. 54.3%). Study design and population Control participants from a West Australian case–con- trol study known as the Breast Cancer Environment and 1 3 428 La radiologia medica (2023) 128:426–433 Results three +) None 87 (8.5) 2 (1.1) 85 (10.2) 0.06 (0.02–0.27)**b 0.06 (0.01–0.25)**c One 71 (7.0) 5 (2.7) 66 (7.9) 0.21 (0.08–0.53)** 0.24 (0.09–0.62)** Two 407 (39.9) 56 (30.4) 351 (42.0) 0.44 (0.31–0.63)** 0.57 (0.39–0.82)** Breastfed (yes) 219 (21.5) 24 (13.0) 195 (23.3) 0.49 (0.31–0.78)** HRT (vs. no) 566 (55.5) 111 (60.3) 455 (54.4) 1.27 (0.92–1.76) Contraception use (vs. no contraception) Combined OC 474 (46.5) 87 (47.3) 387 (46.3) 0.98 (0.65–1.47)d Other hormonal 180 (17.6) 31 (16.8) 149 (17.8) 0.90 (0.54–1.51) Unknown 136 (13.3) 23 (12.5) 113 (13.5) 0.89 (0.51–1.55) Baseline cohort characteristics and associations between BAC and clinical and demographic factors HRT Hormone replacement therapy, OC Oral contraceptive, CI Confidence interval, BAC Breast arterial calcification; Significance is repre- sented by * for p values < 0.05 and ** for p values < 0.01; for non-binary categorical variables, the like likelihood ratio test p values are provided aptrend = 0.0003; bptrend < 0.0001; cptrend < 0.0001; dptrend = 0.96 Table 2   Univariable and multivariate risk of ASCVD in relation to clinical and demographic factors from Cox proportional hazards models ASCVD Atherosclerotic cardiovascular disease, HRT Hormone replacement therapy, OC Oral contraceptive, CI Confidence interval, BAC Breast arterial calcification; Significance is represented by * for p values < 0.05 and ** for p values < 0.01; for non-binary categorical variables, the like likelihood ratio test p values are provided aptrend = 0.11; bptrend = 0.005; cptrend = 0.73; dptrend = 0.12 Risk factor ASCVD (N = 80) Mean ± SD or Count (%) No ASCVD (N = 940) Mean ± SD or Count (%) Univariable analysis Hazard ratio (95% CI) Multivariable analysis Hazard ratio (95% CI) BAC (vs. no) 24 (30.0) 160 (17.0) 1.96 (1.29–2.99)** 1.37 (0.88–2.14) Age (years) 64.2 ± 6.3 60.0 ± 7.0 1.09 (1.06–1.13)** 1.08 (1.04–1.11)** BMI (kg/m2) 28.0 ± 6.6 26.8 ± 5.1 1.02 (0.98–1.05) 1.00 (0.97–1.04) Hypertension (vs no) 44 (55.0) 127 (13.5) 4.15 (2.82–6.12)** 3.35 (2.23–5.04)** Dyslipidemia (vs no) 7 (8.8) 11 (1.2) 3.85 (1.77–8.40)** Diabetes (vs. no) 8 (10.0) 23 (2.5) 2.66 (1.29–5.48)** Smoker (vs. never) Current 5 (6.3) 61 (6.5) 1.43 (0.68–3.02)a 2.45 (1.15–5.22)*b Former 36 (45.0) 292 (31.1) 1.53 (1.02–2.28)* 1.83 (1.22–2.76)** Parity (vs. three +) None 9 (11.2) 78 (8.3) 1.04 (0.53–2.04)c One 5 (6.3) 66 (7.0) 0.84 (0.38–1.85) Two 26 (32.5) 381 (40.5) 0.80 (0.52–1.22) Breastfed (vs. yes) 23 (28.7) 196 (20.9) 1.32 (0.85–2.05) HRT (vs. Results Of the 1789 BCEES controls, 1108 had linked hospital morbidity, mortality data from the Western Australian Department of Health and had their mammogram assessed for BAC. Of these, 57 were diagnosed with ASCVD before their mammogram and were excluded. An additional 31 women were excluded due to incomplete epidemiological data. The final sample size of the dataset for analysis was 1020 (Fig. 2), and of these, 924 had mammographic breast density measures. At the time of baseline assessment, the mean age was 60 (sd = 7.2 years). Overall, the prevalence of cardiovascular risk factors was low with only 1.8% having dyslipidemia and 3% having diabetes. Of the 1020 participants, BAC was found in 184 (18.0%) women. These women were more In the univariable analysis (Table 2), women with BAC had 2.0 (95% CI: 1.29–2.99) times greater risk of developing ASCVD than those without BAC. As age increased, the risk of ASCVD increased by 1.1 times (95% CI: 1.06–1.13) each 1 3 1 3 La radiologia medica (2023) 128:426–433 429 Table 1   Baseline cohort characteristics and associations between BAC and clinical and demographic factors HRT Hormone replacement therapy, OC Oral contraceptive, CI Confidence interval, BAC Breast arterial calcification; Significance is repre- sented by * for p values < 0.05 and ** for p values < 0.01; for non-binary categorical variables, the like likelihood ratio test p values are provided aptrend = 0.0003; bptrend < 0.0001; cptrend < 0.0001; dptrend = 0.96 Risk factor Total Mean ± SD or Count (%) BAC (N = 184) Mean ± SD or Count (%) No BAC (N = 836) Mean ± SD or Count (%) Univariable analysis Odds ratio (95% CI) Multivariable analysis Odds ratio (95% CI) Age (years) 60.3 ± 7.0 65.1 ± 5.5 59.3 ± 6.9 1.15 (1.12–1.19)** 1.15 (1.12–1.19)** BMI (kg/m2) 26.9 ± 5.3 26.3 ± 5.3 27.0 ± 5.3 0.97 (0.94–1.00) 0.97 (0.94–1.00) Hypertension (vs. no) 171 (16.8) 40 (21.7) 131 (15.7) 1.49 (1.01–2.22)* Dyslipidemia (vs. no) 18 (1.8) 2 (1.1) 16 (1.9) 0.56 (0.13–2.47) Diabetes (vs. no) 31 (3.0) 8 (4.4) 23 (2.8) 1.61 (0.71–3.65) Smoker (vs. never) Current 66 (6.5) 5 (2.7) 61 (7.3) 0.29 (0.12–0.76)*a Former 328 (32.2) 44 (23.9) 284 (34.0) 0.56 (0.39–0.82)** Parity (vs. ASCVD Atherosclerotic cardiovascular disease, HRT Hormone replacement therapy, OC Oral contraceptive, CI Confidence interval, BAC Breast arterial calcification; Significance is represented by * for p values < 0.05 and ** for p values < 0.01; for non-binary categorical variables, the like likelihood ratio test p values are provided aptrend = 0.11; bptrend = 0.005; cptrend = 0.73; dptrend = 0.12 BAC and its risk factors year. Hypertension, dyslipidemia or diabetes also resulted in significantly higher risk of ASCVD (HR = 4.15, 95% CI: 2.82–6.12, HR = 3.85, 95% CI: 1.77–8.40 and HR = 2.66, 95% CI: 1.29–5.48, respectively). year. Hypertension, dyslipidemia or diabetes also resulted in significantly higher risk of ASCVD (HR = 4.15, 95% CI: 2.82–6.12, HR = 3.85, 95% CI: 1.77–8.40 and HR = 2.66, 95% CI: 1.29–5.48, respectively). Similar to previous studies [12–15], BAC was associated with age in our study. In contrast to previous cohort studies [10, 13, 16, 17] including a recent systematic review [5], we found no associations of BAC with hypertension or diabetes. However, in studies with relatively healthier populations, no associations between BAC with diabetes, hypertension and dyslipidemia were found [18–20]. This supports our findings as our population were relatively healthy as evidenced by the low prevalence of dyslipidemia (2%) and diabetes (3%). In the multivariable analysis, the association of BAC with ASCVD was no longer statistically significant (HR = 1.37, 95% CI: 0.88–2.14) after adjusting for age, BMI, hyperten- sion and smoking. However, age, hypertension and smok- ing were significantly associated with risk of ASCVD. Dyslipidemia and diabetes were significantly associated with ASCVD risk in the univariate analysis but were omit- ted from the multivariable model due to collinearity with hypertension. Interactions between BAC and hyperten- sion, smoking status and age were explored, but none were considered statistically significant (pBACxhypertension = 0.09, pBACxsmoker = 0.21 and pBACxage = 0.29, respectively). We report a positive association between BAC and par- ity. Reproductive factors, including parity [11, 13, 17, 18, 21–24], have previously been shown to be associated with BAC. A potential mechanism by which parity may induce BAC formation could be the transient increase in calcium required for breastfeeding and fetal growth [22, 25]. We found no association of BAC with HRT use and contracep- tive use although a history of HRT use [11, 14, 16, 22, 26, 27] and oral contraceptive use [14, 24] was inversely asso- ciated with BAC formation in some studies. This suggests that estrogen may not have a role in the formation of BAC. However, studies that have examined HRT and risk of CVD suggest that other factors, which are not accounted for in our analysis, may be important. BAC and its risk factors These include the formula- tion of HRT and duration of HRT use as well as when HRT was started relative to the age of onset of menopause. These factors need to be explored in greater detail to understand if estrogen has a role in BAC formation. g In our subset analysis of the 924 women who had breast density measurements available, the average breast density was 12.9 ­cm2 (sd = 14.6). Breast density was not associated with ASCVD or BAC (Table 3). Results no) 56 (70.0) 510 (54.3) 1.47 (0.99–2.18) Contraception use (vs. no contraception) Combined OC 38 (47.5) 436 (46.4) 0.76 (0.48–1.19)d Other hormonal 4 (5.0) 176 (18.7) 0.45 (0.23–0.90)* Unknown 13 (16.2) 123 (13.1) 0.85 (0.46–1.57) d multivariate risk of ASCVD in relation to clinical and demographic factors from Cox proportional hazards models ASCVD Atherosclerotic cardiovascular disease, HRT Hormone replacement therapy, OC Oral contraceptive, CI Confidence interval, BAC Breast arterial calcification; Significance is represented by * for p values < 0.05 and ** for p values < 0.01; for non-binary categorical variables, the like likelihood ratio test p values are provided aptrend = 0.11; bptrend = 0.005; cptrend = 0.73; dptrend = 0.12 1 3 1 3 430 La radiologia medica (2023) 128:426–433 Discussion This is the first study to examine the associations of BAC with ASCVD risk factors and clinical events in an Australian population. Similar to previous studies conducted in other populations [9, 10], we found that BAC was present in 18% of a sample population of women attending a free mam- mographic screening program, BreastScreen WA. Contrary to previous reports, we found that BAC was not associated with the development of ASCVD events in women with no prior history of ASCVD. However, consistent with a recent meta-analysis [11], we report positive associations between BAC and age and parity. BAC and ASCVD events We report that the association found between BAC and ASCVD, in a population of women without prior ASCVD events, is not independent of age and other risk factors. This finding is in contrast to the first study that reported a Table 3   Associations between breast density and ASCVD/BAC using Cox proportional hazards/logistic regression models for a subset (n = 924) of women BAC Breast arterial calcification, ASCVD Atherosclerotic cardiovascular disease, NA Not applicable. Significance is represented by * for p val- ues < 0.05 and ** for p values < 0.01 † Adjusted for BAC, age, BMI, hypertension, smoking status ‡ Adjusted for age, BMI, parity Cox proportional hazards Outcome: ASCVD Logistic regression Outcome: BAC ASCVD (N = 71) Count (%) No ASCVD (N = 853) Count (%) Univariable Hazard ratio (95% CI) Multivariable† Haz- ard ratio (95% CI) Univariable Odds ratio (95% CI) Multivariable‡ Odds ratio (95% CI) BAC Yes 26 (33.8) 151 (17.7) 2.21 (1.43–3.40)** 1.48 (0.93–2.36) NA NA No 47 (66.2) 702 (82.3) Reference Reference NA NA Dense breasts Yes 25 (35.2) 311 (36.5) 0.86 (0.56–1.32) 1.05 (0.67–1.63) 0.86 (0.61–1.23) 1.21 (0.82–1.79) No 46 (64.8) 542 (64.8) Reference Reference Reference Reference Table 3   Associations between breast density and ASCVD/BAC using Cox proportional hazards/logistic regressio of women 1 3 3 La radiologia medica (2023) 128:426–433 431 2.11-fold increased risk of ASCVD in subjects with BAC [28]. However, that cross-sectional study included 865 women with several cardiovascular risk factors (27% had dyslipidemia, 30% had hypertension, 26% were smokers, 6% had diabetes, 38% had a family history of ASCVD) and a high prevalence of ASCVD (18% of their study population). Grassmann et al. [30] found that dense breast was inversely associated with hypertension, peripheral vascular disease and diabetes mellitus. More studies are needed to assess this association. To our knowledge, we are the first to report that there is no association between breast density and BAC. The relevance of less dense breasts to CVD this remains to be determined but supports the idea that BAC and breast den- sity represent two separate pathophysiological effects. More recently, a large prospective cohort study of 5059 women with no prior history of ASCVD found that BAC was associated with a 1.51-fold increased risk of developing ASCVD after a mean follow-up of 6.5 years [17]. Supplementary Information  The online version contains supplemen- tary material available at https://​doi.​org/​10.​1007/​s11547-​023-​01611-y. Supplementary Information  The online version contains supplemen- tary material available at https://​doi.​org/​10.​1007/​s11547-​023-​01611-y. Author contributions  All authors contributed to the study conception and design. Material preparation, data collection and analysis were per- formed by SCL, SP and JS. The first draft of the manuscript was written by SCL and SP, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript. BAC and ASCVD events Notably, a large proportion of their population at baseline was already on cholesterol lowering drugs (73%) or had hypertension (20%) or diabetes (13%). Similarly, in another recent very large prospective study of 57,867 women who attended screening mammogram in Sweden from January 2011 to March 2013, the presence of BAC was also found to be asso- ciated with a significant 5-year absolute risk of developing ASCVD (HR 1.09 (95% CI 1.05–1.13) and another cardio- vascular risk factor. Those with BAC were also 1.5 times more likely to die from ASCVD. However, in the subset of women with no prior history of ASCVD or cardiovascular risk factors (n = 47,023), these associations were no longer seen with the exception of incident hypertension. These results support our study’s findings as the majority of our study population were relatively healthy, with a low preva- lence of dyslipidemia and diabetes. Taken together, these data suggest that BAC may not be a good marker of future ASCVD events in healthy women. However, BAC may have utility as a marker of future cardiovascular risk in women with established cardiometabolic disease. Limitations As our ASCVD events are determined primarily from data linkage and only events involving hospitalization were reported, it is possible that we have underestimated the num- ber of ASCVD events or prevalence of cardiovascular risk factors, especially the presence of diabetes mellitus as we only had data on the number of newly diagnosed diabetes mellitus cases and not people with pre-existing diabetes mel- litus. There is also a possibility that we have not excluded all women with a history of ASCVD or included all women who developed ASCVD, as they may not have attended a hospital in Western Australia. There are also other potential confounding factors, such as renal disease and statin use, that could not be accounted for in our study as these data were not available. Alternatively, the follow-up duration may not be sufficient to observe an association between BAC and ASCVD.i The quantification of BAC may provide further insight into the association of BAC and ASCVD, but this was not explored in our study. BAC severity, which was not assessed in our study, may have a role in the association of BAC and ASCVD. A systematic review has shown a quantitative association between BAC severity, assessed using subjective methods, and coronary artery disease [29]. A subsequent study using novel techniques to objectively measure BAC showed an association between the presence of BAC and ASCVD but no dose–response relationship [17]. A guideline on quantify- ing and reporting of BAC severity would be useful in future studies to investigate whether BAC severity is a factor in developing ASCVD. In addition, it is important to have long follow-up periods in order to detect a significant association between BAC and the development of ASCVD. In our study of a healthy population who are at low risk of future clinical events, the follow-up may not have been long enough. Conclusion BAC is a marker of increased ASCVD risk, but this is not independent of cardiovascular risk factors. Whether BAC may be used to detect untreated ASCVD risk factors needs further study. The reporting of BAC on routine mammogram will assist in assessing the clinical utility of mammograms to screen for ASCVD. Declarations 10. Schnatz PF, Marakovits KA, Oullivan DM (2011) The association of breast arterial calcification and coronary heart disease. Obstet Gynecol 117:233–241. https://​doi.​org/​10.​1097/​AOG.​0b013​e3182​ 06c8cb Conflict of interest  The authors have no relevant financial or non-fi- nancial interests to disclose. 11. Lee SC, Pirikahu S, Phillips M et al (2021) Reproductive factors and breast arterial calcification: a systematic review and meta- analysis. Climacteric 25:147–154. https://​doi.​org/​10.​1080/​13697​ 137.​2021.​19859​91 Ethical approval  The BCEES study was ethically approved by the Human Research Ethics Committee of the University of Western Aus- tralia and the Department of Health of Western Australia. 12. Loberant N, Salamon V, Carmi N, Chernihovsky A (2013) Preva- lence and degree of breast arterial calcifications on mammogra- phy: a cross-sectional analysis. J Clin Imaging Sci 3:36. https://​ doi.​org/​10.​4103/​2156-​7514.​119013i Consent to participate  Informed consent was obtained from all par- ticipants to participate in the BCEES study. This involved having their mammograms taken and a questionnaire to gather demographic data for research purposes. A waiver of consent was obtained for this study to receive further data on ASCVD events and its risk factors through data linkage. g 13. 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If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. 15. References 18. Maas AHEM, van der Schouw YT, Atsma F et al (2007) Breast arterial calcifications are correlated with subsequent develop- ment of coronary artery calcifications, but their aetiology is pre- dominantly different. Eur J Radiol 63:396–400. https://​doi.​org/​10.​ 1016/j.​ejrad.​2007.​02.​009 1. Australian Institute of Health and Welfare (2018) Cardiovascular disease snapshot, How many Australians have cardiovascular dis- ease?. Australian Institute of Health and Welfare 1. Australian Institute of Health and Welfare (2018) Cardiovascular disease snapshot, How many Australians have cardiovascular dis- ease?. 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Kemmeren JM, van Noord PA, Beijerinck D et al (1998) Arte- rial calcification found on breast cancer screening mammograms and cardiovascular mortality in women: the DOM project. Door- lopend Onderzoek Morbiditeit en Mortaliteit. Am J Epidemiol 147:333–341 17. Iribarren C, Chandra M, Lee C et al (2022) Breast arterial calci- fication: a novel cardiovascular risk enhancer among postmeno- pausal women. Circ Cardiovasc Imaging 15:e013526. https://​doi.​ org/​10.​1161/​CIRCI​MAGING.​121.​013526 Breast density, ASCVD and BAC In our cohort, breast density was not associated with ASCVD or BAC. Interestingly, two prior studies found that women with less dense breasts have a higher risk of CVD [29, 30]. More specifically, among those with no prior his- tory of ASCVD or cardiovascular risk factors (n = 47,023), Funding  Open Access funding enabled and organized by CAUL and its Member Institutions. The original study was funded by a National Health and Medical Research Council Australia (NHMRC) grant 1 3 432 La radiologia medica (2023) 128:426–433 #572530 and by a grant from the Cancer Council Western Australia. However, this post hoc analysis has not received any funding. 9. McLenachan S, Camilleri F, Smith M et al (2019) Breast arte- rial calcification on mammography and risk of coronary artery disease: a SCOT-HEART sub-study. Clin Radiol. https://​doi.​org/​ 10.​1016/j.​crad.​2019.​01.​014 References https://​doi.​org/​ 10.​1038/​bjc.​2013.​544 23. Sedighi N, Radmard AR, Radmehr A et al (2011) Breast arte- rial calcification and risk of carotid atherosclerosis: focusing on the preferentially affected layer of the vessel wall. Eur J Radiol 79:250–256. https://​doi.​org/​10.​1016/j.​ejrad.​2010.​04.​007l j 7. El-Zaemey S, Fritschi L, Heyworth J et al (2020) No asso- ciation between night shiftwork and mammographic density. 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JACC Cardiovasc Imaging 14:426–438. https://​ doi.​org/​10.​1016/J.​JCMG.​2020.​08.​028/​SUPPL_​FILE/​MMC1.​ DOCX j 26. Rotter MA, Schnatz PF, Currier AA, O’Sullivan DM (2008) Breast arterial calcifications (BACs) found on screening mam- mography and their association with cardiovascular disease. Menopause 15:276–281. https://​doi.​org/​10.​1097/​gme.​0b013​e3181​ 405d0a 30. Grassmann F, Yang H, Eriksson M et al (2021) Mammographic features are associated with cardiometabolic disease risk and mor- tality. Eur Heart J 42:3361–3370. https://​doi.​org/​10.​1093/​EURHE​ ARTJ/​EHAB5​02 27. Cox J, Simpson W, Walshaw D (2002) An interesting byproduct of screening: assessing the effect of HRT on arterial calcification in the female breast. J Med Screen 9:38–39. https://​doi.​org/​10.​ 1136/​jms.9.​1.​38 Publisher's Note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 28. Crystal P, Crystal E, Leor J et al (2000) Breast artery calcium on routine mammography as a potential marker for increased risk of cardiovascular disease. Am J Cardiol 86:216–217. https://​doi.​org/​ 10.​1016/​S0002-​9149(00)​00860-2 1 3 1 3 3
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Morphological characteristics of diffuse idiopathic skeletal hyperostosis in the cervical spine
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Results The surface area of the newly formed bone was located symmetrically anterior to the verte- bral body. The ossifications were non-flowing in the sagittal view and no segmental vessels were observed. Substantial displacement of the trachea/esophagus was present in the group with DISH compared to the controls. Copyright: © 2017 Bakker et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Editor: Robert Daniel Blank, Medical College of Wisconsin, UNITED STATES Editor: Robert Daniel Blank, Medical College of Wisconsin, UNITED STATES Received: August 24, 2017 Accepted: November 6, 2017 Published: November 20, 2017 OPEN ACCESS Citation: Bakker JT, Kuperus JS, Kuijf HJ, Oner FC, de Jong PA, Verlaan J-J (2017) Morphological characteristics of diffuse idiopathic skeletal hyperostosis in the cervical spine. PLoS ONE 12 (11): e0188414. https://doi.org/10.1371/journal. pone.0188414 Morphological characteristics of diffuse idiopathic skeletal hyperostosis in the cervical spine Jessica T. Bakker1, Jonneke S. Kuperus1, Hugo J. Kuijf2, F. Cumhur Oner1, Pim A. de Jong3, Jorrit-Jan Verlaan1* Jessica T. Bakker1, Jonneke S. Kuperus1, Hugo J. Kuijf2, F. Cumhur Oner1, Pim A. de Jong3, Jorrit-Jan Verlaan1* 1 Department of Orthopaedics, University Medical Center Utrecht, Utrecht, The Netherlands, 2 Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands, 3 Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands * j.j.verlaan@umcutrecht.nl * j.j.verlaan@umcutrecht.nl a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 Methods Cervical computed tomography (CT) scans were obtained from five patients with dysphagia and DISH and ten control subjects. The location of the vertebral and carotid arteries, surface area of the hyperostosis and distance between the vertebral body and the trachea and esophagus was assessed in the axial view. Objectives Diffuse idiopathic skeletal hyperostosis (DISH) is characterized by anterior ossification of the spine and can lead to dysphagia and airway obstruction. The morphology of the newly formed bone in the cervical spine is different compared to the thoracic spine, possibly due to dissimilarities in local vascular anatomy. In this study the spatial relationship of the new bone with the arterial system, trachea and esophagus was analyzed and compared between subjects with and without DISH. RESEARCH ARTICLE Introduction Diffuse idiopathic skeletal hyperostosis (DISH) is a systemic condition characterized by ossifi- cation of the spine and peripheral entheses [1]. The typical changes related to DISH occur most frequently in the anterolateral part of the thoracic spine, contralateral to the descending thoracic aorta, with bridging ossifications that resemble flowing candle wax in the lateral view (Fig 1) [2,3]. The most commonly used diagnostic criteria for DISH, introduced by Resnick and Niwayama, are met if the ossifications span at least four contiguous vertebrae and do not involve gross degenerative changes in the intervertebral discs or apophyseal and sacroiliac joints [3]. Bone deposition in DISH in the cervical spine is frequently asymptomatic, but can result in dysphagia, aspiration, regurgitation, sleep apnea, upper respiratory tract infection, airway obstruction and difficult intubation [1,4,5]. Verlaan et al. noted in a systematic review that DISH of the cervical spine is an increasing and underappreciated phenomenon [4]. In a Dutch outpatient population older than 50 years the prevalence of DISH based on chest radi- ography was 22.7% in males and 12.1% in females [6]. The prevalence is expected to rise since DISH is correlated with older age, cardiovascular disease and underlying metabolic derange- ment [6,7]. It has been hypothesized that vascular structures act as a natural barrier for the formation of new bone in DISH [8]. This theory is supported by the development of thoracic ossifications mainly contralateral to the aorta. Moreover, the thoracic ossifications are thinnest where the segmental arteries run horizontally across the vertebral bodies, resulting in the typical undulat- ing, flowing pattern [8]. In the cervical spine, however, the vertebral arteries and common, internal and external carotid arteries are located symmetrically and laterally to the vertebral bodies and segmental arteries (at least those of any significant caliber) crossing the vertebral bodies horizontally are absent [9]. If the hypothesis that large vessels prevent the formation of new bone in DISH is true, the newly formed bone in the cervical spine can be expected to be located in the midline and grow in a ventral direction, eventually leading to displacement of esophagus and trachea (Fig 1). Conclusions The hyperostosis at the cervical level was symmetrically distributed anterior to the vertebral bodies without a flowing pattern, in contrast to the asymmetrical flowing pattern typically found in the thoracic spine. The hypothesis that the vascular system acts as a natural barrier against new bone formation in DISH could be further supported with these findings. The sig- nificant ventral displacement of the trachea and esophagus may explain the mechanism of dysphagia and airway obstruction in DISH. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: The authors received no specific funding for this work. Competing interests: The authors have declared that no competing interests exist. 1 / 11 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Morphology of cervical DISH Introduction In this study the location of the newly formed bone in the cervical spine was assessed using computed tomography (CT) scans of subjects with symptomatic DISH and the spatial relation- ship of the new bone with the arterial system, trachea and esophagus was evaluated and com- pared to subjects without DISH. PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Materials and methods Subjects This study was approved by the medical ethical review board of the University Medical Center Utrecht and the need for informed consent was waived (reference number 16/783). This study was performed using the strengthening the reporting of observational studies in epidemiology (STROBE) guidelines [10]. Computed tomography scans of five patients (one female, four males, 65–79 years of age) were selected retrospectively from our outpatient department data- base who had visited our department between 2010 and 2014. All patients had had complaints of dysphagia while eating solid food and were diagnosed with DISH according to the Resnick criteria [3]. Since only the cervical spine was included in the CT scans, evaluation of the sacroil- iac joint was not possible although no signs pointing to the presence of ankylosing spondylitis or spondylosis, such as fused facet joints, were present in any of the patients. Ten subjects (4 females, 6 males, 57–90 years of age) were selected as control group to evaluate the normal ana- tomical location of the vascular system and trachea and esophagus. The control subjects had PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 2 / 11 Morphology of cervical DISH Fig 1. Typical examples of newly formed bone due to DISH in the cervical and thoracic spine. (A) Plain lateral radiograph shows a 69 year old male with DISH in the cervical spine. A solid formation of new bone is extending over at least four vertebral bodies. (B) Computed tomography (CT) visualizes the thoracic spine of a 72 year old male in the sagittal view. The scan shows a flowing ossification of the anterolateral spine with bridging over more than four contiguous vertebral bodies. The intervertebral discs and apophyseal joints are relatively intact in both images. (C + D) The CT scans in axial view demonstrate the differences in position of the new bone formation depending on the region. (C) The CT scan of the cervical spine corresponds to the radiographic Fig 1. Typical examples of newly formed bone due to DISH in the cervical and thoracic spine. (A) Plain lateral radiograph shows a 69 year old male with DISH in the cervical spine. A solid formation of new bone is extending over at least four vertebral bodies (B) Computed tomography (CT) visualizes the thoracic spine of a 72 year old male in the sagittal view The scan shows a Fig 1. Measurements All measurements were performed by two independent observers. In the axial view, the images of all subjects were assessed to locate the position of the main arterial vessels, newly formed bone (if present) and trachea and esophagus. Vertebral levels C4, C5 and C6 were included because the hyperostosis is typically most extensive at these levels [4]. Three axial images, par- allel to the endplates of the pertaining vertebral body, were selected: one adjacent to the cranial endplate, one at the mid-vertebral level and one adjacent to the caudal endplate (Fig 2). In total, nine axial slices were available per subject to analyze the spatial relationship between arterial system, newly formed bone and esophagus/trachea. To describe the location of the different anatomical structures three lines were drawn on each axial image (Fig 3). First, the midsagittal anteroposterior (MAP) line was defined as the line through the spi- nous process, center of the spinal canal and center of the vertebral body (Fig 3E). Additionally, two lines were drawn parallel to the MAP line intercepting the lateral borders of the spinal canal (Fig 3B and 3D). Bone formed between these two lateral lines was considered ‘anterior to the vertebral body’ and bone formed lateral from these two lines was considered ‘lateral to the vertebral body’. The vertebral and carotid arteries were marked manually on the nine axial images of all sub- jects. The arterial blood vessels were considered to be located anterior and/or lateral to the ver- tebral body relative to the two parallel lateral lines (Fig 3B). The presence of segmental vessels (if any) was examined in the sagittal view. In the axial images of the subjects with DISH the outline of the area of newly formed bone was traced manually by the two observers using our software. The total surface area was calculated automatically. The two parallel lateral lines divided the total new bone area in an area anterior to the vertebral body and an area lateral to the vertebral body to assess the distribution of the new bone (Fig 3D). The left and right sur- face areas of the hyperostosis were compared relative to the MAP line to appraise the symme- try of new bone (Fig 3E). Displacement of the trachea and esophagus was assessed by measuring the distance between the center of the vertebral body and the center of the trachea/esophagus in all subjects (Fig 3F and 3H). Imaging The CT imaging of the five subjects with DISH was performed in supine position on a 64-slice calibrated CT scanner (120 kV, 300–375 mAs, 5 mm reconstructed slice thickness; Philips Medical Systems, Cleveland, OH). The study protocol of the CTA scans of the control group has been published previously [11]. Images were analyzed with custom made software based on MeVisLab 2.6 (MeVis Medical Solutions AG, Bremen, Germany [12]) [13]. The vertebral and carotid arteries were identified using Picture Archiving and Communication System (PACS) software (version 17.3, Sectra IDS7, Linko¨ping, Sweden). Materials and methods Subjects Typical examples of newly formed bone due to DISH in the cervical and thoracic spine. (A) Plain lateral radiograph shows a 69 year old male with DISH in the cervical spine. A solid formation of new bone is extending over at least four vertebral bodies. (B) Computed tomography (CT) visualizes the thoracic spine of a 72 year old male in the sagittal view. The scan shows a flowing ossification of the anterolateral spine with bridging over more than four contiguous vertebral bodies. The intervertebral discs and apophyseal joints are relatively intact in both images. (C + D) The CT scans in axial view demonstrate the differences in position of the new bone formation depending on the region. (C) The CT scan of the cervical spine corresponds to the radiographic 3 / 11 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 oi.org/10.1371/journal.pone.0188414 November 20, 201 Morphology of cervical DISH image (A) and demonstrates symmetrical hyperostosis (yellow) anterior to the vertebral body and possible displacement of the trachea. (D) The axial CT of the mid thoracic spine in a 58 year old male with DISH shows the newly formed bone on the right anterolateral side with the aorta clearly located on the left anterolateral side. image (A) and demonstrates symmetrical hyperostosis (yellow) anterior to the vertebral body and possible displacement of the trachea. (D) The axial CT of the mid thoracic spine in a 58 year old male with DISH shows the newly formed bone on the right anterolateral side with the aorta clearly located on the left anterolateral side. https://doi.org/10.1371/journal.pone.0188414.g001 https://doi.org/10.1371/journal.pone.0188414.g001 presented previously to the emergency department with stroke-like symptoms, however no pathologic findings (vascular or musculoskeletal) were detected on computed tomography angi- ography (CTA) of the brain and cervical region. All scans were anonymized prior to analysis. PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Location of arterial vessels At every level in all subjects, the vertebral and carotid arteries were located outside the two par- allel lateral lines and thus lateral to the vertebral body in the cervical spine (Fig 4A). Segmental vessels were not observed in any sagittal plane in any subject. Statistics Data were analyzed by SPSS version 20 software (IBM, Chicago, Illinois, USA). The mean sur- face area was calculated from the surface areas of the newly formed bone in the three axial images in the matching vertebral body and further statistical analyses were performed per ver- tebral level. The data was checked for normality using histograms, Q-Q plots and the Shapiro- Wilk test. The paired samples t-test or the Wilcoxon signed rank test was used to compare new bone anterior and lateral of the parallel lateral lines and left/right from the MAP line. The inde- pendent samples t-test was performed to assess differences in the distance of vertebral body to trachea/esophagus comparing subjects with and without DISH. The statistical significance level was set at p = 0.05 for all analyses and 95% confidence intervals (CI) were presented if relevant. Measurements This measurement was performed in the transverse plane adjacent to the caudal end- plate of C5. 4 / 11 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Morphology of cervical DISH Fig 2. Graphical illustration of the planes used for the measurements. Measurements were performed at three levels in the C4, C5 and C6 vertebral bodies. The axial CT images were reconstructed to planes parallel to the endplate. (A) Sagittal CT image from a 69 year old male. The illustration (B) shows the three levels (C4, C5, C6) and three transverse locations at C5 (1, 2, 3) that were used for the measurements in the axial plane. The dashed line 1 shows the level adjacent to the cranial endplate, line 2 the mid-vertebral level and line 3 the level adjacent to the caudal endplate. The same approach (using the three lines for the transversal levels) was also used for the C4 and C6 vertebral body. https://doi.org/10.1371/journal.pone.0188414.g002 Fig 2. Graphical illustration of the planes used for the measurements. Measurements were performed at three levels in the C4, C5 and C6 vertebral bodies. The axial CT images were reconstructed to planes parallel to the endplate. (A) Sagittal CT image from a 69 year old male. The illustration (B) shows the three levels (C4, C5, C6) and three transverse locations at C5 (1, 2, 3) that were used for the measurements in the axial plane. The dashed line 1 shows the level adjacent to the cranial endplate, line 2 the mid-vertebral level and line 3 the level adjacent to the caudal endplate. The same approach (using the three lines for the transversal levels) was also used for the C4 and C6 vertebral body. https://doi.org/10.1371/journal.pone.0188414.g002 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 https://doi.org/10.1371/journal.pone.0188414.g003 Morphology of cervical DISH Fig 4. Results of the four different types of measurements. The location of the major arteries in the cervical spine was in all cases and at all levels lateral to the parallel lateral lines for the DISH and control group as shown in (A). The median total surface area of the newly formed bone per cervical level was significantly larger at the anterior location compared to the lateral location (B). There was no statistical difference between the left and right side of the MAP line (C). The distance between the center of the vertebral body and the trachea/esophagus was significantly larger in the group with DISH compared to the control group (D). The asterisk represents a p-value  0.05 and the triple asterisk represents a p-value  0.001. The error bars represent the standard error. VB–Vertebral body. https://doi.org/10.1371/journal.pone.0188414.g004 Fig 4. Results of the four different types of measurements. The location of the major arteries in the cervical spine was in all cases and at all levels lateral to the parallel lateral lines for the DISH and control group as shown in (A). The median total surface area of the newly formed bone per cervical level was significantly larger at the anterior location compared to the lateral location (B). There was no statistical difference between the left and right side of the MAP line (C). The distance between the center of the vertebral body and the trachea/esophagus was significantly larger in the group with DISH compared to the control group (D). The asterisk represents a p-value  0.05 and the triple asterisk represents a p-value  0.001. The error bars represent the standard error. VB–Vertebral body. https://doi.org/10.1371/journal.pone.0188414.g004 (IQR 75.3–274.3) and outside the lines 0.2 mm2 (IQR 0–21.4; p = 0.043). At level C5 the median size of the surface area was 272.3 mm2 (IQR 166.1–355.5) between the two parallel lat- eral lines and 0.8 mm2 (IQR 0–27.8; p = 0.043) outside these lines. At level C6 the median size of the surface area between the two lines was 234.5 mm2 (IQR 128.7–343.2) and 23.9 mm2 (IQR 6.6–33.6; p = 0.043) outside the parallel lateral lines. The mean size of the newly formed bone area left and right to the MAP line did not statisti- cally differ for all levels (C4: p = 0.240, C5: p = 0.395, C6: p = 0.083), implying a roughly sym- metrical distribution of the hyperostosis in DISH of the cervical spine (Fig 4C). Distribution of newly formed bone In the subjects with DISH significantly more new bone was formed anterior than lateral rela- tive to the vertebral body at all three vertebral levels of the cervical spine (Fig 4B). At level C4 the median size of the ossification area between the two parallel lateral lines was 113.0 mm2 5 / 11 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Morphology of cervical DISH Fig 3. Graphical illustration of the measurements on the CT images. In (A) the CT scan is shown of a control subject with corresponding illustration (B). The parallel lateral lines are presented in light blue and carotid and vertebral arteries in red. CT scan (C) represents a male subject with DISH (72 years old) and matches illustrations (D and E). The parallel lateral lines (light blue) and the midsagittal anteroposterior (MAP) line (dark blue) were used to compare the different surface areas of newly formed bone (light/dark grey). CT scan (F) shows a male subject with DISH (61 years old) and corresponds to illustrations (G and H). The green lines demonstrate the distances between the center of the vertebral body and the trachea and esophagus, respectively. https://doi.org/10.1371/journal.pone.0188414.g003 Morphology of cervical DISH Fig 3. Graphical illustration of the measurements on the CT images. In (A) the CT scan is shown of a control subject with corresponding illustration (B). The parallel lateral lines are presented in light blue and carotid and vertebral arteries in red. CT scan (C) represents a male subject with DISH (72 years old) and matches illustrations (D and E). The parallel lateral lines (light blue) and the midsagittal anteroposterior (MAP) line (dark blue) were used to compare the different surface areas of newly formed bone (light/dark grey). CT scan (F) shows a male subject with DISH (61 years old) and corresponds to illustrations (G and H). The green lines demonstrate the distances between the center of the vertebral body and the trachea and esophagus, respectively. https://doi.org/10.1371/journal.pone.0188414.g003 https://doi.org/10.1371/journal.pone.0188414.g003 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 6 / 11 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Discussion The results from this study demonstrate that newly formed bone in DISH of the cervical spine occurs mainly anterior to the vertebral bodies. This is in contrast to the pattern of bone deposi- tion at thoracic levels, where new bone is typically formed anterolaterally. Furthermore, the hyperostosis was symmetrically distributed relative to the sagittal midline, again in contrast to the asymmetrical bone depositions in the thoracic spine. The main vessels in the neck were located lateral to the vertebral bodies and segmental arteries were not detected on the sagittal CT images. These results support the hypothesis that arteries may act as a natural barrier for newly formed bone in DISH. The lack of crossing segmental vessels in the cervical spine may permit linear bone growth creating a bar-like structure in contrast to the flowing pattern typi- cal for DISH in the thoracic spine where segmental vessels are present. The unrestricted for- mation of new bone anteriorly could explain the displacement of the trachea and esophagus in a ventral direction. Already in 1950 Forestier and Rotes-Querol, discoverers of the condition currently known as DISH, described that spinal ossifications were often grooved by arterial branching, suggest- ing that the presence of (pulsating) vessels acted as a mechanical barrier for soft tissue ossifica- tion [2]. Their findings were supported by several authors reporting that the anterolateral ossification mass of the thoracic spine was found mainly on the right side of the vertebral col- umn, away from the pulsating aorta [8]. This theory was backed by several observations of left sided hyperostosis of the thoracic spine in patients with situs viscerum inversus, which could be explained by the presence of a right sided aorta [14]. Our findings are in accordance with these studies, as the arteries in the cervical area were located lateral to the vertebral body and the newly formed bone in DISH was located mainly medially and anteriorly to the vertebral body. The displacement of the trachea and esophagus observed in this study was, without doubt, related to the anteriorly located new bone and could help explain the mechanism of dysphagia and airway obstruction sometimes observed in patients with advanced DISH of the cervical spine. The often (sub)acute onset of symptoms, however, implies that mechanical obstruction by (slow) bone growth might not be the only contributor in the pathogenesis of these symp- toms [4]. Displacement of the trachea/esophagus The mean distance from the center of the trachea to the center of the vertebral body was 42.3 mm (±6.6) in subjects with DISH and 31.0 mm (±3.4) in control subjects (p = 0.001; 95%CI 7 / 11 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Morphology of cervical DISH 6–17; Fig 4D). The center of the esophagus to the center of the vertebral body measured 25.9 mm (±7.4) in the patients with DISH, compared to 14.3 mm (±1.6) in the control subjects (p<0.001; 95%CI 7–17). The distance between the vertebral body and the trachea/esophagus in the group with DISH was significantly larger compared to the corresponding distance in the control group. PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Discussion Several authors described other mechanisms that could also contribute to dysphagia or airway obstruction such as inflammation of soft tissues surrounding the ossification, nerve entrapment, limited movement of the epiglottis/larynx and retention of food due to the bone mass [15–18]. In the current study only the contribution of the mechanical obstruction was investigated and only the vertebral levels C4, C5 and C6 were analyzed on the CT images. Dif- ficulties with endotracheal intubation in patients with DISH have been described in multiple case reports in the last decades [5,19–23]. As the presence of cervical hyperostosis could be asymptomatic (or mildly symptomatic), anesthesiologists could encounter unexpected difficul- ties in intubating patients with markedly displaced tracheas due to DISH [5]. Awake (fiberop- tic) intubation is suggested to be a successful resolution in patients with a history of difficult intubation due to DISH [20,22]. The small number of cases with DISH included in this study is the likely result from the mostly asymptomatic natural course of this condition. In the literature only 204 patients with PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 8 / 11 Morphology of cervical DISH dysphagia and/or airway obstruction in combination with DISH are described between 1980 to 2009 [4]. In none of the patients with DISH included in the present study airway obstruction was present and all received surgery to remove the newly formed bone. The current observa- tion of the spatial relationship between new bone and major vessels in the cervical spine cor- roborates previous findings from DISH in the thoracic spine although direct causal evidence cannot, in any way, be concluded from the present work. The anterior location of the newly formed bone could also be due to other causes such as repeated stretching of the degenerated anterior longitudinal ligament leading to subsequent ossification [1,3]. Evidence to support this theory is, however, also lacking. Forestier described the anterior longitudinal ligament to be pushed away by the bony outgrowths, suggesting that the ligament is not directly involved in DISH [2]. Until further studies are performed on the origin of the newly formed bone in DISH, the tentative hypothesis that new bone growth is limited by proximity of the arterial sys- tem may hold. Discussion In conclusion, the new bone in individuals with DISH in the cervical spine is located ante- rior to the vertebral body in a symmetrical order in contrast to the anterolateral formation of bone in the thoracic spine with DISH. The symmetric lateral location of the cervical arteries and the lack of segmental vessels could explain the formation of an anterior bar-like layer of bone in DISH of the cervical spine without the typical flowing pattern observed in the thoracic spine. Both the trachea and esophagus were ventrally displaced in patients with DISH and this displacement is suspected to play an important role in the development of dysphagia. How- ever, the causal relation between the new bone formation in DISH and presence of dysphagia or airway obstruction should be investigated in a longitudinal prospective study design with inclusion of patients with DISH with and without symptoms. References 1. Mader R, Verlaan J-J, Buskila D. Diffuse idiopathic skeletal hyperostosis: clinical features and patho- genic mechanisms. Nat Rev Rheumatol. 2013; 9(12):741–750. https://doi.org/10.1038/nrrheum.2013. 165 PMID: 24189840 2. Forestier J, Rotes-Querol J. Senile ankylosing hyperostosis of the spine. 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Bakker, Jonneke S. Kuperus, Hugo J. Kuijf. Investigation: Jessica T. Bakker, Hugo J. Kuijf. Methodology: Jessica T. Bakker, Jonneke S. Kuperus, Hugo J. Kuijf. Project administration: Jessica T. Bakker, Jonneke S. Kuperus, Jorrit-Jan Verlaan. Supervision: F. Cumhur Oner, Pim A. de Jong, Jorrit-Jan Verlaan. Writing – original draft: Jessica T. Bakker, Jonneke S. Kuperus. Writing – review & editing: Jonneke S. Kuperus, Hugo J. Kuijf, F. Cumhur Oner, Pim A. de Jong, Jorrit-Jan Verlaan. Conceptualization: Jessica T. Bakker, F. Cumhur Oner, Pim A. de Jong, Jorrit-Jan Verlaan. Supervision: F. Cumhur Oner, Pim A. de Jong, Jorrit-Jan Verlaan. Writing – original draft: Jessica T. Bakker, Jonneke S. Kuperus. Writing – original draft: Jessica T. Bakker, Jonneke S. Kuperus. Writing – review & editing: Jonneke S. Kuperus, Hugo J. Kuijf, F. Cumhur Oner, Pim A. de Jong, Jorrit-Jan Verlaan. Writing – review & editing: Jonneke S. Kuperus, Hugo J. Kuijf, F. Cumhur Oner, Pim A. de Jong, Jorrit-Jan Verlaan. PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 9 / 11 Morphology of cervical DISH PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 22. Naik B, Lobato EB, Sulek CA. Dysphagia, obstructive sleep apnea, and difficult fiberoptic intubation secondary to diffuse idiopathic skeletal hyperostosis. Anesthesiology. 2004; 100(5):1311–1312. PMID: 15114233 23. Ozkalkanli MY, Katircioglu K, Ozkalkanli DT, Savaci S. Airway management of a patient with Forestier’s disease. J Anesth. 2006; 20(4):304–306. https://doi.org/10.1007/s00540-006-0418-5 PMID: 17072696 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 References Le AQ, Walcott BP, Redjal N, Coumans J-V. Cervical osteophyte resulting in compression of the jugular foramen. J Neurosurg Spine. 2014; 21(4):565–567. https://doi.org/10.3171/2014.6.SPINE13908 PMID: 25014503 16. Oppenlander ME, Orringer DA, La Marca F, et al. Dysphagia due to anterior cervical hyperosteophy- tosis. Surg Neurol. 2009; 72(3):266–270. https://doi.org/10.1016/j.surneu.2008.08.081 PMID: 19147185 17. Presutti L, Alicandri-Ciufelli M, Piccinini A, et al. Forestier disease: Single-center surgical experience and brief literature review. Ann Otol Rhinol Laryngol. 2010; 119(9):602–608. PMID: 21033027 18. McCafferty RR, Harrison MJ, Tamas LB, Larkins M V. Ossification of the anterior longitudinal ligament and Forestier’s disease: an analysis of seven cases. J Neurosurg. 1995; 83(1):13–17. https://doi.org/ 10.3171/jns.1995.83.1.0013 PMID: 7782829 19. Crosby ET, Grahovac S. Diffuse idiopathic skeletal hyperostosis: an unusual cause of difficult intuba- tion. Can J Anaesth. 1993; 40(1):54–58. https://doi.org/10.1007/BF03009319 PMID: 8425244 20. Palmer JHM, Ball DRR. Awake tracheal intubation with the intubating laryngeal mask in a patient with diffuse idiopathic skeletal hyperotosis. Anaesthesia. 2000; 55(1):70–74. PMID: 10594434 21. Bougaki M, Sawamura S, Matsushita F, Hanaoka K. Difficult intubation due to ossification of the anterior longitudinal ligament [7]. Anaesthesia. 2004; 59(3):303–304. PMID: 14984537 10 / 11 PLOS ONE | https://doi.org/10.1371/journal.pone.0188414 November 20, 2017 Morphology of cervical DISH 11 / 11
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Differential Substrate Usage and Metabolic Fluxes in Francisella tularensis Subspecies holarctica and Francisella novicida
Frontiers in cellular and infection microbiology
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Differential Substrate Usage and Metabolic Fluxes in Francisella tularensis Subspecies holarctica and Francisella novicida Fan Chen 1, Kerstin Rydzewski 2, Erika Kutzner 1, Ina Häuslein 1, Eva Schunder 2, Xinzhe Wang 1, Kevin Meighen-Berger 1, Roland Grunow 3, Wolfgang Eisenreich 1* and Klaus Heuner 2* Fan Chen 1, Kerstin Rydzewski 2, Erika Kutzner 1, Ina Häuslein 1, Eva Schunder 2, Xinzhe Wang 1, Kevin Meighen-Berger 1, Roland Grunow 3, Wolfgang Eisenreich 1* and Klaus Heuner 2* 1 Department of Chemistry, Chair of Biochemistry, Technische Universität München, Garching, Germany, 2 Working Group “Cellular Interactions of Bacterial Pathogens”, ZBS 2, Robert Koch Institute, Berlin, Germany, 3 Centre for Biological Threats and Special Pathogens, Division 2 (ZBS 2), Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany Francisella tularensis is an intracellular pathogen for many animals causing the infectious disease, tularemia. Whereas F. tularensis subsp. holarctica is highly pathogenic for humans, F. novicida is almost avirulent for humans, but virulent for mice. In order to compare metabolic fluxes between these strains, we performed 13C-labeling experiments with F. tularensis subsp. holarctica wild type (beaver isolate), F. tularensis subsp. holarctica strain LVS, or F. novicida strain U112 in complex media containing either [U-13C6]glucose, [1,2-13C2]glucose, [U-13C3]serine, or [U-13C3]glycerol. GC/MS-based isotopolog profiling of amino acids, polysaccharide-derived glucose, free fructose, amino sugars derived from the cell wall, fatty acids, 3-hydroxybutyrate, lactate, succinate and malate revealed uptake and metabolic usage of all tracers under the experimental conditions with glucose being the major carbon source for all strains under study. The labeling patterns of the F. tularensis subsp. holarctica wild type were highly similar to those of the LVS strain, but showed remarkable differences to the labeling profiles of the metabolites from the F. novicida strain. Glucose was directly used for polysaccharide and cell wall biosynthesis with higher rates in F. tularensis subsp. holarctica or metabolized, with higher rates in F. novicida, via glycolysis and the non-oxidative pentose phosphate pathway (PPP). Catabolic turnover of glucose via gluconeogenesis was also observed. In all strains, Ala was mainly synthesized from pyruvate, although no pathway from pyruvate to Ala is annotated in the genomes of F. tularensis and F. novicida. Glycerol efficiently served as a gluconeogenetic substrate in F. novicida, but only less in the F. tularensis subsp. holarctica strains. In any of the studied strains, serine did not serve as a major substrate and was not significantly used for gluconeogenesis under the experimental conditions. Differential Substrate Usage and Metabolic Fluxes in Francisella tularensis Subspecies holarctica and Francisella novicida Rather, it was only utilized, at low rates, in downstream metabolic processes, e.g., via acetyl-CoA in the citrate cycle ORIGINAL RESEARCH published: 21 June 2017 doi: 10.3389/fcimb.2017.00275 Edited by: Alain Charbit, University Paris Descartes, France Edited by: Alain Charbit, University Paris Descartes, France Reviewed by: Christopher Price, University of Louisville, United States Lee-Ann H. Allen, University of Iowa, United States *Correspondence: Wolfgang Eisenreich wolfgang.eisenreich@ch.tum.de Klaus Heuner heunerk@rki.de *Correspondence: Wolfgang Eisenreich wolfgang.eisenreich@ch.tum.de Klaus Heuner heunerk@rki.de Received: 14 April 2017 Accepted: 06 June 2017 Published: 21 June 2017 INTRODUCTION Some of these transporters were characterized in detail only recently (Gesbert et al., 2014, 2015; Ramond et al., 2014, 2015). In particular, serine was shown to be important for intracellularly multiplying Francisella strains (Meibom and Charbit, 2010; Raghunathan et al., 2010; Barel et al., 2012; Gesbert et al., 2013, 2015; Brown et al., 2014), which was also corroborated by a report showing that the SLC family of host amino acid transporters is important for intracellular replication of Fth strain LVS (Barel et al., 2012). Furthermore, it was demonstrated that the glycine cleavage system and the glycine dehydrogenase are also important for replication in serine limiting environments and that a gcvT mutant strain is auxotroph for serine. The glycine cleavage system of Ftt is also required in a murine model of infection (Brown et al., 2014). In addition, Ft requires Ser for growth under in vitro conditions, although Ft is not auxotroph for Ser (Meibom and Charbit, 2010; Brown et al., 2014). The Gram-negative Ftt and Fth are specialized to replicate in the cytosol of host cells, especially of macrophages (for reviews, see Santic et al., 2006; Sjostedt, 2006; Keim et al., 2007; Jones et al., 2012). After engulfment of the pathogens into the macrophages, they form Francisella-containing phagosomes (FCPs) and trigger signals for the induction of the Francisella pathogenicity island (FPI). FPI also encodes a Type 6 secretion system (T6SS) (Chong et al., 2008; Clemens et al., 2015; Rigard et al., 2016) which finally leads to the escape of Ft into the cytosol of the host cell. For successful replication in this niche, the bacteria need to efficiently utilize nutrients from this environment, e.g., for energy generation and biosynthesis purposes. However, the cytosol of a host cell is not a nutrient- rich habitat in which every microorganism is able to grow, as show by injection experiments of e.g., Salmonella typhimurium (Goetz et al., 2001). Some intracellular bacteria including Francisella, Listeria monocytogenes, Shigella, and Rickettsia spp. have managed to exploit the limited nutrient supply of the cytosol for multiplication (Santic and Abu Kwaik, 2013). To efficiently utilize carbon substrates from the cytosolic compartment of the host cell, L. monocytogenes has been shown to take advantage from multiple substrates (e.g., glucose phosphate, glycerol and amino acids) which are shuffled in a bipartite metabolic network to serve specific metabolic traits (Grubmüller et al., 2014). INTRODUCTION phagosomal compartments (Abu Kwaik and Bumann, 2013, 2015; Schunder et al., 2014; Eisenreich and Heuner, 2016; Gillmaier et al., 2016; Häuslein et al., 2016). Francisella tularensis (Ft) is an intracellular Gram-negative pathogen that causes tularemia in many animals including humans (Ellis et al., 2002; Sjostedt, 2011). Ft has a broader host range order than any other known zoonotic pathogenic bacterium and causes the life-threatening disease in approximately 250 wildlife species including mammals, rodents, ticks and other anthropods (Foley and Nieto, 2010; Santic et al., 2010). Transmission mostly occurs via aerosol ingestion or skin inoculation. Due to the high pathogenicity of some strains against humans, F. tularensis is registered as a biological weapon (Dennis et al., 2001). Doses of as low as 10–20 bacteria of Ft subsp. tularensis (Ftt, Ft-type A, mainly found in North America) are infective and can result in lethal tularemia (Ellis et al., 2002). Ft holarctica (Fth, Ft-type B) is still highly infectious and found throughout the Northern hemisphere. Also in Europe, this strain is typically found in infected animals and humans. The bacterium F. novicida has been classified as a separate species, F. novicida (Fno) or as a F. tularensis subspecies novicida (Busse et al., 2010; Johansson et al., 2010; Kingry and Petersen, 2014). Here, we will utilize the nomenclature Fno. In case of Francisella, the relationship between nutrient usage and the in vivo life cycle is still poorly understood (Checroun et al., 2006; Meibom and Charbit, 2010; Santic and Abu Kwaik, 2013; Barel et al., 2015). It is current evidence that Francisella can also exploit some of the metabolic traits described earlier for Listeria. It was demonstrated that multiple substrates including amino acids (e.g., serine, glycine, cysteine, glutamate, glutamine, asparagine), small peptides and other gluconeogenetic substrates like glycerol or glycerol phosphate can also serve as carbon sources for intracellular Ft (Alkhuder et al., 2009; Raghunathan et al., 2010; Brown et al., 2013; Gesbert et al., 2013, 2015; Barel et al., 2015; Brissac et al., 2015; Ramond et al., 2015) (Figure 1). In agreement with this observation is the reported auxotrophy of Ft for several amino acids (e.g., for the branched chain amino acids, arginine, histidine, lysine, methionine and cysteine) and the apparent presence of several MFS-type and APC-type uptake systems for amino acids as seen in the genomes of Ft strains (Alkhuder et al., 2009; Meibom and Charbit, 2010). Citation: Chen F, Rydzewski K, Kutzner E, Häuslein I, Schunder E, Wang X, Meighen-Berger K, Grunow R, Eisenreich W and Heuner K (2017) Differential Substrate Usage and Metabolic Fluxes in Francisella tularensis Subspecies holarctica and Francisella novicida. Front. Cell. Infect. Microbiol. 7:275. doi: 10.3389/fcimb.2017.00275 June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org Chen et al. Metabolic Fluxes in Francisella and for fatty acid biosynthesis, especially in the F. tularensis subsp. holarctica strains. In summary, the data reflect differential metabolite fluxes in F. tularensis subsp. holarctica and F. novicida suggesting that the different utilization of substrates could be related to host specificity and virulence of Francisella. Keywords: Francisella, intracellular bacteria, 13C-labeling, isotopolog profiling, metabolic adaptation, tularemia, metabolic virulence INTRODUCTION Multiple substrate usage might be a general strategy for intracellular bacteria growing in the cytosol, but also in In another agreement with L. monocytogenes, the sequenced genomes of some Francisella also display homologies to glycerol and glycerol phosphate transporters. On this basis, glycerol (and its phosphate) could serve a potential nutrient source at least for some Francisella species and Ft strains. Indeed, glycerol was shown to be metabolized by Ftt, F. hispaniensis, F. philomiragia, Ft subsp. mediasiatica (Huber et al., 2010) and Fno (Brissac et al., 2015). However, all strains of Fth are reported to metabolize glycerol phosphate but not glycerol (Gyuranecz et al., 2010). In contrast to L. monocytogenes, Ft does neither encode potential uptake systems for glucose phosphate such as June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 2 Chen et al. Metabolic Fluxes in Francisella FIGURE 1 | Hypothetical metabolic network of Francisella tularensis. The pathways are predicted on the basis of the genome sequences and earlier biochemical studies (Gyuranecz et al., 2010; Meibom and Charbit, 2010; Raghunathan et al., 2010; Barel et al., 2015). Potential carbon substrates are indicated by red boxes. Major metabolic products are indicated by yellow boxes. Reactions of the glycolytic pathway (EMP) and gluconeogensis (GN) are indicated by red arrows. Reactions of the pentose phosphate pathway (PPP) and the citrate cycle (TCA) are indicated by blue and green arrows, respectively. The interconnection between Gly and Ser includes the glycine cleavage system. FIGURE 1 | Hypothetical metabolic network of Francisella tularensis. The pathways are predicted on the basis of the genome sequences and earlier biochemical studies (Gyuranecz et al., 2010; Meibom and Charbit, 2010; Raghunathan et al., 2010; Barel et al., 2015). Potential carbon substrates are indicated by red boxes. Major metabolic products are indicated by yellow boxes. Reactions of the glycolytic pathway (EMP) and gluconeogensis (GN) are indicated by red arrows. Reactions of the pentose phosphate pathway (PPP) and the citrate cycle (TCA) are indicated by blue and green arrows, respectively. The interconnection between Gly and Ser includes the glycine cleavage system. UhpT, nor PTS-type or non-PTS-type transporters of glucose. Despite this apparent lack of glucose or glucose phosphate uptake systems, glucose was shown to be metabolized by some Francisella strains. Determination of Protein-Bound Amino Acids 50 µL of autoclaved medium T was dried under N2 flux. The residue was suspended in 0.5 mL of 6 M hydrochloric acid and hydrolyzed for 15 h at 105◦C. The hydrolysate was dried under N2 flux. The residue was suspended in 200 µL of 50% acetic acid using an ultrasonic bath for 3 min. The solution was centrifuged and the supernatant was applied onto a small column of Dowex 50W X8 (7 × 10 mm; 200–400 mesh, 34–74 µm, H+-form). The column was first washed with 2 mL H2O, then eluted with 1 mL 4 M aqueous ammonia. 5 µL of 10 mM Analysis of Medium T Determination of Free Amino Acids y Determination of Free Amino Acids Determination of Free Glucose and Glucose from Acid-Labile Polysaccharides Strains used in this study were Fno strain U112 (ATCC 15482; Larson et al., 1955), Fth strain LVS (ATCC 29684) and Fth wild type strain (“Beaver” isolate; Ft-type B) (Schulze et al., 2016). Francisella strains were cultivated in medium T (Pavlovich and Mishan’kin, 1987; Becker et al., 2016) containing 1% brain heart infusion broth (Difco Laboratories, Inc., Sparks, MD, USA), 1% bacto tryptone (Difco), 1% technical casamino acids (Difco), 0.005 g of MgSO4, 0.01% FeSO4, 0.12% sodium citrate, 0.02% KCl, 0.04% K2HPO4, 0.06% L-cysteine and 1.5% glucose at 37◦C. 100 µL of 10 mM fructose solution (internal standard) was added to 1 mL of autoclaved medium T, the mixture was dried under N2 flux. 1 mL of a solution of acetone containing 2% sulfuric acid was added. After 1 h at room temperature, 2 mL of saturated NaCl solution and 2 mL of saturated NaCO3 solution were added. The reaction mixture was extracted two times with 3 mL of ethyl acetate. The organic phase was collected and dried under N2 flux. The residue was reacted with 100 µL of acetyl anhydride at 60◦C in 100 µL of water free ethyl acetate for 16 h. The reaction mixture was dried under N2 flux, dissolved in 100 µL of water free ethyl acetate and subjected to GC-MS analysis. Labeling Experiments of Francisella Strains 1 L of growth medium (medium T) was supplemented with 2 g of [U-13C6]glucose (11 mM), 2 g of [1,2-13C2]glucose (11 mM), 0.3 g of [U-13C3]Ser (3 mM), or 2.5 g of [U-13C3]glycerol (25 mM), respectively. Volumes of 250 ml of supplemented medium T were inoculated with 2–4 ml of an over-night culture of the Francisella strains. Incubation was carried out at 37◦C and 220 rpm. The optical density at 600 nm (OD600) was determined at regular intervals. An OD600 of ∼1.8 correlated with stationary growth. Cultures in medium T reached stationary growth at 26 h. Before harvesting, a culture aliquot was plated onto lysogeny broth (LB) agar (Bertani, 1951, 2004) to rule out the possibility of contamination. The bacteria were pelleted at 4,700 g and 4◦C for 15 min. The supernatant was discarded and the bacterial pellet was autoclaved at 120◦C for 20 min. Then, the pellet was resuspended in 3 ml of water and lyophilized. INTRODUCTION All of the Fth isolates were able to utilize glucose, whereas no strain could metabolize glucose 6-phosphate (Gyuranecz et al., 2010; Gesbert et al., 2014). In contrast to Fth, Fno could use cellobiose, galactose, and sucrose (Huber et al., 2010). On the basis of the genomes, all of these sugars can be degraded by the glycolytic pathway (EMP pathway) and/or the non-oxidative pentose phosphate pathway (PPP), but not via the Entner-Doudoroff pathway (ED) and the oxidative branch of the PPP. Further downstream, a complete citrate cycle (TCA) appears to be important to provide NADH for energy production. Anaplerotic reactions could interconnect the EMP with the TCA. A schematic overview of the key metabolic pathways is given in Figure 1. These metabolic capacities already point at a highly versatile and maybe species- and strain-dependent substrate usage of Ft. Interestingly, the genetic analysis of the Ftt Schu S4 genome revealed an unusually high amount of disrupted biosynthetic pathways which could indicate that Ftt is an obligate host- dependent bacterium in its natural life cycle (Larsson et al., 2005; Meibom and Charbit, 2010). However, the details of metabolic fluxes in Ft are still rather obscure. It is not known whether the usage of substrates is related to virulence of different Francisella species. In order to shed light onto this item and to study the metabolism of Ft in general, we applied comparative isotopolog profiling experiments with a highly pathogenic Fth strain recovered recently from a beaver (Schulze et al., 2016), an attenuated live vaccine strain (LVS) of Fth, and the (for humans) almost apathogenic Fno strain U112 (Larson et al., 1955; Hollis et al., 1989; Clarridge et al., 1996). Thereby, a rather detailed view into the metabolic network of Fth and Fno could be made with June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 3 Metabolic Fluxes in Francisella Chen et al. some remarkable metabolic differences between Fth and Fno, suggesting that substrate usage and metabolic fluxes could also trigger pathogenesis of different Francisella species. norvaline solution (internal standard) was added to the eluate and the mixture was dried under N2 flux at 55◦C. The residue was treated with 50 µL of N-(tert-butyldimethylsilyl)-N-methyl- trifluoroacetamide containing 1% tert-butyldimethylsilylchloride and 50 µL of water free acetonitrile at 70◦C for 30 min. The TBDMS-derivatives of amino acids were then quantified by GC-MS. Analysis of Medium T Analysis of Medium T Determination of Free Amino Acids Methanolic Cell Extraction and Analysis of Polar Metabolites 1 mL of autoclaved medium T was dried under N2 flux. The residue was suspended in 1 mL of methanol and was centrifuged (10,000 g for 20 min, 4◦C). 5 µL of a 10 mM norvaline solution (internal standard) was added to the supernatant. The mixture was then dried under N2 flux. The residue was treated with 50 µL of N-(tert-butyldimethylsilyl)-N-methyl- trifluoroacetamide containing 1% tert-butyldimethylsilylchloride and 50 µL of water free acetonitrile at 70◦C for 1 h. The TBDMS- derivatives of amino acids were then quantified by GC-MS. About 30 mg of bacterial sample (lyophilized cell pellet) and 500 µL of glass beads (0.25–0.5 mm) were suspended in 1 mL of methanol. The mixture was subjected to mechanical disruption using a ribolyser system (6.5 s−1, 20 s, 27◦C, three times). The mixture was centrifuged (10,000 g for 20 min, 4◦C) and the supernatant was then dried under N2 flux. The residue was treated with 50 µL of N-(tert-butyldimethylsilyl)-N-methyl- trifluoroacetamide containing 1% tert-butyldimethylsilylchloride and 50 µL acetonitrile at 70◦C for 1 h. The resulting TBDMS- derivatives were then analyzed by GC-MS. Workup of Francisella Cells Aqueous Cell Extraction and Analysis of Free Fructose About 30 mg of bacterial sample (lyophilized cell pellet) and 500 µL of glas beads (0.25–0.5 mm) were suspended in 1 mL of H2O. The mixture was subjected to mechanical disruption using a ribolyser system (6.5 s−1, 20 s, 27◦C, three times). The mixture was centrifuged (10,000 g for 20 min, 4◦C) and the supernatant was then dried under N2 flux. The residue was treated with 100 µL of methoxamine hydrochloride pyridine solution (40 mg/mL) at 30◦C for 90 min. The reaction mixture was dried under N2 flux. Finally, the residue was treated with 100 µL of N-methyl-N-trifluoroacetamide at 37◦C for 45 min and subjected to GC-MS analysis. Analysis of TMS-Sugars The column was first developed at 70◦C for 5 min, then using a gradient of 5◦C min−1 to 310◦C where it was hold for 1 min. RESULTS About 5 mg of bacterial sample (lyophilized cell pellet) was hydrolyzed for 15 h with 0.5 mL of 3 M methanolic HCl at 80◦C. The reaction mixture was centrifuged (10,000 g for 20 min, 4◦C) and the supernatant was dried using a stream of dry N2 gas. 1 mL of a solution of acetone containing 2% sulfuric acid was added. After 1 h at room temperature, 2 mL of saturated NaCl solution and 2 mL of saturated NaCO3 solution were added. The reaction mixture was extracted two times with 3 mL of ethyl acetate. The organic phase was collected and dried under N2 flux. The residue was reacted with 100 µL of acetyl anhydride at 60◦C in 100 µL of water-free ethyl acetate for 16 h. The reaction mixture was dried under N2 flux and resolved in 100 µL of water free ethyl acetate for GC-MS analysis. GC-MS and Isotopolog Analysis All derivatives mentioned above were analyzed by GC-MS using a GCMS-QP 2010 Plus spectrometer (Shimadzu, Duisburg, Germany) as described earlier (Häuslein et al., 2016). All data were collected using LabSolution software (Shimadzu). The samples were analyzed three times as technical replicates. The overall 13C excess (mol-%) and the relative contributions of isotopomers (%) were computed by an Excel-based in-house software package (Eylert et al., 2008) according to Lee et al. (1991). Total Hydrolysis and Analysis of Protein-Derived Amino Acids About 2 mg of bacterial sample (lyophilized cell pellet) were suspended in 1 mL of 6 M hydrochloric acid and hydrolyzed for 15 h at 105◦C. The reaction mixture was dried under N2 flux. The residue was suspended in 200 µL of 50% acetic acid using an ultrasonic bath for 3 min. The solution was June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 4 Chen et al. Metabolic Fluxes in Francisella Analysis of TBDMS-Amino Acids The column was first developed at 150◦C for 3 min, then using a gradient of 7◦C min−1 to 280◦C where it was hold for 3 min. Analysis of TBDMS-Amino Acids The column was first developed at 150◦C for 3 min, then using a gradient of 7◦C min−1 to 280◦C where it was hold for 3 min. centrifuged and the supernatant was applied onto a small column of Dowex 50W X8 (7 × 10 mm; 200–400 mesh, 34–74 µm, H+-form). The column was first washed with 2 mL H2O, then eluted with 1 mL 4 M aqueous ammonia. 5 µL of 10 mM norvaline solution (internal standard) was added to the eluate and the mixture was dried under N2 flux at 55◦C. The residue was treated with 50 µL of N-(tert-butyldimethylsilyl)-N-methyl- trifluoroacetamide containing 1% tert-butyldimethylsilylchloride and 50 µL of water free acetonitrile at 70◦C for 30 min. The TBDMS-derivatives of amino acids were then quantified by GC-MS (Eylert et al., 2010). Hydrolysis of Cell Wall and Analysis of Cell-Wall Sugars About 15 mg of bacterial sample (lyophilized cell pellet) was hydrolyzed for 15 h in 0.5 mL of 6 M hydrochloric acid at 105◦C. The reaction mixture was filtered and the filtrate was dried under N2 flux. The residue was treated with 100 µL hexamethyldisilazane at 120◦C for 3 h. The resulting TMS- derivatives were analyzed by GC-MS. Analysis of Diisopropylidene/Acetate Derivatives of Glucose The column was first developed at 150◦C for 3 min, then using a gradient of 10◦C min−1 to 220◦C, then by 50◦C min−1 to 280◦C where it was hold for 3 min. Experimental Approach p pp To investigate the usages of possible substrates, i.e., of glucose, serine or glycerol, we performed labeling experiments with different Francisella strains growing in medium T in the presence of [U-13C6]glucose, [1,2-13C2]glucose, [U-13C3]serine, or [U- 13C3]glycerol as tracers. More specifically, we supplemented the highly pathogenic Fth WT strain (beaver isolate) (Schulze et al., 2016), the Fth life vaccine strain LVS, or the less pathogenic Fno strain U112 with 11 mM [U-13C6]glucose, 11 mM [1,2- 13C2]glucose, 3 mM [U-13C3]serine, or 25 mM [U-13C3]glycerol, respectively. In each of the labeling experiments, the strains were grown at 37◦C for 26 h. The growth curves of Fth and Fno were apparently identical in each of the labeling experiments (data not shown). The cells were harvested at final optical densities (OD600) of approximately 1.8 (stationary phase). The bacteria were pelleted, autoclaved and lyophilized affording about 100 mg of dry cell pellet from a given experiment. From the dried cell pellets, polar metabolites including free fructose were extracted. Proteins, cell wall, or acid-labile polysaccharides were then hydrolyzed and amino acids, glucosamine, muramic acid and glucose were isolated from the respective hydrolysates. The isolated metabolites were converted into appropriate derivatives which were finally analyzed by GC/MS spectrometry (for details, see Materials and Methods). Each of the labeling experiments was done at least two times, in most of the settings three times (biological replicates). Each of the GC-MS samples was analyzed three times (technical replicates). On this basis, the data given below represent mean values and standard deviations using six to nine experimental values for each metabolite under study (see also Supplemental Tables S1–S27 for numerical data). This provided a robust basis for the comparative approach. Labeling Experiments with [U-13C6]Glucose Analysis of MEOX-TMS-Fructose and TBDMS-Derivatives of Polar Metabolite Mixtures The column was first developed at 100◦C for 2 min, then using a gradient of 3◦C min−1 to 234◦C, followed by 1◦C min−1 to 237◦C and 3◦C min−1 to 260◦C. Finally, the column was heated at a gradient of 10◦C min−1 to a final temperature of 320◦C where it was hold for 2 min. Analysis of MEOX-TMS-Fructose and TBDMS-Derivatives of Polar Metabolite Mixtures Isotopolog Profiles of Free Polar Metabolites Isotopolog Profiles of Free Polar Metabolites In the aqueous and methanolic cell extracts, we focused on about 20 metabolites including free amino acids, lactate, glycerol, succinate, malate, and fatty acids. Generally, the 13C-enrichments and isotopolog profiles of free amino acids resembled those from the protein-bound amino acids (Figure 2A). The 13C- excess values and isotopolog compositions of lactate and glycerol resembled that of alanine indicating a quasi-equilibrium state of isotope distribution between these related metabolites. Fatty acids and 3-hydroxybutyrate were also highly 13C- enriched (6–12%) suggesting efficient usage of [U-13C6]glucose for fatty acids biosynthesis by glucose degradation leading to [U-13C2]acetyl-CoA precursors. Carbon flux via [U-13C2]acetyl- CoA into the TCA cycle is also seen in the labeling profiles of succinate and malate with high fractions of M+2 (like in the TCA-derived amino acid aspartate). As shown in Figure 2, the values for the metabolites from Fth or Fno were again very similar, with a slight tendency of higher incorporation into metabolites from Fno. In any of the detected amino acids, there were no significant differences in the overall 13C-enrichments (Figure 2A) and the isotopolog profiles as well (Figure 2B) between Fth LVS and the highly pathogenic beaver isolate of Fth. In contrast, significant differences could be noticed when comparing the Fth strains with Fno. More specifically, the 13C excess values from protein-derived amino acids (especially of Ala, Ser, and Tyr) using glucose as the substrate were higher in Fno than in the Fth strains. From the MS traces, the relative fractions of 13C-isotopologs in the 13C- enriched amino acids could be determined (Figure 2B). Again, the relative fractions of the isotopologs were highly similar when comparing the Fth strains, but significantly different for some amino acids when comparing Fth with Fno. In total, the labeling patterns of multiple metabolites obtained from the labeling experiment with 11 mM [U-13C6]glucose suggested its efficient uptake and direct usage for polysaccharide synthesis, but also its degradation via the glycolytic pathway to pyruvate/Ala and, at lower rates, to acetyl-CoA as a precursor for fatty acids or as a substrate for the TCA cycle. Moreover, the observed complex isotopolog compositions in cell wall sugars, glucosamine and muramic acid, indicated direct incorporation of the intact hexose tracer, but also glycolytic turnover e.g., via the PPP and/or gluconeogenesis. Analysis of MEOX-TMS-Fructose and TBDMS-Derivatives of Polar Metabolite Mixtures Isotopolog Profiles of Free Fructose, Glucose from Acid-Labile Polysacharides, and Amino Sugars from the Cell Wall Isotopolog Profiles of Free Fructose, Glucose from Acid-Labile Polysacharides, and Amino Sugars from the Cell Wall The column was first developed at 100◦C for 2 min, then using a gradient of 3◦C min−1 to 234◦C, followed by 1◦C min−1 to 237◦C and 3◦C min−1 to 260◦C. Finally, the column was heated at a gradient of 10◦C min−1 to a final temperature of 320◦C where it was hold for 2 min. Hexoses could be isolated in form of free fructose (isolated from the aqueous cell extracts), polysaccharide-derived glucose obtained by mild acidic hydrolysis and cell wall-derived amino sugars (i.e., glucosamine and muramic acid) by harsh acidic June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 5 Metabolic Fluxes in Francisella Chen et al. treatment. Each of the sugars displayed high 13C-enrichments (about 10–12%, Figure 2A) reflecting efficient uptake and usage of exogenous glucose by any of the Fth and Fno strains under study. The incorporation rates were slightly higher in the Fth strains (11.2 ± 0.9% averaged over the four hexoses) in comparison to Fno (10.5 ± 1.1%) (See also Supplemental Table S9). The major isotopolog in free fructose was M+6 (Figure 2B) by conversion of [U-13C6]glucose into [U-13C6]fructose probably via glucose 6-phosphate and fructose 6-phosphate. However, significant metabolic turnover in hexose metabolism (i.e., degradation to triose phosphates and subsequent reformation of hexoses) became evident on the basis of the detected M+1 to M+5 isotopologs in free fructose (20–30%) and glucose from the polysaccharides (20–50%) and even more pronounced in glucosamine and muramic acid from the cell wall (60–90%) (Figure 2B). The relative fractions of the isotopologs reflecting this glycolytic cycling were apparently similar for Fth and Fno, with the notable exception of polysaccharide-derived glucose from Fno showing significantly lower rates. enzymes for the usage of glucose by glycolysis (EMP pathway) and the non-oxidative PPP are present in the genomes of the sequenced Francisella strains (Figure 1). Surprisingly, however, genes encoding alanine dehydrogenase and Glu/Asp transaminase converting [U-13C3]pyruvate into [U-13C3]-Ala are not annotated in the Francisella genomes. The lower relative amounts of 13C2- and 13C1-Ala can be explained by the expected pyruvate formation via Asp by an aspartate 4- decarboxylase as also reflected in the genomes (Figure 1). Frontiers in Cellular and Infection Microbiology | www.frontiersin.org Analysis of MEOX-TMS-Fructose and TBDMS-Derivatives of Polar Metabolite Mixtures The observed ratio of 13C2- and 13C1-Ala in the global 13C- excess of Ala-260 suggested that approximately 35% of Ala were synthesized from Asp, and 65% from pyruvate in Fth, whereas the pyruvate contribution was slightly higher in Fno (about 75%). Subsequently, 13C from pyruvate could enter the TCA cycle mainly via [U-13C2]acetyl-CoA as reflected by the detected 13C2-Glu (M+2, Figure 2B) formed from 13C2-α-ketoglutarate, and 13C2-Asp (M+2) formed from 13C2- oxaloacetate. The labeling profiles of Tyr were more complex and contained a large fraction of M+4 that could be explained by the shikimate/chorismate pathway using [U-13C4]erythrose 4- phosphate as a precursor which could be synthesized via the PPP (forming [U-13C4]erythrose 4-phosphate from [U-13C6]fructose 6-phosphate by the transketolase reaction). The M+2 and M+3 fraction could arise by incorporation of [U-13C3]PEP, one of which becomes decarboxylated during the chorismate route. Isotopolog Profiles of Protein-Derived Amino Acids Harsh acidic hydrolysis of the bacterial pellet afforded a mixture of amino acids mostly (>90 %) derived from the protein fraction. By silylation, these amino acids were converted into TBDMS- derivatives that could be analyzed by GC/MS following our standard protocols. Since Trp and Cys were destroyed during the acidic hydrolysis, we could not obtain data for these amino acids. Asn and Gln were converted into Asp and Glu, respectively, and the reported values for Asp and Glu therefore represent averages for Asn/Asp and Gln/Glu, respectively. GC/MS analysis of 15 TBDMS-amino acids revealed 13C enrichments (and therefore de novo biosynthesis) in 7 amino acids from the Fth strains: Ala > Glu > Asp > Tyr > Thr > Phe > Gly = Ser (8–0.1%) and in Fno: Ala > Glu > Tyr >> Thr = Asp = Gly = Ser > Phe) (9–0.1%) (Figure 2A). His, Ile, Leu, Val, Lys, and Pro were apparently unlabeled (Supplemental Table S1) demonstrating that these amino acids were derived from unlabeled substrates (e.g., amino acids or peptides) present in brain heart infusion broth, bacto trypton and casamino acids of medium T (see also Supplemental Tables S25, S26). Isotopolog Profiles of Free Polar Metabolites In comparison of the strains, usage of glucose appears to be more directed for cell wall synthesis in the Fth strains, whereas degradation and downstream usage seems to be more pronounced in Fno. The high fractions of [U-13C3]-Ala (M+3) in the fragment containing all three carbon atoms of the original alanine molecule (Ala-260) indicated efficient usage of glucose present in the complex medium and the formation of [U-13C3]pyruvate by degradation of [U-13C6]glucose (see below). Genes encoding June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 6 Chen et al. Metabolic Fluxes in Francisella FIGURE 2 | (A) 13C-Excess (mol%) and (B) the fractional isotopolog distributions (%) in key metabolites of Francisella tularensis subspecies holartica WT strain (beaver isolate) (Fth Beaver, 1), the Francisella tularensis subspecies holartica life vaccine strain LVS (Fth LVS, 2), or the less pathogenic Francisella novicida strain U112 (Fno, 3) grown in medium T supplied with 11 mM [U-13C6]glucose. 13C-Excess (mol%) and relative fractions of isotopologs (%) were determined by GC/MS of silylated derivatives at the indexed m/z values. Error bars indicate standard deviations from the means of 6 to 9 values 2–3 × biological replicates, 3 × technical replicates. M+1, M+2, M+3, etc. indicate isotopologs carrying 1, 2, 3, etc. 13C-atoms. For numerical values, see Supplemental Tables S1, S5, S9, S13, S17, S21. FIGURE 2 | (A) 13C-Excess (mol%) and (B) the fractional isotopolog distributions (%) in key metabolites of Francisella tularensis subspecies holartica WT strain (beaver isolate) (Fth Beaver, 1), the Francisella tularensis subspecies holartica life vaccine strain LVS (Fth LVS, 2), or the less pathogenic Francisella novicida strain U112 (Fno, 3) grown in medium T supplied with 11 mM [U-13C6]glucose. 13C-Excess (mol%) and relative fractions of isotopologs (%) were determined by GC/MS of silylated derivatives at the indexed m/z values. Error bars indicate standard deviations from the means of 6 to 9 values 2–3 × biological replicates, 3 × technical replicates. M+1, M+2, M+3, etc. indicate isotopologs carrying 1, 2, 3, etc. 13C-atoms. For numerical values, see Supplemental Tables S1, S5, S9, S13, S17, S21. Labeling Experiments with [1,2-13C2]Glucose mass (Ala-232) carrying C-2 and C-3 of Ala showed a similarly high fraction for M+2 which is only possible when C-1 of Ala was not 13C-labeled (Figure 3A). It can therefore be concluded that 13C from [1,2-13C2]glucose was predominantly, if not entirely, transferred into the positions 2 and 3 of Ala (Figure 3A). This pattern excludes the Entner-Doudoroffpathway, since cleavage of [1,2-13C2]glucose would then lead to [1,2-13C2]pyruvate and [1,2-13C2]Ala finally affording M+1 in the Ala-232 fragment, but not M+2 (Figure 3B). However, glycolysis yields [2,3- 13C2]pyruvate/Ala from [1,2-13C2]glucose, in line with our experimental data (Figure 3B). Degradation of [1,2-13C2]glucose via the PPP would results in single labeled or unlabeled triose phosphates and subsequently pyruvate/Ala. On this basis, a major contribution of the PPP in the formation of the precursors Since the labeling profiles in metabolites from [U-13C6]glucose could not discriminate between glucose degradation via glycolysis, the PPP or the Entner-Doudoroffpathway, we performed additional experiments with [1,2-13C2]glucose. As a key analyte to distinguish between these routes, we had a detailed look at Ala which displayed in the mass spectrum of its TBDMS-derivative a fragment at m/z of 232 which is devoid of C-1 (Figure 3A). In comparison to the mass trace at m/z of 260 showing all three carbon atoms of the original alanine molecule, some positional 13C-assignment can be made on this basis. As expected, the Ala-derivative carrying all three C-atoms (Ala-260) displayed high fractions of M+2. The fragment with the smaller June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 7 Metabolic Fluxes in Francisella Chen et al. FIGURE 3 | Transfer of 13C-label from [1,2-13C2]glucose into alanine of Fth Beaver (1), Fth LVS (2), or Fno (3). (A) 13C-Excess (mol%) and the fractional isotopolog distributions (%) in the silylated fragments Ala-260 and Ala-232 carrying C1-C3 and C2-C3 of the original alanine carbon chain, respectively. (B) Conversion of [1,2-13C2]glucose into pyruvate and alanine via glycolysis (EMP) (left, with red bars indicating the 13C-labels) or the Entner-Doudoroff pathway (ED) (right, with green bars indicating the 13C-labels). The observed label distribution with 13C at C2 and C3 (indicated by red bars in panel A), only matches the predicted pattern via the EMP in panel (B). For more details, see also text. FIGURE 3 | Transfer of 13C-label from [1,2-13C2]glucose into alanine of Fth Beaver (1), Fth LVS (2), or Fno (3). Labeling Experiments with [1,2-13C2]Glucose (A) 13C-Excess (mol%) and the fractional isotopolog distributions (%) in the silylated fragments Ala-260 and Ala-232 carrying C1-C3 and C2-C3 of the original alanine carbon chain, respectively. (B) Conversion of [1,2-13C2]glucose into pyruvate and alanine via glycolysis (EMP) (left, with red bars indicating the 13C-labels) or the Entner-Doudoroff pathway (ED) (right, with green bars indicating the 13C-labels). The observed label distribution with 13C at C2 and C3 (indicated by red bars in panel A), only matches the predicted pattern via the EMP in panel (B). For more details, see also text. of Ala can also be excluded. Thus, glycolysis (EMP pathway) is the predominant route for glucose usage in Francisella. However, the metabolic degradation of serine became evident from the detected 13C-enrichments in a set of metabolites including glycine (Figure 4A) that can be derived from serine by a hydroxymethytransferase. Amino acids derived from pyruvate (Ala) and the TCA (Asp and Glu), fatty acids (derived from acetyl-CoA), and some polar metabolites directly related to pyruvate (lactate from the Fno strain) or fatty acid metabolism (3-hydroxybutyrate) also acquired significant 13C-label from serine (Figure 4A). However, amino acids derived from the PPP (Phe and Tyr) and any of the analyzed sugars (free fructose, glucose from glycogen and amino sugars from the cell wall) were apparently unlabeled (Supplemental Tables S3, S7, S11) suggesting that serine is not serving as a glucogenic substrate, under our experimental conditions. Labeling Experiments with [U-13C3]Serine Using our experimental system, we showed that exogenous 3 mM [U-13C3]serine is taken up by Fth and Fno as reflected by the 13C-enrichments in serine isolated from the methanolic cell extracts (Fth beaver isolate, 10%; Fth LVS, 6%, Fno, 20%) (See also Supplemental Table S7) (Figure 4A). The usage of serine for protein biosynthesis was also gleaned from the 13C-enrichments in protein-bound Ser (Fth strains, 12%; Fno, 16%) (See also Supplemental Table S3). The predominant isotopologs in any of the serine samples were the M+3 species indicating less metabolic turnover leading to M+1 or M+2 serine (Figure 4B). June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 8 Metabolic Fluxes in Francisella Chen et al. FIGURE 4 | (A) 13C-Excess (mol%) and (B) the fractional isotopolog distributions (%) in key metabolites of Fth Beaver (1), Fth LVS (2), or Fno (3) grown in medium T supplied with 3 mM [U-13C3]serine. For numerical values, see Supplemental Tables S3, S7, S11, S15, S19, S23. For more details, see also legend to Figure 2. FIGURE 4 | (A) 13C-Excess (mol%) and (B) the fractional isotopolog distributions (%) in key metabolites of Fth Beaver (1), Fth LVS (2), or Fno (3) grown in medium T supplied with 3 mM [U-13C3]serine. For numerical values, see Supplemental Tables S3, S7, S11, S15, S19, S23. For more details, see also legend to Figure 2. in the free short living metabolites, probably because no further 13C-Ser was available at this late growth phase of Fth. Compared to the Fth strains, Fno exhibited a different pattern of 13C-excess with [U-13C3]-Ser as a substrate. In the Fth strains, there was more flux from Ser directly into the biosynthesis of proteins (with the exception of glycine), via the precursors, pyruvate and oxaloacetate used for amino acid biosynthesis, and into acetyl-CoA used for fatty acid biosynthesis. In Fno, however, the free amino acids Ala, Ser and Gly, as well as lactate acquired much more (> factor 3) 13C-label from [U-13C3]-Ser. Interestingly, in Fth there was less 13C flux from Ser to Gly, than from Ser to Ala, in Fno it was vice versa (Figure 4A). Labeling Experiments with [U-13C3]Serine Probably, in Fth, Ser is more effectively used as a substrate during the exponential phase of growth with high rates of protein and lipid biosynthesis, but less in post-exponential or stationary phase of growth (sampling point), as reflected by the lower enrichments Frontiers in Cellular and Infection Microbiology | www.frontiersin.org Labeling Experiments with [U-13C3]Glycerol Using 25 mM [U-13C3]glycerol as a substrate, GC/MS analysis suggests efficient incorporation into the cell on the basis of 93% and 59% 13C excess in glycerol (Figure 5A) (mainly as M+3 isotopologs, Figure 5B) from the methanolic cell extracts of the Fth strains and Fno, respectively. Conversion of labeled glycerol into [U-13C3]pyruvate could be demonstrated by 13C-incorporation into Ala (protein-bound and in the free form) mainly as M+3 isotopologs. Carbon flux via [U-13C2]- acetyl-CoA into the TCA and fatty acid biosynthesis is also June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 9 Metabolic Fluxes in Francisella Chen et al. FIGURE 5 | (A) 13C-Excess (mol%) and (B) the fractional isotopolog distributions (%) in key metabolites of Fth Beaver (1), Fth LVS (2), or Fno (3) grown in medium T supplied with 25 mM [U-13C3]glycerol. For numerical values, see Supplemental Tables S4, S8, S12, S16, S20, S24. For more details, see also legend to Figure 2. FIGURE 5 | (A) 13C-Excess (mol%) and (B) the fractional isotopolog distributions (%) in key metabolites of Fth Beaver (1), Fth LVS (2), or Fno (3) grown in medium T supplied with 25 mM [U-13C3]glycerol. For numerical values, see Supplemental Tables S4, S8, S12, S16, S20, S24. For more details, see also legend to Figure 2. FIGURE 5 | (A) 13C-Excess (mol%) and (B) the fractional isotopolog distributions (%) in key metabolites of Fth Beaver (1), Fth LVS (2), or Fno (3) grown in medium T supplied with 25 mM [U-13C3]glycerol. For numerical values, see Supplemental Tables S4, S8, S12, S16, S20, S24. For more details, see also legend to Figure 2. clearly reflected by the M+2 isotopologs of Glu (derived from α-ketoglutarate), Asp (derived from oxaloacetate), succinate, malate, fatty acids, and 3-hydroxybutyrate. Generally, the 13C-enrichment values of these metabolites were much higher in Fno (by a factor of 2–5) in comparison to Fth. This is a clear indication for the better usage of glycerol by the less pathogenic Francisella strain Fno. The same holds true for products derived via glucogenesis and the PPP. In Fno, significant incorporation was found in Tyr (mainly as M+3 and M+2 from either PEP or the erythrose 4-phosphate precursor, respectively), in Ser and Gly (via the glucogenic intermediate, 3-phosphoglycerate), in glucosamine and muramic acid and, at lower rates, in free fructose and glucose from acid-labile polysaccharides. Frontiers in Cellular and Infection Microbiology | www.frontiersin.org DISCUSSION Pathogenic intracellular bacteria of the family Francisella can grow in the cytosolic compartments of different cell types (e.g., macrophages) in a high variety of host organisms (Santic et al., 2006; Sjostedt, 2006; Keim et al., 2007). It can be assumed that these different environments provide versatile and changing nutrient supplies. This host plasticity points at a high degree of metabolic robustness and adaptation capacities of the bacteria. The highly conserved genomes of Francisella strains reflect the potential usage of amino acids, glucose and glucogenetic substrates (e.g., glycerol or pyruvate) as major carbon substrates feeding a highly interconnected metabolic network. Earlier studies have indeed confirmed the role of amino acids, glucose, and glycerol as nutrients (Checroun et al., 2006; Meibom and Charbit, 2010; Santic and Abu Kwaik, 2013; Barel et al., 2015). On the other hand, the metabolic network structure of Fth and Fno could in principle allow the usage of a single carbon substrate to satisfy all metabolic demands (i.e., as a source for the generation of energy and biomass). Since multiple substrate usages have been shown in other intracellular bacterial pathogens characterized by similar metabolic capacities, it was therefore in order to analyze metabolite fluxes from the carbon sources glucose, serine, and glycerol. To this aim, we used isotopolog profiling experiments with three Francisella strains, i.e., the highly pathogenic F. tularensis subsp. holarctica wild type (isolated from a beaver deceased from tularemia), the attenuated live vaccine F. tularensis subsp. holarctica strain LVS, or the for humans less pathogenic F. novicida strain U112. As a benefit of the 13C-method, metabolic pathways and fluxes can be rather directly determined in contrast to transcriptomic, proteomic or metabolomic methods. Comparing the labeling profiles between the strains under study, the method should also be conducive to correlate metabolism with pathogenicity. Glycerol could not be detected in any of these fractions, whereas glucose was found, in free form, in amounts of 75.3 mM. Free serine was present at a concentration of 0.5 mM, after total hydrolysis of medium T, the concentration raised to 3.1 mM. On this basis, in the labeling experiments the total concentration of glycerol was 25 mM (with 100% [U-13C3]glycerol), glucose was present at a total concentration of 94.4 mM (with 11.8% [U-13C6]glucose), and the overall concentration of serine (free form and in peptides) was 3.4 mM (with 84.3% [U-13C3]serine) (Supplemental Tables S25, S26). Differential Substrate Usage metabolic network in Fth (i.e., with glucose feeding directly the formation of polysaccharides, and serine adding more carbon for pyruvate and actyl-CoA metabolism) in comparison to the less human-pathogenic Fno. Glycerol was a generally less efficient substrate in Fth than in Fno. This was especially true for cell wall sugars indicating that glucogenesis from glycerol is not a major process in Fth under the experimental conditions. g Since medium T (see also Supplemental Tables S25, S26) contains poorly defined components such as bacto trytone (10 g/L), casamino acids (10 g/L), and brain heart infusion broth (10 g/L), it was necessary to experimentally determine the amounts of glucose, serine and glycerol in this medium. These values were important in order to normalize the incorporation rates described above for the respective 13C-tracers. For this purpose, medium T (without the 13C-tracers) was prepared following the same protocol described for the labeling experiments (with the exception of not adding the 13C-labeled substrates) and autoclaved. After lyophilization, a fraction was silylated as described in the Materials Methods section and analyzed by GC- MS for quantifying the amounts of free glucose, glycerol, and amino acids, e.g., serine, respectively. Another fraction of the lyophilized medium was dissolved and heated in 6 M HCl in order to hydrolyze proteins and peptides present in the medium. Subsequently, the hydrolysate was lyophilized, derivatized and again analyzed by GC-MS. DISCUSSION On the basis of these findings, the 13C-enrichment values were normalized. For the 13C-glucose experiment, the measured 13C-enrichments values were multiplied by a factor of 8.5, for the 13C-serine experiment by a factor of 1.15, and for the 13C- glycerol experiment by a factor of 1. The normalized values are shown in Figures 6A,B for Fth and Fno, respectively. The relative fluxes are also indicated in Figures 6A,B by the arrow widths. It is immediately obvious that the cell wall sugars of Fth and Fno were predominantly (>85%) derived from the glucose supply present in medium T. Major fluxes were also observed from glucose to alanine and fatty acids (>50%). In Fth and Fno, exogenous serine (in free form or from the peptides present in medium T) was incorporated into the metabolic network only at lower rates (<10%). Similar low fluxes (<5%) were found from exogenous glycerol into the network of Fth. In Fno, however, glycerol contributed to biosynthesis at higher rates (up to 55% in cell wall sugars). Frontiers in Cellular and Infection Microbiology | www.frontiersin.org Labeling Experiments with [U-13C3]Glycerol Again, the M+3 isotopologs were the most prominent ones, but M+1 and M+2 also made substantial fractions in the amino sugars (Figure 5B) again indicating metabolic turnover during the amino sugar biosynthesis using glycerol as a precursor. In summary, the results demonstrate that glycerol is used for gluconeogenesis quite efficiently in Fno, but only at minor rates in Fth. June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 10 Metabolic Fluxes in Francisella Chen et al. Glucose From the analysis of genome data, it was speculated that gluconeogenesis and not glycolysis is important for intracellular replication, because no phosphofructokinase was annotated within the genomes of Ftt, Fth, and Fno until recently, and genes of gluconeogenesis/glycolysis pathways have been shown to be expressed and important for intracellular growth (Meibom and Charbit, 2010; Raghunathan et al., 2010). Mutant strains of glpX encoding the fructose-1,6-bisphosphatase, were shown to be hampered in growth under in vitro and in vivo conditions (Kadzhaev et al., 2009; Brissac et al., 2015). On the other hand, there are general differences between the human pathogenic Ftt and Fth species and the mice pathogenic Fno species in Differences in the metabolic fluxes are displayed in Figure 6C. The numbers indicate the differences between the normalized 13C-enrichments in Fth and Fno (Fth–Fno). Higher fluxes in Fth are indicated by normal arrows, whereas lower fluxes are shown by dashed arrows. It becomes evident that Fth is characterized by a slightly higher flux of glucose into the cell wall, but reduced fluxes (with the exception of Asp for unknown reasons) into any other metabolite under study. Moreover, higher fluxes were gleaned from serine into the downstream pathways of Fth (i.e., the lower part of EMP, formation of acetyl-CoA and fatty acids), but not into cell wall sugars. This points at a more bipartite June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 11 Metabolic Fluxes in Francisella Chen et al. FIGURE 6 | Observed metabolic pathways and fluxes in (A) Fth Beaver/Fth LVS, and (B) Fno from exogenous glucose (red arrows), serine (green arrows), and glycerol (blue arrows). (C) Differences in the metabolic fluxes between Fth and Fno (Fth–Fno). Metabolites studied by GC-MS-based isotopolog profiling are indicated by black boxes. The numbers indicate normalized overall 13C-enrichments (from labeled glucose, glycerol and serine in red, blue and green, respectively). The arrow widths roughly indicate the relative fluxes. Fluxes conducive to enrichments <1% are not shown. In (C) the numbers indicate the differences in the normalized overall 13C-enrichments (Fth–Fno). Higher fluxes in Fth are indicated by normal arrows, lower fluxes by dashed arrows. FIGURE 6 | Observed metabolic pathways and fluxes in (A) Fth Beaver/Fth LVS, and (B) Fno from exogenous glucose (red arrows), serine (green arrows), and glycerol (blue arrows). (C) Differences in the metabolic fluxes between Fth and Fno (Fth–Fno). Frontiers in Cellular and Infection Microbiology | www.frontiersin.org Glycerol It was recently shown that glycerol is metabolized by Fno, mainly for gluconeogenesis during intracellular replication (Kadzhaev et al., 2009; Brissac et al., 2015). Indeed, glpD (glycerol-3-P dehydrogenase) is necessary for the utilization of glycerol in Fno (Brissac et al., 2015). Carbon flux from Ser to some protein-derived amino acids (e.g., Ala and Asp) was higher in Fth than in Fno. The carbon flux from Ser to Gly, however, was much higher in Fno than in Fth. For Fth, it was shown that the glycine cleavage system (GCS) is important for replication in Ser-limiting environments and that a gcvT mutant strain is auxotrophic for Ser, indicating the importance of the Ser to Gly (and vice versa) converting systems (Meibom and Charbit, 2010; Brown et al., 2014). Glycine- dependent Ser production in E. coli is only apparent when the Ser biosynthesis pathway (serABC) is disrupted (Ravnikar and Somerville, 1987). In addition, the GCS is the only source of Ser biosynthesis in Fth, but surprisingly also in Ftt containing a complete serABC pathway (Brown et al., 2014). In Fth, the Ser synthesis pathway (from 3-PG) is incomplete, due to a pseudo serB gene (P-serine phosphatase [serB]). This is in agreement with our results of no 13C flux to Ser using glucose or glycerol as a substrate. Our results confirmed these and earlier data (Petersen and Schriefer, 2005; Marinov et al., 2009; Gyuranecz et al., 2010; Huber et al., 2010), but also provided additional insights into details of species-specific differences in glycerol metabolism. As expected, carbon flux from glycerol was much higher in Fno than in Fth, and glycerol was efficiently used for gluconeogenesis, also in the presence of (unlabeled) glucose in the medium T (Figure 6C). 13C-Excess values of 4–5% in muramic acid and Ala from Fth grown in the presence of [U-13C3]glycerol clearly demonstrated that glycerol was also metabolized by Fth. This is noteworthy since Fth is known to be negative for the fermentation and metabolism of glycerol (Biolog system), but able to metabolize glycerol phosphate (Petersen and Schriefer, 2005; Gyuranecz et al., 2010; Huber et al., 2010) probably due to the presence of a glycerol phosphate transporter GlpT (see also Supplemental Figure S1) which is also necessary for the uptake of fosmidomycin (Mackie et al., 2012). Glucose Metabolites studied by GC-MS-based isotopolog profiling are indicated by black boxes. The numbers indicate normalized overall 13C-enrichments (from labeled glucose, glycerol and serine in red, blue and green, respectively). The arrow widths roughly indicate the relative fluxes. Fluxes conducive to enrichments <1% are not shown. In (C) the numbers indicate the differences in the normalized overall 13C-enrichments (Fth–Fno). Higher fluxes in Fth are indicated by normal arrows, lower fluxes by dashed arrows. carbohydrate metabolism (for review, see Kingry and Petersen, 2014). More specifically, Fth strains seem to metabolize glucose, but not glucose-6-phosphate in vitro. Only F. hispaniensis and F. philomiragia were shown to be able to metabolize glucose-1-phosphate and glucose-6-phosphate (Gyuranecz et al., 2010). Only in 2012, a gene encoding a phosphofructokinase (FTN_1210) was identified in Fno (Enstrom et al., 2012) providing evidence for the role of glycolysis at least in Fno, also confirmed by elegant labeling studies (Brissac et al., 2015). not only in Fno, but also in Fth when growing in the complex medium T. There were no significant differences between the Fth LVS and the Fth wild-type strain indicating that the reduced virulence of Fth LVS is not (strongly) related to glucose usage. However, as pointed out above, the direct transfer of exogenous glucose into cell wall sugars is slightly higher in Fth than in Fno (Figure 6C). The pathways of glucose degradation follow the same routes in Fth and Fno, i.e., via the EMP, but not the ED or PPP. Carbon flux from glucose to amino acids via pyruvate and intermediates of the TCA is lower in Fth than in Fno with the exception of Asp (Figure 6C). This could indicate We could now demonstrate by isotopolog profiling that exogenous glucose is by far the most efficient carbon substrate June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 12 Metabolic Fluxes in Francisella Chen et al. that Fth utilizes additional carbon substrates for the energy generating sections of metabolism (see below) following the concepts of a bipartite metabolism in L. pneumophila (Gillmaier et al., 2016; Häuslein et al., 2016) and Chlamydia trachomatis (Mehlitz et al., 2017). Although not annotated within the genome, we could provide evidence for the presence of a putative Ala dehydrogenase or Glu/Pyr transaminase. Nevertheless, the results also demonstrate the expected activity of an aspartate 4-decarboxylase (see Figure 1). Glucose the SLC family of host amino acid transporters is important for intracellular replication of Fth strain LVS (Barel et al., 2012). Interestingly, although Fth replicates in the cytosol, a similar finding of the usage of amino acids during intracellular growth and the involvement of SLC proteins of the host cell was found for L. pneumophila, a human pathogenic bacterium which replicates within a vacuole in alveolar macrophages (Wieland et al., 2005; Eisenreich and Heuner, 2016). Under the in vitro growth conditions used in our experiments, there was only a very low flux from 13C-Ser into the downstream metabolites in Fth and especially in Fno, as well as a very low (if at all) flux via gluconeogenesis in both species (as gleaned e.g., from the apparently unlabeled cell wall-derived carbohydrates). This also came as a surprise, since gluconeogenesis is present under the in vitro growth conditions used here as gleaned from the glycerol experiments (Figures 6A,B). Glycerol However, there is also a glpF gene annotated in the genomes of Francisella, coding for an aquaglyceroporin involved in glycerol and water transport (Raghunathan et al., 2010). Moreover, three strains of Fth were reported to be able to produce acid from glycerol as a substrate (Marinov et al., 2009). On this basis, it is not surprising that Fth is using glycerol, rather it remains unclear, why Fth strains are only less able to utilize glycerol, also taking into account that all genes for the metabolism of glycerol are present in the genomes of Fth (see Supplemental Figure S1). In F. tularensis subsp. tularensis (Ftt), gfpK and glpD are separated by an IS-Ftu1 element, as well as in Fth LVS, but there, the operon is also disconnected spatially. Nevertheless, in all strains analyzed in this study, the genes for glycerol uptake and usage are present and seem to encode putative functional enzymes. Further experiments are therefore necessary to elucidate the reason for the low rate of glycerol utilization in Fth. We could now demonstrate that this is not true for Fno, since we obtained carbon flux from glucose and glycerol to Ser. Isotopolog profiles of protein derived Ser using 13C-Ser as a substrate indicated synthesis of Ser from Gly (i.e., displaying M+1 and M+2 fractions), but this was not true for free Ser collected at the stationary phase (Figure 4B). In addition, the free amino acids Ala, Ser, and Gly, as well as lactate, acquired much more 13C-label from Ser in Fno. In Fth, label from serine was more effectively transferred into most amino acids from the protein fraction. This may indicate that amino acids (Ser) are more efficiently used in the replicative phase of growth of Fth, but less in stationary phase of growth. Similar results were obtained recently for L. pneumophila (Gillmaier et al., 2016). This could point again at a shift to a bipartite metabolism in Fth as in L. pneumophila, using amino acids as carbon and energy source in the exponential phase and more glucose during the post-exponential phase of growth (Eisenreich and Heuner, 2016; Gillmaier et al., 2016; Häuslein et al., 2016). In this context, it is noteworthy that species-specific differences in the metabolism of glucose were also found for different Legionella species (Brzuszkiewicz et al., 2013) in analogy to Francisella strains (Gyuranecz et al., 2010; Huber et al., 2010). REFERENCES MBio 3, e00001–e00012. doi: 10.1128/mBio.00001-12 Bertani, G. (1951). Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J. Bacteriol. 62, 293–300. Eylert, E., Herrmann, V., Jules, M., Gillmaier, N., Lautner, M., Buchrieser, C., et al. (2010). Isotopologue profiling of Legionella pneumophila: role of serine and glucose as carbon substrates. J. Biol. 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It is tempting to speculate whether the detected metabolic differences between Fth and Fno are also related to host-specific virulence, and whether the concept of metabolic virulence is a key feature for the pathogenicity of Francisella. Further metabolic analyses of Francisella strains during replication in different host cells could finally elucidate the different nutrition strategies of Francisella strains. This work was supported by the Deutsche Forschungsgemeinschaft (EI 384/11) and the Robert Koch Institute. WE and IH were also supported by the Bundesministerium für Bildung und Forschung (BMBF) through ERA-NET Infect-ERA in the context of the EUGENPATH network. This work was supported by the Deutsche Forschungsgemeinschaft (EI 384/11) and the Robert Koch Institute. WE and IH were also supported by the Bundesministerium für Bildung und Forschung (BMBF) through ERA-NET Infect-ERA in the context of the EUGENPATH network. AUTHOR CONTRIBUTIONS The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fcimb. 2017.00275/full#supplementary-material KH, WE, and RG designed the study and provided facility and equipment. FC, KR, EK, IH, ES, XW, and KM performed the experiments. KH and WE wrote the paper. Serine Amino acids (Ser) are well-known to be important for intracellular multiplying Francisella (Meibom and Charbit, 2010; Raghunathan et al., 2010; Barel et al., 2012, 2015; Steele et al., 2013; Brown et al., 2014; Ramond et al., 2014; Gesbert et al., 2015). This was strongly supported by a report showing that In conclusion, our findings are in agreement with multiple substrate usage by Francisella and species-dependent carbon June 2017 | Volume 7 | Article 275 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 13 Metabolic Fluxes in Francisella Chen et al. REFERENCES Evol. 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Mass isotopomer analysis: theoretical and practical considerations. Biol. Mass Spectrom. 20, 451–458. doi: 10.1002/bms.1200200804 Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Mackie, R. S., McKenney, E. S., and Van Hoek, M. L. (2012). Resistance of Francisella novicida to fosmidomycin associated with mutations in the glycerol-3-phosphate transporter. Front. Microbiol. 3:226. doi: 10.3389/fmicb.2012.00226 Copyright © 2017 Chen, Rydzewski, Kutzner, Häuslein, Schunder, Wang, Meighen- Berger, Grunow, Eisenreich and Heuner. 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Employability Paradox: The Effect of Development Idiosyncratic Deals on Recipient Employees’ Turnover Intention
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*Correspondence: Hui Deng Keywords: development idiosyncratic deals, internal employability, external employability, turnover intention, opportunity to perform Specialty section: This article was submitted to Organizational Psychology, a section of the journal Frontiers in Psychology Received: 16 April 2021 Accepted: 08 July 2021 Published: 04 August 2021 Specialty section: This article was submitted to Organizational Psychology, a section of the journal Frontiers in Psychology Employability Paradox: The Effect of Development Idiosyncratic Deals on Recipient Employees’ Turnover Intention Xiaoyan Zhang, Hui Deng*, Yuhuan Xia and Yuanyuan Lan* School of Economics and Management, Beijing Jiaotong University, Beijing, China Xiaoyan Zhang, Hui Deng*, Yuhuan Xia and Yuanyuan Lan* School of Economics and Management, Beijing Jiaotong University, Beijing, China Applied social cognitive theory, this study built a moderated mediation model to explain how and when development idiosyncratic deals (i-deals) affect recipients’ turnover intention. Specifically, this study proposed two paths that linked development i-deals with the recipients’ turnover intention. One path was a retention path via perceived internal employability and another path was a turnover path via perceived external employability. This study tested the hypotheses with a sample of 337 employees from three companies in China. The results showed that development i-deals improved recipients’ perception of internal and external employability both. Perceived internal employability predicted low risk of turnover, but perceived external employability predicted high risk of turnover. And perceived internal and external employability played mediating roles in the relationship between development i-deals and turnover intention. Furthermore, the recipients’ perception of opportunity to perform in current organization strengthened the relationship between perceived internal employability and turnover intention, but weakened the relationship between perceived external employability and turnover intention. Theoretical and practical implications of these findings were discussed. Keywords: development idiosyncratic deals, internal employability, external employability, turnover intention, opportunity to perform INTRODUCTION Idiosyncratic deals (i-deals) are voluntary and personalized agreements of a non-standard nature negotiated between individual employees and employers regarding employment terms that can benefit each party (Rousseau et al., 2006). Development i-deals refer to the individualized opportunities to develop working skills, enhance professional competencies, and meet personal career aspirations, which are essential for higher performance, greater occupational success, and a larger space for promotion (Zhang et al., 2020). In human resource management practice, development i-deals often manifest as challenging work assignments, special training opportunities, or career development opportunities in the organization (Marescaux et al., 2019; Zhang et al., 2020). Received: 16 April 2021 Accepted: 08 July 2021 Published: 04 August 2021 ORIGINAL RESEARCH published: 04 August 2021 doi: 10.3389/fpsyg.2021.696309 Edited by: Melinde Coetzee, University of South Africa, South Africa Reviewed by: Ingrid Potgieter, University of South Africa, South Africa Michael Tomlinson, University of Southampton, United Kingdom *Correspondence: Hui Deng 19113068@bjtu.edu.cn Yuanyuan Lan 16113168@bjtu.edu.cn Reviewed by: Ingrid Potgieter, University of South Africa, South Africa Michael Tomlinson, University of Southampton, United Kingdom *Correspondence: Hui Deng Citation: Zhang X, Deng H, Xia Y and Lan Y (2021) Employability Paradox: The Effect of Development Idiosyncratic Deals on Recipient Employees’ Turnover Intention. Front. Psychol. 12:696309. doi: 10.3389/fpsyg.2021.696309 Zhang X, Deng H, Xia Y and Lan Y (2021) Employability Paradox: The Effect of Development Idiosyncratic Deals on Recipient Employees’ Turnover Intention. Front. Psychol. 12:696309. doi: 10.3389/fpsyg.2021.696309 As an effective human resources management tool, development i-deals have been shown to have significant effects on recipient employees (Hornung et al., 2010, 2011). The majority of existing August 2021 | Volume 12 | Article 696309 Frontiers in Psychology | www.frontiersin.org 1 Development I-Deals and Turnover Intention Zhang et al. studies have tended to focus on the positive effects of development i-deals on the recipients’ work-related behaviors, such as constructive voice behavior (Ng and Feldman, 2015), helping behavior (Guerrero and Challiol-Jeanblanc, 2016), creativity (Wang et al., 2018), in-role performance, and organizational citizenship behavior (Anand et al., 2010, 2018). Only a few studies have noted that these i-deals can also exert some negative impacts on the recipients. For example, current research has indicated that development i-deals can increase recipients’ working stress and work-family conflicts (Hornung et al., 2014), feeling of being envied (2017), and even unethical pro-organizational behavior (Jiang and Zhang, 2020). However, thus far, empirical research on the potential costs and risks of granting development i-deals still remains in its infancy. this paper speculated that recipients’ improved perception of internal employability may increase recipients’ retention, which brings benefits to the organization, but the perception of external employability may increase recipients’ turnover, which brings some costs to the organization. Consistent with previous research, such a dilemma between the benefits and costs of recipients’ development i-deals can be referred to as the employability paradox (Nelissen et al., 2017). Further, this study examined the moderating effect of recipients’ perception of opportunity to perform in current organization on the relationship between perceived employability and turnover intention. The opportunity to perform refers to the extent to which individuals believe they have sufficient opportunities to demonstrate their abilities, skills, and knowledge in the current organization (Schleicher et al., 2006; Ingold et al., 2016). Existing research has emphasized the importance of opportunity to perform, indicating that lack of opportunity to perform is related to performance decrements (Ford et al., 2006), which may affect employees’ willingness to remain. Citation: Thus, this study included opportunity to perform as a moderator in the model, and argued that high level of opportunity to perform may strengthen the negative relationship between perceived internal employability and turnover intention, but weaken the positive relationship between perceived external employability and turnover intention. Development i-deals were originally used for retaining the employees that supervisors valued (Rousseau et al., 2006). Indeed, empirical research has shown that i-deals are effective in boosting recipients’ job motivation and commitment to the current organization (Bal et al., 2012). However, there is a common phenomenon that many recipient employees who are valued by their supervisors leave their organizations after obtaining special career development or training opportunities. To date, the research examining how and when development i-deals shape the recipients’ turnover intention is relatively rare (Brzykcy et al., 2019). Exploring the process through which development i-deals impact recipients’ turnover intention has important significance (Ng, 2017). Authorizing development i-deals to particular employees not only means that supervisors provide training and career development opportunities to those employees, but also means that the organization invests substantial direct and indirect money and time on the recipient employees (Rousseau et al., 2006). Therefore, once the recipients leave, it will result in costs to the organization. Thus, to advance the understanding of whether, how, and when development i-deals influence recipients’ turnover intention, a deeper investigation is warranted. In sum, this paper applied social cognitive theory to explore the relationship between development i-deals and recipient employees’ turnover intention by uncovering the potential mediating cognitive mechanism of employability paradox and moderating effect of opportunity to perform. This provides a new theoretical perspective to understand the relationship between development i-deals and recipients’ behaviors. Figure 1 shows the conceptual model. Frontiers in Psychology | www.frontiersin.org LITERATURE REVIEW AND HYPOTHESES DEVELOPMENT Accordingly, this study presents a framework based on social cognitive theory to reveal the cognitive and psychological mechanisms through which development i-deals may affect recipients’ turnover intention. The social cognitive theory posits that the development of individuals’ self-efficacy may be a conduit between environmental cues and their behavioral outcomes (Bandura, 1986). Obtaining development i-deals can be regarded as a valuable environmental cue because it provides desired resources to the recipients; thus, it will be more likely to boost their self-efficacy (Wang et al., 2018). Scholars have indicated that the conception of perceived employability is a form of self-efficacy (Nelissen et al., 2017). Rothwell and Arnold (2007) stated that perceived employability emphasizes the extent to which individuals believe that they have the ability to meet the requirements of the job they have (i.e., perceived internal employability) or the extent to which the individuals believe that they have the capability to attain the requirements of a certain new job that they desire (i.e., perceived external employability). Thus, this paper proposed that recipients’ cognition of their working capability may serve as a mediating variable, such that development i-deals may have positive effects on recipients’ perceived internal and external employability. Subsequently, I-deals may take many forms in management practice (Rousseau et al., 2006). In terms of the content, scholars identified three types of i-deals, namely development i-deals (or task i-deals), flexibility i-deals, and reduced workload i-deals (Rousseau and Kim, 2006; Hornung et al., 2009). Based on this, Rosen et al. (2013) modified and broadened the previous scale of i-deals to cover four dimensions, namely schedule flexibility i-deals, location flexibility i-deals, task and work i-deals, and financial incentives i-deals. This study mainly focused on development i-deals. That is because, conceptually, development i-deals refer to the customized but limited opportunities in the organization that can increase the recipients’ working skills or promote their career development, while flexibility i-deals provide recipients with discretion to personalize working schedules or working locations to better fit personal needs (Hornung et al., 2014). Reduced workload i-deals are used to individually adjust the quantity or quality of workload, such as shorter workdays or less strenuous tasks (Hornung et al., 2009), and financial incentives i-deals allow employees to negotiate the terms of their August 2021 | Volume 12 | Article 696309 2 Development I-Deals and Turnover Intention Zhang et al. FIGURE 1 | Theoretical model. FIGURE 1 | Theoretical model. LITERATURE REVIEW AND HYPOTHESES DEVELOPMENT compensation plans (Rosen et al., 2013). From the perspective of involved content, relative to other three types of i-deals, development i-deals may be more closely associated with perceived workability (Brzykcy et al., 2019), and may be more instrumental in facilitating recipients’ career development and future performance (Guerrero and Challiol-Jeanblanc, 2016; Liao et al., 2016; Kong et al., 2020). Furthermore, a recent study indicated that flexibility i-deals and reduced workload i-deals may help individuals to focus on other areas in life, such as caring for elderly parents or young baby, and balancing work and family (Bal et al., 2021). Thus, the positive effects of such two types of i-deals may not be visible inside organizations, but may extend beyond organizations. Besides, there usually has a pay or compensation privacy policy in modern organizations, and it is difficult to do compensation research. Therefore, this research explored the influences of development i-deals on recipients’ perceived employability and turnover intention. have recognized perceived employability as a form of self- efficacy (Nelissen et al., 2017). Given that development i-deals can be viewed as an important contextual factor that can exert significant effects on recipient employees’ self-efficacy (Wang et al., 2018), it is assumed that development i-deals may have a positive influence on their perceived employability. This study speculates that development i-deals can positively impact recipients’ perceived internal employability for the following reasons. g First, as mentioned above, development i-deals refer to employers offering customized opportunities in order to promote particular employees’ working skills and career development, such as on-the-job training, promotion opportunities, or challenging work assignments (Hornung et al., 2009; Zhang et al., 2020). From the perspective of the content, development i-deals may be helpful to increase the recipients’ work ability, and thus enhance their perceived internal employability. Second, the resources that development i-deals involved are usually limited, that is, for example, one employee’s obtaining promotion opportunities may mean that his or her coworkers cannot be raised (Kong et al., 2020). Therefore, granting development i-deals to employees not only means that the recipients can obtain working resources or opportunities that they desire, but also has some invisible implications beyond the actual resources (Srikanth et al., 2020). In other words, authorizing development i-deals delivers a signal that supervisors value and trust the recipients (Rousseau et al., 2006). LITERATURE REVIEW AND HYPOTHESES DEVELOPMENT And obtaining development i-deals can also be viewed as the important evidence of supervisors’ recognition of the i-dealers’ contribution to the organization, their special status in supervisors’ eyes, and supervisors’ expectations of their future performance (Vidyarthi et al., 2016). Those cues from supervisors may cause the recipients’ perception that they are essential for the organization, thus enhancing their assessments of internal employability. Third, development i-deals encourage the recipient employees to participate in their career management (Rousseau et al., 2006). Thus, providing development i-deals may show that the supervisors care about the recipients’ employability. This may strengthen recipients’ beliefs that the employer wants to build a long-term employment relationship with them, which may improve their perception of internal employability. Empirical studies also provide support for this proposition, that individual career management practices Frontiers in Psychology | www.frontiersin.org The Retention Path via Perceived Internal Employability p y y Drawing on social cognitive theory (Bandura, 1986; Wang et al., 2018), this study proposed two paths that linked development i-deals with recipients’ turnover intention via their cognitive processes of perceived employability. The first is a retention path via perceived internal employability, and the second is a turnover path via perceived external employability. In general terms, perceived employability refers to individuals’ evaluations of “capacity to control one’s employment options through the creation, identification, and realization of career opportunities” (Direnzo and Greenhaus, 2011, p. 571). Perceived employability concerns individuals’ perceptions about the possibilities to obtain new employment (De Cuyper et al., 2012). The possibility at their current organization can be referred to as perceived internal employability, and the possibility at another organization can be referred to as perceived external employability (Rothwell and Arnold, 2007; De Cuyper and De Witte, 2010). The difference between them is that the former concerns the transfer of skills within organizational boundaries and the latter outside organizational boundaries. According to social cognitive theory, Bandura (1978) indicated self-efficacy as a motivational pathway that links contextual factors with individuals’ behaviors. Many scholars August 2021 | Volume 12 | Article 696309 Frontiers in Psychology | www.frontiersin.org 3 Development I-Deals and Turnover Intention Zhang et al. could increase their perceptions of internal employability (Soares and Mosquera, 2021). Accordingly, this paper hypothesizes that: employability, employees’ perceived external employability refers to their perception of finding a comparable desired new job with another employer (Rothwell and Arnold, 2007; De Cuyper and De Witte, 2010). Based on the rationale of social cognitive theory (Bandura, 1978), this study posits that development i-deals not only increase the recipient employees’ perceived internal employability, but also increase their external employability at the same time. Hypothesis 1a: Development i-deals are positively related to recipient employees’ perceived internal employability. Hypothesis 1a: Development i-deals are positively related to recipient employees’ perceived internal employability. According to social cognitive theory (Bandura, 2006), belief in one’s efficacy is a key personal resource in personal development and change, and such a belief can affect people’s motivation, expectations, and selection. Based on this, this study proposes that perceived internal employability will reduce recipient employees’ turnover intention. Turnover intention is defined as employees’ conscious and deliberate willingness to leave the organization (Tett and Meyer, 1993; Egan et al., 2004). The Retention Path via Perceived Internal Employability And existing empirical research has shown that increasing an individual’s organizational commitment may be helpful to lower their turnover intention (Kim and Beehr, 2020). Turnover intention and turnover are two distinct concepts, but higher turnover intention is a key element that can predict employees’ turnover behavior (Egan et al., 2004). First, as noted above, obtaining development i-deals means the supervisors value the recipient employees, that is supervisors recognize the recipients’ contribution to the organization and trust their personal competencies (Rousseau et al., 2006; Vidyarthi et al., 2016). Those clues may improve the recipient employees’ evaluations of their working abilities and self-worth, thus increasing their confidence to find a new job in the external labor market. Second, the within-group heterogeneity nature of development i-deals reveals that development i-deals are not available for every employee, but for someone who is professional or valuable (Marescaux et al., 2019, 2021). Because of this nature, development i-deals may have broader significance and implications beyond the current organization (Bal and Rousseau, 2015). Besides, receiving special work arrangements vis-à-vis career development and skill improvement also shows the recipients’ capabilities and worth to other employers to some degree. In other words, employers can observe the recipient employees’ positive and valuable characteristics, competencies, and attitudes through their experience of obtaining development i-deals. Such experience delivers a powerful signal of the recipient employees’ abilities, worth, and potential to prospective employers (Ho and Kong, 2015). When recipient employees perceive development i-deals as valuable signs of their ability to other employers, the self-perceived external employability may be enhanced. Previous research has provided empirical support for this proposition, that development i-deals could boost recipients’ perception of skill acquisition and occupational self-efficacy (Hornung et al., 2014). Thus, this paper hypothesizes that: g Employees who received development i-deals may possess more valuable resources and greater development space than their coworkers who did not obtain i-deals (Huo et al., 2014; Zhang et al., 2020). Those recipients may view leaving the current organization as a risk and a personal loss of resources, and therefore they may not be inclined to leave (De Cuyper and De Witte, 2011). Moreover, based on previous i-deals research, this negative relationship between internal employability and recipient employees’ turnover intention can also be explained through social exchange mechanisms (Liu et al., 2013; Ng and Feldman, 2015; Vidyarthi et al., 2016). The Retention Path via Perceived Internal Employability Those i-deals studies have shown that when employees successfully negotiate i-deals with their supervisors, they may perceive that their organization values them, trusts them, and provides desired opportunities to facilitate their career development and improve their future performance. As a result, they may feel obliged to respond reciprocally, and thus increase their intention to remain. Furthermore, many scholars have explicitly stated that perceived internal employability can decrease individuals’ intention to leave (Kammeyer-Mueller et al., 2005). A recent study also demonstrated the association between perceived internal employability and lower turnover intention, as well as the mediating role of perceived internal employability in the relationship between career development management and turnover intention (Soares and Mosquera, 2021). Therefore, this paper hypothesizes that: Hypothesis 2a: Development i-deals are positively related to recipient employees’ perceived external employability. Hypothesis 2a: Development i-deals are positively related to recipient employees’ perceived external employability. According to social cognitive theory, the extent to which individuals believe in their capacity will determine their motivation, affect, and what they decide to do with their abilities, skills, and knowledge (Bandura, 1978, 2006). Bandura (2006) also stated that employees’ cognition about the future could be brought into the present as guides and motivators of current behaviors. Based on these rationales of social cognitive theory, it is speculated that recipient employees’ perceived external employability may increase the risk of their turnover. Hypothesis 1b: Perceived internal employability is negatively related to recipient employees’ turnover intention. Hypothesis 1b: Perceived internal employability is negatively related to recipient employees’ turnover intention. Hypothesis 1c: Perceived internal employability mediates the relationship between development i-deals and turnover intention. Hypothesis 1c: Perceived internal employability mediates the relationship between development i-deals and turnover intention. Drawing on social cognitive theory, recipient employees with a higher-level perception of external employability may be more likely to feel confident about their working abilities. Such confidence may enhance their self-expectation, which may trigger a belief that they deserve a better organizational platform or a higher position that they desire. Therefore, those recipient employees may be inclined to keep their eyes on job alternatives across organizational boundaries and seek more The Moderating Role of Opportunity to Perform Based on social cognitive theory (Bandura, 1986; Wang et al., 2018), as an important contextual factor, opportunity to perform in current organization may have a significant impact on recipient employees’ cognition, which may alter their reaction toward self-evaluation. The opportunity to perform refers to recipient employees’ perceptions concerning whether they have adequate opportunity to demonstrate their knowledge, skills, and abilities in the current organization (Schleicher et al., 2006; Ingold et al., 2016). And lack of opportunities has long been associated with deviant or counterproductive behaviors (Khan et al., 2017). This study proposes that recipient employees’ perceptions of opportunity to perform in the current organization may moderate the relationships between perceived internal and external employability and turnover intention. To reduce the potential common method bias, the research team collected two waves of data and the interval between each wave was 1 month. At time 1, researchers distributed 410 questionnaires, and asked the participants to report their development i-deals, perceptions of opportunity to perform in the current organization, their organizational commitment, and demographic variables. At time 2, researchers asked them to report their perceived internal and external employability, and their turnover intention. Finally, the research team obtained a complete set of valid responses from 337 individuals (82.20% of the initial sample). Overall, 52.82% were male, and the average age was 36.93. Their average organizational tenure was 8.04 years, and 50.45% held a master’s degree or above. In terms of the position, 29.38% of them were in management positions, 21.96% were designers, 8.90% were financial staff, 28.19% were engaged in research and development, and 11.57% were engaged in product operations. p y y Recipient employees’ perceptions of opportunity to perform emphasize the extent to which they perceive that their current circumstances allow them to express themselves (Schleicher et al., 2006). Recipient employees with a high level of opportunity to perform may perceive that they not only have special opportunities for training or improving their work-related skills, but also the opportunities to develop advanced skills and knowledge to optimize the completion of tasks, thus demonstrating or showing their abilities (Ford et al., 2006). Moreover, the i-deals literature has indicated that i-deals can deliver a signal to the recipient employees that they may have a broader development space than their coworkers (Zhang et al., 2020). And recipient employees’ perceptions of high opportunity to perform may further enhance such cognition. Participants and Procedures The sample covers three companies in Shandong, China. One of them is a high-tech company with about 200 employees, the second one is a traditional textile company with around 800 employees, and the third one is a wholly-owned subsidiary of a large-scale 3C products R&D and manufacturing company, with about 1,500 employees. As a first step, permission was obtained from the CEO of each company to collect the required data. The researchers randomly selected and interviewed a small number of managers and employees from those companies to ensure that development i-deals were a feature of each company. Then the research team acquired lists identifying all participants, and assigned a four-digit code to each of them. With the assistance of the human resource department in each company, all participants were invited into a large conference room. Next, the research team distributed printed questionnaires, gift incentives, and introduced the purpose and procedures of the survey. Participation was voluntary and individuals were assured that their data would remain confidential. After completed the questionnaires, they put them in sealed envelopes and handed them directly to the research team. Hypothesis 2b: Perceived external employability is positively related to recipient employees’ turnover intention. Hypothesis 2b: Perceived external employability is positively related to recipient employees’ turnover intention. Hypothesis 2c: Perceived external employability mediates the relationship between development i-deals and turnover intention. The Turnover Path via Perceived External Employability Similar to perceived internal employability, perceived external employability can also be viewed as a form of self- efficacy (Nelissen et al., 2017). According to the research on August 2021 | Volume 12 | Article 696309 Frontiers in Psychology | www.frontiersin.org 4 Development I-Deals and Turnover Intention Zhang et al. the recipient employees’ intention to remain. Thus, this study hypothesizes that: the recipient employees’ intention to remain. Thus, this study hypothesizes that: opportunities outside their own organization, causing their turnover intention to increase. Furthermore, previous research has linked employees’ perceptions of job alternatives to turnover intention, thus providing some support for this proposition. For example, March and Simon (1958) indicated that employees’ perceptions of a number of external alternatives may be an important predictor shaping their turnover intention. Thus, the more alternatives the recipient employees perceive, the more likely they will quit. Many empirical studies have also demonstrated a positive relationship between perceived external employability and turnover intention (Steel and Griffeth, 1989; Hom et al., 1992; Nelissen et al., 2017). Accordingly, this paper hypothesizes that: Hypothesis 3a: Opportunity to perform strengthens the negative effect of perceived internal employability on turnover intention. Hypothesis 3b: Opportunity to perform weakens the positive effect of perceived external employability on turnover intention. Hypothesis 3a: Opportunity negative effect of perceived turnover intention. Hypothesis 3b: Opportunity to effect of perceived external intention. Hypothesis 3a: Opportunity to perform strengthens the negative effect of perceived internal employability on turnover intention. Hypothesis 3b: Opportunity to perform weakens the positive effect of perceived external employability on turnover intention. The Moderating Role of Opportunity to Perform When recipient employees perceive an optimistic picture in the near future, they may be more likely to remain in the current organization, rather than leaving and taking a risk. That is, even though development i-deals can impact recipient employees’ perceptions of their internal and external employability, a high level of opportunity to perform in the current organization may be helpful to increase Frontiers in Psychology | www.frontiersin.org Confirmatory Factor Analysis Development i-deals were measured with Rousseau and Kim (2006) 4-item scale. The effectiveness of this scale has been confirmed by Wang et al. (2018) and Zhang et al. (2020). And a sample item is “To what extent have you asked for and successfully negotiated with your supervisor for training opportunities” (α = 0.743). This study analyzed the data using Mplus 7 and SPSS 25. Before testing the hypotheses, a confirmatory factor analysis (CFA) was conducted to examine the validity of the six key variables in the model (development i-deals, perceived internal employability, perceived external employability, turnover intention, organizational commitment, and opportunity to perform in current organization). Chi-square, the Tucker–Lewis index (TLI), the comparative fit index (CFI), the root mean square error of approximation (RMSEA), and the standardized root mean residual (SRMR) were used to assess model fit. As shown in Table 1, the proposed six-factor model showed a good overall fit to the data with χ2/df = 1.112, CFI = 0.992, TLI = 0.991, RMSEA = 0.018, SRMR = 0.037, and all factor loadings were significant. Descriptive Analyses Means, standard deviations, zero-order Pearson correlations, and scale reliabilities for each variable are shown in Table 2. Recipient employees’ development i-deals are positively correlated with their perceived internal employability (r = 0.192, p < 0.01), and their perceived external employability (r = 0.227, p < 0.01). Recipient employees’ perceived internal employability is negatively correlated with turnover intention (r = −0.344, p < 0.01). These results provide preliminary support for the study’s hypotheses. Hypotheses Testing To test the proposed hypotheses, the PROCESS macro in SPSS 25 (Hayes, 2013) with a 5,000-resample bootstrap method was used to construct 95% bias-corrected confidence intervals (CIs). If the CI did not include 0, the null hypothesis of no (conditional) indirect effect was rejected (Preacher et al., 2007). Control Variables Most of the effect sizes of focal variables are in the range of “small” and “medium” sized effects. Specifically, the absolute value of correlations between development i-deals and other focal variables ranges from 0.129 to 0.227, which fits into Rhoades and Eisenberger (2002) interpretation of Cohen (1988) small effect size range (i.e., | r| < 0.24). The absolute value of correlations between predictors and turnover intention is higher, ranging from 0.129 to 0.344. Among them, the 0.344 is the medium effect size according to Rhoades and Eisenberger (2002) interpretation of Cohen (1988) medium effect size range (i.e., 0.24 < | r| < 0.36), and the rest are the small effect size. Following Liu et al. (2013) which explored the effects of i-deals on recipient employees, this study controlled for employee demographics, including age, gender, education level, and organizational tenure. In addition, previous research has suggested that employees’ commitment may have a significant direct impact on their turnover intention (Chang, 1999). Thus, this study included recipient employees’ organizational commitment to the current organization as a control variable, using a six-item scale from Meyer et al. (1993). A sample item is “I would be very happy to spend the rest of my career with this organization” (α = 0.905). Turnover Intention A 4-item scale from O’Reilly et al. (1991) was used to measure turnover intention. This scale’s high reliability has been proved by Ferreira et al. (2017). A sample item is “I prefer another more ideal job than the one I now work in” (α = 0.754). Perceived Internal and External Employability Perceived internal employability was measured with a 4-item scale from De Cuyper and De Witte (2010). This scale has been shown a high reliability in Nelissen and colleagues’ work (2017). A sample item is “I am optimistic that I would find another job with this employer, if I looked for one” (α = 0.819). The items measuring perceived external employability were comparable except for the reference to “another employer” or “elsewhere”. A sample item is “I am optimistic that I would find another job elsewhere, if I looked for one” (α = 0.882). To determine the discriminant validity of the six constructs, competing models were constructed. As shown in Table 1, the six-factor model fits the data better than other competing models, indicating that the proposed six constructs have good discriminant validity. Therefore, these six constructs were used in the subsequent data analysis. Measures Because all the measures this study used were originally specified in English, back-translation was used to create accurate and understandable Chinese versions (Brislin, 1980). All items were rated on a 7-point Likert-type scale ranging from 1 August 2021 | Volume 12 | Article 696309 Development I-Deals and Turnover Intention Zhang et al. (completely disagree or not at all) to 7 (completely agree or to a very great extent). (completely disagree or not at all) to 7 (completely agree or to a very great extent). which was less than 40% of the critical standard. Thus, there was no serious common method bias in this study. Opportunity to Perform Opportunity to perform was measured with the Chance to Perform Scale by Bauer et al. (2001). This 4-item scale has been employed by Ingold et al. (2016) in their study to measure employees’ perceptions of opportunity to perform in the current organization. A sample item is “I could really show my skills and abilities in the current organization” (α = 0.901). Frontiers in Psychology | www.frontiersin.org Common Method Bias Test Given that all variables in this study were self-reported by recipient employees, Harman’s single factor test was used to examine whether there is a problem of common method bias. The results showed that the variance interpretation rate of the largest factor in the four factors isolated in this study was 26.45%, To test direct and indirect effects, PROCESS model 4 was executed. Specifically, in PROCESS model 4, mediators (M) mediate the relationship between the independent variable (X) and dependent variable (Y). As shown in Table 3, August 2021 | Volume 12 | Article 696309 Frontiers in Psychology | www.frontiersin.org 6 Development I-Deals and Turnover Intention Zhang et al. external employability (β = 0.347, 95% CI = [0.218, 0.475]), and recipient employees’ perceived external employability was positively related to their turnover intention (β = 0.305, 95% CI = [0.216, 0.400]). Thus, H2a and H2b were supported. recipient employees’ development i-deals were positively related to perceived internal employability (β = 0.244, 95% CI = [0.124, 0.357]), and recipient employees’ perceived internal employability were negatively related to their turnover intention (β = −0.442, 95% CI = [−0.563, −0.326]). Thus, H1a and H1b were supported. Table 3 also showed that recipient employees’ development i-deals were positively associated with perceived H1c predicted the mediating role of recipient employees’ perceived internal employability in the relationship between development i-deals and turnover intention, and H2c predicted TABLE 1 | Results of confirmatory factor analysis. Common Method Bias Test One-factor model = DI + PIE + PEE + TI + OP + OC; two-factor model-1 = DI + PIE + PEE + TI + OP, and OC; two-factor model-2 = DI + PIE + PEE + TI + OC, and OP; three-factor model-1 = DI + PIE + PEE + TI, OP, and OC; three-factor model-2 = DI, PIE + PEE + TI + OP, and OC; three-factor model-3 = DI, PIE + PEE + TI + OC, and OP; four-factor model-1 = DI + PIE + PEE, TI, OP, and OC; four-factor model-2 = DI + TI + OC, PIE, PEE, and OP; four-factor model-3 = DI, PIE + PEE + TI, OP, and OC; four-factor model-4 = DI + TI + OP, PIE, PEE, and OC; five-factor model-1 = DI, PIE + PEE, OP, TI, and OC; five-factor model-2 = DI, PIE, PEE, OP, and TI + OC; five-factor model-3 = DI + OP, PIE, PEE, TI, and OC; five-factor model-4 = DI + TI, PIE, PEE, OP, and OC; six-factor Model = DI, PIE, PEE, TI, OP, and OC. DI, development i-deals; PIE, perceived internal employability; PEE, perceived external employability; TI, turnover intention; OP, opportunity to perform; OC, organizational commitment. TABLE 2 | Means, standard deviations, and correlations. Variable M SD 1 2 3 4 5 6 7 8 9 10 11 (1) Age 36.93 6.87 – (2) Gendera 0.53 0.50 −0.006 – (3) Educationb 2.38 0.69 0.283** −0.036 – (4) Tenure 8.04 4.27 0.675** −0.030 −0.101 – (5) Positionc 2.71 1.44 0.031 0.080 0.062 −0.029 – (6) Organizational commitment 4.30 1.09 −0.042 −0.035 −0.011 −0.071 −0.001 0.905 (7) Development i-deals 4.14 0.99 −0.041 −0.093 −0.002 −0.011 −0.024 0.027 0.743 (8) Perceived internal employability 4.82 1.27 −0.041 −0.015 −0.025 −0.018 0.046 0.134* 0.192** 0.819 (9) Perceived external employability 4.41 1.50 −0.001 −0.021 0.017 −0.007 −0.051 −0.026 0.227** 0.617** 0.882 (10) Turnover intention 3.65 1.06 0.026 0.025 0.110* −0.009 −0.033 −0.512** −0.129* −0.344** 0.091 0.754 (11) Opportunity to perform 3.72 1.31 −0.089 −0.017 −0.082 −0.084 −0.078 −0.008 0.150** 0.228** 0.177** −0.219** 0.901 Cronbach’s alphas are shown along the diagonal in italics; ** p < 0.01, * p < 0.05, the same is true for the tables below. a0 = female and 1 = male. b1 = associate degree or below, 2 = undergraduate degree, 3 = master degree or above. Common Method Bias Test Model χ2 df CFI TLI RMSEA SRMR Six-factor model 315.895 284 0.992 0.991 0.018 0.037 Five-factor model-1 574.268 289 0.931 0.922 0.054 0.064 Five-factor model-2 579.488 289 0.930 0.921 0.055 0.065 Five-factor model-3 598.951 289 0.925 0.915 0.056 0.071 Five-factor model-4 605.945 289 0.923 0.914 0.057 0.074 Four-factor model-1 822.938 293 0.871 0.857 0.073 0.080 Four-factor model-2 877.236 293 0.858 0.843 0.077 0.094 Four-factor model-3 995.610 293 0.830 0.811 0.084 0.119 Four-factor model-4 1061.815 293 0.813 0.793 0.088 0.123 Three-factor model-1 1238.557 296 0.771 0.749 0.097 0.128 Three-factor model-2 1767.720 296 0.643 0.608 0.121 0.142 Three-factor model-3 2131.071 296 0.555 0.511 0.136 0.169 Two-factor model-1 2005.381 298 0.586 0.548 0.130 0.149 Two-factor model-2 2373.598 298 0.496 0.451 0.144 0.175 One-factor model 3138.535 299 0.311 0.251 0.168 0.191 One-factor model = DI + PIE + PEE + TI + OP + OC; two-factor model-1 = DI + PIE + PEE + TI + OP, and OC; two-factor model-2 = DI + PIE + PEE + TI + OC, and OP; three-factor model-1 = DI + PIE + PEE + TI, OP, and OC; three-factor model-2 = DI, PIE + PEE + TI + OP, and OC; three-factor model-3 = DI, PIE + PEE + TI + OC, and OP; four-factor model-1 = DI + PIE + PEE, TI, OP, and OC; four-factor model-2 = DI + TI + OC, PIE, PEE, and OP; four-factor model-3 = DI, PIE + PEE + TI, OP, and OC; four-factor model-4 = DI + TI + OP, PIE, PEE, and OC; five-factor model-1 = DI, PIE + PEE, OP, TI, and OC; five-factor model-2 = DI, PIE, PEE, OP, and TI + OC; five-factor model-3 = DI + OP, PIE, PEE, TI, and OC; five-factor model-4 = DI + TI, PIE, PEE, OP, and OC; six-factor Model = DI, PIE, PEE, TI, OP, and OC. DI, development i-deals; PIE, perceived internal employability; PEE, perceived external employability; TI, turnover intention; OP, opportunity to perform; OC, organizational commitment. Common Method Bias Test FIGURE 3 | The moderating effect of opportunity to perform on the relationship between perceived external employability and turnover intention. FIGURE 2 | The moderating effect of opportunity to perform on the relationship between perceived internal employability and turnover intention. the mediating role of recipient employees’ perceived external employability in the relationship between development i-deals and turnover intention. Table 3 not only lists the estimates of Stage I effects (independent variable [IV] →mediator [Me]) and Stage II effects (Me →dependent variable [DV]), but also the indirect effects (IV →Me →DV). As hypothesized, perceived internal employability exerted significant mediation effects on the relationship between development i-deals and recipient employees’ turnover intention (indirect effect = −0.108, 95% CI = [−0.173, −0.051]), and perceived external employability also exerted significant mediation effects on the relationship between development i-deals and recipient employees’ turnover intention (indirect effect = 0.106, 95% CI = [0.060, 0.161]). Thus, H1c and H2c were supported. FIGURE 2 | The moderating effect of opportunity to perform on the relationship between perceived internal employability and turnover intention. pp PROCESS model 14 was executed to test H3a and H3b. Specifically, in this model, one moderator (W) moderates the relationship between the mediators (M1, M2) and dependent variable (Y). As shown in Table 4, it was revealed that the interaction between perceived internal employability and recipient employees’ perceptions of opportunity to perform in the current organization is negatively related to recipient employees’ turnover intention (β = −0.072, SE = 0.034, p < 0.01), and the interaction between perceived external employability and recipient employees’ perceptions of opportunity to perform is also negatively related to recipient employees’ turnover intention (β = −0.066, SE = 0.030, p < 0.01). Thus, recipient employees’ perceptions of opportunity to perform in the current organization strengthened the negative effect of perceived internal employability on turnover intention, and weakened the positive effect of perceived external employability on turnover intention, supporting H3a and H3b. FIGURE 3 | The moderating effect of opportunity to perform on the relationship between perceived external employability and turnover intention. Common Method Bias Test c1 = management positions, 2 = designers, 3 = financial staff, 4 = research and development, 5 = product operations. TABLE 2 | Means, standard deviations, and correlations. Cronbach’s alphas are shown along the diagonal in italics; ** p < 0.01, * p < 0.05, the same is true for the tables below. a0 = female and 1 = male. b1 = associate degree or below, 2 = undergraduate degree, 3 = master degree or above. c1 = management positions, 2 = designers, 3 = financial staff, 4 = research and development, 5 = product operations. August 2021 | Volume 12 | Article 696309 7 Frontiers in Psychology | www.frontiersin.org Development I-Deals and Turnover Intention Effect Boot SE Boot LL 95% CI Boot UL 95% CI 0.244 0.059 0.124 0.357 −0.442 0.061 −0.563 −0.326 −0.108 0.031 −0.173 −0.051 0.347 0.065 0.218 0.475 0.305 0.047 0.216 0.400 0.106 0.026 0.060 0.161 −0.123 0.044 −0.211 −0.036 LL, lower level. UL, upper level. CI, confidence interval. FIGURE 2 | The moderating effect of opportunity to perform on the relationship between perceived internal employability and turnover intention. FIGURE 3 | The moderating effect of opportunity to perform on the relationship between perceived external employability and turnover intention. employees with higher perceptions of opportunity to perform in the current organization than those with lower such perceptions. DISCUSSION Development I-Deals and Turnover Intention Zhang et al. TABLE 3 | Bootstrapping results for mediation relationship tests. Path Effect Boot SE Boot LL 95% CI Boot UL 95% CI Development i-deals →Perceived internal employability 0.244 0.059 0.124 0.357 Perceived internal employability →Turnover intention −0.442 0.061 −0.563 −0.326 Development i-deals →Perceived internal employability →Turnover intention −0.108 0.031 −0.173 −0.051 Development i-deals →Perceived external employability 0.347 0.065 0.218 0.475 Perceived external employability →Turnover intention 0.305 0.047 0.216 0.400 Development i-deals →Perceived external employability →Turnover intention 0.106 0.026 0.060 0.161 Development i-deals →Turnover intention −0.123 0.044 −0.211 −0.036 All coefficients are unstandardized. Boot, bootstrapped estimate. SE, standard error. LL, lower level. UL, upper level. CI, confidence interval. TABLE 3 | Bootstrapping results for mediation relationship tests. 0.305 0.047 0.216 0.400 0.106 0.026 0.060 0.161 −0.123 0.044 −0.211 −0.036 LL, lower level. UL, upper level. CI, confidence interval. FIGURE 2 | The moderating effect of opportunity to perform on the relationship between perceived internal employability and turnover intention. Frontiers in Psychology | www.frontiersin.org Common Method Bias Test FIGURE 3 | The moderating effect of opportunity to perform on the relationship between perceived external employability and turnover intention To further test the moderating effect, this study conducted a simple slope analysis (Aiken et al., 1991), demarcating between high (one standard deviation above the mean) and low (one standard deviation below the mean) levels of recipient employees’ perceptions of opportunity to perform in the current organization. As shown in Figure 2, the negative influence of perceived internal employability on recipient employees’ turnover intention is weaker for recipient employees with lower perceptions of opportunity to perform than those with higher perceptions of opportunity to perform. Figure 3 shows that the positive influence of perceived external employability on recipient employees’ turnover intention is weaker for recipient employees with higher perceptions of opportunity to perform in the current organization than those with lower such perceptions. DISCUSSION Drawing on social cognitive theory, the current research proposed and tested a moderated mediation model to explain the mechanisms through which development i-deals affect recipient employees’ turnover intention. Specifically, this study proposed August 2021 | Volume 12 | Article 696309 8 Development I-Deals and Turnover Intention Zhang et al. TABLE 4 | Moderating effect of opportunity to perform on the relationship between perceived employability and turnover intention. Variable Effect Boot SE Boot LL 95% CI Boot UL 95% CI Y: Turnover intention Constant 5.809 0.361 5.105 6.523 X: Development i-deals −0.107 0.040 −0.186 −0.026 M1: Perceived internal employability −0.407 0.061 0.526 −0.290 M2: Perceived external employability 0.277 0.046 0.188 0.361 W: Opportunity to perform −0.120 0.037 −0.192 −0.044 Interaction 1: M1 × W −0.072 0.034 −0.138 −0.004 Interaction 2: M2 × W −0.066 0.030 −0.122 −0.007 TABLE 4 | Moderating effect of opportunity to perform on the relationship between perceived employability and turnover intention. two paths that linked development i-deals with turnover intention: a retention path via perceived internal employability and a turnover path via perceived external employability. Through a time-lagged research design, the results supported proposed hypotheses, showing that the effects of development i-deals on recipients’ turnover intention may be complex. The results found that development i-deals can improve recipients’ perception of internal employability, which is negatively related to their turnover intention. This finding is consistent with previous i-deals studies which hold the argument that customized development work arrangements are associated with lower turnover intention (Hornung et al., 2014; Liao et al., 2016). And this finding is also in accordance with the work of Hornung et al. (2010), showing that development i-deals can increase recipient employee’s work engagement. Besides, different from traditional assumptions, the results also found that development i-deals can enhance recipients’ perception of external employability, which is positively related to turnover intention. This finding is parallel with that of Rodrigues et al. (2020), who suggested that individuals can benefit from organizational investment in their career development practices, such as feel highly employable, and their perceived external employability is positively associated with intention to quit. Furthermore, the results confirmed the moderating effects of opportunity to perform in current organization on the relationships between perceived employability and turnover intention. This finding supports literature suggesting that a positive perception of the availability of career opportunities within one’s organization is critical to retaining employees (Rasheeda et al., 2020). of turnover. DISCUSSION This study responds to the call proposed by Ng (2017) that more research should be conducted to explore the potential negative effects of granting i-deals. Thus, this study extends i-deals literature by investigating the effect of development i-deals on recipients’ turnover intention, revealing the benefits and risks that development i-deals may bring to the organization. Second, this study contributes to social cognitive theory by examining the mediating roles of recipients’ cognitive processes which can be conceptualized as the employability paradox in the relationship between development i-deals and turnover intention. Previous research on i-deals is dominated by mediating mechanisms pertaining to social exchange, social identity, or social comparison perspectives (Ng and Feldman, 2015; Vidyarthi et al., 2016; Zhang et al., 2020). However, this study tries to explore how receiving development i-deals shapes the i-dealers’ self-cognition, and thus their turnover intention. This research adds the limited mediating mechanisms linking development i-deals with recipients’ behaviors from a social cognitive perspective. Thus, it responds to scholars’ calls (Bal and Rousseau, 2015; Liao et al., 2016) that more research should drill down into the mechanisms through which i-deals have an impact on outcomes from different theoretical perspectives, and it also enriches social cognitive theory by applying this theory into the i-deals context. Third, this study increases the understanding of human resource development by investigating the relationship between development i-deals and the recipients’ perceived employability. That is, granting individualized work terms about career development to employees can boost both their perceptions of internal and external employability. This study explains the phenomenon that why some employees remain and why some leave after they were given development i-deals, providing theoretical support for this employability paradox. Besides, this study also examined the boundary effects of opportunity to perform in current organization. And it responds to the suggestion of Liao et al. (2016) that greater consideration was needed of contextual moderators in research on i-deals. The results showed that for recipients who perceive more opportunity to perform in current organization, the positive relationship between perceived external employability and turnover intention can be weaker. This finding provides some theoretical evidence about how to avoid the potential Frontiers in Psychology | www.frontiersin.org Practical Implications This research may have some limitations. The first is that all variables in the model were assessed with self-reported responses. This paper addressed recipient employees’ receiving development i-deals and their psychological cognitive process, so self-reporting of these variables was not unreasonable, even though this may raise the possibility of common method bias (Podsakoffet al., 2003). Indeed, it may be difficult to argue that others could provide an accurate evaluation of recipient employees’ subjective feelings. This study tried to minimize the potential influence of common method bias on the results by separating the data collection into two measurement waves and randomizing the order of scale items in the survey instrument. This study has some practical implications for managers and organizations. First, the results of this research showed that development i-deals can increase recipient employees’ perceptions of internal employability, and subsequently enhance their willingness to remain. This finding revealed the benefits that development i-deals bring for the organization, and verified the original assumption that i-deals can be used to help retain valued employees. Therefore, for those organizations focusing on employee retention, development i-deals can be an instrumental tool to achieve such aims. For instance, managers can provide individualized work arrangements for key employees who have higher working skills, core technologies, professional knowledge, or higher competitiveness. This may be a win-win strategy for employees and managers, that is employees can obtain customized work items and managers retain the talents. Second, this study was conducted only in Shandong, China, which may limit the generalizability of the results in some degree. Future studies could reexamine whether development i-deals may influence recipient employees’ turnover intention via employability paradox, in other areas of China or other country settings. Besides, this research examined the effect of development i-deals on recipients’ turnover intention, revealing the possible risk that development i-deals bring for the organizations. Future research is needed to explore whether and in which conditions, development i-deals can lead to recipients’ actual turnover behaviors by utilizing a longitudinal tracing design. Moreover, this study only focused on development i-deals, and future research could investigate the influence of other types of i-deals on the recipients’ perceived employability and turnover intention, and compare such influence with that of development i-deals. Yet, i-deals have negative ramifications too. Theoretical Implications This study has several theoretical implications. First, it contributes to i-deals literature by building a model to reveal the process through which development i-deals impact recipients’ turnover intention. Previous studies indicated that development i-deals satisfy the i-dealers’ personal needs, thus increasing their commitment and willingness to remain (Liu et al., 2013; Las Heras et al., 2017). Consistent with previous studies, this research proposed a retention path and the results found that development i-deals can improve recipients’ perceived internal employability, which in turn reduce their turnover intention. Besides, this paper also verified a turnover path that development i-deals can increase i-dealers’ perceived external employability and thus the risk August 2021 | Volume 12 | Article 696309 Frontiers in Psychology | www.frontiersin.org 9 Development I-Deals and Turnover Intention Zhang et al. turnover risks and how to maximize the effectiveness of development i-deals. their willingness to build a long-term employment relationship with current employer. Practical Implications Challenging traditional wisdom, it was found that development i-deals can also increase recipient employees’ evaluations of their external employability, and thus increase the risk of turnover intention. This finding revealed the potential cost of providing employees with development i-deals. Thus, when authorizing i-deals, managers should undertake a balanced analysis of benefits and risks. For example, managers could sign a supplementary and reciprocal contract about i-deals with recipients, which specify obligations and duties of the both parties. More specifically, both parties could negotiate the service period before employees are given the special training opportunities, and once they are in violation of the service period stipulation, he or she shall pay the organization a penalty for breach of contract as stipulated. Besides, when authorizing i-deals, managers also should be cautious about the individual difference of i-dealers, such as organizational commitment, loyalty, or identification. Third, this study used social cognitive theory to introduce the recipients’ perceived employability paradox as the theoretically- driven mediators that linked development i-deals and turnover intention. However, there may exist other theoretical frameworks that can be used to understand the employability paradox. For example, future research could analyze the employability paradox by using social exchange theory. In addition, many scholars have indicated that i-deals have broader implications beyond the recipient employees (Marescaux et al., 2021). Thus, it is encouraged that future research could explore the impacts of authorizing i-deals on the i-dealers’ coworkers or supervisors themselves. Moreover, the results verified the moderating effect of opportunity to perform in current organization, and showed that the opportunity to perform can alter the effect of perceived employability on recipient employees’ turnover intention. Overall, it is demonstrated that employees with a perception of high level of opportunity to perform are more likely to show greater willingness to remain in the current organization. This finding suggests that in order to maximize the effectiveness of development i-deals, managers and organizations should create more opportunities for i-deals recipients. For example, after the special training, managers should be aware of providing some practice opportunities for those recipient employees to apply the knowledge or skills that they learned from the training courses. Managers also should pay attention to the recipients’ psychological and developmental needs. 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YX contributed to the collection of the data. YL contributed to the revision of the manuscript. All authors contributed to the article and approved the submitted version. CONCLUSION Drawing on social cognitive theory, this study revealed the mechanism of the mediating effects of the employability paradox between development i-deals and recipient employee’s turnover intention. This study also found that recipient’s perception of opportunity to perform in current organization plays a moderating role. The results advance collective understandings of how development i-deals impact recipient’s turnover intention, providing insights that could be leveraged by human resource personnel. August 2021 | Volume 12 | Article 696309 10 Development I-Deals and Turnover Intention Zhang et al. REFERENCES doi: 10.1177/0894845309357051 Huo, W., Luo, J., and Tam, K. L. (2014). Idiosyncratic deals and good citizens in China: The role of traditionality for recipients and their coworkers. Internat. J. Hum. 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Perceived organizational support: A review of the literature. J. Appl. Psychol. 87, 698–714. doi: 10.1037//0021-9010.87.4.698 August 2021 | Volume 12 | Article 696309 Frontiers in Psychology | www.frontiersin.org 12
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A Web-Based Psychosocial Intervention for Family Caregivers of Older People: Results from a Mixed-Methods Study in Three European Countries
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Corresponding Author: Corresponding Author: Francesco Barbabella, PhD Centre for Socio-Economic Research on Ageing National Institute of Health and Science on Ageing (INRCA) Via S. Margherita 5 Ancona, 60126 Italy Phone: 39 0718004799 Fax: 39 07135941 Email: f.barbabella@inrca.it Corresponding Author: Francesco Barbabella, PhD Centre for Socio-Economic Research on Ageing National Institute of Health and Science on Ageing (INRCA) Via S. Margherita 5 Ancona, 60126 Italy Phone: 39 0718004799 Fax: 39 07135941 Email: f.barbabella@inrca.it JMIR RESEARCH PROTOCOLS JMIR RESEARCH PROTOCOLS Barbabella et al Original Paper A Web-Based Psychosocial Intervention for Family Caregivers of Older People: Results from a Mixed-Methods Study in Three European Countries Francesco Barbabella1,2, PhD; Arianna Poli1,3, MPsych; Frida Andréasson2,4, MA Sociology; Benjamin Salzmann1,5, MSW; Roberta Papa1, BSc; Elizabeth Hanson2,4,6, PhD; Areti Efthymiou6,7, MPsych; Hanneli Döhner5,6, PhD; Cristina Lancioni1, MSc (Tech); Patrizia Civerchia8, MPsych; Giovanni Lamura1, PhD 1Centre for Socio-Economic Research on Ageing, National Institute of Health and Science on Ageing (INRCA), Ancona, Italy 2Department of Health and Caring Sciences, Linnaeus University, Kalmar, Sweden 3National Institute for the Study of Ageing and Later Life, Linköping University, Norrköping, Sweden 4Swedish Family Care Competence Centre (NKA), Kalmar, Sweden 5wir pflegen e.V., Berlin, Germany 6Eurocarers, Brussels, Belgium 7Cyprus University of Technology, Limassol, Cyprus 8Neurology Unit National Institute of Health and Science on Ageing (INRCA) Ancona Italy 8Neurology Unit, National Institute of Health and Science on Ageing (INRCA), Ancona, Italy http://www.researchprotocols.org/2016/4/e196/ JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.1 (page number not for citation purposes) Introduction A significant portion of adult individuals worldwide are experiencing increasing responsibilities of, and effects from being involved in, informal care for relatives with long-term care needs. For instance, it is estimated that the number of family caregivers over 18 years of age who care for older people and disabled adults are around 58 million in the European Union (EU) (15% of the adult population) [1] and 34 million (14% of the adult population) in the United States [2]. In the European context, the number of family caregivers is twice the entire health care workforce, with the economic value of informal care covering between 50% and 90% of overall costs for long-term care in EU member states [3]. The impact of caregiving on individuals’ lives is often remarkable and associated with different health and social issues. The prevalence of mental health problems among caregivers seems to be 20% higher than among noncaregivers [4], especially in terms of anxiety, depression, and distress attributed to their caring situation. Other risks for caregivers concern the possibility of encountering financial problems and difficulties in reconciling care with family activities and social life [4-6]. As part of the wider INNOVAGE project, cofunded by the European Union, we addressed this systematic lack of online supports for caregivers by promoting a new social innovation at the European level (ie, an innovative solution to meet health and social needs of caregivers, to sustain their empowerment, and to improve their well-being) [23]. This social innovation was constituted by the new InformCare Web platform, which was intended to act as a first point of access to a variety of information, education, and social support opportunities at the country level for family caregivers, as well as an opportunity for formal services and nonprofit organizations in the field. Our research had the ultimate goal to implement the InformCare Web platform in 27 European countries in their official languages in order to allow caregivers from any involved nation to benefit from a set of minimum information and support. Research, development, and implementation activities were coordinated by the Italian National Institute of Health and Science on Ageing (INRCA) and the European nonprofit organization Eurocarers, with the support of the Swedish Family Care Competence Centre (NKA) and a wide network of national nonprofit organizations in the European Union. KEYWORDS caregivers; frail elderly; Internet; social support; social networking; health education of a general lack of formal support services dedicated to family caregivers [5,6]. This is further exacerbated in some EU countries—especially in Southern and Eastern Europe—by low policy, social, and cultural recognition of family caregivers’ roles, including a lack of legal rights, benefits, and support actions from public institutions and society [3]. (JMIR Res Protoc 2016;5(4):e196) doi:10.2196/resprot.5847 (JMIR Res Protoc 2016;5(4):e196) doi:10.2196/resprot.5847 http://www.researchprotocols.org/2016/4/e196/ Abstract The analysis suggested the intervention was useful and appropriate, also stimulating a better self-efficacy and reappraisal of the caregivers’ role. identified five main themes: online social support, role awareness, caregiving activities, psychological well-being, and technical concerns. The analysis suggested the intervention was useful and appropriate, also stimulating a better self-efficacy and reappraisal of the caregivers’ role. Conclusions: The intervention seemed to contribute to the improvement of family caregivers’ awareness, efficacy, and empowerment, which in turn may lead to a better self-recognition of their own needs and improved efforts for developing and accessing coping resources. A major implication of the study was the finalization and implementation of the InformCare Web platform in 27 European countries, now publicly accessible (www.eurocarers.org/informcare). JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.2 (page number not for citation purposes) Abstract Background: Informal caregiving is the main source of care for older people in Europe. An enormous amount of responsibility and care activity is on the shoulders of family caregivers, who might experience problems in their psychological well-being and in reconciling caregiving and their personal sphere. In order to alleviate such burden, there is increasing interest and growing research in Europe on Web-based support addressing family caregivers and their needs. However, the level of development and penetration of innovative Web-based services for caregivers is still quite low and the access to traditional face-to-face services can be problematic for logistic, availability, and quality reasons. Objective: As part of the European project INNOVAGE, a pilot study was conducted for developing and testing a Web-based psychosocial intervention aimed at empowering family caregivers of older people in Italy, Sweden, and Germany. The program offered information resources and interactive services to enable both professional and peer support. Methods: A mixed-methods, sequential explanatory design was adopted. Caregivers’ psychological well-being, perceived negative and positive aspects of caregiving, and social support received were assessed before and after the 3-month intervention. Poststudy, a subsample of users participated in focus groups to assist in the interpretation of the quantitative results. Results: A total of 94 out of 118 family caregivers (79.7%) from the three countries used the Web platform at least once. The information resources were used to different extents in each country, with Italian users having the lowest median number of visits (5, interquartile range [IQR] 2-8), whereas German users had the highest number (17, IQR 7-66) (P<.001). The interactive services most frequently accessed (more than 12 times) in all countries were the social network (29/73, 40%) and private messages (27/73, 37%). The pretest-posttest analysis revealed some changes, particularly the slight worsening of perceived positive values of caregiving (Carers of Older People in Europe [COPE] positive value subscale: P=.02) and social support received (COPE quality-of-support subscale: P=.02; Multidimensional Scale of Perceived Social Support subscale: P=.04), in all cases with small effect size (r range -.15 to -.18). Focus groups were conducted with 20 family caregivers and the content analysis of discussions JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.1 (page number not for citation purposes) XSL•FO RenderX JMIR RESEARCH PROTOCOLS Barbabella et al identified five main themes: online social support, role awareness, caregiving activities, psychological well-being, and technical concerns. Introduction Recently, research in the European Union has increasingly concentrated on the development and testing of innovative solutions for providing support services to family caregivers of older people, especially in terms of Web-based programs with psychoeducational and psychotherapeutic purposes [7,8], or with multicomponent approaches including both professional and peer online support [9-11]. Although reviews in this field recommend more in-depth research for clarifying the effectiveness of Web-based interventions, preliminary evidence at the international level suggests that these should be multicomponent and tailored to caregivers’ actual needs and preferences, in order to impact effectively on caregivers’ psychological well-being, self-efficacy, and social inclusion [12-17]. This can be achieved by integrating the availability of information and educational modules with both professional and peer support, for instance, via interactive tools like discussion forums, chat rooms, and group videoconferencing [10,11,18-20]. Thus, this article reports the results from the pilot-testing in three European countries of a multicomponent, Web-based intervention delivered through the InformCare Web platform. The work is based on the assumption that caregiving activities can lead the caregiver to experience both negative feelings, such as subjective burden, stress, and depression [24,25], and positive ones, for instance, gain, reward, and satisfaction [26,27]. The goal of this pilot study was to verify the impact of the Web-based psychosocial intervention on caregivers, primarily in terms of benefits for psychological well-being, self-efficacy, and self-perception of both negative and positive aspects of caregiving, and secondarily as a potential driver of personal development and access to coping resources. So far, however, the level of development and coverage of Web-based programs for family caregivers has been rather low and fragmented in the European Union, with a number of small initiatives having limited scope and being sustained by poor funds and resources [21,22]. This fits into the broader picture XSL•FO RenderX JMIR RESEARCH PROTOCOLS Barbabella et al languages was carried out by national project staff and double-checked by senior project staff. Sample The recruitment process adopted a convenience sample approach. Brochures and promotional materials were distributed in order to reach caregivers through available institutional and informal channels. In Italy, all participants were recruited through the Alzheimer Evaluation Unit at INRCA in Ancona, thus including family caregivers of people with Alzheimer’s disease or other dementias. In Sweden, caregivers were enrolled by exploiting existing networks of the NKA, the Swedish Dementia Association, Carers Sweden, and Linnaeus University in Kalmar and Växjö. In Germany, the nonprofit caregiver organization wir pflegen e.V. and local social care services contributed to recruitment by approaching family caregivers through their networks and websites. Design The interactive services area enabled communication among caregivers, as well as between caregivers and professional staff. The area included a set of Web tools: a dedicated social network, a forum, a private message feature, a chat feature, and a videochat feature. Interactive services were aimed specifically at improving caregivers’ psychological well-being, self-efficacy, and self-perception of caregiving situation. These services were delivered by means of individual and group online support provided in terms of information, advice, counseling, and emotional and social support. In each country, an interactive services area was managed by a professional moderator—a psychologist in Italy, and social workers in Sweden and Germany—who acted as an online counselor. The multicenter pilot study was conducted in Italy, Sweden, and Germany, and employed a mixed-methods, sequential explanatory design. Structured questionnaires with quantitative measures of the main outcomes were administered to enrolled family caregivers both at baseline and at 3-months postintervention; the study took place from April to July 2014. Postintervention, results from the structured questionnaires were used to organize a focus group in each country, at which a subgroup of users participated. The aim was to gain a more in-depth understanding of caregivers’ experiences, support the final analysis, and better interpret the results. The design and methods of the study were evaluated by competent local ethics committees in each country. Some additional structured services and tasks were also proposed in order to better customize service provision to the sociocultural peculiarities and digital skills of national samples (see Table 1). The choice of services and tasks took into account that the main profiles of caregivers recruited in the three countries differed in terms of age and relationship with the older person, as well as of education and employment status, confirming what was highlighted by a previous European study [5,32]. Development of the Web Platform The design and development of the Web platform was based on a review of the main needs and preferences expressed by family caregivers [5,28], as well as the areas of online health information and support [15,29-31]. A consultation process was also carried out via online surveys administered to 58 family caregivers, external experts, and stakeholders from different European countries, reached by means of national and international networks of partner organizations, in order to identify Web tools to include for addressing caregivers’ needs. Guidelines for moderators, who were trained prior to the intervention, were developed based on the main recommendations available in the field [33-35]. This aimed to clarify how support and interactions with users should be performed by moderators, and to set limits and standards of such support. Individual user tests with 10 family caregivers were conducted on a first prototype of the Web platform in order to gain preliminary insights on its usability. Based on the feedback received, the platform was further refined for the pilot intervention. JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.3 (page number not for citation purposes) http://www.researchprotocols.org/2016/4/e196/ Intervention Conditions In all three countries, the Web platform included both information resources and interactive services areas, developed in their national official languages. Access was restricted by means of an individual username and password given to each caregiver at the beginning of the study. An overview of the main characteristics of the information and services and a screenshot of the home page are provided in Table 1 and Figure 1, respectively. Within the information resources area, four main sections were developed in order to improve knowledge and self-awareness, mainly concerning the caregiver’s role, coping strategies, and support available. Contents regarding the national range of services, benefits, and contacts available were appositely written by project staff and double-checked by external experts. Contents concerning general information on diseases, coping, and reconciliation strategies were provided by selected reliable websites in English managed by nonprofit organizations with a long-standing expertise in this field. Translation into national Selection criteria for including family caregivers in the study were the following: (1) providing informal caregiving in activities of daily living (ADLs) and/or instrumental activities of daily living (IADLs) for an older person aged 60 years or more; (2) having basic digital skills, allowing the use of an Internet browser on a computer and/or mobile device; (3) having ordinary access to a computer and/or mobile device with Internet connection. JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.3 (page number not for citation purposes) http://www.researchprotocols.org/2016/4/e196/ XSL•FO RenderX XSL•FO RenderX JMIR RESEARCH PROTOCOLS Barbabella et al Figure 1. Screenshot of the home page of the InformCare Web platform for family caregivers of older people (example of Italian version). hot of the home page of the InformCare Web platform for family caregivers of older people (example of Italian version). Figure 1. Screenshot of the home page of the InformCare Web platform for family caregivers of older people (example of Italian version). Figure 1. Screenshot of the home page of the InformCare Web platform for family caregivers of older people (exampl Procedure At the outset, each participant caregiver signed an informed consent form and received a guide for accessing and using the platform in both paper and electronic versions. Preliminary face-to-face or videoconferencing meetings were organized on an individual or group basis for presenting and showing the platform. Additional structured services (country specific) E-learning: multimedia training units with a focus on caregiving activities and long-term care services Virtual desk: weekly availability of moderator and other psychologists via chat, videochat, and forum for providing individual support E-learning: multimedia training units with a focus on caregiving activities and long-term care services Virtual desk: weekly availability of moderator and other psychologists via chat, videochat, and forum for providing individual support Writing tasks in forum (Sweden) Biweekly writing exercises alternating time management and emotional writing, managed by the moderator Two weekly videoconferencing groups with three family caregivers each, managed by the moderator Videoconferencing groups (Germany) Technical support was guaranteed by both the moderator—for immediate help and clarification—and the Web developer—for fixing technical problems. A set of earphones was given to each caregiver allowing for the use of videochat and videocommunication tools. http://www.researchprotocols.org/2016/4/e196/ http://www.researchprotocols.org/2016/4/e196/ JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.4 (page number not for citation purposes) JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.4 (page number not for citation purposes) JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.4 (page number not for citation purposes) XSL•FO RenderX XSL•FO RenderX JMIR RESEARCH PROTOCOLS Barbabella et al Table 1. Characteristics of information resources and interactive services. Characteristics of information resources and interactive services. JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.5 (page number not for citation purposes) Characteristics Resources and services Information resources Symptoms, diagnosis, and treatments of the 10 most common chronic conditions Long-term care services at country level Environmental security Caring for the older person Coping strategies Reconciliation with family and work Physical exercise Your own needs Legal issues (eg, responsibility, rights, and competency) Economic and social insurance benefits Support by the state Contacts for crisis or emergency List of relevant nonprofit associations List of other Web-based support programs Get help Interactive services Channel: asynchronous group communication Possible user’s tasks: to see and read other caregivers’ profiles and posts; to post, comment, and share information and multimedia on personal and others’ walls Moderator’s role: to post regularly, both useful information (from the Web and the information resources area) and emotional statements; to interact with users by commenting on their posts and periodically leaving messages on their walls Social network Channel: asynchronous group communication Possible user’s tasks: to open discussion threads on personal doubts and requests; to comment on others’ open threads Moderator’s role: to stimulate interactions by opening new discussion threads and/or commenting ap- propriately on users’ threads and comments Forum Channel: asynchronous interpersonal or group communication Possible user’s tasks: to ask for direct support from the moderator; to contact other users Moderator’s role: to monitor and support users by sending periodical or ad hoc messages Private messages/emails Channel: synchronous interpersonal or group communication Possible user’s tasks: to ask for direct support from the moderator; to contact other users Moderator’s role: to support users by participating in individual or group discussions Chat and videochat/ videocommunication tools Additional structured services (country specific) E-learning: multimedia training units with a focus on caregiving activities and long-term care services Virtual desk: weekly availability of moderator and other psychologists via chat, videochat, and forum for providing individual support E-learning course and virtual desk (Italy) Biweekly writing exercises alternating time management and emotional writing, managed by the moderator Writing tasks in forum (Sweden) Two weekly videoconferencing groups with three family caregivers each, managed by the moderator Videoconferencing groups (Germany) Procedure At the outset, each participant caregiver signed an informed consent form and received a guide for accessing and using the Technical support was guaranteed by both the moderator—for immediate help and clarification—and the Web developer—for fixing technical problems. A set of earphones was given to each e i e ll i f the e f ide h t d Table 1. Characteristics Resources and services Information resources Symptoms, diagnosis, and treatments of the 10 most co Long-term care services at country level Environmental security Caring for the older person Coping strategies Reconciliation with family and work Physical exercise Your own needs Legal issues (eg, responsibility, rights, and competency Economic and social insurance benefits Support by the state Contacts for crisis or emergency List of relevant nonprofit associations List of other Web-based support programs Get help Interactive services Channel: asynchronous group communication Possible user’s tasks: to see and read other caregivers’ p information and multimedia on personal and others’ wa Moderator’s role: to post regularly, both useful informati area) and emotional statements; to interact with users b leaving messages on their walls Social network Channel: asynchronous group communication Possible user’s tasks: to open discussion threads on perso open threads Moderator’s role: to stimulate interactions by opening n propriately on users’ threads and comments Forum Channel: asynchronous interpersonal or group commun Possible user’s tasks: to ask for direct support from the Moderator’s role: to monitor and support users by send Private messages/emails Channel: synchronous interpersonal or group communi Possible user’s tasks: to ask for direct support from the Moderator’s role: to support users by participating in in Chat and videochat/ videocommunication tools Additional structured services (country specific) E-learning: multimedia training units with a focus on ca Virtual desk: weekly availability of moderator and othe for providing individual support E-learning course and virtual desk (Italy) Biweekly writing exercises alternating time manageme moderator Writing tasks in forum (Sweden) Two weekly videoconferencing groups with three fami Videoconferencing groups (Germany) h i l Symptoms, diagnosis, and treatments of the 10 most common chronic conditions Long-term care services at country level Environmental security Coping strategies Reconciliation with family and work Physical exercise Legal issues (eg, responsibility, rights, and competency) Economic and social insurance benefits Contacts for crisis or emergency List of relevant nonprofit associations List of other Web-based support programs Channel: asynchronous group communication Possible user’s tasks: to see and read other caregivers’ profiles and posts; to post, comment, and share information and multimedia on personal and others’ walls Moderator’s role: to post regularly, both useful information (from the Web and the information resources area) and emotional statements; to interact with users by commenting on their posts and periodically leaving messages on their walls Social network Channel: asynchronous group communication Possible user’s tasks: to open discussion threads on personal doubts and requests; to comment on others’ open threads Moderator’s role: to stimulate interactions by opening new discussion threads and/or commenting ap- propriately on users’ threads and comments Forum Channel: asynchronous interpersonal or group communication Possible user’s tasks: to ask for direct support from the moderator; to contact other users Moderator’s role: to monitor and support users by sending periodical or ad hoc messages Private messages/emails Channel: synchronous interpersonal or group communication Possible user’s tasks: to ask for direct support from the moderator; to contact other users Moderator’s role: to support users by participating in individual or group discussions Chat and videochat/ videocommunication tools Additional structured services (country specific) E-learning: multimedia training units with a focus on caregiving activities and long-term care services Virtual desk: weekly availability of moderator and other psychologists via chat, videochat, and forum for providing individual support E-learning course and virtual desk (Italy) Biweekly writing exercises alternating time management and emotional writing, managed by the moderator Writing tasks in forum (Sweden) Two weekly videoconferencing groups with three family caregivers each, managed by the moderator Videoconferencing groups (Germany) Possible user’s tasks: to see and read other caregivers’ profiles and posts; to post, comment, and share nformation and multimedia on personal and others’ walls Moderator’s role: to post regularly, both useful information (from the Web and the information resources area) and emotional statements; to interact with users by commenting on their posts and periodically leaving messages on their walls Possible user’s tasks: to open discussion threads on personal doubts and requests; to comment on others’ open threads Moderator’s role: to stimulate interactions by opening new discussion threads and/or commenting ap- propriately on users’ threads and comments Possible user’s tasks: to ask for direct support from the moderator; to contact other users Moderator’s role: to monitor and support users by sending periodical or ad hoc messages Possible user’s tasks: to ask for direct support from the moderator; to contact other users Moderator’s role: to support users by participating in individual or group discussions Quantitative Measures and Statistical Analysis The primary outcome measures were represented by the caregivers’ psychological well-being and self-perception of both negative and positive aspects of caregiving. A secondary outcome was the social support the caregiver perceived from significant others and from services. Variables were measured with a structured questionnaire administered to all participants, Participants were invited to use the Web platform whenever they needed to find information, ask advice, or get support. Stimulation strategies were planned according to social and cultural preferences (eg, short message service [SMS] text messages and emails). JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.5 (page number not for citation purposes) XSL•FO RenderX JMIR RESEARCH PROTOCOLS Barbabella et al both prior to and after the 3-month intervention, through an online system or, if requested, by post or email. both prior to and after the 3-month intervention, through an online system or, if requested, by post or email. number of times participants used single features of each interactive service were self-reported, then summed and categorized for each service as follows: never (no use), low use (6-12 times), and medium-high use (more than 12 times). Sociodemographic characteristics and health problems of family caregivers and of their cared-for older persons—with the caregiver answering as a proxy—were asked through ad hoc categorical or binary questions. Other details were also asked about the care setting and access to public services (eg, home care and care allowances) and private services (eg, privately employed care assistant). As for the older person, ADLs and IADLs were measured, respectively, by means of the Barthel Index [36] (range 0-20, where 20 refers to a person who is independent in all activities) and the Duke Older Americans’ Resources and Services (OARS) scale [37] (range 0-6, where 6 is the highest number of activities for which the person needs help). Health status of the caregiver was assessed through a single item—health status 1 variable (HS1): self-perceived general health—retrieved from the Minimum European Health Module [38], whose results were recoded in three categories: good, fair, and bad. The Kolmogorov-Smirnov test was used to check for normal distribution of quantitative data. Data were expressed as frequencies for categorical variables, and as median (interquartile range [IQR]) and mean (SD) for continuous ones. Focus Groups and Qualitative Data Analysis A focus group was organized in each country after the intervention for further evaluation, especially with regard to the aspects of self-efficacy and support received online. Standard operative guidelines and a common set of topics to be covered were adopted for all focus groups, including the following: (1) appropriateness and usefulness of the intervention to meet own needs, (2) personal evaluation of using online services, and (3) perceived changes and improvements connected to the use of the services. Moderators of focus groups were senior project staff, whereas other trained researchers participated as observers and note takers. The Carers of Older People in Europe (COPE) Index (15 items) [40,41] was included to ask about the perceived impact of the caregiving situation. The COPE Index uses a 4-point Likert scale (ranging from never to always) and includes three subscales concerning the following: negative impact, with seven items such as “Do you find caregiving too demanding?” (score range 7-28); positive value, with four items such as “Do you find caregiving worthwhile?” (score range 4-16); and quality of support, with four items such as “Do you feel well supported by friends or neighbors?” (score range 4-16). Negatively worded items of the negative impact subscale were reverse coded. A high score in a subscale indicated the following: low level of subjective burden (negative impact subscale); high level of positive feelings (positive value); and high level of support received by community, including family, friends, and formal services (quality of support). Participants constituted a subgroup of the overall sample of family caregivers who used the platform. All focus groups took approximately 90-120 minutes; discussions were audiotaped and transcribed, with the support of field notes. Transcriptions and field notes were used for a conventional content analysis [43], based on a constant comparative approach [44], which aimed at exploring similarities and differences across the three country samples. By making systematic comparisons across units of data—participants’ comments and answers, and observations—researchers subsequently identified themes of discussion and selected relevant quotes from the focus groups [44,45]. http://www.researchprotocols.org/2016/4/e196/ Quantitative Measures and Statistical Analysis Bivariate analysis was performed between the country variable and both sociodemographic characteristics and usage of the platform using the chi-square or Kruskal-Wallis tests for categorical or continuous variables, respectively. Comparison of paired data—medians before and after the intervention—on the primary outcome variables was carried out by the nonparametric Wilcoxon signed-rank test for dependent samples; effect size (r) was calculated as the Z value divided by the square root of the number of observations. A value of P<.05 was accepted as statistically significant. SPSS for Windows, version 16.0 (SPSS Inc) was used for the creation of the database, data cleaning, and data analysis. Among the outcome measures, the 5-item World Health Organization Well-being Index (WHO-5) [39] was used to assess the level of psychological well-being perceived by the caregiver. It uses a 6-point Likert scale (ranging from at no time to all of the time) to rate statements such as “I have felt cheerful and in good spirits” and “I have felt calm and relaxed,” referring to the last 2-week period. Its percentage score was calculated by multiplying the raw score by 4 (ranging from 0 to 25). Focus Groups and Qualitative Data Analysis Credibility of qualitative research was assured mainly by the following: prolonged engagement (eg, project staff’s long-standing experience of research and practice on Web-based support for caregivers); persistent observation (eg, direct knowledge gained by moderators and researchers on Web platform usage by caregivers, including types and frequency of peer and professional interactions); and peer debriefing, including the continuous involvement of an external advisory board (15 international experts) and the validation of final study results in an expert evaluation meeting (6 international experts) [46]. Furthermore, the Multidimensional Scale of Perceived Social Support (MSPSS) (12 items) [42] measured the level of perceived social support received by the family caregiver. The MSPSS uses a 7-point Likert scale (ranging from very strongly disagree to very strongly agree) and includes three subscales asking to rate family (four items; eg, “My family really tries to help me”), friends (four items; eg, “I have friends with whom I can share my joys and sorrows”), and social support (four items; eg, “I have a special person who is a real source of comfort to me”). Each subscale ranges from 4 to 48 points, where 48 is the best support received, and a total score was calculated by summing the scores from all subscales. The analysis of qualitative data integrated quantitative results in an explanatory sequential process [47]. Data about access to the information resources area of the platform were tracked through Google Analytics software. The JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.6 (page number not for citation purposes) XSL•FO RenderX JMIR RESEARCH PROTOCOLS Barbabella et al providing medium-low intensity of informal care. German caregivers were mostly unemployed children or children-in-law with a medium-high education, whereas the Swedish subsample included mostly retired spouses with high education. Descriptive Statistics Overall, 123 family caregivers were initially recruited to the study—59 in Italy, 44 in Sweden, and 20 in Germany—completing both the informed consent form and baseline questionnaire. A total of 5 participants dropped out during the intervention—1 in Italy, 3 in Sweden, and 1 in Germany—due to the death of the older person, changed life circumstances, or lack of time. At the end of the intervention, 94 out of 118 caregivers (79.7%) had accessed the Web platform at least once—42 in Italy, 36 in Sweden, and 16 in Germany. JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.7 (page number not for citation purposes) http://www.researchprotocols.org/2016/4/e196/ Usage Table 3 shows how access to the two areas of the Web platform varied across countries. In general, the majority of caregivers in all countries accessed the platform two or more times—74% in Italy, 83% in Sweden, and 94% in Germany. Concerning the information resources area, German and Swedish users made more visits than Italian ones in absolute terms (P<.001). The median number of visits ranged between 5 (IQR 2-8) in Italy and 17 (IQR 7-66) in Germany, with relevant differences in the number of pages visited (P=.001) and overall time spent (P=.002). In terms of interactive services, social network and private messages were used by the majority of participants. In particular, Swedish caregivers tended to use the forum more often (58% overall), followed by the chat feature (62%), and the videochat feature or other videocommunication tools (31%). German users displayed similar behaviors, whereas Italian caregivers hardly used the videochat feature (only 3% accessed it) and reported lower levels of access to both the forum and the chat feature (20% and 26%, respectively). Table 2 describes the sociodemographic characteristics of both the participating caregivers and the older persons they cared for. The median age of the older persons in the total sample was 80 years (IQR 74-85), the group consisted of mostly women in both Italy and Germany (79% and 69%, respectively), and they had different levels of ADL and IADL dependency. Family caregivers who used the Web platform at least once were mostly women (64/94, 68%) with a median age of 58 years (IQR 51-69). In Italy, participants were mostly children and children-in-law of the older person, with low confidence with the Internet and high participation rates in the labor market, XSL•FO RenderX XSL•FO RenderX JMIR RESEARCH PROTOCOLS Barbabella et al Table 2. Characteristics of older persons, family caregivers, and care settings by country. Usage Pa value Total (n=94) Germany (n=16) Sweden (n=36) Italy (n=42) Participant and setting characteristics Older person <.001 57 (61) 11 (69) 13 (36) 33 (79) Gender (woman), n (%) .03 80 (74-85) 82 (69-87) 76 (72-82) 82 (76-87) Age (years), median (IQRb) <.001 13 (5-18) 5 (1-8) 11 (4-17) 15 (11-18) ADLc index, median (IQR) .05 4 (2-6) 6 (4-6) 4 (2-6) 4 (2-6) IADLd index, median (IQR) Family caregiver .73 64 (68) 10 (63) 26 (72) 28 (67) Gender (woman), n (%) <.001 58 (51-69) 56 (53-67) 68 (57-73) 53 (47-58) Age (years), median (IQR) <.001 Relationship to the older person, n (%) 31 (34) 3 (19) 27 (75) 1 (2) Spouse/partner 48 (51) 10 (63) 7 (19) 31 (74) Child/child-in-law 15 (16) 3 (19) 2 (6) 10 (24) Other .20 70 (75) 9 (56) 30 (83) 31 (74) Children (yes), n (%) <.001 34 (36) 2 (13) 22 (61) 10 (24) Grandchildren (yes), n (%) .11 Health status, n (%) 7 (7) 2 (13) 4 (11) 1 (2) Bad 38 (40) 8 (50) 17 (47) 13 (31) Fair 49 (52) 6 (38) 15 (42) 28 (67) Good <.001 Education, n (%) 14 (15) 2 (13) 3 (8) 9 (21) Low 37 (39) 5 (31) 7 (19) 25 (60) Medium 43 (46) 9 (56) 26 (72) 8 (19) High .04 44 (47) 4 (25) 15 (42) 25 (60) Employment (yes), n (%) .002 Living status (with respect to cared-for person), n (%) 41 (44) 8 (50) 24 (67) 9 (21) Same household 22 (23) 5 (31) 4 (11) 13 (31) Within walking distance 31 (33) 3 (19) 8 (22) 20 (48) Beyond walking distance <.001 Confidence with Internet, n (%) 12 (13) 1 (6) 1 (3) 10 (24) None/low 40 (43) 8 (50) 8 (22) 24 (57) Medium 42 (45) 7 (44) 27 (75) 8 (19) High Care setting .02 15 (6-40) 30 (9-144) 32 (6-70) 12 (6-24) Informal care provided per week (hours), median (IQR) .09 4 (2-5) 7 (2-9) 3 (2-7) 3 (2-4) Duration of caregiving period (years), median (IQR) <.001 22 (23) 6 (38) 14 (39) 2 (5) Home care (yes), n (%) <.001 38 (40) 12 (75) 4 (11) 22 (52) Cash allowances received by older people and/or family caregivers (yes), n (%) .38 36 (38) 7 (44) 11 (31) 18 (43) Privately employed care assistant (yes), n (%) aResults of chi-square or Kruskal-Wallis tests for categorical and continuous variables, respectively. http://www.researchprotocols.org/2016/4/e196/ Usage Sum of percentages may not be 100% becau rounding. bIQR: interquartile range. Barbabella JMIR RESEARCH PROTOCOLS Table 2. Characteristics of older persons, family caregivers, and care settings by country. JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.8 (page number not for citation purposes) XSL•FO RenderX JMIR RESEARCH PROTOCOLS JMIR RESEARCH PROTOCOLS Barbabella et al dIADL: instrumental activities of daily living. Table 3. Usage of the online information resources and interactive services by country. Pa value Total (N=94) Germany (n=16) Sweden (n=36) Italy (n=42) Usage of resources and ser- vices Information resources area, median (IQRb ) <.001 7 (2-20) 17 (7-66) 13 (3-41) 5 (2-8) Number of visits .001 157 (67-362) 423 (121-926) 267 (66-790) 123 (75-186) Number of pages visited .002 139 (57-405) 432 (113-689) 177 (65-755) 102 (53-163) Time spent (minutes) .07 22 (14-35) 21 (11-25) 20 (13-34) 25 (18-40) Pages per visit .048 21 (14-29) 19 (10-25) 19 (10-27) 24 (16-30) Time per visit (minutes) Interactive services area (Italy n=35; Sweden n=26; Germany n=12; total n=73), n (%) .001 Social network 26 (35) 4 (33) 2 (8) 20 (57) Never 18 (25) 2 (17) 8 (31) 8 (23) Low use 29 (40) 6 (50) 16 (61) 7 (20) Medium-high use .007 Private messages 26 (36) 6 (50) 4 (15) 16 (46) Never 20 (27) 0 (0) 8 (31) 12 (34) Low use 27 (37) 6 (50) 14 (54) 7 (20) Medium-high use .006 Forum 44 (60) 5 (42) 11 (42) 28 (80) Never 18 (25) 5 (42) 7 (27) 6 (17) Low use 11 (15) 2 (16) 8 (31) 1 (3) Medium-high use .02 Chat 43 (59) 7 (58) 10 (38) 26 (74) Never 19 (26) 3 (25) 8 (31) 8 (23) Low use 11 (15) 2 (17) 8 (31) 1 (3) Medium-high use <.001 Videochat/ videocommunication tools 57 (78) 5 (42) 18 (69) 34 (97) Never 7 (10) 2 (16) 4 (15) 1 (3) Low use 9 (12) 5 (42) 4 (15) 0 (0) Medium-high use Specific country services or tasks, n (%) N/A N/A N/Ac 25 (60) E-learning course (Italy) (yes) N/A N/A 8 (22) N/A Writing task in forum (Sweden) (yes) N/A 6 (38) N/A N/A Videoconferencing sessions (Germany) (yes) aResults of chi-square or Kruskal-Wallis tests for categorical and continuous variables, respectively. Sum of percentages may not be to 100% because of rounding Table 3. aResults of chi-square or Kruskal-Wallis tests for categorical and continuous variables, respectively. Sum of percentages may not be to 100% because of rounding. b Outcomes Primary and secondary outcomes were assessed before (T0) and after (T1) the 3-month Web-based intervention (see Table 4). At baseline, the median scores of negative impact and positive value COPE subscales were relatively high (13 out of 16 points, negative impact; 21 out of 28 points, positive value), indicating quite low levels of subjective burden and a high positive experience of caregiving. The level of perceived social support was moderate, as suggested by midrange values in the COPE quality-of-support subscale and MSPSS, whereas the level of psychological well-being was quite low (median 40 out of 100 in the WHO-5 Index). 1. Online Social Support A consensus across the three focus groups was reported about the positive effects on social inclusion and support derived from using the interactive services. The platform was perceived as a safe virtual environment, which addressed caregivers’ needs to communicate with others and share personal experiences, more than any other available, mainstream, open-access social network (ie, Facebook). The possibility to interact in a protected environment with other people experiencing similar issues—although users did not know each other at first—led to increased mutual learning and understanding, as well as the recognition of not being alone in this condition. Both group and individual support provided by professional counselors was considered optimal and brought clear benefits. In particular, Swedish caregivers openly described that social recognition and confirmation by peers was useful for raising their own self-esteem, mastery over life, and sense of competence. Concerning the pretest-posttest scores, the analysis showed that participants changed their perception toward different aspects. There was a statistically significant decrease of values concerning the positive value of caregiving (-1; P=.02) and the quality of support received by significant others (-1; P=.02) (COPE Index subscales), as well as by family (-2; P=.04) and social support in general (-2; P=.04) (MSPSS subscales). A small effect size [48] was found for all significant variables (ranging from -.15 to -.18). The scores concerning the other scales related to the negative impact of caregiving, support by friends, and psychological well-being showed no changes in values. On other platforms, when I write something about my situation I have to explain. On this platform I don’t need to explain why I feel like I do, the other caregivers understand and know we have difficult times now and then. [Nils, Swedish adult son] http://www.researchprotocols.org/2016/4/e196/ O JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.10 (page number not for citation purposes) Usage Usage of the online information resources and interactive services by country. Interactive services area (Italy n=35; Sweden n=26; Germany n=12; total n=73), n (%) JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.9 (page number not for citation purposes) JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.9 (page number not for citation purposes) http://www.researchprotocols.org/2016/4/e196/ http://www.researchprotocols.org/2016/4/e196/ XSL•FO RenderX XSL•FO RenderX JMIR RESEARCH PROTOCOLS Table 4. Impact of the Web-based intervention on users. Effect size, rc Pb value Postintervention measurement (T1) Baseline measurement (T0) Outcomes Median (IQR) Mean (SD) Median (IQRa) Mean (SD) -.06 .41 40 (24-60) 43.4 (23.0) 40 (24-60) 44.5 (24.2) WHO-5d COPEe Index -.09 .22 21 (18-23) 20.4 (4.2) 21 (19-24) 20.9 (4.1) Negative impact -.18 .02 12 (11-14) 12.1 (2.1) 13 (11-14) 12.6 (2.2) Positive value -.18 .02 9 (8-12) 9.8 (2.7) 10 (8-12) 10.4 (2.8) Quality of support MSPSSf -.15 .04 20 (16-25) 20.1 (5.9) 22 (17-26) 21.0 (5.8) Family -.03 .71 18 (13-22) 17.5 (6.1) 18 (13-23) 17.8 (6.1) Friends -.16 .04 21 (17-26) 21.1 (5.5) 23 (18-27) 21.9 (5.8) Social support -.12 .11 60 (47-69) 58.7 (14.2) 63 (50-73) 60.7 (14.2) Total score aIQR: interquartile range. bWilcoxon signed-rank test for dependent samples, calculated between median values before and after the intervention. cEffect size, r, is calculated as the Z value divided by the square root of the number of observations. dWHO-5: 5-item World Health Organization Well-being Index. eCOPE: Carers of Older People in Europe. fMSPSS: Multidimensional Scale of Perceived Social Support. Table 4. Impact of the Web-based intervention on users. aIQR: interquartile range. fMSPSS: Multidimensional Scale of Perceived Social Support. activities, psychological well-being, and technical concerns. Theme analysis and relevant quotes are provided below (users’ names are fictional). JMIR RESEARCH PROTOCOLS Barbabella et al I feel less stressed and that can be a result of other people’s posts that I allow myself to have negative feelings and thoughts. [Anna, Swedish older female spouse] Discussion I have felt that my experiences are worth something, that I am not only an old lady in her 70s who should just sit and be quiet. [Lisa, Swedish older female spouse] Results from our pilot study showed a statistically significant change of the perception by caregivers of some aspects related to the caregiving context. At the end of the intervention, caregivers reported slightly lower levels of positive feelings and social support received, whereas subjective burden and psychological well-being did not change. On the other hand, qualitative findings from the focus groups pointed out the usefulness and appropriateness of support received by caregivers from information and communication with moderators and peers. The major benefit for users seemed to be their empowerment, by means of increased self-efficacy, role awareness, and social recognition. 5. Technical Concerns Despite the majority of participants who judged the usability of the platform as sufficient or good, some of them did mention technical or usability issues as a reason for not having used some of the available interactive services more. In particular, Swedish users reported problems with using the mobile version and specific features of some services (eg, uploading pictures on the social network, and using the chat and videochat features), whereas in Italy some caregivers found it difficult to find and reach some internal pages or services. In Sweden, an alternative videocommunication system was used with the moderator in order to overcome technical issues arising with the videochat feature. Support guaranteed by the moderator was in any case highly appreciated by all users across the three countries. You got the impression that you are understood, able to talk openly and got to reflect on your own situation. This motivates you to take on new steps to improve your personal situation. [Stefanie, German adult daughter] 2. Role Awareness Caregivers expressed that they felt a change in their understanding of their caregiving situation, claiming especially of having been stimulated to reflect about and understand more their own condition and needs. In Italy and Germany, participants agreed that reading and sharing caregivers’ experiences was emotionally difficult, but helpful in order to understand and better appraise their roles. Furthermore, many caregivers expressed that they had a better understanding about the future development of the older person’s condition, and what they could expect to face in the months or years to come. In Sweden, older female spouses emphasized the valorization of their role as a direct effect of online interactions, one of them even reporting that she could now see her activity more as a proper “job” and better accept this role. 3. Caregiving Activities Most caregivers in Italy and Germany underlined that information available on the platform, as well as tips and advice from other users, were useful to improve caregiving activities and better approach the cared-for person. Talking retrospectively, many users said their lives could have changed if they had had access to the platform earlier, because it could have helped them to recognize certain symptoms and help provide the older person with more adequate care. An interpretation of these ambivalent results can be that the intervention actually stimulated a new appraisal of the caregiving situation, including coping resources and social support available in the community, with caregivers recognizing ultimately a lack of adequate (external and/or professional) support from family, significant others, and formal services. The online information and support received via the platform could have produced a reappraisal of their own situation, thus allowing participants to identify more clearly and/or for the first time multiple issues of caregiving previously unrecognized, and to understand hidden needs for support. My caregiving situation has improved by the tips I got from the other caregivers. [Phillip, German older male spouse] My caregiving situation has improved by the tips I got from the other caregivers. [Phillip, German older male spouse] If this Web platform existed when our mum looked upset without any clear reasons, we would have realized more easily what she needed and would have avoided her having to suffer so much. [Roberta, Italian adult daughter] http://www.researchprotocols.org/2016/4/e196/ Content Analysis of Focus Groups Even just knowing that these kinds of support services exist and trustworthy people are working behind them, it is really important and helpful for family caregivers. [Patrizia, Italian adult daughter] A total number of 20 caregivers attended the focus groups: 7 in Italy, 7 in Germany, and 6 in Sweden. All participants in the three countries generally had a positive and satisfying experience with the platform, although there were slight differences in the emphasis of certain aspects. Data analysis identified five main themes: online social support, role awareness, caregiving XSL•FO RenderX JMIR RESEARCH PROTOCOLS JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.11 (page number not for citation purposes) 4. Psychological Well-being In terms of subjective well-being, some users in Sweden (both children and spouses) said they felt less burdened after the intervention, especially because they could better accept both positive and negative feelings arising from the caregiving situation. The possibility to express and share them with others, without being judged but rather receiving social recognition and confirmation of their own efforts by peers, helped them to cope with the situation and to reduce their perceived stress. Our results seem to be in line with previous international research in this field. Studies delivering multicomponent programs comparable to our intervention, that included unstructured support by professionals and peers, did not show significant changes in psychological well-being and burden [49], especially over a short time frame [9,11]. Overall, only some structured psychoeducational and psychotherapeutic programs were found to have an impact on caregiver burden and psychological well-being outcomes [7,18,19,50-52], whereas other studies highlighted mainly mixed or inconclusive results [8,53-56]. I feel happier and calmer when I can share the positive and negative things that happen in my situation as a caregiver. I don't know if I would have coped with the situation [without the platform] actually. [Nils, Swedish adult son] Furthermore, there is a lack of empirical literature regarding the effect of Web-based programs on perceived positive aspects of JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.11 (page number not for citation purposes) XSL•FO RenderX XSL•FO RenderX JMIR RESEARCH PROTOCOLS Barbabella et al caregiving [13], which limits the possibility of comparisons with our partly unexpected findings. However, another short-term study found that some caregivers receiving the Web-based program had higher levels of stress at the end of the intervention than at baseline [8], a result that has been similarly explained as the possible consequence of caregivers’ enhanced awareness of their challenging caring situation. However, the worsening of positive feelings toward caregiving was narrow (median decreased from 13 to 12 in the 4-16 subscale range) and did not imply serious consequences for caregivers, also given the high level of initial scores and the qualitative findings collected in this respect. and cannot therefore exclude the influence of external variables on the outcomes. Fourth, only a subgroup of caregivers could be enrolled in the focus groups; indeed, we cannot fully exclude the influence of a selection bias in the qualitative findings. 4. Psychological Well-being In general, the recruitment process was based on a convenience sample approach and bias in the profiles of the recruited caregivers was possible. Difficulties in approaching family caregivers [5], especially in testing Web-based services [7,8], are well-known in the literature, and they might have led to a slight imbalance of country subsamples concerning numbers and characteristics of caregivers involved. Despite these limitations, it should be underlined that only a few studies have been able to involve similar or higher numbers of family caregivers in Web-based intervention research [7,9,19,50], and almost none have had a multi-country perspective [9]. Furthermore, the refinement and implementation of the InformCare Web platform at the European level within the INNOVAGE project was a direct consequence of this study. Based on results and indications from the pilot intervention, the project team managed an adjustment of information resources and a revision of guidelines for implementing and moderating interactive services, an effort conducted together with a network of appointed stakeholders—nonprofit organizations and experts—in the EU countries. This constitutes a remarkable, concrete added value of this research, since the platform has been accessible since mid-2015 in 27 EU countries via the Eurocarers website [60]. It includes 32 national versions, with some countries having more than one official language, and more than 2500 Web pages in the information resources area, which are publicly available and tailored to country characteristics. According to the availability and resources of national nonprofit organizations appointed in each country, a selection of interactive services may have been activated for national caregivers as well. Therefore, this study represents a unique example of translational research, which aims to contribute to the overcoming of social and cultural barriers for family caregivers that still exist in many countries by exploiting the potential of Web-based support. Future work might be based on this pilot experience and the implementation of the InformCare Web platform for conducting more in-depth and robust studies, especially on how to provide effective and tailored support for family caregivers, as well as for enabling cross-country, comparability research with a common set of intervention tools and guidelines. Available literature also suggests that guidance from a professional counselor or coach is an effective way to address specific needs of caregivers [13,57]. As well, peer support in online communities can lead to increased confidence and self-efficacy [13-16,30], sense of belonging, and social inclusion [11,20,31]. 4. Psychological Well-being Qualitative findings from our pilot study seemed to confirm these positive effects in the three countries, with major benefits for addressing social isolation for Swedish older spouses, also in line with available research [58]. Despite the lack of evidence in terms of burden and psychological well-being, the piloted intervention seemed able to provide useful and adequate online support services for family caregivers of older people, even in a short-term time frame, which might lead to increased efforts to alleviate stress by accessing coping resources and social support in the community [20,24,59]. In this respect, however, the challenge of tailoring the Web platform and tools to users’ digital skills and preferences represents a crucial issue to be considered for guaranteeing their usability and friendliness. This is especially true for caregivers with little experience of using Web services [10,15], as shown by the problems experienced by the Italian subsample, mainly due to low digital skills. This study has some limitations to be taken into account and results cannot be generalized without caution. First, the study was conceived as a pilot test of a new Web-based program, able to carry out only a short-term and limited assessment of the intervention. Second, although the adopted mixed-methods approach gave the opportunity to integrate quantitative and qualitative results, associations between variables and causal relations could only be inferred. Third, despite the fact that the study was designed to include the main variables of interest, due to project constraints we could not include a control arm http://www.researchprotocols.org/2016/4/e196/ JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.12 (page number not for citation purposes) Acknowledgments The research leading to these results has received funding from the European Union’s Seventh Framework Programme for Research and Technological Development (FP7/2007-2013) under grant agreement No. 306058 (HEALTH-F3-2012-306058). Additional funding for publication was granted by the FP7 postgrant Open Access Pilot under the OpenAIRE2020 project (H2020-EINFRA-2014-1, 643410). The authors would like to thank the family caregivers involved in the study; the experts who were involved in the consultation process, especially Elsa Marziali (University of Toronto) and Madeleine Starr (Carers UK) for their valuable feedback and support; Matteo Annibali (INRCA), Aidan Paul MacNally, and Alessio Ritucci (Eurocarers) for their contribution to the development and implementation of the InformCare Web platform in 27 European countries; Frank Goodwin, Stecy Yghemonos, and Francesca Centola (Eurocarers) for their support during the development and implementation phases; Cinzia Giuli and Silvia Valenza JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.12 (page number not for citation purposes) XSL•FO RenderX XSL•FO RenderX Barbabella et al JMIR RESEARCH PROTOCOLS (INRCA), and Paul Svensson (NKA) for their contribution to field research; and the Italian nonprofit organization Anziani e Non Solo, which offered one of its e-learning courses to be tested during our intervention. (INRCA), and Paul Svensson (NKA) for their contribution to field research; and the Italian nonprofit organization Anziani e Non Solo, which offered one of its e-learning courses to be tested during our intervention. References 1. Glendinning C, Tjadens F, Arksey H, Morée M, Moran N, Nies H. Care Provision Within Families and its Socio-Economic Impact on Care Providers. York, UK: University of York; 2009 May. URL: http://europa.eu/epic/docs/eu-2342-care-provision. pdf [accessed 2016-04-07] [WebCite Cache ID 6gaeCUB38] 2. NAC, AARP Public Policy Institute. Caregiving in the US. Bethesda, MD; Washington, DC: National Alliance for Caregiving (NAC) and AARP Public Policy Institute; 2015 Jun. URL: http://www.aarp.org/content/dam/aarp/ppi/2015/ caregiving-in-the-united-states-2015-report-revised.pdf [WebCite Cache ID 6jcCiJFMs] 3. European Commission. Long-Term Care in Ageing Societies - Challenges and Policy Options. Brussels, Belgium: European Commission; 2013 Feb 20. 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Abbreviations ADL: activities of daily living COPE: Carers of Older People in Europe EU: European Union FP7: Seventh Framework Programme HS1: health status 1 variable IADL: instrumental activities of daily living INRCA: Italian National Institute of Health and Science on Ageing IQR: interquartile range MSPSS: Multidimensional Scale of Perceived Social Support N/A: not applicable NISAL: National Institute for the Study of Ageing and Later Life NKA: Swedish Family Care Competence Centre OARS: Older Americans’ Resources and Services ADL: activities of daily living COPE: Carers of Older People in Europe EU: European Union FP7: Seventh Framework Programme HS1: health status 1 variable IADL: instrumental activities of daily living INRCA: Italian National Institute of Health and Science on Ageing IQR: interquartile range MSPSS: Multidimensional Scale of Perceived Social Support N/A: not applicable NISAL: National Institute for the Study of Ageing and Later Life NKA: Swedish Family Care Competence Centre OARS: Older Americans’ Resources and Services JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.15 (page number not for citation purposes) Barbabella et al JMIR Res Protoc 2016 | vol. 5 | iss. 4 | e196 | p.16 (page number not for citation purposes) http://www.researchprotocols.org/2016/4/e196/ JMIR RESEARCH PROTOCOLS SMS: short message service T0: baseline measurement point T1: postintervention measurement point WHO-5: 5-item World Health Organization Well-being Index Edited by G Eysenbach; submitted 07.04.16; peer-reviewed by M Erol, C Barker, R Hawkins; comments to au version received 11.08.16; accepted 24.08.16; published 06.10.16 Please cite as: Barbabella F, Poli A, Andréasson F, Salzmann B, Papa R, Hanson E, Efthymiou A, Döhner H, Lancioni C, Civerchia P, Lamura G A Web-Based Psychosocial Intervention for Family Caregivers of Older People: Results from a Mixed-Methods Study in Three European Countries JMIR Res Protoc 2016;5(4):e196 URL: http://www.researchprotocols.org/2016/4/e196/ doi:10.2196/resprot.5847 PMID: a F, Poli A, Andréasson F, Salzmann B, Papa R, Hanson E, Efthymiou A, Döhner H, Lancioni C, Civerchia P, Lamura G sed Psychosocial Intervention for Family Caregivers of Older People: Results from a Mixed-Methods Study in Three C t i ©Francesco Barbabella, Arianna Poli, Frida Andréasson, Benjamin Salzmann, Roberta Papa, Elizabeth Hanson, Areti Efthymiou, Hanneli Döhner, Cristina Lancioni, Patrizia Civerchia, Giovanni Lamura. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 06.10.2016. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in JMIR Research Protocols, is properly cited. The complete bibliographic information, a link to the original publication on http://www.researchprotocols.org, as well as this copyright and license information must be included. ©Francesco Barbabella, Arianna Poli, Frida Andréasson, Benjamin Salzmann, Roberta Papa, Elizabeth Hanson, Areti Efthymiou, Hanneli Döhner, Cristina Lancioni, Patrizia Civerchia, Giovanni Lamura. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 06.10.2016. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in JMIR Research Protocols, is properly cited. The complete bibliographic information, a link to the original publication on http://www.researchprotocols.org, as well as this copyright and license information must be included. http://www.researchprotocols.org/2016/4/e196/ XSL•FO RenderX XSL•FO RenderX
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УДК (582.52+582.61)581.95(517.3) УДК (582.52+582.61)581.95(517.3) Новые находки во флоре Монголии. Часть 2 А. А. Кечайкин1, 7*, А. И. Шмаков1, 8, А. А. Баткин1, 9, В. Гундэгмаа2, 10, Ш. Баасанмунх3, 11, Б. Оюунцэцэг4, 12, Х. Ч. Чой3, 13, Т. Грэгор5, 14, Ю. Пауле5, 15, Д. Н. Шауло6, 16, А. Ю. Королюк6, 17, Е. Г. Зибзеев6, 18, Т. А. Синицына1, 19, С. В. Смирнов1, 20 1 Южно-Сибирский ботанический сад, Алтайский государственный университет, пр. Ленина, д. 61, г. Барнаул, 656049, Россия 1 Южно-Сибирский ботанический сад, Алтайский государственный университет, пр. Ленина, д. 61, г. Барнаул, 656049, Россия 2 Факультет биологии, Школа математики и естественных наук, Монгольский национальный педагогический университет, г. Улан-Батор, 14191, Монголия 2 Факультет биологии, Школа математики и естественных наук, Монгольский национальный педагогический университет, г. Улан-Батор, 14191, Монголия 3 Факультет биологии и химии, Чханвонский национальный университет, Чангвондэхак-ро Уичан-гу, 20, Кенсан-Намдо, г. Чханвон, 51140, Южная Корея 4 Факультет биологии, Школа искусства и науки, Монгольский национальный университет, ул. Университетская, д 1, г. Улан-Батор, 14201, Монголия у р р 5 Факультет ботаники и молекулярной эволюции, Научно-исследовательский институт Зенкенберга и Музей естественной истории Франкфурта, Зенкенберганлаге, д. 25, г. Франкфурт-на-Майне, 60325, Германи Центральный сибирский ботанический сад СО РАН, ул. Золотодолинская, д. 101, г. Новосибирск, 630090, Росс 7 E-mail: alekseikechaikin@mail.ru; ORCID iD: https://orcid.org/0000-0002-0754-4698 8 ORCID iD: https://orcid.org/0000-0002-1052-4575; 9 ORCID iD: https://orcid.org/0000-0001-5628-0089 10 ORCID iD: https://orcid.org/0000-0001-9883-2451; 11 ORCID iD: https://orcid.org/0000-0003-4224-9376 12 ORCID iD: https://orcid.org/0000-0003-3772-3301; 13 ORCID iD: https://orcid.org/0000-0003-3644-6795 14 ORCID iD: https://orcid.org/0000-0001-7692-8348; 15 ORCID iD: https://orcid.org/0000-0001-5375-7689 16 ORCID iD: https://orcid.org/0000-0002-1835-8532; 17 ORCID iD: https://orcid.org/0000-0003-4646-4698 18 ORCID iD: https://orcid.org/0000-0002-7135-0724; 19 ORCID iD: https://orcid.org/0000-0002-7644-9176 20 ORCID iD: https://orcid.org/0000-0002-9657-3959 * Автор для переписки Ключевые слова: Алтай, редкие виды, флористические находки, Хангай, Центральная Азия, эндемики. у р ц Принято к публикации 10.03.2022 Поступило в редакцию 01.03.2022  Принято к публикации 10.03.2022 Поступило в редакцию 01.03.2022  Turczaninowia 25, 1: 105–123 (2022) DOI: 10.14258/turczaninowia.25.1.9 http://turczaninowia.asu.ru Turczaninowia 25, 1: 105–123 (2022) DOI: 10.14258/turczaninowia.25.1.9 http://turczaninowia.asu.ru ISSN 1560–7259 (print edition) TURCZANINOWIA ISSN 1560–7267 (online edition) ISSN 1560–7259 (print edition) TURCZANINOWIA ISSN 1560–7267 (online edition) ISSN 1560–7259 (print edition) TURCZANINOWIA ISSN 1560–7267 (online edition) Keywords: Altai, Central Asia, endemics, floristic findings, Khangai, rare species. Summary. New data on the distribution of 40 species from the families Asteraceae, Cystopteridaceae, Dryopteri- daceae, Euphorbiaceae, Poaceae, Rosaceae, and Woodsiaceae in Mongolia are presented in the article. For the first time, Centaurea cyanus, Cystopteris almaatensis, Potentilla × habievii, Potentilla salsa, and Potentilla smirnovii are indicated for the flora of the country. 19 species previously known in the flora of Mongolia are new for its separate botanical and geographical regions. Of these, 7 taxa were found for the first time in the Khuvsgul, 5 – in the Khovd, 4 – in the Gobi Altai and 3 – in the Mongolian Altai regions, 2 each – in the Khangai, Khentei, and Dzungarian Gobi, 1 – in the Middle Khalkha. New locations were registered for 19 rare and endemic species of the study region. There are narrow local national endemics: Potentilla coriacea, P. inopinata, P. laevipes, and P. schmakovii, among them. The findings are divided into three groups in the article. Comments about the range, relationships and main morphological differences are given for each species. Photographic materials of Potentilla salsa made in nature on the territory of Mongolia are demonstrated for the first time. лючевые слова: Алтай, редкие виды, флористические находки, Хангай, Центральная Азия, эндемик Аннотация. Приводятся новые данные о распространении 40 видов из семейства Asteraceae, Cystopterida- ceae, Dryopteridaceae, Euphorbiaceae, Poaceae, Rosaceae и Woodsiaceae на территории Монголии. Впервые для флоры страны указываются Centaurea cyanus, Cystopteris almaatensis, Potentilla × habievii, Potentilla salsa и Potentilla smirnovii. 19 видов, ранее известные во флоре Монголии, являются новыми для ее отдельных бота- нико-географических районов. Из них 7 таксонов обнаружено впервые в Прихубсугульском, 5 – в Кобдосском, 4 – в Гоби-Алтайском и 3 – в Монгольско-Алтайском районах, по 2 – в Хангайском, Хэнтэйском и Джунгар- ской Гоби, 1 – в Средней Халке. Зарегистрированы новые местонахождения для 19 редких и эндемичных ви- дов исследуемого региона. Среди них узколокальные национальные эндемики Potentilla coriacea, P. inopinata, P. laevipes и P. schmakovii. Соответствующие находки распределены в статье на три группы. К каждому виду даются комментарии об ареале, родственных связях и главных морфологических отличиях. Впервые демон- стрируются фотоматериалы Potentilla salsa, сделанные в природе на территории Монголии. Поступило в редакцию 01.03.2022  Принято к публикации 10.03.2022 Submitted 01.03.2022 Accepted 10.03.2022 106 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 South-Siberian Botanical Garden, Altai State University, Lenina Pr. 61, Barnaul, 656049, Russian Federation 2 Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, 14191, Mongolia 3 Department of Biology and Chemistry, Changwon National University, 20 Changwondaehak-ro Uichang-gu, Gyeongsangnam-do, Changwon, 51140, South Korea Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, 14201, Mongolia 5 Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage, 25, Frankfurt am Main, 60325, Germany 6 Central Siberian Botanical Garden SB RAS, Zolotodolinskaya St. 101, Novosibirsk, 630090, Russian Federation New findings in the flora of Mongolia. Part 2 А. А. Kechaykin1, А. I. Shmakov1, А. А. Batkin1, V. Gundegmaa2, Sh. Baasanmunkh3, B. Oyuntsetseg4, H. J. Choi3, Тh. Gregor5, J. Paule5, D. N. Shaulo6, А. Yu. Korolyuk6, Е. G. Zibseev6, Т. А. Sinitsyna1, S. V. Smirnov1 Материалы и методы Для написания этой работы были использо- ваны материалы, собранные во время флористи- ческих исследований Монголии в разные годы и хранящиеся в Гербариях ALTB, FR, GAT, HAL, LE, NS (Gatilova, 2021), MW (Seregin, 2022), UBA, UBU. Акронимы Гербариев приведены согласно Index Herbariorum (Thiers, 2022). Рас- пространение видов дано по ботанико-географи- ческим районам Монголии, предложенным В. И. Грубовым и А. А. Юнатовым (Grubov, Yunatov, 1952) и впоследствии уточненным в отноше- нии их границ В. И. Грубовым (Grubov, 1955), которые традиционно используются в работах по флоре страны. После авторства таксона ука- зывается общепринятое название ботанико-гео- графического района Монголии (подчеркнутый текст), в котором было собрано данное растение, на русском и английском языках, затем приво- дятся данные гербарной этикетки с указанием места хранения образца. Отдельно без цитирова- ния этикетки приводится прямая ссылка на гер- барный образец, данные о котором выставлены на сайте «Global Biodiversity Information Facil- ity» (GBIF. URL: https://www.gbif.org/). Это от- носится лишь к материалам из FR. Для удобства названия семейств, родов и видов внутри разде- лов перечислены в алфавитном порядке. Сystopteridaceae (Payer) Schmakov Сystopteridaceae (Payer) Schmakov Cystopteris almaatensis Kotukhov: Монголь- ско-Алтайский (Mongolian Altai) – «Кобдосский аймак, Монгольский Алтай, хр. Батар-Хайрхан, дол. р. Мэрэнгийн-Амны-Гол близ выхода из гор, 1750–2300 м над ур. м., 47°00ʹ3ʺ с. ш. 92°49ʹ58ʺ в. д. МШК 197. 3 VIII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB); Джунгарская Гоби (Dzungarian Gobi) – «Кобдосский аймак, Монгольский Алтай, сред- нее течение р. Баян-гол, долина правого при- тока Улястыйн-Сала, хребет Аршантын-Нуру, г. Могойн-Улан-Ула близ вершины, субальпий- ские и альпийские луга, скалы, 2200–2500 м над ур. м., 46°23ʹ с. ш. 91°14ʹ в. д. 27 VI 2004. С. А. Дьяченко, П. А. Косачев» (ALTB). – Описан из Юго-Восточного Казахстана по сбору в урочи- ще Чимбулак на Заилийском Алатау (Kotukhov, 1966), но впоследствии был сведен в синонимы к Cystopteris fragilis (L.) Bernh. (Bobrov, 1984). Опубликованные позже материалы подтверди- ли видовую самостоятельность C. almaatensis, а новые находки значительно расширили его ареал (Gureeva, Kuznetsov, 2015; Gureeva et al., 2015). К отличительным признакам C. almaaten- sis относятся крупные вайи до 50 см с ланцето- видными, широко отставленными друг от друга (особенно нижняя пара) перьями; покрывальца яйцевидные, на конце разорваны на неравные зубчатые доли, округло-выпуклые у основания; споры мелкоморщинистые, почковидно-оваль- ные с периспорием по краю в виде выгрызено- крылатых гребешков (Kotukhov, 1966). Вид по морфологии тройчато-рассеченных вай близок к C. fragilis, по морфологии спор схож с C. dickieana R. Sim. Для последнего присущи небольшие раз- меры вай с двойным рассечением. Также у видов C. dickieana и C. almaatensis наблюдаются раз- личия в размерах спор и структуре периспория (Ulko et al., 2017; Batkin et al., 2020). Как само- стоятельный вид C. dickieana приводится для Прихубсугульского и Хангайского р-нов Мон- голии (Gubanov, 1996). Во «Флоре Алтая» этот вид указан уже и для Западной Монголии по сбо- рам, соответствующим Монгольско-Алтайскому р-ну, Джунгарской Гоби и Котловине Больших Озер (Shmakov, 2005a). В «Conspectus of the Vascular Plants of Mongolia» самостоятельность C. dickieana не признается, и он синонимизи- Введение Резко континентальная Монголия с ее уни- кальными степными экосистемами и котлови- нами, окруженными различными по происхож- дению горными хребтами, остается перспектив- ным регионом для изучения эволюции флоры и фауны Евразии. Развитие цифровых технологий в значительной мере упрощает эту задачу. Так, общедоступная мировая база данных «Global Biodiversity Information Facility» (GBIF. URL: https://www.gbif.org/) позволяет провести анализ разнообразных коллекций, собранных на терри- тории Монголии. Большая часть этих материа- лов, выставленная в цифровом формате, безус- ловно, представляет интерес для систематиков и флористов. После выхода «Conspectus of the Vascular Plants of Mongolia» (Urgamal et al., 2014) актив- ные исследования флоры Монголии продолжа- ются. Опубликованы крупные работы, посвя- щенные отдельным группам растений (German, 2015; Ovczinnikova, 2019; Baasanmunkh et al., 2020, 2021a, 2021c; Shiga et al., 2020; Troshki- na, 2021) и ботанико-географическим районам (Baasanmunkh et al., 2021b), а также эндемич- ным и редким видам (Baasanmunkh et al., 2021d, 2022a). Критически пересмотренный и обнов- ленный контрольный список сосудистых рас- тений природной флоры Монголии включает 3041 таксон из 653 родов и 111 семейств (Baas- anmunkh et al., 2022b). Настоящая статья отра- жает максимальное количество результатов фло- ристического исследования данной территории, обнародованных после 2014 г. Настоящая работа является продолжени- ем цикла регистрации новых находок во флоре Монголии, первая часть которого была опубли- кована ранее (Kechaykin et al., 2014b). Стиму- лом к созданию очередной части послужила Turczaninowia 25, 1: 105–123 (2022) 107 расположен в Европе, во многих странах Азии успешно натурализовался после интродукции и заносов. совместная германско-российская научная экс- педиция в малоисследованные районы горных массивов Хархира и Батар-Хайрхан в 2017 г. В ходе этой экспедиции было собрано более 1500 гербарных листов, которые хранятся в Гербари- ях ALTB (Россия, г. Барнаул) и FR (Германия, г. Франкфурт-на-Майне). Стоит отметить, что данные о материалах, хранящихся в FR, вы- ставлены на сайте GBIF.org (Senckenberg, Her- barium Senckenbergianum (FR). URL: https://doi. org/10.15468/ucmdjy). Сystopteridaceae (Payer) Schmakov Новые виды для флоры Монголии Asteraceae Bercht. et J. Presl Centaurea cyanus L.: Котловина Больших Озер (Depression of Great Lakes) – «Кобдос- ский аймак, г. Кобдо, заброшенные участки возле гостиницы, 1400 м над ур. м., 48°00ʹ11ʺ с. ш. 91°38ʹ34ʺ в. д. 17 IX 2018. А. И. Шмаков» (ALTB). – Новый адвентивный вид для флоры Монголии, где, по всей видимости, является ксе- ноэргазиофитом. Естественный ареал C. cyanus 108 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 с. ш. 93°46ʹ44ʺ в. д. 8 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Гоби-Алтайский ай- мак, окр. оз. Алаг-Нур, 1040 над ур. м., 45°09ʹ04ʺ с. ш. 94°29ʹ51ʺ в. д. 10 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Кобдоский аймак, бас- сейн р. Бодончийн-Гол близ родника Эргийн ус, 1760 м над ур. м., 46°06ʹ59ʺ с. ш. 92°31ʹ01ʺ в. д. 4 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Ховдинский аймак, прав. приток р. Увичийн- Гол, 46°15ʹ с. ш. 92°03ʹ в. д. 22 VII 2009. И. А. Шерин, А. П. Шалимов» (ALTB); «Ховдин- ский аймак, 7 км сев.-вост. горы Алаг-Тэгт-Ула, р. Хэндлэн, 1620 м над ур. м., 46°07ʹ с. ш. 92°30ʹ в. д. Псаммо-петрофитные степи, близ обнаже- ния скал. 7 VII 2009. И. А. Шерин, А. П. Ша- лимов» (ALTB); Кобдосский (Khovd) – «Баян- Ульгийский аймак, пойма р Кобдо-Гол между г. Сул-Ула и вершиной 2163.0, 1597 м над ур. м., 49°07ʹ56ʺ с. ш. 90°20ʹ05ʺ в. д. МШК 1. 29 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Си- ницына, А. А. Баткин» (ALTB); «Westliche Mon- golei, Uvs aimak, N-Ufer des Chjargas nuur, Termis. Senke zwischen Strandwällen. 29 VIII 1976. W. Hilbig, Z. Schamsran» (HAL); Джунгарская Гоби (Dzungarian Gobi) – «Кодбосский аймак, дол. р. Уенч в 10 км ниже пос. Уенч, 1301 м над ур. м., 45°59ʹ273ʺ с. ш. 91°57ʹ963ʺ в. д. МКД 433. 9 VII 2013. А. И. Шмаков, А. А. Кечайкин» (ALTB); «Хобдосский аймак, Булугун сомон, пойма р. Булугун в 3–4 км выше зимней стоянки со- мона, пырейные луга на супесчаных аллювиях. № 13576. 28 VII 1947. А. А. Юнатов» (LE); Котловина Больших Озер (Depression of Great Lakes) – «Гоби-Алтайский аймак, Хасагту сомон, Шаргани-Гоби, долина Шаргани-Гола у Сундул- ту-Байгиниг, по берегам и днищу ороситель- ного канала. № 5706. 4 IX 1948. В. И. Грубов» (LE); «Гоби-Алтайский аймак, Хасагту сомон, Шаргани-Гоби, долина Шаргани-Гола у Сун- дулту-Байгиниг, по берегу арыка. № 5655. 5 IX 1948. В. И. Новые виды для флоры Монголии Грубов» (LE); Гоби-Алтайский (Gobi Altai) – «Баян-Хонгорский аймак, Баин-Лэг со- мон, Гобийский Алтай: низкий хребет Баин- Цаган, Ширикийн-худук. Каменистые холмы. № 17053. 3 IX 1927. М. Симукова» (LE). – Вид описан по единственному сбору с юго-восточ- ных предгорий хребта Азутау в Восточном Ка- захстане вблизи границы с Китаем и более никем не приводился. В первоисточнике указывается, что P. salsa не имеет родства среди известных таксонов рода Potentilla (Kotukhov, 1992). Ис- с е о а е а а о И Со обоз а а а э руется с C. fragilis (Urgamal et al., 2014). В «The vascular plant diversity of Dzungarian Gobi in west- ern Mongolia, with an annotated checklist» C. dick- ieana, к сожалению, также не приводится как от- дельный вид (Baasanmunkh et al., 2021a). Rosaceae Juss. Rosaceae Juss. Potentilla × habievii Kechaykin: Кобдосский (Khovd) – «Баян-Ульгийский аймак, хр. Кара- лахту, перевал Оботын-Даба, 2640 м над ур. м., 49°19ʹ15ʺ с. ш. 89°49ʹ42ʺ в. д. МШК 281. 6 VIII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Си- ницына, А. А. Баткин» (ALTB); там же, «8 км южнее перевала Оботын-Даба, 2285 м над ур. м., 49°14ʹ47ʺ с. ш. 89°50ʹ46ʺ в. д. МКД 640. 18 VII 2013. А. И. Шмаков, А. А. Кечайкин» (ALTB); «Убсунурский аймак, массив Хархира, дол. р. Иргийн-Голын-Сала в среднем течении, 2622 м над ур. м., 49°38ʹ17ʺ с. ш. 91°12ʹ45ʺ в. д. МШК 27. 30 VII 2017. А. И. Шмаков, А. А. Ке- чайкин, Т. А. Синицына, А. А. Баткин» (ALTB); там же, «хр. Тургэний-Нуру, подножье южного макросклона, 2650–2750 м над ур. м., 49°38ʹ34ʺ с. ш. 91°15ʹ07ʺ в. д. МШК 84. 31 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB); там же, «хр. Хархира-Ула, се- верный макросклон вершины 3687.4, 2700–3000 м над ур. м., 49°35ʹ57ʺ с. ш. 91°16ʹ28ʺ в. д. МШК 55. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB, FR-0130810 [https://www.gbif.org/occurrence/3046086513]); Монгольско-Алтайский (Mongolian Altai) – «Монгольский Алтай, хребты. Склон CСВ экспо- зиции, крутизна 14°. Злаково-кобрезиево-осоко- вый альпийский луг, 2654 м над ур. м., 48.32347° с. ш. 90.31017° в. д. Z17-049. 21 VII 2017. Е. Г. Зибзеев» (ALTB, NS). – Нотовид был описан по многочисленным гербарным образцам из Юго- Восточного Алтая в пределах России. Большая часть типового материала собрана на плоско- горье Укок вблизи границ с Казахстаном, Кита- ем и Монголией. По данным А. А. Кечайкина, P. × habievii представляет собой межсекционный гибрид между P. multifida L. и P. exuta Soják (Ke- chaykin, 2015a). Действительно, гибрид имеет промежуточные признаки относительно предпо- лагаемых родительских видов и собран в Монго- лии на контакте их популяций. Potentilla salsa Kotukhov: Монгольско-Ал- тайский (Mongolian Altai) – «Гоби-Алтайский аймак, хр. Монгольский Алтай, верхнее тече- ние р. Могоийн-Гол, 2286 м над ур. м., 45°50ʹ42ʺ Turczaninowia 25, 1: 105–123 (2022) 109 var. gobica Soják» (образцы № 13576, 5706, 5655 и 17053 из LE, цитируемые выше) или «P. gobica Soják» (образец из HAL, цитируемый выше), однако впоследствии под названием P. gobica он описал совершенно другой вид, близкий к P. desertorum Bunge. А. А. Кечайкин также сбли- жает это растение с P. virgata Lehm. (Kechaykin, 2018). Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Rosaceae Juss. При абсолютно схожих условиях произ- растания (сырые луговины по берегам водоемов и солончаки) эти виды отличаются лишь морфо- логией листовых пластинок. У обоих таксонов прикорневые листья пальчато-сложные. Однако у P. salsa они всегда с пятью листочками, имею- щими 2–6 зубцов с каждой стороны (рис. 1Б), а у P. virgata – с 5–9 листочками, число зубцов ко- торых обычно 5–13 с каждой стороны и часто с дополнительным рассечением. С большой долей уверенности можно утверждать о вероятности нахождения P. salsa во флоре Китае в бассейнах рек Урунгу и Черный Иртыш. Нами впервые приводится изображение этого вида в природе, сделанное в окр. родника Сухайтын Хоолой в сомоне Цээл Гоби-Алтайского аймака (рис. 1). Данный пункт расположен на территории Мон- гольско-Алтайского р-на на границе с Заалтай- ской Гоби (Transaltai Gobi). Рис. 1. Potentilla salsa: А – внешний вид; Б – листовая пластинка (вид с нижней стороны) (фото С. Баасанмун- ха: Сухайтын Хоолой, 7 июля 2019 г.). Рис. 1. Potentilla salsa: А – внешний вид; Б – листовая пластинка (вид с нижней стороны) (фото С. Баасанмун- ха: Сухайтын Хоолой, 7 июля 2019 г.). Potentilla smirnovii Kechaykin: Кобдосский (Khovd) – «Баян-Ульгийский аймак, хр. Кара- лахту, перевал Оботын-Даба, 2640 м над ур. м., 49°19ʹ15ʺ с. ш. 89°49ʹ42ʺ в. д. МШК 281. 6 VIII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Си- ницына, А. А. Баткин» (ALTB); Монгольско- Алтайский (Mongolian Altai) – «Khovdo aimag, Bulgan sum, stony slopes, 2796 m. 45°01ʹ10.56ʺN, 92°01ʹ0.16ʺE. 18 VII 2014. D. Urangoo» (UBA); Джунгарская Гоби (Dzungarian Gobi) – «Кобдо- ский аймак, хр. Байтаг-Богдо, басс. р. Баруук- Харгайтын-Гол, дол. левого притока, беруще- го начало на г. Алтан-Обо, 2132 м над ур. м., 45°15ʹ005ʺ с. ш. 90°56ʹ195ʺ в. д. МКД 182. 5 VII 2013. А. И. Шмаков, А. А. Кечайкин» (ALTB). – Вид был описан по двум сборам с плоскогорья Укок в пределах России вблизи границ с Мон- голией и Китаем (Kechaykin, Kutsev, 2015). Наи- более близкими к P. smirnovii являются P. multi- fida и P. habievii. От первого вида он отличается прикорневыми листовыми пластинками с 3–5 парами боковых листочков (не 2–3-парными), от второго – отсутствием железистого опушения и более мелкими лепестками. 110 Новые виды для отдельных ботанико- географических районов Монголии Rosaceae Juss. Potentilla acervata Soják: Прихубсугульский (Khuvsgul) – «Хубсугульский аймак, левобере- жье р. Аригийн-Гол у горы Цэгэр-Ула, 1140–1300 м над ур. м., 50°30ʹ44ʺ с. ш. 101°27ʹ57ʺ в. д. СМЭ 1030. 7 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Каме- лина, В. И. Дорофеев» (ALTB); «Хубсугульский аймак, правый берег р. Ур-Гол близ устья р Хух- Гол, 1172 м над ур. м., 50°45ʹ42ʺ с. ш. 101°31ʹ28ʺ в. д. СМЭ 1472. 14 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB). – Вид был описан по многочисленным сборам из Восточной Сибири, Северной Монго- лии и Маньчжурии. По данным И. Сояка, P. acer- vata возник в результате скрещbивания P. longi- folia Willd. ex D. F. K. Schltdl. и P. tanacetifolia Willd. ex D. F. K. Schltdl. (Soják, 1970, 2012а), а P. chenteica Soják, описанный им из окр. Тэрэлжа к северо-востоку от г. Улан-Батора, относится к этому же виду (Soják, 2012b). Листовые пластин- ки P. acervata по форме и характеру опушения черешков схожи с P. longifolia, но рыхлое соцве- тие и крупные лепестки такие же, как у P. tanac- etifolia. В Монголии этот вид встречается во многих районах за исключением западной части. Dryopteridaceae Herter Dryopteris fragrans (L.) Schott: Прихубсугуль- ский (Khuvsgul) – «Хубсугульский аймак, берег оз. Хубсугул южнее устья р. Хэгцер-Гол, 1675 м над ур. м., 50°34ʹ10ʺ с. ш. 100°28ʹ04ʺ в. д. СМЭ 812. 4 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дарийма, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB). – Распро- странен во многих северных районах Монголии. Euphorbiaceae Juss. Euphorbia potaninii Prokh.: Джунгарская Гоби (Dzungarian Gobi) – «Кобдоский аймак, Ал- тай сомон, северо-западный макросклон хребта Их-Хавтаг-Уул в 4 км южнее заставы Зээгийн, урочище “Яргайтын сайр”, каменистые остеп- ненные склоны ущельев и щебнистые днища пересыхающих ручьев (с участием зарослей можжевельника, жимолости, спиреи и розы), 1850–2200 м над ур. м., 45°05ʹ96ʺ с. ш. 92°15ʹ43ʺ в. д. 27 V 2015 А. А. Кечайкин» (ALTB). – Су- бэндемик Монголии, описанный по сбору из окрестностей (вероятнее всего, южных) оз. Уу- рэг-Нуур. Poaceae Barnhart crebridens приведены в работе С. В. Смирнова и др. (Smirnov et al., 2021). (Mongolian Altai) – «Bayan-Ulgii aimag, Tsengel sum, Axsu, in Larch forest, 2200 m, 48°53ʹ941ʺN, 88°04ʹ63.2ʺE. 9 VIII 2016. V. Gundegmaa» (UBA201689). – Описан из Восточной Сибири по сборам в среднем течении р. Иркут. Во флоре Монголии вид был известен для Прихубсугуль- ского, Хангайского и Хэнтэйского р-нов, а также Котловины Больших Озер. Подробные коммен- тарии о распространении, основных морфоло- гических отличиях от близких таксонов и среде обитания P. crebridens приведены в работе С. В. Смирнова и др. (Smirnov et al., 2021). ского Алтая. Информация об общем распростра- нении, морфологии и разновидностях P. chamae- leo приведена в другом источнике (Kechaykin et al., 2019). ского Алтая. Информация об общем распростра- нении, морфологии и разновидностях P. chamae- leo приведена в другом источнике (Kechaykin et al., 2019). Potentilla chionea Soják: Монгольско-Алтай- ский (Mongolian Altai) – «Гоби-Алтайский ай- мак, хр. Хасагт-Хайрхан, южнее пос. Сумийн- ден, 2594 м над ур. м., 46°59ʹ19ʺ с. ш. 95°48ʹ32ʺ в. д. 19 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Кобдосский аймак, Цэцэг сомон, близ н. п. Цэцэг, гора Цаст-Богдо-Ула, пойма ручья, склоны и скалы. № 961. 28 VII 1975. О. В. Жур- ба» (MW0181759). – Описан из Монголии по многочисленным экземплярам, собранным в окр. Хубсугула и представляет собой гибридо- генный таксон, возникший в результате скре- щивания между P. crebridens Juz. и P. sericea L. (Soják, 1970). В монгольской флоре распростра- нен в северных, западных и южных районах. На- хождение P. chionea в Монгольско-Алтайском регионе было лишь делом времени. Этот вид приводился также для Кобдосского ботанико- географического района по сбору в северной части хр. Тургэний-Нуру (Gundegmaa, Urgamal, 2016), однако соответствующие данные не ука- заны в работе Baasanmunkh et al. (2022b). Приме- чания об общем распространении и экологиче- ских предпочтениях P. chionea указаны в работе С. В. Смирнова и др. (Smirnov et al., 2021). Potentilla × drymeja Soják: Прихубсугульский (Khuvsgul) – «Хубсугульский аймак, берег оз. Хубсугул южнее устья р. Хэгцэр-Гол, 1675 м над ур. м., 50°34ʹ10ʺ с. ш. 100°28ʹ04ʺ в. д. СМЭ 730. 4 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Да- риймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камели- на, В. И. Дорофеев» (ALTB). – По данным И. Со- яка, это гибридогенный таксон, возникший в ре- зультате скрещивания между P. arenosa (Turcz.) Juz. и P. crebridens Juz. (Soják 1970). Poaceae Barnhart Описан из Монголии по сборам из двух точек: горы Богд- Хан-Уул южнее Улан-Батора и Северный Хангай в окр. пос. Баян-Агт. В «Conspectus of the Vascu- lar Plants of Mongolia» (Urgamal et al., 2014) до- пущена ошибка: в работе Кечайкина и Шмакова этот таксон не приводится для Гоби-Алтайского (Gobi Altai) р-на (Kechaykin, Shmakov, 2013). Распространен от Северной Монголии до аркти- ческих территорий Азии. Potentilla crebridens Juz.: Кобдосский (Khovd) – «Убсунурский аймак, массив Хархи- ра, хр. Хархира-Ула, северный макросклон вер- шины 3687.4, 2700–3000 м над ур. м., 49°35ʹ57ʺ с. ш. 91°16ʹ28ʺ в. д. МШК 67. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB, FR-0130794 [https://www.gbif. org/occurrence/3046150515], FR-0130795 [https:// www.gbif.org/occurrence/3046152512]); «Убсу- нурский аймак. Тугрэн сомон. Долина р. Тур- гэн. Разнотравно-злаков. лиственничник. 2070 м над ур. м. № 4440. 7 VII 1973. [Д.] Банзрагч, [З. В.] Карамышева, [С.] Мунхбаяр, [Ц.] Цэгмид» (NS0026197); «[Убсунурский аймак] Mongolia borealis. Circa lacus Ubsa. Южный берег Хархи- ра. 23 VII 1879. G. N. Potanin» (LE); «Uvs aimag, Kharkhiraa-Turgen Mt., 1949 m, 49°53ʹ53.21ʺN, 91°24ʹ06.13ʺE. 14 VII 2017. V. Gundegmaa» (UBA177141); «Uvs aimag, Emchiin am of Kharkhiraa-Turgen Mt., in Larch forests, 2411 m, 49°55ʹ3.18ʺN, 91°15ʹ13.40ʺE. 14 VII 2017. V. Gun- degmaa» (UBA1707141); Монгольско-Алтайский Potentilla fragarioides L.: Прихубсугульский (Khuvsgul) – «Хубсугульский аймак, правый берег р. Ур-Гол близ устья р. Хух-Гол, 1172 м над ур. м., 50°45ʹ42ʺ с. ш. 101°31ʹ28ʺ в. д. СМЭ 1407. 14 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB). – Широко распространенный в Азии вид. Приурочен к лес- ным и кустарниковым сообществам на равнинах и в среднегорьях от Западной Сибири и Казах- стана до Дальнего Востока. Во флоре Монголии P. fragarioides встречается дизъюнктивно с запа- да на восток в основном севернее 47 параллели, не имеет близкородственных или схожих по га- битусу таксонов, легко определяемый. Potentilla fragarioides L.: Прихубсугульский (Khuvsgul) – «Хубсугульский аймак, правый берег р. Ур-Гол близ устья р. Хух-Гол, 1172 м над ур. м., 50°45ʹ42ʺ с. ш. 101°31ʹ28ʺ в. д. СМЭ 1407. 14 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB). – Широко распространенный в Азии вид. Приурочен к лес- ным и кустарниковым сообществам на равнинах и в среднегорьях от Западной Сибири и Казах- стана до Дальнего Востока. Во флоре Монголии P. Poaceae Barnhart Potentilla chalchorum Soják: Прихубсугуль- ский (Khuvsgul) – «Хубсугульский аймак, лево- бережье р. Аригийн-Гол у горы Цэгэр-Ула, 1140– 1300 м над ур. м., 50°30ʹ44ʺ с. ш. 101°27ʹ57ʺ в. д. СМЭ 1029. 7 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB). – Этот вид был описан по многочисленным сбо- рам с юга Средней Сибири, из Даурии и Север- ной Монголии (Soják, 1970). Во флоре Монголии был известен для Монгольско-Алтайского, Хан- гайского, Хэнтэйского и Восточно-Монгольско- го р-нов (Baasanmunkh et al., 2022b). Подробные данные о распространении, родстве и основных отличительных признаках P. chalchorum указаны в работе Kechaykin et al. (2021). Poaceae Barnhart Poa sergievskajae Probat.: Хэнтэйский (Khen- tei) – «Монголия, Селенгинский аймак, сум Ероо. Урочище Хонин Нуг (Хониний-Ноганы), левый берег р. Ероо-гол. Березово-сосновый лес, 882 м над ур. м., 49°05ʹ с. ш. 107°18ʹ в. д. 17 VI 2012. Д. Н. Шауло» (NS). – Распростра- нен в Восточной Сибири и на Дальнем Востоке (Tzvelev, Probatova, 2019). Единичные находки известны в Западном Саяне (Shaulo, 2006). Для флоры Монголии приводился в качестве под- вида P. pratensis L. по сборам из Монгольско- Даурского и Прихинганского р-нов (Urgamal et al., 2014), а также в монографической обработке М. В. Олоновой, но без точного указания ме- стонахождений (Olonova, 2016). Предполага- ется, что вид морфологически очень близок P. pratensis и отличия заключаются лишь в сте- пени опушения нижних цветковых чешуй и ши- рине листовых пластинок (Olonova, 2012, 2016). Но, по мнению Н. Н. Цвелева и Н. С. Пробато- вой (Tzvelev, Probatova, 2019), вид более близок к P. sabulosa (Roshev.) Roshev., при этом габиту- ально имеет значительное сходство с P. sibirica Roshev. Potentilla chamaeleo Soják: Гоби-Алтайский (Gobi Altai) – «Баин Xонгop аймак, Баин Гоби сомон, хр. Ихэ-Богдо (Гобийский Алтай). Верх- ний пояс. Плато в верховьях пади Ихэ Хуримт, типцово-кобрезиевая высокогорная степь, на россыпях. № 8697. 28 VI 1945. А. А. Юнатов» (LE01017069 – Holotypus). – Субэндемик Монго- лии, описан по сборам из Монгольского и Гобий- Turczaninowia 25, 1: 105–123 (2022) 111 (Mongolian Altai) – «Bayan-Ulgii aimag, Tsengel sum, Axsu, in Larch forest, 2200 m, 48°53ʹ941ʺN, 88°04ʹ63.2ʺE. 9 VIII 2016. V. Gundegmaa» (UBA201689). – Описан из Восточной Сибири по сборам в среднем течении р. Иркут. Во флоре Монголии вид был известен для Прихубсугуль- ского, Хангайского и Хэнтэйского р-нов, а также Котловины Больших Озер. Подробные коммен- тарии о распространении, основных морфоло- гических отличиях от близких таксонов и среде обитания P. Poaceae Barnhart Wolf, от которого отличается нежелезисты- ми черешками, листочками и чашелистиками, а также не утолщенными в основании столбиками (Soják, 2003). Вид ранее приводился для Алтая, но без указания конкретных местонахождений (Kechaykin, Shmakov, 2020). с. ш. 91°16ʹ28ʺ в. д. МШК 57. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB). – Вид описан по сборам с юго- западного берега Хубсугула в 20 км севернее по- селка Хатгал и считается эндемиком Монголии (Baasanmunkh et al., 2021d). По мнению И. Со- яка, P. hubsugulica произошел от гибридизации между P. crebridens Juz. и P. gelida C. A. Mey., но по внешнему виду наиболее близок к P. evestita Th. Wolf, от которого отличается нежелезисты- ми черешками, листочками и чашелистиками, а также не утолщенными в основании столбиками (Soják, 2003). Вид ранее приводился для Алтая, но без указания конкретных местонахождений (Kechaykin, Shmakov, 2020). Т. А. Синицына, А. А. Баткин» (ALTB); «Uvs aimag, Sagil sum, in rocky slopes at Ÿltiin-am of Tsagaan-Shuvuut Mt., 2311 m. 50°15ʹ53.1ʺN, 91°16ʹ46.6ʺE. 28 VII 2014. V. Gundegmaa» (UBA14756); Монгольско-Алтайский (Mongo- lian Altai) – «Баян-Улэгэйский аймак, верхнее течение р. Цаган-Гол, лев. бер., южный макро- склон вершины 3483 м, 49°08ʹ с. ш. 88°12ʹ в. д. ШАМ 1793. 3 VIII 2001. Р. В. Камелин, А. И. Шмаков, В. И. Дорофеев, М. Г. Куцев, И. Н. Чу- баров, С. А. Костюков, С. А. Дьяченко, П. А. Ко- сачев, Д. А. Герман, А. А. Скачко» (ALTB); «Ба- ян-Ульгийский аймак, Сагсай сомон. Монг. Ал- тай. Оз. Хулган-Нур близ Даян-Нура. № 1268. 29 VII 1974. О. В. Журба» (MW0181888). – Описан с плоскогорья Укок по сборам в долине р. Калгу- ты. Во флоре Монголии указывался для Джун- гарской Гоби (Kechaykin et al., 2014a), Хангай- ского (Gubanov, 1996) и Монгольско-Алтайского р-нов (Urgamal et al., 2014). Однако последние данные мы предлагаем считать ошибочными, так как вид в действительности нигде не при- водился с указанием каких-либо точек сборов или полевых наблюдений из этого района. Тем самым, мы впервые приводим здесь P. kryloviana для Монгольско-Алтайской территории с указа- нием конкретных местонахождений. Этот вид был также обнаружен в Монгольском Алтае в пределах Китая примерно в 10 км от границы с Монголией (Kechaykin et al., 2014a). Мы придер- живаемся мнения Сояка о том, что P. kryloviana – это, вероятнее всего, гибридогенный таксон, ко- торый мог возникнуть от скрещивания P. exuta и P. gelida (Soják, 1986). Такое утверждение требу- ет специальных исследований. Potentilla jenissejensis Polozhij et W. Poaceae Barnhart Smirnova: Джунгарская Гоби (Dzungarian Gobi) – «Кобдос- ский аймак, хр. Аршантын-Нуру, дол. ручья Уля- стыйн-сала (прав. прит. р. Баян-Гол), 1700–2300 м над ур. м., 46°22ʹ с. ш. 91°14ʹ в. д. 21 VII 2009. И. А. Шерин, А. П. Шалимов» (ALTB). – Описан с юга Красноярского края. Распространен много- численными популяциями в Южной Сибири на Алтае и Саянах, во флоре Монголии известен по сборам лишь из четырех пунктов в Монголь- ском Алтае (Kechaykin et al., 2014b; Bekket et al., 2015) и двух в Котловине Больших Озер из окр. оз. Хяргас-Нуур (Soják, 2012) и Холбоо-Нуур (Soják, 1987). В «Conspectus of the Vascular Plants of Mongolia» (Urgamal et al., 2014) для Кобдос- ского р-на приводится ошибочно: в работе Ке- чайкина и Шмакова этот таксон не указывался для данного региона (Kechaykin, Shmakov, 2013). Наиболее близким к P. jenissejensis по габитусу и экологической приуроченности (вероятно, и по филогении) является P. agrimonioides M. Bieb. Важно отметить, что из котловины оз. Холбоо- Нуур (пункта, упомянутого выше) И. Сояком была описана разновидность P. agrimonioides var. kobdoensis Soják, которую он впоследствии синонимизировал с P. jenissejensis (Soják, 2012b). Potentilla mongolica Krasch.: Гоби-Алтайский (Gobi Altai) – «Sudgobi-Aimak: Jamcat-Massiv, Bergsteppe, N-hang, 2400 m. Nr. 1114. 24 VI 1962. C. Davazame, P. Hanelt» (GAT). – Эндемик Цен- тральной и Южной Монголии, описан по сбо- рам из юго-восточных отрогов Хангая. Наибо- лее близким к P. mongolica по габитусу является P. sericea L., о чем свидетельствуют частые не- верные определения последнего вида. У P. mon- golica каудекс разветвленный, образует много- численные партикулы (обычно 7–10), которые в 3–4 раза длиннее, чем у P. sericea. Кроме этого, у первого вида остатки отмерших прилистников светло-коричневого или соломенного цвета и гу- сто опушены беловатыми волосками. У второго таксона каудекс в основном с 2–5 укороченными партикулами, покрытыми темно-бурыми остат- Potentilla kryloviana Th. Wolf: Кобдосский (Khovd) – «Убсунурский аймак, массив Хархи- ра, хр. Тургэний-Нуру, подножье южного макро- склона, 2650–2750 м над ур. м., 49°38ʹ34ʺ с. ш. 91°15ʹ07ʺ в. д. МШК 88 и 97. 31 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB); там же, «хр. Хархира-Ула, се- верный макросклон вершины 3687.4, 2700–3000 м над ур. м., 49°35ʹ57ʺ с. ш. 91°16ʹ28ʺ в. д. МШК 56. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Potentilla kryloviana Th. Wolf: Кобдосский (Khovd) – «Убсунурский аймак, массив Хархи- ра, хр. Тургэний-Нуру, подножье южного макро- склона, 2650–2750 м над ур. м., 49°38ʹ34ʺ с. ш. 91°15ʹ07ʺ в. д. Poaceae Barnhart fragarioides встречается дизъюнктивно с запа- да на восток в основном севернее 47 параллели, не имеет близкородственных или схожих по га- битусу таксонов, легко определяемый. Potentilla hubsugulica Soják: Кобдосский (Khovd) – «Убсунурский аймак, массив Хархи- ра, хр. Хархира-Ула, северный макросклон вер- шины 3687.4, 2700–3000 м над ур. м., 49°35ʹ57ʺ 112 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Т. А. Синицына, А. А. Баткин» (ALTB); «Uvs aimag, Sagil sum, in rocky slopes at Ÿltiin-am of Tsagaan-Shuvuut Mt., 2311 m. 50°15ʹ53.1ʺN, 91°16ʹ46.6ʺE. 28 VII 2014. V. Gundegmaa» (UBA14756); Монгольско-Алтайский (Mongo- lian Altai) – «Баян-Улэгэйский аймак, верхнее течение р. Цаган-Гол, лев. бер., южный макро- склон вершины 3483 м, 49°08ʹ с. ш. 88°12ʹ в. д. ШАМ 1793. 3 VIII 2001. Р. В. Камелин, А. И. Шмаков, В. И. Дорофеев, М. Г. Куцев, И. Н. Чу- баров, С. А. Костюков, С. А. Дьяченко, П. А. Ко- сачев, Д. А. Герман, А. А. Скачко» (ALTB); «Ба- ян-Ульгийский аймак, Сагсай сомон. Монг. Ал- тай. Оз. Хулган-Нур близ Даян-Нура. № 1268. 29 VII 1974. О. В. Журба» (MW0181888). – Описан с плоскогорья Укок по сборам в долине р. Калгу- ты. Во флоре Монголии указывался для Джун- гарской Гоби (Kechaykin et al., 2014a), Хангай- ского (Gubanov, 1996) и Монгольско-Алтайского р-нов (Urgamal et al., 2014). Однако последние данные мы предлагаем считать ошибочными, так как вид в действительности нигде не при- водился с указанием каких-либо точек сборов или полевых наблюдений из этого района. Тем самым, мы впервые приводим здесь P. kryloviana для Монгольско-Алтайской территории с указа- нием конкретных местонахождений. Этот вид был также обнаружен в Монгольском Алтае в пределах Китая примерно в 10 км от границы с Монголией (Kechaykin et al., 2014a). Мы придер- живаемся мнения Сояка о том, что P. kryloviana – это, вероятнее всего, гибридогенный таксон, ко- торый мог возникнуть от скрещивания P. exuta и P. gelida (Soják, 1986). Такое утверждение требу- ет специальных исследований. с. ш. 91°16ʹ28ʺ в. д. МШК 57. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB). – Вид описан по сборам с юго- западного берега Хубсугула в 20 км севернее по- селка Хатгал и считается эндемиком Монголии (Baasanmunkh et al., 2021d). По мнению И. Со- яка, P. hubsugulica произошел от гибридизации между P. crebridens Juz. и P. gelida C. A. Mey., но по внешнему виду наиболее близок к P. evestita Th. Poaceae Barnhart МШК 88 и 97. 31 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB); там же, «хр. Хархира-Ула, се- верный макросклон вершины 3687.4, 2700–3000 м над ур. м., 49°35ʹ57ʺ с. ш. 91°16ʹ28ʺ в. д. МШК 56. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Turczaninowia 25, 1: 105–123 (2022) 113 сожалению, данная информация оказалась упу- щенной во многих крупных флористических сводках исследуемой территории. Кроме Гобий- ского Алтая, вид известен из нескольких пунктов для Монгольско-Алтайского р-на и по единич- ным сборам для Кобдосского, Джунгарской Гоби и Котловины Больших Озер (Hilbig, Schamsran, 1980; Kechaykin et al., 2014a; Bekket et al., 2015). Подробные сведения об общем распростране- нии, близких таксонах и главных отличительных признаках P. pamirica обнародованы в других ис- точниках (Soják, 2007; Kechaykin et al., 2019). ками голых (или с немногочисленными волоска- ми) прилистников (нами исследовано более 50 гербарных образцов из различных районов Мон- голии). Стоит также отметить, что P. mongolica, в отличие от P. sericea, никогда не собирался выше 2400 м над ур. м. ками голых (или с немногочисленными волоска- ми) прилистников (нами исследовано более 50 гербарных образцов из различных районов Мон- голии). Стоит также отметить, что P. mongolica, в отличие от P. sericea, никогда не собирался выше 2400 м над ур. м. Potentilla multicaulis Bunge: Гоби-Алтайский (Gobi Altai) – «Sudgobi-Aimak: Dund-Sajchan, Bognin-chjar, ca. 25 km sudl. Bulgan, Trocken- tal. Nr. 2078. 28 V 1962. C. Davazame, P. Hanelt» (GAT); «Умнеговь аймак, Булган сомон, Бог- нийн хяр» (UBA). – Вид был описан по сборам из окр. г. Пекина в 1833 г. и лишь спустя более 150 лет впервые приводится для флоры Монго- лии по сборам из Северного Хангая (Byazrov et al., 1989). Странно, что его первые местонахож- дения относятся не к приграничным районам с Китаем, а к бореальной зоне. К сожалению, гер- барных образцов P. multicaulis из Монголии в LE и MW нами не обнаружено. Таксон широко представлен во многих северных и центральных районах Китая. Распространение его во флоре Монголии, как и определение ранее собранных образцов, требует уточнений. Этому вопросу бу- дет посвящена отдельная работа. Potentilla stepposa Soják: Хангайский (Khan- gai) – «Ара-Хангайский аймак, Люнг сомон. Долина р. Орхон-гол у монастыря Эрдэни-дзу. Каменистый склон левого берега над руслом. № 7332. 21 VI 1948. А. А. Юнатов» (LE); «Ба- ян-Хонгор аймак, Жаргалант сомон. В 10–13 км восточнее Баин-Хонгора по дороге на Арбай Хэрэ. Полынно-ковыльная степь. № 11253. 29 VIII 1943. А. А. Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 49°24ʹ с. ш. 89°04ʹ в. д. ШАМ 1994 и 1981. 5 VIII 2001. Р. В. Камелин, А. И. Шмаков, В. И. Дорофе- ев, М. Г. Куцев, А. Е. Бородина-Грабовская, Н. А. Усик, Ш. Дариймаа, С. А. Дьяченко, А. А. Скач- ко» (ALTB);. – Редкий вид, описанный по сбо- рам из Восточного Тянь-Шаня и Монгольского Алтая. Во флоре Монголии был известен лишь в двух пунктах: гора Алтан-Обо на хр. Байтаг-Бог- до и перевал между Индертийн-Гол и Тумурту- Гол. Подробные комментарии о P. turkestanica даны в работе Soják et al. (2011). 49°24ʹ с. ш. 89°04ʹ в. д. ШАМ 1994 и 1981. 5 VIII 2001. Р. В. Камелин, А. И. Шмаков, В. И. Дорофе- ев, М. Г. Куцев, А. Е. Бородина-Грабовская, Н. А. Усик, Ш. Дариймаа, С. А. Дьяченко, А. А. Скач- ко» (ALTB);. – Редкий вид, описанный по сбо- рам из Восточного Тянь-Шаня и Монгольского Алтая. Во флоре Монголии был известен лишь в двух пунктах: гора Алтан-Обо на хр. Байтаг-Бог- до и перевал между Индертийн-Гол и Тумурту- Гол. Подробные комментарии о P. turkestanica даны в работе Soják et al. (2011). на этикетке указан Ара-Хангайский (Архангай) аймак, но монастырь Эрдэни-Дзу находится в аймаке Уверхангай у административного центра сомона Хархорин на правом берегу р. Орхон. на этикетке указан Ара-Хангайский (Архангай) аймак, но монастырь Эрдэни-Дзу находится в аймаке Уверхангай у административного центра сомона Хархорин на правом берегу р. Орхон. Potentilla tergemina Soják: Прихубсугульский (Khuvsgul) – «Хубсугульский аймак, левобере- жье р. Аригийн-Гол у горы Цэгэр-Ула, 1140–1300 м над ур. м., 50°30ʹ44ʺ с. ш. 101°27ʹ57ʺ в. д. СМЭ 1015. 7 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB); «Хубсугуль- ский аймак, пойменный берег р. Аригийн-Гол в 4 км от устья, галечник и пойменные заросли, 1126 м над ур. м., 50°29ʹ51ʺ с. ш. 101°32ʹ26ʺ в. д. СМЭ 1661. 18 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB); «Хубсугуль- ский аймак, правый берег р. Ур-Гол близ устья р. Хух-Гол, 1172 м над ур. м., 50°45ʹ42ʺ с. ш. 101°31ʹ28ʺ в. д. СМЭ 1395 и 1448. 14 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Доро- феев» (ALTB). Woodsiaceae Herter Woodsiaceae Herter Woodsia asiatica Shmakov et Kiselev: Хан- гайский (Khangai) – «Булганский аймак, долина р. Их-Тулбэрцйн-Гол ниже бригады Уньт, 1160 м над ур. м., 49°10ʹ02ʺ с. ш. 102°51ʹ40ʺ в. д. СМЭ 1853. 21 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дарийма, А. В. Ваганов, Р. А. Зубов, О. П. Ка- мелина, В. И. Дорофеев» (ALTB); Прихубсугуль- ский (Khuvsgul) – «Хубсугульский аймак, берег оз. Хубсугул южнее устья р. Хэгцер-Гол, 1675 м над ур. м., 50°34ʹ10ʺ с. ш. 100°28ʹ04ʺ в. д. СМЭ 801. 4 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дарийма, А. В. Ваганов, Р. А. Зубов, О. П. Ка- мелина, В. И. Дорофеев» (ALTB). – Вид приво- дился для Монголии во «Flora Altaica» (Shmakov, 2005b) по сборам из бассейна р. Цаган-Ус и окр. г. Цаган-Ула, что соответствует Монгольско- Алтайскому р-ну. Однако W. asiatica по каким- то причинам не указан Urgamal et al. (2014) и Baasanmunkh et al. (2022b). Новые местонахождения редких и эндемичных видов в отдельных ботанико- географических районах Монголии Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 – Описан из Монголии, Сибири и Российского Дальнего Востока. Наиболее близ- кими к P. tergemina во флоре Монголии являются P. multifida и P. ornithopoda Tausch., от которых он отличается более длинными (почти в 2 раза) горизонтально расположенными волосками на черешках и стеблях. У последних видов воло- ски короткие и прижатые. В исследуемом реги- оне вид распространен в основном по северным и северо-восточным районам. Произрастает на суходольных лугах, остепненных щебнистых склонах, по опушкам и берегам рек, на выгонах, вдоль дорог и железнодорожных путей, часто на нарушенных местообитаниях. Poaceae Barnhart Юнатов» (LE); «Хубсугульский аймак, сомон Их-Ула, левобережье р. Селенга, подножье г. Хундлэн-Их-Ула, 1005–1050 м над ур. м., 49°25ʹ01ʺ с. ш. 101°54ʹ23ʺ в. д. СМЭ 253. 27 VI 2007. Р. В. Камелин, А. И. Шмаков, Ш. Да- риймаа, А. В. Ваганов, Р. А. Зубов, О. П. Каме- лина, В. И. Дорофеев» (ALTB); «Хубсугульский аймак, левобережье р. Селенга, хребет Доло- дын-Нуру, южная часть, 1150–1300 м над ур. м., 49°18ʹ16ʺ с. ш. 100°54ʹ57ʺ в. д. СМЭ 541. 30 VI 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дарий- маа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB); Средняя Халка (Middle Khalkha) – «Центральный аймак, Баин-Баратуин сомон, тракт Улан-Батор-Далан-Дзадагад, 150 километр. Злаково-карагановая степь. № 1785. 12 VI 1945. А. А. Юнатов» (LE). – По данным И. Сояка, множество образцов P. stepposa было собрано из Монголии и Южной Сибири, однако в протологе процитирован лишь один экземпляр, обнаруженный им на северных склонах гор Богд- Хан-Уул (Soják, 1992). Этот пункт соответствует Хэнтэйскому (Khentei) ботанико-географическо- му району Монголии, кроме этого, сборы P. step- posa приводились для Монгольско-Алтайского и Котловины Больших Озер (Kechaykin et al., 2014b). В одной из работ А. А. Кечайкина этот вид впервые указывается для флоры Казахстана, там же указаны его общее распространение и ос- новные отличительные признаки от близкород- ственных таксонов (Kechaykin, 2016). Отметим, что для сбора № 7332 из LE, цитируемого выше, Potentilla ozjorensis Peschkova: Кобдосский (Khovd) – «Uvs aimag, Turgen sum, Emchiin-am of Kharkhiraa-Turgen Mt., in wet meadows, 2142 m, 49°55ʹ14.2ʺN, 91°15ʹ15.5ʺE. 27 VI 2014. V. Gun- degmaa» (UBA146678). – Южносибирско-мон- гольский вид, описанный из Восточной Сибири с берегов Байкала на территории Ольхонского р-на. Сборы этого вида во флоре Монголии еди- ничны и относятся в основном к северным ре- гионам от Хубсугула до Хэнтея, в одном пункте был зарегистрирован также для Монгольско-Ал- тайского р-на. Наиболее близок к P. multifida L., от которого отличается тройчатосложными ли- стовыми пластинками (не перистосложными). Вероятнее всего, более детальное исследование гербарных образцов последнего вида позволит выявить новые находки P. ozjorensis в Южной Сибири и Монголии. Potentilla pamirica Th. Wolf: Гоби-Алтайский (Gobi Altai) – «S. Mong.: the summit of Baga-Bogd- ul mountains in Gobi Altai; 44°55ʹN, 101°35ʹE. № 7493. 20 VIII 1966. J. Soják, V. Vasák» (PR). – Эта точка сбора была опубликована в работе Měsíček, Soják (1969) и является первым досто- верным указанием P. pamirica для Монголии. К 114 Новые местонахождения редких и эндемичных видов в отдельных ботанико- географических районах Монголии Гурван-Улиасын-Гол, 2849 м над ур. м., 45°49ʹ58ʺ с. ш. 95°35ʹ14ʺ в. д. 14 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Гоби- Алтайский аймак, хр. Хасагт-Хайрхан, южнее пос. Сумийнден, 2594 м над ур. м., 46°59ʹ19ʺ с. ш. 95°48ʹ32ʺ в. д. 19 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Гоби-Алтайский аймак. В 40 км к ССВ от сомона Цогт. Хр. Гичгенийн- Нуру (Монгольский Алтай). Дриадовый кобрез- ник на склоне. Скалы. 3100 м над ур. м. № 6035. 12 VIII 1973. Исаченко, Рачковская» (NS); «Ховд сомон, 70–75 км южнее с. Манхан, окр. Давст- Нур, привершинная часть гряды, округлые гра- нитные глыбы = 10–15, др = 50, перевыпас, 2715 м над ур. м. 46.74904° с. ш. 92.26491° в. д. Оп. 17–299. 19 VII 2017. А. Королюк, Е. Королюк» (ALTB, NS); Кобдосский (Khovd) – «Баян-Улэ- гэйский аймак, хр. Сайлюгем, северный макро- склон г. Гурбан-Гайшинсар-Ула, 49°24ʹ с. ш. 89°04ʹ в. д. ШАМ 2001. 5 VIII 2001. Р. В. Камелин, А. И. Шмаков, В. И. Дорофеев, М. Г. Куцев, А. Е. Бородина-Грабовская, Н. А. Усик, Ш. Дариймаа, С. А. Дьяченко, А. А. Скачко» (ALTB); «Убсунур- ский аймак, массив Хархира, хр. Тургэний-Нуру, подножье южного макросклона, 2650–2750 м над ур. м., 49°38ʹ34ʺ с. ш. 91°15ʹ07ʺ в. д. МШК 90. 31  VII 2017. А. И. Шмаков, А. А. Кечай- кин, Т. А. Синицына, А. А. Баткин» (ALTB, FR- 0130787 [https://www.gbif.org/occurrence/ 3046080515]). – Примечание см. выше. Potentilla crantzii (Crantz) Beck ex Fritsch: Мон- гольско-Алтайский (Mongolian Altai) – «Гоби- Алтайский аймак, хр. Хара-Адзрагын-Нуру, вер- ховья р. Гурван-Улиасын-Гол, 2849 м над ур. м., 45°49ʹ58ʺ с. ш. 95°35ʹ14ʺ в. д. 14 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); Кобдосский (Khovd) – «Убсунурский аймак, массив Хархи- ра, хр. Тургэний-Нуру, подножье южного ма- кросклона, 2650–2750 м над ур. м., 49°38ʹ34ʺ с. ш. 91°15ʹ07ʺ в. д. МШК 85. 31 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB); там же, «хр. Хархира-Ула, северный макросклон вершины 3687,4, 2700– 3000 м над ур. м., 49°35ʹ57ʺ с. ш. 91°16ʹ28ʺ в. д., МШК 58. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB). – Широко распространенный голаркти- ческий вид, наиболее близкий к P. gelida C. A. Mey., от которого отличается лишь наличием в прикорневой розетке пальчатосложных листо- вых пластинок (у второго вида тройчатослож- ные). В Монголии P. Новые местонахождения редких и эндемичных видов в отдельных ботанико- географических районах Монголии Rosaceae Juss. Potentilla angustiloba T. T. Yu et C. L. Li: Джунгарская Гоби (Dzungarian Gobi) – «Кобдос- ский аймак, хр. Аршантын-Нуру, дол. ручья Уля- стыйн-сала (прав. прит. р. Баян-Гол), 1700–2300 м над ур. м., 46°22ʹ с. ш. 91°14ʹ в. д. 21 VII 2009. И. А. Шерин, А. П. Шалимов» (ALTB); «Ховдин- ский аймак, прав. приток р. Увичийн-Гол, 46°15ʹ с. ш. 92°03ʹ в. д. 22 VII 2009. И. А. Шерин, А. П. Шалимов» (ALTB). – Описан по сборам из гор- ного хребта Циляньшань на севере Китая (ве- роятно, в провинции Ганьсу) и Синьцзян-Уй- гурского автономного р-на. Распространен от Пакистана до Центрального Китая, приводится также для юга Западной Сибири, но без указа- ния конкретных местонахождений (Soják, 2004, Potentilla turkestanica Soják: Кобдосский (Khovd) – «Баян-Ульгийский аймак, хр. Кара- лахту, перевал Оботын-Даба, 2640 м над ур. м., 49°19ʹ15ʺ с. ш. 89°49ʹ42ʺ в. д. МШК 288. 6 VIII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Сини- цына, А. А. Баткин» (ALTB, FR-0129925 [https:// www.gbif.org/occurrence/3046155461]); «Убсу- нурский аймак, массив Хархира, дол. р. Ир- гийн-Голын-Сала в среднем течении, 2622 м над ур. м., 49°38ʹ17ʺ с. ш. 91°12ʹ45ʺ в. д. МШК 22. 30 VIII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB, FR-0129926 [https://www.gbif.org/occurrence/3046157493]); «Баян-Улэгэйский аймак, хр. Сайлюгем, се- верный макросклон г. Гурбан-Гайшинсар-Ула, Turczaninowia 25, 1: 105–123 (2022) 115 P. × drymeja. От первого вида P. coriacea отлича- ется по габитусу, опушенными стеблями и чаше- листиками без войлочка; от последнего – жест- кими, кожистыми листочками, а также чашечкой, опушенной кроме прямых волосков, курчавыми. По данным И. Сояка, эти признаки устойчивы и стабильны даже в условиях интродукции (Soják, 1970). Совершенно необоснованно и без каких- либо комментариев P. coriacea включен в сино- нимы к P. leucophylla (Gubanov, 1992; Urgamal et al., 2014). Возможно, что P. coriacea является результатом гибридизации между P. × drymeja и P. leucophylla. Вероятнее всего, сбор Клеменцов (детерминированный, кстати, самим автором вида И. Сояком) относится к сомону Ихтамир на территории Архангайского аймака. 2012b). Во флоре Монголии известен по сборам с хребта Байтаг-Богдо и в долинах рек Баян-Гол и Барлагийн-Гол (Kechaykin et al., 2014b). По дан- ным И. Сояка, P. angustiloba представляет собой гибридогенный таксон, возникший от скрещива- ния между P. multifida и P. virgata (Soják, 1988). Подробная информация о главных отличитель- ных признаках P. angustiloba опубликована в других работах (Soják, 1988; Kechaykin, 2016). Potentilla chamaeleo Soják: Монгольско- Алтайский (Mongolian Altai) – «Гоби-Алтай- ский аймак, хр. Хара-Адзрагын-Нуру, верховья р. Новые местонахождения редких и эндемичных видов в отдельных ботанико- географических районах Монголии Хархира-Ула, север- ный макросклон вершины 3687.4, 2700–3000 м над ур. м., 49°35ʹ57ʺ с. ш. 91°16ʹ28ʺ в. д. МШК 70. над ур. м., 49 35 57 с. ш. 91 16 28 в. д. МШК 70. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB, FR-0130800 [https://www.gbif.org/occurrence/3046148509]); Монгольско-Алтайский (Mongolian Altai) – «Ба- ян-Улэгэйский аймак, верховья р. Цаган-Гол, морены близ ледника Потанина, 49°07ʹ с. ш. 87°58ʹ в. д. ШАМ 1910. 3 VIII 2001. Р. В. Каме- лин, А. И. Шмаков, В. И. Дорофеев, М. Г. Ку- цев, И. Н. Чубаров, С. А. Костюков, С. А. Дья- ченко, П. А. Косачев» (ALTB); «Монгольский Алтай. Водораздельный гребень хребта Мунх- Хайрхан. Котловина Их-Хатгар-Нур в Кобдос- ском аймаке. Склон юго-западной экспозиции, 2900 м над ур. м. № 406. 4 VIII 1991. Г. Н. Огу- реева» (MW0181830); «Баян-Ульгийский аймак, Сагсай сомон. Монг. Алтай. Южн. берег Даян- Нур, болото. № 1273. 29 VII 1974. О. В. Журба» (MW0181826); Хангайский (Khangai) – «Ара- Хангайский аймак. Восточный Хангай, верши- на горы Хайрхан. Высокогорная лужайка среди камней, 2500 м над ур. м. № 1791. 14 VIII 1980. И. А. Губанов» (MW0181831). – Описан по мно- гочисленным сборам из Монголии, Киргизии и Восточного Саяна. Во флоре первого региона встречается в Джунгарской Гоби, Гобийском и Монгольском Алтае, на Хангае, а также в горах, окаймляющих оз. Уурэг-Нуур на юго-западе. Произрастает P. exuta в высокогорных тундрах и так называемых тундростепях, вблизи ледников и снежников. От наиболее близкого P. kryloviana отличается листовыми пластинками обычно с 4–5 парами боковых листочков (не с 2–3 пара- ми). Видовой самостоятельности P. exuta будет посвящена отдельная работа. Potentilla inopinata Soják: Монгольско-Ал- тайский (Mongolian Altai) – «Кобдосский ай- мак, Монгольский Алтай, хр. Батар-Хайрхан, дол. р. Мэрэнгийн-Амны-Гол близ выхода из гор, 1750–2300 м над ур. м., 47°00ʹ23ʺ с. ш. 92°49ʹ58ʺ в. д. МШК 212. 3 VIII 2017. А. И. Шма- ков, А. А. Кечайкин, Т. А. Синицына, А. А. Бат- кин» (ALTB, FR-0130811 [https://www.gbif.org/ occurrence/3046078514]); «Кобдосский аймак, дол. р. Хонго-гол в месте выхода из гор, правый и левый берег, каменистые склоны и скалы, 48°23ʹ с. ш. 91°06ʹ в. д. 22 V 2002. С. В. Смирнов, Д. А. Герман, С. А. Дьяченко, П. А. Косачев» (ALTB). – Эндемик Западной Монголии, описанный по единственному сбору из Кобдосского ботанико- географического района в южной части хребта Чихачева. Кроме этого, P. inopinata был зареги- стрирован в Монгольско-Алтайском р-не на за- падном склоне массива Цагдуулт (Kechaykin, 2015b). Новые местонахождения редких и эндемичных видов в отдельных ботанико- географических районах Монголии crantzii крайне редок и был зарегистрирован лишь на двух участках: гора Ца- ган-Ула (Kechaykin, Shmakov, 2013) и северный макросклон хребта Тургэний-Нуру (Gundegmaa, Urgamal, 2016). Potentilla exuta Soják: Кобдосский (Khovd) – «Убсунурский аймак, массив Хархира, дол. р. Иргийн-Голын-Сала в среднем течении, 2622 м над ур. м., 49°38ʹ17ʺ с. ш. 91°12ʹ45ʺ в. д. МШК 26. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Синицына, А. А. Баткин» (ALTB); там же, «хр. Тургэний-Нуру, подножье южного макро- склона, 2650–2750 м над ур. м., 49°38ʹ34ʺ с. ш. 91°15ʹ07ʺ в. д. МШК 97. 31 VII 2017. А. И. Шма- Potentilla coriacea Soják: Хангайский (Khan- gai) – «На С.-З. склоне гор, окаймляющих до- лину правого берега р. Хойту-Тамир. № 62 в. 1 VI 1894. Д. А. и Е. Н. Клеменцы» (LE). – Ред- чайший эндемик Северной Монголии, опи- санный по сборам из единственной точки в со- моне Тариалан аймака Хувсгел. Принадлежит секции Niveae A. Nelson, из которой наиболее близкими к нему являются P. leucophylla Pall. и Potentilla coriacea Soják: Хангайский (Khan- gai) – «На С.-З. склоне гор, окаймляющих до- лину правого берега р. Хойту-Тамир. № 62 в. 1 VI 1894. Д. А. и Е. Н. Клеменцы» (LE). – Ред- чайший эндемик Северной Монголии, опи- санный по сборам из единственной точки в со- моне Тариалан аймака Хувсгел. Принадлежит секции Niveae A. Nelson, из которой наиболее близкими к нему являются P. leucophylla Pall. и 116 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 р. Арбурюка, на каменистой почве. № 50. 15 VI 1896. E. Klementz» (LE); «Хубсугульский ай- мак, горы между р. Джаргалант-Гол и оз. Цаган- Нур, 1813 м над ур. м., 49°25ʹ34ʺ с. ш. 98°06ʹ29ʺ в. д. СМЭ 164. 24 VI 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зу- бов, О. П. Камелина, В. И. Дорофеев» (ALTB). – Субэндемик Монголии, описан по сборам с хребта Хан-Хухийн-Ула. Кроме Монголии рас- пространен на юге Сибири в Республиках Алтай и Тыва (Kurbatskiy, 2007; Kechaykin, 2012). От наиболее близких P. jenissejensis Polozhij et W. Smirnova и P. pensylvanica L. отличается следу- ющими признаками: стабильно мелкие растения 4–10 см высотой с малоцветковыми (обычно 2–6 цветка) соцветиями, листочки в числе 2–3 пар с 2–3 зубцами. Судя по приграничному сбору СМЭ 164, цитируемому выше, нахождение вида возможно также в Прихубсугульском р-не. ков, А. А. Кечайкин, Т. А. Синицына, А. А. Бат- кин» (ALTB); там же, «хр. Новые местонахождения редких и эндемичных видов в отдельных ботанико- географических районах Монголии Давст-Нур, выположен- ная вершина гребня среди останцов и глыб, 3188 м над ур. м., 46.78297° с. ш. 89.20683° в. д. Оп. 17–47. 18 VII 2017. Е. А. Басаргин» (ALTB, NS); «Ховд сомон, окр. Давст-Нур, верхняя часть СВ склона у подножья останца, 3087 м над ур. м., 46.78277° с. ш. 92.21369° в. д. Оп. 17–46. 18 VII 2017. Е. А. Басаргин» (ALTB, NS); «Ховд сомон, 70–75 км южнее с. Манхан, окр. Давст- Нур, привершинная часть гряды, округлые гра- нитные глыбы = 10–15, др = 50, перевыпас, 2715 м над ур. м., 46.74904° с. ш. 92.26491° в. д. Оп. 17–299. 19 VII 2017. А. Королюк, Е. Королюк» (ALTB, NS); «Монгольский Алтай, хребты в окр. оз. Дават Нуур. Склон СВ экспозиции, крутиз- на 8°. Криофильная степь, 2777 м над ур. м., 46.46598° с. ш. 92.13437° в. д. Z17–033. 18 VII 2017. Е. Г. Зибзеев» (ALTB, NS); «Монгольский Алтай, хребты в окр. оз. Дават Нуур. Склон ВСВ экспозиции, крутизна 20°. Разнотравно-овсяни- цевая степь, 2946 м над ур. м., 46.46538° с. ш. 92.13096° в. д. Z17–035. 18 VII 2017. Е. Г. Зибзе- Potentilla jenissejensis Polozhij et W. Smirnova: Монгольско-Алтайский (Mongolian Altai) – «Го- би-Алтайский аймак, хр. Монгольский Алтай, верхнее течение р. Могоийн-Гол, 2286 м над ур. м., 45°50ʹ42ʺ с. ш. 93°46ʹ44ʺ в. д. 8 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Bayan- Ulgij distr., Mongolian Altai, 25 km S Bayan-Ulgij, 48°83ʹN, 89°57ʹE, cryophytic steppe and meadow spots near the pass. 10 VI 2004. S. A. Dyachenko, P. A. Kosachev» (ALTB); «Hovd aimak, Mongo- lian Altai Mts., 40 km on southwest from settlement Manchan, stony slopes of mountains. 28 V 2011. P. Kosachev, A. Schalimov» (ALTB); «Баян-Улэ- гэйский аймак, сев.-зап. склон г. Баян-Дзурх- Ула, лиственничник и степной склон, 48°41ʹ с. ш. 88°45ʹ в. д. ШАМ 284. 27 VII 2001. Р. В. Каме- лин, А. И. Шмаков, В. И. Дорофеев, М. Г. Куцев, Н. А. Усик, С. А. Дьяченко, Д. А. Герман, И. Н. Чубаров, С. А. Костюков, П. А. Косачев» (ALTB); Котловина Больших Озер (Depression of Great Lakes) – «Северная Монголия. Убсунурская кот- ловина. Полынно-ковыльная каменистая степь, 50°40ʹ с. ш. 92°35ʹ в. д. 14 VIII 1995. Н. Артемов» (NS). – Примечание см. выше. P. Kosachev, A. Schalimov» (ALTB); «Khobdo dis- tr., Mongolian Altai, Baga-Ulan-Daba pass (2845 m a. s. l.), kryoxerophytic communities with dominance of Smelowskia alba, 46°42ʹN, 92°18ʹE. 13 VI 2004. S. A. Dyachenko, P. A. Новые местонахождения редких и эндемичных видов в отдельных ботанико- географических районах Монголии Вид был описан без данных по морфоло- гии лепестков в связи с их отсутствием у типо- вого материала (Soják, 1986). Здесь мы впервые сообщаем об их характеристике: лепестки 6–7 мм длиной и 5–6 мм шириной, в 1,5 раза пре- вышающие чашечку, широко обратносердцевид- ные с хорошо заметной выемкой на верхушке, светло-желтые. Образцы P. inopinata из ALTB (МШК 212) и FR, цитируемые выше, собраны на границе районов Монгольско-Алтайского и Котловины Больших Озер, поэтому нахождение данного вида на территории последнего вполне ожидаемо. Potentilla gracillima Kamelin: Монгольско- Алтайский (Mongolian Altai) – «Гоби-Алтай- ский аймак, хр. Хасагт-Хайрхан, южнее пос. Сумийнден, 2594 м над ур. м., 46°59ʹ19ʺ с. ш. 95°48ʹ32ʺ в. д. 19 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Гоби-Алтайский аймак, Монгольский аймак, перевал Тамчи-Даба. В 60 км южнее пос. Тонхил, на склонах, 2851 м над. ур. м. 24 VII 1978. И. А. Губанов» (MW0181874); Хангайский (Khangai) – «[Архангай аймак] Mon- golia borealis. На одном из утесов, окаймляю- щих долину правого берега р. Тэрхи. 12 VI 1896. E. Klementz» (LE); «[Архангай аймак] Mongolia borealis. В долине р. Тэрхи, верст 5–6 выше устья 117 Turczaninowia 25, 1: 105–123 (2022) А. А. Скачко» (ALTB); Монгольско-Алтайский (Mongolian Altai) – «Гоби-Алтайский аймак, хр. Хасагт-Хайрхан, южнее пос. Сумийнден, 2594 м над ур. м., 46°59ʹ19ʺ с. ш. 95°48ʹ32ʺ в. д. 19 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Гоби-Алтайский аймак, хр. Хара-Адзрагын-Ну- ру, верховья р. Гурван-Улиасын-Гол, 2849 м над ур. м., 45°49ʹ58ʺ с. ш. 95°35ʹ14ʺ в. д. 14 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB); «Баян- Улэгэйский аймак, хр. Тэшир-Хэрбэйн-Нуру, перевал Ачагардаг-Даба, 48°58ʹ с. ш. 89°22ʹ в. д. ШАМ 1343. 1 VIII 2001. Р. В. Камелин, А. И. Шмаков, В. И. Дорофеев, М. Г. Куцев, С. А. Ко- стюков, П. А. Косачев, С. А. Дьяченко, Д. А. Гер- ман, И. Н. Чубаров, А. А. Скачко» (ALTB); «Go- bi-Altai aimak, Adzh-Bogdo Mts. (NE slope), valley of the river Dzagolyn-gol, near Khalba-Khairkhan Mt., 1700–3000 m, 45°03ʹN, 94°59ʹE. 4 VI 2011. P. Kosachev, A. Schalimov» (ALTB); «Khobdo dis- tr., Mongolian Altai, Baga-Ulan-Daba pass (2845 m a. s. l.), kryoxerophytic communities with dominance of Smelowskia alba, 46°42ʹN, 92°18ʹE. 13 VI 2004. S. A. Dyachenko, P. A. Kosachev» (ALTB); «Ховд сомон, 70–75 км южнее с. Манхан, окр. Давст- Нур, каменистая седловина между вершинами, 3028 м над ур. м., 46.78652° с. ш. 92.444483° в. д. Оп. 17–55. 19 VII 2017. Е. А. Басаргин» (ALTB, NS); «Ховд сомон, окр. Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Розеточные листья P. stepposa снизу серо-белые или беловатые, с густым опушением, где между жилками преоб- ладают короткие волоски, сегменты листочков обычно тупые, лепестки примерно 5 мм длиной. У P. serrata розеточные листья снизу серо-зеле- ные или серые, с редким опушением и преоб- ладанием между жилками длинных волосков, сегменты листочков часто довольно острые, ле- пестки обычно 6–7 мм длиной. Оба таксона от- личаются от P. sericea железистыми чашелисти- ками. Сбор СМЭ 208 из долины р. Мурэн – это первая находка P. serrata Хубсугульском аймаке в пределах Хангайского ботанико-географиче- ского района. км выше сомона Бурэн-Тогтох, пойма, 1380 м над ур. м., 49°34ʹ06ʺ с. ш. 99°24ʹ08ʺ в. д. СМЭ 208. 25 VI 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB); «Восточ- ный Хангай, 15–20 км на юго-восток от пос. Тэв- шрулэг Архангайского аймака. В степи. № 1759. 31 VII 1980. И. А. Губанов» (MW). – Субэнде- мик Монголии, описанный из Хангая по сборам из двух пунктов: окр. Арвайхээра и Улзийта. Первый относится к Уверхангайскому аймаку, второй – к Архангайскому. По данным Сояка, P. serrata – это гибридный вид, возникший от скрещивания P. sericea и P. tanacetifolia (Soják, 1994). Наиболее близким к нему по габитусу является P. stepposa, также гибридного проис- хождения с участием P. sericea, но с совершенно другим вторым родительскими видом (примеча- ние к P. stepposa см. выше). Розеточные листья P. stepposa снизу серо-белые или беловатые, с густым опушением, где между жилками преоб- ладают короткие волоски, сегменты листочков обычно тупые, лепестки примерно 5 мм длиной. У P. serrata розеточные листья снизу серо-зеле- ные или серые, с редким опушением и преоб- ладанием между жилками длинных волосков, сегменты листочков часто довольно острые, ле- пестки обычно 6–7 мм длиной. Оба таксона от- личаются от P. sericea железистыми чашелисти- ками. Сбор СМЭ 208 из долины р. Мурэн – это первая находка P. serrata Хубсугульском аймаке в пределах Хангайского ботанико-географиче- ского района. Potentilla soongorica Bunge: Джунгарская Гоби (Dzungarian Gobi) – «Кобдосский аймак, Монгольский Алтай, ср. теч. р. Баян-гол, дол. правого притока Улястыйн-Сала, хр. Аршан- тын-Нуру, сев. макросклон г. Могойн-Улан-Ула, остепненные луга, 2000 м над ур. м., 46°23ʹ с. ш. 91°14ʹ в. д. 21 VI 2004. S. A. Dyachenko, P. A. Kosachev» (ALTB); «Ховдский аймак, хр. Ар- шантын-Нуру, р. Баян-гол, приток р. Булган-гол, 1900 м над ур. м., 46°21ʹ с. ш. 91°08ʹ в. д. 9–10 VI 2011. P. Kosachev, A. Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Potentilla rigidula Th. Wolf: Монгольско- Алтайский (Mongolian Altai) – «Кобдосский аймак, Монгольский Алтай, хр. Батар-Хайр- хан, дол. р. Мэрэнгийн-Амны-Гол близ выхода из гор, 1750–2300 м над ур. м., 47°00ʹ23ʺ с. ш. 92°49ʹ58ʺ в. д. МШК 168. 3 VIII 2017. А. И. Шма- ков, А. А. Кечайкин, Т. А. Синицына, А. А. Бат- кин» (ALTB, FR-0129919 [https://www.gbif.org/ occurrence/3046149471]); Котловина Больших Озер (Depression of Great Lakes) – «Убсунурский аймак, левобережье р. Намирын-Гол (сев.-зап. оз. Хара-Ус-Нур), 1660 м над ур. м., 49°13ʹ28ʺ с. ш. 91°39ʹ28ʺ в. д. 20 VI 2007. СМЭ 27. Р. В. Ка- мелин, А. И. Шмаков, Ш. Дариймаа, А. В. Вага- нов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB). – Субэндемик Монголии, описанный по единственному экземпляру, собранному с Алтая. Распространен от Чуйской степи в Республике Алтай до восточной части аймака Ховд. Впер- вые для Монголии конкретное местонахождение P. rigidula приводит И. А. Губанов, основываясь на сбор Г. Н. Огуреевой из верховий р. Хархира (хранится в MW), что соответствует Хобдосско- му ботанико-географическому р-ну (Gubanov, 1996). Данный гербарный образец нам удалось исследовать, и соответствует он P. pamirica. Согласно этому, мы впервые приводим здесь P. rigidula для аймака Увс. Информация о нахож- дении P. rigidula в Монгольско-Алтайском р-не (Kechaykin, 2013; Kechaykin et al., 2014b; Gun- degmaa, Urgamal, 2016) оказалась неучтенной в работе Baasanmunkh et al. (2022b). Подробные данные об изучении этого вида на Алтае опубли- кованы в другой работе (Kechaykin, 2013). Сбор МШК 168, цитируемый выше, является на дан- ный момент самым южным в ареале P. rigidula. км выше сомона Бурэн-Тогтох, пойма, 1380 м над ур. м., 49°34ʹ06ʺ с. ш. 99°24ʹ08ʺ в. д. СМЭ 208. 25 VI 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ваганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофеев» (ALTB); «Восточ- ный Хангай, 15–20 км на юго-восток от пос. Тэв- шрулэг Архангайского аймака. В степи. № 1759. 31 VII 1980. И. А. Губанов» (MW). – Субэнде- мик Монголии, описанный из Хангая по сборам из двух пунктов: окр. Арвайхээра и Улзийта. Первый относится к Уверхангайскому аймаку, второй – к Архангайскому. По данным Сояка, P. serrata – это гибридный вид, возникший от скрещивания P. sericea и P. tanacetifolia (Soják, 1994). Наиболее близким к нему по габитусу является P. stepposa, также гибридного проис- хождения с участием P. sericea, но с совершенно другим вторым родительскими видом (примеча- ние к P. stepposa см. выше). Новые местонахождения редких и эндемичных видов в отдельных ботанико- географических районах Монголии Kosachev» (ALTB); «Ховд сомон, 70–75 км южнее с. Манхан, окр. Давст- Нур, каменистая седловина между вершинами, 3028 м над ур. м., 46.78652° с. ш. 92.444483° в. д. Potentilla laevipes Soják: Монгольско-Алтай- ский (Mongolian Altai) – «Ховд сомон, 70–75 км южнее с. Манхан, окр. Давст-Нур, днище доли- ны, засоленные луга, 2500 м над ур. м., 46.749° с. ш. 92.265° в. д. Оп. 17–310. 19 VII 2017. А. Королюк, Е. Королюк» (ALTB, NS). – Энде- мик центральной части Монгольского Алтая, описан из верховий р. Уенч. Своеобразный вид, не имеющий аналогов среди лапчаток Монголии и сопредельных территорий. Все известные ра- нее местонахождения и некоторые морфологи- ческие отличия P. laevipes приведены в работе А. А. Кечайкина (Kechaykin, 2015b). 18 VII 2017. Е. А. Басаргин» (ALTB, NS); «Ховд сомон, 70–75 км южнее с. Манхан, окр. Давст- Нур, привершинная часть гряды, округлые гра- нитные глыбы = 10–15, др = 50, перевыпас, 2715 м над ур. м., 46.74904° с. ш. 92.26491° в. д. Оп. Potentilla ozjorensis Peschkova: Монгольско- Алтайский (Mongolian Altai) – «Баян-Ульгий- ский аймак, 4 км северо-восточнее сомона Тол- бо, 2230 м над ур. м., 48°25ʹ36ʺ с. ш. 90°20ʹ23ʺ в. д. 1 VII 2010. А. А. Кечайкин, А. В. Галькин» (ALTB). – Примечание см. выше. Potentilla pamirica Th. Wolf: Кобдосский (Khovd) – «Баян-Улэгэйский аймак, хр. Сайлю- гем, северный макросклон г. Гурбан-Гайшин- сар-Ула, 49°24ʹ с. ш. 89°04ʹ в. д. ШАМ 2002. 5 VIII 2001. Р. В. Камелин, А. И. Шмаков, В. И. Дорофеев, М. Г. Куцев, А. Е. Бородина-Грабов- ская, Н. А. Усик, Ш. Дариймаа, С. А. Дьяченко, 118 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 soongorica не поднимается выше 2000 м над ур. м., о чем указывают данные гербарных этикеток и наши многочисленные по- левые наблюдения. От близких P. agrimonioides M. Bieb., P. jenissejensis и P. multicaulis этот вид отличается отсутствием многочисленных круп- ных железок, от P. sericea – отсутствием корот- ких щетинистых волосков на нижней поверх- ности листочков. Таким образом, маловероятно, что обильно железистые растения, собранные на Алтае и конкретно в Монголии в цветущем со- стоянии в летние месяцы на высоте более 2000 м над ур. м., окажутся P. soongorica. расположена в 35 км сев.-зап. от колодца Хетел- Ус – первого пункта сбора данного вида в этом районе (Kechaykin et al., 2014b). Другие приме- чания см. выше. расположена в 35 км сев.-зап. от колодца Хетел- Ус – первого пункта сбора данного вида в этом районе (Kechaykin et al., 2014b). Другие приме- чания см. выше. расположена в 35 км сев.-зап. от колодца Хетел- Ус – первого пункта сбора данного вида в этом районе (Kechaykin et al., 2014b). Другие приме- чания см. выше. Potentilla tytthantha (Soják) Kechaykin: Коб- досский (Khovd) – «Убсунурский аймак, массив Хархира, хр. Хархира-Ула, северный макро- склон вершины 3687,4, 2700–3000 м над ур. м., 49°35ʹ57ʺ с. ш. 91°16ʹ28ʺ в. д., МШК 54. 30 VII 2017. А. И. Шмаков, А. А. Кечайкин, Т. А. Сини- цына, А. А. Баткин» (ALTB, FR-0130788 [https:// www.gbif.org/occurrence/3046087503]); Монголь- ско-Алтайский (Mongolian Altai) – «Монголь- ский Алтай, хребет Хуйтэн-Хошуу, каменистая горная степь со скальными выходами, листвен- ничник, 2100–2700 м ур. м., 46°51ʹ с. ш. 91°10ʹ в. д. № ЕК 14. 8 VII 2015. P. Kosachev, I. Evdo- kimov» (ALTB); «Кобдосский аймак, Цэцэг со- мон, близ н. п. Цэцэг, гора Цаст-Богдо-Ула, пой- ма ручья, склоны и скалы. № 1014. 28 VII 1975. О. В. Журба» (MW0181752). – На основании ряда морфологических признаков был выде- лен в самостоятельный вид из разновидности P. chamaeleo (Kechaykin et al., 2019). Тип таксона был собран в южной части Монгольского Алтая в бассейне р. Булган и хранится в LE, кроме это- го, вид дважды отмечался на перевале Оботын- Даба (образцы МКД 649 и МШК 284 в ALTB). На данный момент ареал P. tytthantha ограничен только Западной Монголией. Woodsiaceae Herter Woodsia calcarea (Fomin) Schmakov: Хан- гайский (Khangai) – «Булганский аймак, долина р. Их-Тулбэрцйн-Гол ниже бригады Уньт, 1160 м над ур. м., 49°10ʹ02ʺ с. ш. 102°51ʹ40ʺ в. д. СМЭ 1851. 21 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дарийма, А. В. Ваганов, Р. А. Зубов, О. П. Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Schalimov» (ALTB); «Кобдосский аймак, Булган сомон, 7 км северо- западнее п. Буглан, 1250 м над ур. м., 46°07ʹ01ʺ с. ш. 91°28ʹ15ʺ в. д. 14 V 2012. А. А. Кечайкин» (ALTB); «Кобдосский аймак, хр. Аршантын-Ну- ру, 8 км на юго-восток от вершины Могойн-Улан- Ула, перевал 1598, сев. макросклон, каменистые склоны, скалы, 46°16ʹ с. ш. 91°17ʹ в. д. 12 V 2002. С. В. Смирнов, Д. А. Герман, С. А. Дьяченко, Potentilla schmakovii Kechaykin: Монголь- ско-Алтайский (Mongolian Altai) – «Кобдосский аймак, дол. р. Хонго-гол в месте выхода из гор, галечник по берегу, 48°23ʹ с. ш. 91°06ʹ в. д. 22 V 2002. С. В. Смирнов, Д. А. Герман, С. А. Дьячен- ко, П. А. Косачев» (ALTB). – Эндемик Западной Монголии, описан из центральной части Мон- гольского Алтая. Недавно был обнаружен так- же в Джунгарской Гоби на хребте Байтаг-Богдо (Baasanmunkh et al., 2021a). Новое местонахождение P. schmakovii рас- положено в 40 км к юго-востоку от ближайшего locus classicus. Potentilla serrata Soják: Хангайский (Khan- gai) – «Хубсугульский аймак, дол. р. Мурэн в 17 Turczaninowia 25, 1: 105–123 (2022) 119 П. А. Косачев» (ALTB); «Кобдосский аймак, Джунгарская Гоби, г. Увход-Ула, глинисто-щеб- нистая, местами мелкоземисто-песчанистая пу- стыня у подножья, 45°49ʹ с. ш. 91°05ʹ в. д. 17 V 2002. С. В. Смирнов, Д. А. Герман, С. А. Дьячен- ко, П. А. Косачев» (ALTB). – Туранско-джунгар- ский вид, описанный из восточной части Казах- стана и распространенный от северо-восточного Ирана до Западной Монголии. По данным Р. В. Камелина и др., указания P. soongorica для не- которых северных и центральных территорий Монголии основаны на неверных определениях; авторы также приводят, по их мнению, первый и единственный на тот момент сбор этой лапчат- ки для страны из бассейна р. Булган в низовьях Дзун-Хадз-Ула (Kamelin et al., 1985), что отно- сится к Джунгарской Гоби. С этими фактами мы полностью согласны. Р. В. Камелин очень активно работал в Средней Азии и хорошо по- нимал многие лапчатки этого региона, в част- ности, P. soongorica. Об этом свидетельствуют многочисленные образцы данного вида, точ- но определенные им в Гербариях ALTB, LE и MW. Potentilla soongorica на территории Боль- шого Алтая – это ранневесеннее растение с ос- новным периодом вегетации в мае, иногда при благоприятных условиях может зацветать уже в конце апреля. В середине лета обнаружить ее практически невозможно, т. к. к концу июля от растений остаются лишь несколько незаметных невысоких иссохших побегов с увядшей розет- кой прикорневых листьев. Стоит также отме- тить, что на Алтае P. REFERENCES / ЛИТЕРАТУРА Baasanmunkh S., Oyuntsetseg B., Tsegmed Z., Oyundelger K., Urgamal M., Gantuya B., Javzandolgor J., Nyambayar N., Kosachev P., Choi H. J. 2022a. Distribution of vascular plants in Mongolia − I Part. Mongolian Jour- nal of Biological Sciences 20, 1: 3–28. DOI: 10.22353/mjbs.2022.20.01 Baasanmunkh S., Kovtonyuk N. K., Oyuntsetseg B., Tsegmed Z., Han I. V., Choi H. J. 2020. Diversity and dis- tribution of the genus Primula L. (Primulaceae) in Mongolia. Journal of Asia-Pacific Biodiversity 13: 687–700. DOI: 10.1016/j.japb.2020.09.002i Baasanmunkh S., Oyuntsetseg B., Efimov P., Tsegmed Z., Vandandorj S., Oyundelger K., Urgamal M., Undruul A., Khaliunaa K., Namuulin T., Choi H. J. 2021a. Orchids of Mongolia: taxonomy, species richness, and conserva- tion status. Diversity 13: 302. DOI: 10.3390/d13070302 Baasanmunkh S., Oyuntsetseg B., Oyundari C., Oyundelger K., Urgamal M., Darikhand D., Soninkhishig N., Nyambayar D., Khaliunaa K., Tsegmed Z., Kechaykin A. A., Shmakov A. I., Erst A. S., Friesen N., Ritz C. M., We- sche K., Choi H. J. 2021b. The vascular plant diversity of Dzungarian Gobi in western Mongolia, with an annotated checklist. Phytotaxa 501, 1: 1–55. DOI: 10.1016/j.japb.2020.09.002 Baasanmunkh S., Oyuntsetseg B., Urgamal M., Norris J., Shiga T., Choi H. J. 2021c. Notes on the taxonomy of Nymphaeaceae and Menyanthaceae in Mongolia. Journal of Asia-Pacific Biodiversity 15: 129–137. DOI: 10.1016/j. japb.2021.09.011 Baasanmunkh S., Urgamal M., Oyuntsetseg B., Grabovskaya-Borodina A., Oyundelger K., Tsegmed Z., Gun- demgaa V., Kechaykin A. A., Pyak A. I., Zhao L. Q., Choi H. J. 2021d. Updated checklist of vascular plants endemic to Mongolia. Diversity 301: 619. DOI: 10.3390/d13120619 Baasanmunkh S., Urgamal M., Oyuntsetseg B., Sukhorukov A. P., Tsegmed Z., Son D. C., Erst A., Oyundelger Kh., Kechaykin A. A., Norris J., Kosachev P., Ma J.-Sh., Chang K. S., Choi H. J. 2022b. Flora of Mongolia: anno- tated checklist of native vascular plants. PhytoKeys 192: 63–169. DOI: 10.3897/phytokeys.192.79702 Batkin A. A., Vaganov A. V., Kechaykin A. A., Shmakov A. I. 2020. Spore morphology of some species of the genus Сystopteris Bernh. from the territory of Altai-Sayan and Trans-Ili Alatau. Problems of Botany of South Sibe- ria and Mongolia 19, 2: 102–107. [in Russian] (Баткин А. А., Ваганов А. В., Кечайкин А. А., Шмаков А. И. Морфология спор некоторых представителей рода Сystopteris Bernh. с территории Алтае-Саянского региона и Заилийского Алатау // Проблемы ботаники Южной Сибири и Монголии, 2020. Т. 19, № 2. С. 102–107). DOI: 10.14258/pbssm.2020085il Bekket U., Kechaykin A. A., Yevdokimov I. Yu., Kosachev P. Благодарности Авторы благодарят кураторов фондовых кол- лекций гербариев GAT, HAL, LE, NS и MW за оказанную помощь при исследовании монголь- ских образцов Potentilla. Отдельную благодар- ность авторы выражают д. б. н., проф. В. И. До- рофееву за помощь в поисках местоположений некоторых административных пунктов, д. б. н. Д. В. Гельтману за определение собранных нами молочаев, а также к. б. н. Д. А. Герману за лю- безно предоставленные ценные литературные данные и фотоматериалы. Woodsia heterophylla (Turcz. ex Fomin) Sch- makov: Прихубсугульский (Khuvsgul) – «Хуб- сугульский аймак, правый берег р. Ур-Гол близ устья р. Хух-Гол, 1223 м над ур. м., 50°45ʹ08ʺ с. ш. 101°30ʹ56ʺ в. д. СМЭ 1990. 15 VII 2007. Р. В. Камелин, А. И. Шмаков, Ш. Дариймаа, А. В. Ва- ганов, Р. А. Зубов, О. П. Камелина, В. И. Дорофе- ев» (ALTB). – Один из редчайших папоротников Монголии, известный на ее территории лишь из одной точки в предгорьях хр. Хорьдол-Сарьдаг. Новое местонахождение расположено примерно в 140 км к западу от этого пункта. Работа выполнена в рамках гранта РФФИ при финансовой поддержке научного проекта № 20- 04-00183_А. Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 не указано в работах Urgamal et al. (2014) и Baasanmunkh et al. (2022b). не указано в работах Urgamal et al. (2014) и Baasanmunkh et al. (2022b). Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 Ка- мелина, В. И. Дорофеев» (ALTB); Монгольско- Алтайский (Mongolian Altai) – «Баян-Улэгэйский аймак, хребет Монгольский Алтай, верховья р. Цаган-Ус, 48°57ʹ с. ш. 88°03ʹ в. д. ШАМ 1162. 30 VII 2001. Р. В. Камелин, А. И. Шмаков, В. И. Дорофеев, М. Г. Куцев, С. А. Костюков, П. А. Косачев, С. А. Дьяченко, Д. А. Герман, И. Н. Чу- баров, А. А. Скачко» (ALTB). – Редкий вид во флоре Монголии, распространенный в северной части и после некоторой дизъюнкции на западе в Монгольском Алтае в среднем течении р. Цаган- Ус, бассейне Ёлт-Гол и окр. горы Цаган-Ула (Shmakov, 2005b). О нахождении W. calcarea на территории Монгольско-Алтайского р-на Potentilla stepposa Soják: Котловина Больших Озер (Depression of Great Lakes) – «Кобдосский аймак, хр. Дзун-Джаргалант, дол. р. Ар-Шаатын- Гол, 2000–2500 м над ур. м., 49°44ʹ442ʺ с. ш. 92°26ʹ965ʺ в. д. МКД 522. 12 VII 2013. А. И. Шмаков, А. А. Кечайкин» (ALTB). – Это вторая находка P. stepposa в Котловине Больших Озер, 120 REFERENCES / ЛИТЕРАТУРА New findings of Cinquefoils (Potentilla L., Rosaceae) in the Middle Asia and south-east of West Siberia. Turczaninowia 15, 4: 48–51. [In Russian] (Кечайкин А. А. 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Findings to the flora of Russia and adjacent countries: New national and regional vascular plant records, 3. Botanica Pacifica 10, 1: 94–95. DOI: 10.17581/bp.2021.10110 122 Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 DOI: 10.1016/j.japb. 2020.06.008 Shmakov A. I. 2005a. Cystopteridaceae. In: R. V. Kamelin (Ed.). Flora Altaica. Vol. 1. Barnaul: Azbuka. Pp. 205–220. [In Russian] (Шмаков А. И. Сем. Cystopteridaceae – Пузырниковые // Флора Алтая. Под ред. Р. В. Камелина. Т. 1. Барнаул: Азбука, 2005. С. 205–220). р у у ) Shmakov A. I. 2005b. Woodsiaceae. In: R. V. Kamelin (Ed.). Flora Altaica. Vol. 1. Barnaul: Azbuka. Pp. 223–232. [In Russian] (Шмаков А. И. Woodsiaceae – Вудсиевые // Флора Алтая. Под ред. Р. В. Камелина. Т. 1. Барнаул: Азбука, 2005. С. 223–232). Smirnov S. V., Kechaykin A. A., Tenigin V. S., Shestakov I. A., Shmakov A. I. 2021. New records of vascular plants in the West Altai. Turczaninowia 24, 4: 131–139. [In Russian] (Смирнов С. В., Кечайкин А. А., Тенигин В. С., Шестаков И. А., Шмаков А. И. Новые находки сосудистых растений на Западном Алтае // Turcza- ninowia, 2021. Т. 24, № 4. С. 131–139). DOI: 10.14258/turczaninowia.24.4.13. , , ) Soják J. 1970. Potentilla mongolicae novae. Folia Geobotanica et Phytotaxonomica 5: 99–114. Soják J. 1986. Notes on Potentilla (Rosaceae) II. Some new species from Mongolia. Willdenowia 16: 12 Turczaninowia 25, 1: 105–123 (2022) 123 J. 1987. Notes on Potentilla. V. Potentilla pensylvanica group in the Old World. Preslia 59: 289–305. Soják J. 1988. Notes on Potentilla (Rosaceae). VII. Some Himalayan taxa. Candollea 43: 437–453. Sojak J. 1992. Notes on Potentilla XIII. Further new taxa from Asia. Preslia 64(3): 211–222. Soják J. 1994. Notes on Potentilla X–XII. – X. The section Dumosae. XI. The P. microphylla and P. stenophylla groups (sect. Pentaphylloides). XII. Key to the taxa of P. sect. Pentaphylloides (Anserina). Botanische Jahrbücher fur Systematik, Pflanzengeschichte und Pflanzengeographie 116(1): 11–81. Soják J. 2003. Some new taxa Potentilla (Rosaceae) from New Guinea, Asia and Canada (Notes on Potentilla XV). Willdenowia 33: 409–423.i Soják J. 2004. Potentilla L. (Rosaceae) and related genera in the former USSR (identification key, checklist and figures). Notes on Potentilla XVI. Botanische Jahrbücher fur Systematik, Pflanzengeschichte und Pflanzengeographie 125(3): 253–340. Soják J. 2007. Potentilla (Rosaceae) in China. Notes on Potentilla XIX. Harvard Papers in Botany 324. Soják J. 2012a. Copies of seven species and twenty hybrids of Potentilla (Rosaceae) obtained through experimen- tal hybridization (Notes on Potentilla XXVI). Thaiszia 22(1): 33–48. Soják J. 2012b. Potentilla L. (Rosaceae) and related genera in Asia (excluding the former USSR), Africa and New Guinea. Notes on Potentilla XXVIII. Plant Diversity and Evolution 130(1–2): 7–157. Кечайкин А. А. и др. Новые находки во флоре Монголии. Часть 2 DOI: 10.1127/1869- 6155/2012/0130-0060l Soják J., Danihelka J., Haek M. 2011. Potentilla turkestanica, a rare species new to the flora of Ru ninowia 14, 1: 101–105.f Thiers B. M. [2022]. Index Herbariorum: A global directory of public herbaria and associated staff. Bronx, New York, USA: New York Botanical Garden's Virtual Herbarium, New York Botanical Garden. URL: http://sweetgum. nybg.org/science/ih/ (Accessed 10 January 2022).l Troshkina V. I. 2021. Taxonomic revision of the family Geraniaceae in the flora of Mongolia. Turczaninowia 24, 1: 9–20. [In Russian] (Трошкина В. И. Таксономическая ревизия семейства Geraniaceae во флоре Монголии // Turczaninowia, 2021. Т. 24, № 1. С. 9–20). DOI: 10.14258/turczaninowia.24.1.2i Tzvelev N. N., Probatova N. S. 2019. Grasses of Russia. Moscow: KMK Scientific Press Ltd. 646 pp. [In Russian] (Цвелëв Н. Н., Пробатова Н. С. Злаки России. М.: Тов-во науч. изд. КМК, 2019. 646 с.). Ulko D. O., Gureeva I. I., Shmakov A. I., Romanets R. S. 2017. Spore morphology of subgenus Cystopteris spe- cies (Cystopteris Bernh., Cystopteridaceae). Turczaninowia 20, 2: 5–15. [In Russian] (Улько Д. О., Гуреева И. И., Шмаков А. И., Романец Р. С. Морфология спор видов подрода Cystopteris (Cystopteris Bernh., Cystopterida- ceae) // Turczaninowia, 2017. Т. 20, № 2. С. 5–15). DOI: 10.14258/turczaninowia.20.2.1 Urgamal M., Oyuntsetseg B., Nyambayar D., Dulamsuren C. 2014. Conspectus of the Vascular Pl golia. Ulaanbaatar: Admon. 334 pp.
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https://zenodo.org/record/6465683/files/ACA_article_84506.pdf
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A new endemic dormouse species in Anatolia
ARPHA Conference Abstracts
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A new endemic dormouse species in Anatolia Ortaç Çetintaş , Sercan Irmak , Ferhat Matur , Mustafa Sözen ‡ § | ‡ ‡ Zonguldak Bülent Ecevit University, Zonguldak, Turkey § Balıkesir University, Balıkesir, Turkey | Dokuz Eylül University, İzmir, Turkey Corresponding author: Ortaç Çetintaş (ortaccetintas@gmail.com) Received: 28 Mar 2022 | Published: 15 Apr 2022 Citation: Çetintaş O, Irmak S, Matur F, Sözen M (2022) A new endemic dormouse species in Anatolia. ARPHA Conference Abstracts 5: e84506. https://doi.org/10.3897/aca.5.e84506 Received: 28 Mar 2022 | Published: 15 Apr 2022 Citation: Çetintaş O, Irmak S, Matur F, Sözen M (2022) A new endemic dormouse species in Anatolia. ARPHA Conference Abstracts 5: e84506. https://doi.org/10.3897/aca.5.e84506 © Çetintaş O et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ARPHA Conference Abstracts 5: e84506 doi: 10.3897/aca.5.e84506 Conference Abstract A new endemic dormouse species in Anatolia Ortaç Çetintaş , Sercan Irmak , Ferhat Matur , Mustafa Sözen ‡ Zonguldak Bülent Ecevit University, Zonguldak, Turkey § Balıkesir University, Balıkesir, Turkey | Dokuz Eylül University, İzmir, Turkey Corresponding author: Ortaç Çetintaş (ortaccetintas@gmail.com) Received: 28 Mar 2022 | Published: 15 Apr 2022 Citation: Çetintaş O, Irmak S, Matur F, Sözen M (2022) A new endemic dormouse species in Anatolia. ARPHA Conference Abstracts 5: e84506. https://doi.org/10.3897/aca.5.e84506 ‡ § | ‡ ARPHA Conference Abstracts 5: e84506 doi: 10.3897/aca.5.e84506 Conference Abstract A new endemic dormouse species in Anatolia Ortaç Çetintaş , Sercan Irmak , Ferhat Matur , Mustafa Sözen ‡ Zonguldak Bülent Ecevit University, Zonguldak, Turkey § Balıkesir University, Balıkesir, Turkey | Dokuz Eylül University, İzmir, Turkey Corresponding author: Ortaç Çetintaş (ortaccetintas@gmail.com) Received: 28 Mar 2022 | Published: 15 Apr 2022 Citation: Çetintaş O, Irmak S, Matur F, Sözen M (2022) A new endemic dormouse species in Anatolia. ARPHA Conference Abstracts 5: e84506. https://doi.org/10.3897/aca.5.e84506 ‡ § | ‡ ARPHA Conference Abstracts 5: e84506 doi: 10.3897/aca.5.e84506 Conference Abstract Conference Abstract Keywords Phylogeography, endemic mammals, molecular ecology, Alpine species, evolutionary history Presenting author Ortaç Çetintaş Ortaç Çetintaş Çetintaş O et al Çetintaş O et al Çetintaş O et al 2 Abstract Molecular studies provide very useful information on predicting the evolutionary history of species, species ecology and for describing new species. Dryomys laniger is an alpine species that is endemic to Anatolia, inhabiting high rocky areas. Its known distribution consists of fragmented and isolated populations. In order to determine the evolutionary history of the species, a phylogenetic tree was created with one mtDNA and two nuDNA. Thirty-one samples were collected from 6 populations of Dryomys laniger distributed in Anatolia. Among these 6 populations, Subaşı plateau (Antalya) and Çiçekliboyun plateau (Niğde) populations are new distribution records for the species. According to the result of this study the genetic distance between Eastern lineage and Western lineage is 7%. Beside this genetic distance, two clades are morphologically significantly different from each other. Based on the differences, the Eastern lineage was defined as a new Dryomis species. The two lineages appear in the evolutionary tree as two monophyletic lineages and no common haplotype is shared between these lineages. According to the data available in the literature, and provided in this study, the westernmost distribution limit of Dryomys laniger is around the Subaşı plateau (Antalya), and the easternmost distribution limit is probably the Saimbeyli-Tufanbeyli line. The distribution area of the new Dryomys species is Tahtalı Mountains on the Adana-Kahramanmaraş border in the west, and the Erzurum region in the east. This study strongly suggests the importance of Anatolian high mountain ecosystems in terms of biodiversity, their potential to host new species, and the need for careful conservation. Presented at Oral presentation at the 11 International Dormice Conference (May 9-13, 2022) th
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https://www.bio-conferences.org/articles/bioconf/pdf/2020/02/bioconf_vizr2020_00009.pdf
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Insect parasites in multicomponent systems and development of new bioinsecticides
Bio web of conferences/BIO web of conferences
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* Corresponding author: skif@eco.nsc.ru Viktor Glupov 1,*, Vyacheslav Martemyanov1, and Vadim Kryukov1 1Institute of Systematics and Ecology of Animals SB RAS, 630091 Novosibirsk, Russia Abstract. Stable and dynamic interactions among plants, herbivorous insects, parasites and associated microbes are formed in natural habitats. The study of these interactions in multicomponent models is required to develop integrated methods for the management of insect pest populations. In this work, we summarize our studies on the influence of different factors, such as hygrothermal conditions, host development, host microbiota, plant quality, and concomitant infections, on interactions between insects and their parasites, such as fungi, bacteria, viruses and parasitoids. Some approaches for developing complex products for biocontrol are also discussed. For example, the use of natural compounds with immunosuppressive effects may enhance the efficacy of microbial agents toward pest insects. © The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (http://creativecommons.org/licenses/by/4.0/). BIO Web of Conferences 18, 00009 (2020) IV All-Russian Plant Protection Congress BIO Web of Conferences 18, 00009 (2020) IV All-Russian Plant Protection Congress https://doi.org/10.1051/bioconf/20201800009 1 Introduction In natural ecosystems and agroecosystems, insects and their parasites are exposed to a broad range of factors, such as temperature, solar radiation, plant and microbial metabolites, as well as insecticides. Complicated interrelations in the host-parasite systems are therefore established. These systems exhibit intriguing models for ecological and immunological studies. The ecological properties and virulence of microorganisms are dependent on the species and strain. It is quite natural that these particular features should be considered for strains of bioinsecticide products [1]. Plants and insects have been coexisting for more than 400 million years; therefore, they form stable dynamic systems in which endosymbionts and parasites also participate [2-3]. Among the parasites involved in this system, we can find species of various taxonomic groups ranging from viruses, bacteria and fungi to protists and invertebrates (e.g., nematodes and parasitic insects). These organisms can form associations with both plants and insects, causing changes in various parts of the systems [4-5]. Moreover, in these systems, the role of certain components can change; for example, entomopathogenic microorganisms entering into association with plants will enhance plant growth and resistance to diseases. Therefore, to create new bioinsecticides and approaches for their use, it is necessary to study the multicomponent systems as a whole. However, we need to know the properties of certain components, that is, plants, insects and microorganisms, including how they can change under the influence of certain conditions. https://doi.org/10.1051/bioconf/20201800009 BIO Web of Conferences 18, 00009 (2020) IV All-Russian Plant Protection Congress IV All-Russian Plant Protection Congress 2 Pathogen virulence and ecological fitness It is well known that strains of one species or cryptic species of one genus may significantly differ in virulence, which is mediated by environmental adaptations. For example, cryptic species of the fungus Metarhizium have different hygrothermal preferences and may be associated with different habitats [6]. We have shown that the virulence of the cryptic species M. brunneum and M. robersii toward Colorado potato beetle (CPB) was mediated by hygrothermal conditions [7]. M. robersii was active against the CPB under both humid and arid regimes, although M. brunneum was less virulent under arid conditions than under humid conditions. Therefore, using M. robertsii will be more effective against CPB larvae in open ground under continental climate conditions. Similar effects were shown for natural isolates of Beauveria bassiana s.l. In particular, steppe isolates were more thermotolerant and most virulent toward wax moth and CPB under arid regimes as compared to forest and forest- tundra isolates [8]. Population differences of viral entomopathogens in terms of virulence are partially determined by their genetic differences. In particular, the strains of Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV, Baculoviridae) isolated in North America possess higher virulence than the Asian strain because of vef-1 gene deletion [9-10]. However, the phenotypic expression of these genetic differences does not depend on the host population [10]; conversely, it is ruled by the environmental conditions. In particular, sunlight easily decreases the potency of the American strain by UV even after 15 min of exposure, while the Asian strain possesses higher UV tolerance [11]. These features of highly potent strains should be considered for the producers of bioformulations for pest control. 4 Interactions between parasites and host microbial communities Insect symbiotic bacteria may inhibit or promote the development of parasitoids and pathogenic microorganisms [17-18]. Recent studies have shown intriguing interactions between gut microbiota of the host and its fungal pathogens [18]. In particular, the penetration of the fungus through integuments may lead to an increase in the gut bacterial load that promotes fungal infection [19]. Inhibition of gut bacteria with antibiotics enhances insect survival after topical application of fungi [20]; however, the opposite effect is usually observed after oral administration of the fungi [e.g., 21]. We showed that the envenomation of wax moth larvae by the parasitoid Habrobracon hebetor as well as a combination of envenomation and B. bassiana infection led to a shift in the balance among Enterococcus, Enterobacter and Serratia in the wax moth midgut [22]. Envenomation causes uncontrolled proliferation of gut bacteria; however, the strong activation of antimicrobial peptides in the midgut was observed. We suggest that the activation of wax moth gut immunity prevents the bacterial decomposition of envenomated larvae, thus permitting the development of parasitoids and fungi. Moreover, the oral administration of predominant bacteria (Enterococcus, Enterobacter and Serratia) to the wax moth larvae synergistically increased susceptibility to the fungi [22]. Thus, the changes in the midgut bacterial community may promote death of larvae induced by the fungi. Interestingly, the combined treatment of the larvae with the aforementioned symbiotic bacteria and Bacillus thuringiensis led to antagonistic effects on mortality (O. Polenogova, unpublished). In other experiments, we demonstrated that the diversity of bacteria in the L. dispar midgut was decreased by the consumption of low-quality leaves and was associated with a decrease in the susceptibility of the insects to the entomopathogenic bacterium B. thuringiensis [23]. 3 Physiological state of hosts The immuno-physiological state of insect hosts plays a crucial role in the development of pathogenesis. Host populations and ontogenetic stages differ significantly in their susceptibility to infections. For example, wax moths demonstrate different immune responses to fungal infection under an active state and under a facultative diapause [12]. Larval diapause induced by decreasing temperature was most favorable for the development of the fungus Cordyceps militaris due to a decrease in phenoloxidase activity and encapsulation rate. Additionally, while fought off in the active state of the host, the infection could still be activated in the diapause state. Interestingly, viral pathogenesis does not depend on the phenoloxidase activity that was shown on L. dispar larvae using several lines of evidence [13]. The larvae of CPB demonstrated strong differences in susceptibility to the fungus Metarhizium during the intermolt period of the last instar due to the changes in integument thickness and epicuticular hydrocarbon contents (which determine the level of conidial adhesion) as well as changes in cellular immunity [14]. The solitaria phase of migratory locust was more resistant to fungi (Metarhizium and Beauveria) than to gregaria [15]. In experiments with another pest species (L. dispar), we did not demonstrate the effect of gregariously reared larvae on susceptibility to an entomopathogenic virus as compared to the larvae reared solitarily [16]. 2 2 BIO Web of Conferences 18, 00009 (2020) IV All-Russian Plant Protection Congress https://doi.org/10.1051/bioconf/20201800009 ( ) IV All-Russian Plant Protection Congress 5 Interactions among insects, parasites and plants The host plant-mediated modification of an insect’s innate immunity status is one of the mechanisms determining the outcome of insect-pathogen interactions [23]. 6 Multicomponent approaches in biological control The study of interactions in multicomponent systems allows the development of new products for biocontrol. For example, the use of natural compounds with immunosuppressive effects may enhance the efficacy of microbial agents toward insect pests. We studied the effects of different microbial and plant metabolites (e.g., Streptomyces toxins, usnic acid derivatives, and Cordyceps extracts) as well as mixed infections on the defense systems and development of pathogeneses in different insects such as wax moth, CPB and four-eyed fir bark beetle Polygraphus proximus, and mosquito Aedes aegypti [35-40]. The synergy between pathogenic fungi (Metarhizium, Beauveria) and bacteria (B. thuringiensis) or between these fungi and the aforementioned metabolites was shown. We found that the synergy is caused by changes in cellular and humoral immunity responses, gut microbiota, morphological and biochemical properties of integuments that stipulate fungal adhesion, penetration and colonization. We also suggest that the disturbance in larval development caused by these metabolites and bacteria has a great impact on immunity, integument properties and susceptibility to fungi [14]. The investigated combinations provide a stable synergy in laboratory and field experiments. These combinations may be promising for the development of efficient products to manage pest insects. The study was supported by the Russian Science Foundation (project № 19-14-00138). 5 Interactions among insects, parasites and plants It is known that the host plant quality may affect both the primary and the higher level (secondary) consumers [24-25]. However, the expression of this effect strongly depends on many factors, including the species involved and the weather conditions. For example, defoliation of oak Quercus rubra by L. dispar may induce an increase in the phenolic concentration in leaves that will inhibit both the life history traits of herbivores and their susceptibility to LdMNPV [26]. Alternatively, when the host plant is silver birch Betula pendula, the induction of phenolics (and possibly another phytochemicals) synthesis leads to a negative effect on herbivores [27-29] but has no effect on the interaction between L. dispar and LdMNPV [28] or the entomopathogenic bacteria Bacillus thuringiensis [30]. One chemical defense mechanism triggered by defoliation, which was shown for B. pendula, is the trade-off between glycosides and aglycons of flavonoids [27]. Synthesis of monoterpens is also induced by tree defoliation, especially at the moment of defoliation, which may be the chemical signal attracting parasitoids to the location of defoliators [27, 31]. The interactions between host plants, herbivores and pathogens/parasites significantly depend on the weather conditions, which may i) directly modify the traits of each participant of the food chain and ii) indirectly synchronize or desynchronize the phenological development of plants and herbivores, which is related to the dynamics of plant phytochemistry during a season. The effect of weather-induced asynchrony between the phenological development of plants and insects on insect survival via the dynamics of plant chemicals was demonstrated approximately 50 years ago [32] and provided the start of a new direction in ecology, i.e., chemical ecology. However, we recently showed that a mismatch in synchrony may spread further though the food chain, effecting the interaction between insects and entomopathogens [23, 33-34]. Moreover, this effect will depend on the type of pathogen involved in this interaction. For example, viruses have the advantage when insects appear asynchronously 3 3 BIO Web of Conferences 18, 00009 (2020) IV All-Russian Plant Protection Congress https://doi.org/10.1051/bioconf/20201800009 (because of cold weather) with the host plants [33], while this is disadvantageous for bacteria [33]. The host plant-mediated modification of an insect’s innate immunity status is one of the mechanisms determining the outcome of insect-pathogen interactions [23]. (because of cold weather) with the host plants [33], while this is disadvantageous for bacteria [33]. References 1. L.A. Lacey, D. Grzywacz, D.I. Shapiro-Ilan, R. Frutos, M. Brownbridge, M.S. Goettel, J. Invertebr. Pathol. 132, 1-41 (2015) http://doi/org/10.1016/j.jip.2015.07.009 ( ) p g j j p 2. A. Sugio, G. Dubreuil, D. Giron, J.-C. Simon. J. Experimen. Bot. 66, 467–478 (2015) http://doi/org/10.1093/jxb/eru435 3. J. Lazebnik, E. Frago, M. Dicke, J.J.A. van Loon. J. Chem. 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Zhang, S. Zhang, J. Lu, Y.M. Xia, Y.H. Huang, X.J Wang, Pest Manag. Sci. 74, 438-447 (2018) http://doi/org/10.1002/ps.4726 22. O.V. Polenogova, M.R. Kabilov, M.V. Tyurin, U.N. Rotskaya, A.V. Krivopalov, V.V. Morozova, K. Mozhaitseva, N.A. Kryukova, T. Alikina, V.Yu. Kryukov, V.V. Glupov, Sci. Rep. 9, 4012 (2019) http://doi/org/10.1038/s41598-019-40301-6 p ( ) p g 23. V.V. Martemyanov, I.A. Belousova, S.V. Pavlushin, I.M. Dubovskiy, N.I. Ershov, T.Y. Alikina, M.R. Kabilov, V.V. Glupov, Ecol. Evol. 6, 7298-7310 (2016) http://doi/org/10.1002/ece3.2460 24. J.S. Cory, K. Hoover, Trends Ecol. Evol. 21, 278–286 (20 http://doi/org/10.1016/j.tree.2006.02.005 25. T.C.J. Turlings, M. Erb, Annu. Rev. Entomol. 63, 433-452 (2018) http://doi/org/10.1146/annurev-ento-020117-043507 26. M.D. Hunter, J.C. Schultz, Oecologia. 94, 195–203 (1993) http://doi/org/10.1007/BF00341317 27. V.V. Martemyanov, I.M. Dubovskiy, I.A. Belousova, S.V. Pavlushin, D.V. Domrachev, M.J. Rantala, J-P, Salminen, S.A. Bakhvalov, V.V. Glupov, Arthropod-Plant Interact. 6, 507–518 (2012). http://doi/org/10.1007/s11829-012-9202-7 28. V.V. Martemyanov, I.M. Dubovskiy, M.J. Rantala, J.P. Salminen, I.A. Belousova, S.V. Pavlushin, S.A. Bakhvalov, V.V. Glupov, J. Chem. Ecol. 38, 295–305 (2012) http://doi/org/10.1007/s10886-012-0090-1 29. V.V. Martemyanov, S.V. Pavlushin, I.M. Dubovskiy, I.A. Belousova, Y.V. Yushkova, S.V. Morosov, E.I. Chernyak, V.V. Glupov, PLoS One. 10, e0121917 (2015) http://doi/org/10.1371/journal.pone.0121917 30. I.A. Belousova, V.V. Martemyanov, V.V. Glupov, Russ. J. Ecol. 48, 116-121 (2017) http://doi/org/10.1134/S1067413617020047 5 5 https://doi.org/10.1051/bioconf/20201800009 BIO Web of Conferences 18, 00009 (2020) IV All-Russian Plant Protection Congress 31. V.V. Martemyanov, D.V. Domrachev, S.V. Pavlushin, I.A. Belousova, S.A. Bakhvalov, A.V. Tkachev, V.V. Glupov, Dokl. Biol. Sci. 435, 407–410 (2010) http://doi/org/10.1134/S0012496610060104 32. P.P. Feeny, Ecology 51, 565–581 (1970) 33. V.V. Martemyanov, S.V. Pavlushin, I.M. Dubovskiy, Y.V. Yushkova, S.V. Morosov, E.I. Chernyak, V.M Efimov, T. Ruuhola, V.V. Glupov, PLoS One. 10, e0130988 (2015) http://doi/org/10.1371/journal.pone.0130988 34. E.I. Chernyak, Yu.V. Yushkova, S.V. Pavlushin, S.O. Nikolenko, V.V. Martemyanov, S.V. Morozov, Chem. Nat. Compd. 52, 193-198 (2016) http://doi/org/10.1007/s10600- 016-1592-9 35. O.G. Tomilova, V.Yu. Kryukov, B.A. Duisembekov, O.N. Yaroslavtseva, M.V. Tyurin, N.A. Kryukova, V. Skorokhod, I.M. Dubovskiy, V.V. Glupov, J. Invertebr. Pathol. 140. 8–15 (2016) http://doi/org/10.1016/j.jip.2016.08.008 36. O.N. Yaroslavtseva, I.M. Dubovskiy, V.P. Khodyrev, B.A. Duisembekov, V.Yu. Kryukov, V.V. Glupov, J. Insect. Physiol. 96, 14–20 (2017) http://doi/org/10.1016/j.jinsphys.2016.10.004 37. V.Yu. Kryukov, O.N. Yaroslavtseva, I.M. Dubovskiy, M.V. Tyurin, N.A. Kryukova, V.V. Glupov, Biol. Bull. 41, 276–283 (2014) http://doi/org/10.1134/S1062359014020046 38. V.Yu. Krukov, O.G. Tomilova, O.A. Luzina, O.N. Yaroslavtseva, Yu.B. Akhanaev, M.V. Tyurin, B.A. Duisembekov, N.F. Salakhutdinov, V.V. Glupov, Pest Manag. Sci. References 74, 598- 606 (2018) DOI:10.1002/ps.4741 39. I.A. Kerchev, N.A. Kryukova, V.Yu. Kryukov, V.V. Glupov, ISJ 14, 324-329 (20 40. Y.A. Noskov, O.V. Polenogova, O.N. Yaroslavtseva, O.E. Belevich, Y.A. Yurchenko, E.A. Chertkova, N.A. Kryukova, V.Yu Kryukov, V.V. Glupov, PeerJ 7, e7931 (2019) DOI. 10.7717/peerj.7931 6 6
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Kragvelde binne die wêreld van F. M. Dostojewski
Tydskrif vir letterkunde
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Dolf van Niekerk Dolf van Niekerk (geb. 1929) is ’n veelbekroonde skrywer van onder meer Gannavlei (1958), Skepsels (1962), Die son struikel (1960) en jeugverhale soos Die haasvanger (1985). Kragvelde binne die wêreld van F. M. Dostojewski Deur watter stiltes moes hy gaan van daadlose vernedering, tot hierdie vreemde diep bestaan: dat só sy deemoed hom omring – ’n wit kelk van geborgenheid waarin hy lê, van alle drang en trots vervreemd en wil tot stryd –, dat só in hom die stroom en dwang van mens-wees tot die yswit stand van roerlose waatre kon verloop. Geen smaadwoord beef tot deur die wand waaragter hy skuil teen die Hoop en al haar laatre bitterheid; want alles het gegroei in hom tot dié geduld-in-lydsaamheid waaraan die goue vreugde blom. “Dostojewski” Uit: N.P. van Wyk Louw, Die halwe kring (1947) “Dostojewski” – uit Die halwe kring, my eerste digbundel wat ek as student met drie maande se sakgeld gekoop het – skep ’n beeld van ’n onbekende gees wat later in my jongmensbestaan sou ingryp, en vanweë die krag daarvan, vandag nog deel van my bewussynswêreld uitmaak.1 “Dostojewski” – uit Die halwe kring, my eerste digbundel wat ek as student met drie maande se sakgeld gekoop het – skep ’n beeld van ’n onbekende gees wat later in my jongmensbestaan sou ingryp, en vanweë die krag daarvan, vandag nog deel van my bewussynswêreld uitmaak.1 My eerste kennismaking met ’n werk van F. M. Dostojewski was in meer as een opsig nogal dramaties. Dit was in die vorm van ’n radiodrama, verwerk en in Afri- kaans vertaal deur F. J. van der Merwe. Ek het pas by die SAUK as omroeper-regisseur begin werk en het elke geleentheid aangegryp om die werkinge van die radiome- dium te leer ken, ook wat regie betref. Die radiodrama ter sprake was Misdaad en straf, TYDSKRIF VIR LETTERKUNDE • 43 (2) • 2006 204 en die regie is waargeneem deur Anna Neethling-Pohl, toe reeds ’n beroemde aktris en die regie is waargeneem deur Anna Neethling-Pohl, toe reeds ’n beroemde aktrise – ’n feit wat my bra sku teenoor haar gemaak het. Tog laat sy my toe om die repetisies by te woon en stop boonop een aand ’n kopie van die teks in my hand. g g g , – ’n feit wat my bra sku teenoor haar gemaak het. Tog laat sy my toe om die repetisie by te woon en stop boonop een aand ’n kopie van die teks in my hand. Misdaad en straf het my soos ’n donderslag getref – intellektueel en geestelik. Kragvelde binne die wêreld van F. M. Dostojewski My klein wêreld van literêre ervaring is tot in sy fondamente geskud deur ’n skrywer wat, selfs in dialoogvorm, prosa maak soos ek nog nooit onder oë gehad het nie. Drie figure groei uit die teks: Machiavelli, Nietzsche en Jesus Christus. Drie geeste, drie idees: die man van absolute mag, die supermens, en die nederige man aan die kruis – al drie in ’n enkele karakter geteleskopeer. Raskolnikof verklaar dat alles toelaatbaar is, selfs moord. Daarmee konstateer hy sy absolute mag oor homself, sy medemens en die wêreld. Maar dan die pynlike oomblik van waarheid: sy daad ly nie tot die gewaande hoogtes van ’n mens-god nie, maar tot die duisternis van eensame aan- houding en berou. Hy word gedwing tot die besef dat die mens nie God is nie – die eerste stap om God te leer ken. Die mislukking van geweld gee aanleiding tot nede- righeid en selfverloëning – Dostojewski se voorwaarde vir wedergeboorte. Reeds tydens die lees van die radioteks het gedagtes oor die eksistensiële pro- bleem by my opgekom. Dit is versterk met die lees van ’n Duitse vertaling van Misdaad en straf. Daarna het ’n tydperk van Dostojewski-koors gevolg. Nagte, weke en maande lank het ek sy werk gelees en herlees, afgewissel met ’n studie van sy lewe wat nie minder aangrypend en tragies was as dié van sy groot karakters nie. Eers jare later, toe ek Dostojewski se werk in historiese perspektief kon plaas, het ek besef in watter mate karakters soos Raskolnikof in Misdaad en straf, Stavrogin, Shatof en Kirillof in Die duiwels, Mishkin in Die idioot, Ivan, Dmitri en andere in Die Karamasof-broers, die groot dilemma van Dostojewski se tyd weerspieël het: die mens wat vasgevang is tussen die argetipes van die supermens en die messiaanse mens – ’n kardinale faktor in die geestelike skeiding tussen die Ooste en die Weste. Wat konsep, opset en nood- wendigheid betref, kan Dostojewski se werk as tragedies bestempel word wat die Russiese mens voor ’n wesenlike probleem te staan bring. Sy hoofkarakters is draers van die soewereiniteit van die rede, en hulle lewens word in gebrokenheid gedom- pel deur die innerlike stryd tussen die gees van die Ooste en die nuwe gees van die Weste. Dostojewski se siening van die konflik tussen die rede en vryheid word aan- grypend weergegee in Aantekeninge uit die ondergrondse. Kragvelde binne die wêreld van F. M. Dostojewski By die lees van dié werk het ek so sterk onder die indruk van die probleem van die enkeling, die buitestaander of uithuisige figuur gekom, dat ek op grond daarvan’n magisterstudie aangepak het oor vryheid as ’n fundamenteel eksistensiële prinsipe soos aan die orde gestel in Aanteken- inge uit die ondergrondse. In daardie stadium het die eksistensiële probleem reeds neer- slag gevind in Gannavlei (1958) en Die son struikel (1960). Ek beskou Dostojewski geensins as ’n eksistensialis nie, maar ek onderskryf Kaufmann se siening: “I can see TYDSKRIF VIR LETTERKUNDE • 43 (2) • 2006 205 no reason for calling Dostojevsky an existentialist, but I do think that Part One of Notes from Underground is the best overture for existentialism ever written .” Friedrich Nietzsche, onbetwiste argitek van eksistensiële denke, erken Dostojewski se invloed, met besondere verwysing na Aantekeninge uit die ondergrondse. Die lees van Die duiwels, Die idioot en Die Karamazof-broers kan ek beskryf as ’n volgehoue proses van intellektuele en geestelike suiwering. Dostojewski se boeiende ontleding van die Russiese psige begelei as ’t ware sy beskrywing van die messiaaanse mens uit die Ooste. Raskolnikof beliggaam die ideaal van die soewereine mens; Stav- rogin en andere in Die duiwels verkondig die ideaal van die magstaat. Hierdie karak- ters is nie tot berou in staat nie, en uiteindelik wreek die gees van geweld hom op sy voorstanders. Soos reeds aangedui, was Machiavelli en Nietzsche in die gedagte teen- woordig by die lees van Misdaad en straf. In die geval van Die duiwels was dit die figuur van Karl Marx, vader van ateïstiese sosialisme en profeet van die hemel op aarde, wat opgedoem het. In historiese perspektief beskou, het Dostojewski in Die duiwels ’n blik gewerp op die tragiese verband tussen die koud-rasionele inhoud van die Westerse denke en die brandende begeerte by die messiaanse mens om te glo. In sowel Misdaad en straf as Die idioot triomfeer die messiaanse mens. As kind is ek geboei maar ook in ’n mate ontstel deur die Bergpredikasie (1933- vertaling), in die besonder die vers in Mattheüs 5: “Salig is die wat arm van gees is, want aan hulle behoort die koninkryk van die hemele.” Ware begrip vir dié woorde het jare later gekom met die lees van Die idioot. Kragvelde binne die wêreld van F. M. Dostojewski Dié verhaal het my dae lank laat loop en dink aan die geheimenisse wat in die siel en verstand opgeroep is van dié man-na- die-beeld-van-Christus wat as ’n idioot beskou is, maar wat in sy kinderlike onskuld en vertroue – miskien ook as gevolg van die epilepsie wat hom telkens na ’n hoër vlak van innerlike kontemplasie voer – die simbool van die wedergebore mens geword het. Die invloed van Mishkin op die ander karakters, insluitend ’n moordenaar en ’n histeriese courtisane, asook andere op die drumpel van waansin, het my by die eerste deurlees verstom. Deur liefde en begrip lei hy hierdie verlore siele op ’n soektog na die waarheid. Die boodskap is duidelik: nederigheid en lyding kan die mens tot herrysenis lei. Die Mishkin-tema keer in Die Karamazof-broers terug. Dié verstommende werk het ek aan die einde van die eerste Dostojewski-leeskoors ter hand geneem. Ek moes die boek ’n paar keer lees om perspektief te kry op die inslag van ’n prosawerk soos ek nog nie tot in daardie stadium gelees het nie. Ek het as ’t ware deel geword van ’n univer- sum van denke, menslike lyding, tragedie en verlossing – alles in ’n enkele bewussyns- oomblik vasgevang. Dit was inderdaad ’n roerende en openbarende ervaring. Ek be- skou Die Karamzof-broers steeds as een van die grootste prosawerke van alle tye. Ek het algaande begryp dat dié werk alles beliggaam wat Dostojewski die denker sy eie ge- maak het. Soos iemand dit gestel het: Die Karamazof- broers is die bergpiek waarvandaan die organiese eenheid van Dostojewski se hele skeppende lewe oorskou kan word. TYDSKRIF VIR LETTERKUNDE • 43 (2) • 2006 206 Die uitgawe van Die Karamazof- broers in my besit bevat as epigram die woorde van Johannes 12, vers 24: “Voorwaar, voorwaar ek sê vir julle, as die koringkorrel nie in die grond val en sterwe nie, bly dit alleen; maar as dit sterf, dra dit veel vrug.” Tydens die leesproses het dié woorde my bygebly, en hulle verwoord waarskynlik Dostojewski se nalatenskap. Al die swaar wat Dostojewski moes ly, alles wat hy geskryf het, wil ’n mens met Motsjoelski laat saamstem dat Dostojewski ’n plek verdien naas Christenskrywers soos Dante, Pascal en Milton. Hy is die profeet van die lewende mens, van vryheid, nederigheid, selfverloëning en wedergeboorte van die mensdom. g 1. Hierdie artikel is ’n verwerkte weergawe van ’n lesing wat die skrywer by geleentheid van ’n uitstalling van Suid-Afrikaanse jeugboeke in Moskou sou lewer. Die besoek aan Rusland sou studiebesoeke aan die Dostojewski-museums in Sint Petersburg en Omsk insluit. Weens skielike ongesteldheid kon die reis na Rusland nie plaasvind nie. Kragvelde binne die wêreld van F. M. Dostojewski Die meeste skrywers van die jare sestig was ernstig gemoeid met die probleem van die buitestaander (outsider), veral onder die invloed van Franse skrywers soos Sartre en Camus. In my geval was dit Nietszche en Dostojewski. In Die son struikel is God vir Diederik dood soos hy vir Nietzsche was in die magstaat van Bismarck. En Diederik se sterwe in sy soeke na God in sy versplinterde wêreld, is in wese sy wedergeboorte. Aantekeninge uit die ondergrondse het my eie beeld van die afgeslote, uithuisige mens wat oorhoops is met homself en met die wêreld, as ’t ware gevoed. Dostojewski se “man onder die vloerplanke” worstel met die rede en met vryheid, vasgevang in die rasionalisme en meganistiese denkwyses van sy tyd. In Die moeder (1965) is die naam- lose man in gevangeskap aan die worstel met die mag van die wetenskap (die atoom- bom), dekadensie en verwording wat sy verwoeste wêreld gedryf het. Dostojewski se ondergrondse wese is nie in geskiedenis of die wetenskap geïnte- resseerd nie. Hy redeneer onder meer dat wanneer geloof in die wetenskap en die suiwer rede tussen die mens en vryheid staan, isoleer dit die mens van homself. Vir hom is die menslike bestaan in wese ’n moeisame proses waarin vryheid die grond- slag vir selfverwesenliking vorm. Op die keper beskou is Aantekeninge uit die onder- grondse ’n geloofsbelydenis, terwyl in Misdaad en straf, Die idioot, Die duiwels en Die Karamazof-broers die vryheidsprinsipe tot lewe kom, telkens in ’n ander wêreld. Uitein- delik, volgens Dostojewski, regverdig die vryheid om te kies – wat dikwels ’n skrik- wekkende keuse is – nie slegs die bestaan van die mens nie, maar ook die bestaan van God. Aantekening TYDSKRIF VIR LETTERKUNDE • 43 (2) • 2006 207
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https://academicworks.cuny.edu/cgi/viewcontent.cgi?article=1211&context=hc_pubs
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Harnessing gene expression to identify the genetic basis of drug resistance
Molecular systems biology
2,009
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17,989
City University of New York (CUNY) City University of New York (CUNY) CUNY Academic Works CUNY Academic Works City University of New York (CUNY) City University of New York (CUNY) CUNY Academic Works CUNY Academic Works Hunter College Publications and Research Harnessing gene expression to identify the genetic basis of drug Harnessing gene expression to identify the genetic basis of drug resistance resistance Noel L. Goddard CUNY Hunter College How does access to this work benefit you? Let us know! More information about this work at: https://academicworks.cuny.edu/hc_pubs/191 Discover additional works at: https://academicworks.cuny.edu Authors Authors Bo-Juen Chen, Helen C. Causton, Denesy Mancenido, Noel L. Goddard, Ethan O. Perlstein, and Dana Pe'er Authors Authors Bo-Juen Chen, Helen C. Causton, Denesy Mancenido, Noel L. Goddard, Ethan O. Perlstein, and Dana Pe'er This article is available at CUNY Academic Works: https://academicworks.cuny.edu/hc_pubs/191 Harnessing gene expression to identify the genetic basis of drug resistance Helen C Causton1, Denesy Mancenido1, Noel L Goddard4, Ethan O Perlstein5 and Dana Pe’er1,3,* Bo-Juen Chen1,2,3, Helen C Causton1, Denesy Mancenido1, Noel L Goddard4, Ethan O Perlstein5 and D 1 Department of Biological Sciences, Columbia University, New York, NY, USA, 2 Department of Biomedical Informatics, Columbia University, New York, NY, USA, 3 Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA, 4 Department of Physics and Astronomy, Hunter College, 695 Park Avenue, 1225 Hunter North, New York, NY, USA and 5 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA * Corresponding author. Department of Biological Sciences, Columbia University, 2960 Broadway, 607D Fairchild Center, MC 2461, New York, NY 10027, USA. Tel.: þ 1 212 854 4397; Fax: þ 1 212 865 8246; E-mail: dpeer@biology.columbia.edu Received 20.3.09; accepted 24.8.09 Received 20.3.09; accepted 24.8.09 The advent of cost-effective genotyping and sequencing methods have recently made it possible to ask questions that address the genetic basis of phenotypic diversity and how natural variants interact with the environment. We developed Camelot (CAusal Modelling with Expression Linkage for cOmplex Traits), a statistical method that integrates genotype, gene expression and phenotype data to automatically build models that both predict complex quantitative phenotypes and identify genes that actively influence these traits. Camelot integrates genotype and gene expression data, both generated under a reference condition, to predict the response to entirely different conditions. We systematically applied our algorithm to data generated from a collection of yeast segregants, using genotype and gene expression data generated under drug-free conditions to predict the response to 94 drugs and experimentally confirmed 14 novel gene–drug interactions. Our approach is robust, applicable to other phenotypes and species, and has potential for applications in personalized medicine, for example, in predicting how an individual will respond to a previously unseen drug. g olecular Systems Biology 5:310; published online 13 October 2009; doi:10.1038/msb.2009.69 bject Categories: functional genomics Molecular Systems Biology 5:310; published online 13 October 2009; doi:10.1038/msb.2009.69 Subject Categories: functional genomics g Keywords: complex trait analysis; drug target/off-target discovery; genetical genomics This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. Creation of derivative works is permitted but the resulting work may be distributed only under the same or similar licence to this one. Harnessing gene expression to identify the genetic basis of drug resistance This licence does not permit commercial exploitation without specific permission. Authors Authors Molecular Systems Biology 5; Article number 310; doi:10.1038/msb.2009.69 Citation: Molecular Systems Biology 5:310 y gy & 2009 EMBO and Macmillan Publishers Limited All rights reserved 1744-4292/09 www.molecularsystemsbiology.com & 2009 EMBO and Macmillan Publishers Limited Introduction contribute significantly to the phenotype. Gene expression has proven a potent predictor of phenotype, most notably in cancer genomics, where gene expression is used to build classifiers that predict response to therapy (Alizadeh et al, 2000; van’t Veer et al, 2002; Kutalik et al, 2008). While relatively accurate, these predictors typically consist of 4100 genes and do not provide mechanistic insight regarding the genes responsible for this response. Ground breaking approaches in the genetics of gene expression (Brem et al, 2002; Cheung and Spielman, 2002; Dixon et al, 2007) have recently been used to show that gene expression can be used to associate genes with disease phenotypes (Mehrabian et al, 2005; Schadt et al, 2005; Chen et al, 2008; Emilsson et al, 2008); however, these methods only identify the genes involved and do not directly predict multi- gene traits from the genotype. Understanding how differences in genotype account for the wide range of phenotypic diversity between individuals is one of the fundamental challenges of biology. With the advent of high-throughput sequencing, the number of available geno- types is increasing at a staggering rate, and we are nearing the point where DNA sequence represents individuals rather than organisms, providing a toehold towards answering this question. Most traits are determined by multiple genes whose identities are largely unknown; therefore, the challenge of predicting an individual’s phenome (i.e., spectrum of traits) from its genome requires both identification of the genes that influence the trait, and models that describe how they interact to determine the trait (Gabriel et al, 2002; Maller et al, 2006). Our approach is to combine genotype and gene expression data to associate genetic factors with the downstream changes in phenotype. Our premise is that gene expression is useful because it integrates information from multiple loci that are individually too weak to detect but which, in combination, Understanding how differences in genotype account for the wide range of phenotypic diversity between individuals is one of the fundamental challenges of biology. With the advent of high-throughput sequencing, the number of available geno- types is increasing at a staggering rate, and we are nearing the point where DNA sequence represents individuals rather than organisms, providing a toehold towards answering this question. Introduction Most traits are determined by multiple genes whose identities are largely unknown; therefore, the challenge of predicting an individual’s phenome (i.e., spectrum of traits) from its genome requires both identification of the genes that influence the trait, and models that describe how they interact to determine the trait (Gabriel et al, 2002; Maller et al, 2006). We developed Camelot (CAusal Modelling with Expression Linkage for cOmplex Traits) and applied it to genotype, gene expression and phenotype (growth in the presence of drug) data from segregants obtained from a cross between two diverse strains of Saccharomyces cerevisiae (Brem and Kruglyak, 2005; Our approach is to combine genotype and gene expression data to associate genetic factors with the downstream changes in phenotype. Our premise is that gene expression is useful because it integrates information from multiple loci that are individually too weak to detect but which, in combination, Molecular Systems Biology 2009 1 Identifying the genetic basis of drug resistance B-J Chen et al Perlstein et al, 2007). The genotypic differences in these strains manifest in rich phenotypic diversity in the segregants. To our knowledge, Camelot is the first method that automatically builds a model based on both gene expression and genotype, selects genes that actively influence the phenotype and accurately predicts complex quantitative phenotypes. Having ‘trained’ a model, we can use it to accurately predict the growth of a new strain with an entirely different genotype. This is demonstrated by correctly predicting growth, in the presence of each of a panel of drugs, for segregants not used during training. Most importantly, the majority of genes used for predicting growth are causal factors. Thus, genetic manipulation of these genes (deletion or allele swap, that is, replacement of the causal gene with the same gene from the other parental strain) leads to a change in phenotype (e.g., drug resistance/sensitivity) matching our prediction. segregant grown in the absence of drug, and use this to derive a quantitative prediction of the strain’s phenome, its response to each drug in a panel of drugs. We seek to identify a small set of features, either genotypic markers or single genes (transcripts in the gene expression data) that influence growth in the presence of each drug, and to explain the observed differences between segregants. We use the term ‘causal’ to describe a feature that not only correlates with and predicts the phenotype, but which actively influences it. Introduction We define a feature as ‘causal’ if genetic manipulation of this feature, for example, by allele swap or gene deletion, changes the phenotype, as predicted by the model. Identifying a predictive model defines a task of selecting a sparse set of features from a pool of markers and a precompiled list of transcripts that together predict growth in the presence of drug D. Although the true relationship may not be linear, we use linear models as these can be robustly inferred from the data (Hastie et al, 2001). Camelot selects a sparse set of features, markers {L} and transcripts {E} so that DB{L} þ {E} (Box 1B). An important distinguishing feature of Camelot is that it integrates genotype and gene expression data, generated under drug-free conditions, to detect causal genes and predicts the response to an entirely different condition, growth in the presence of a drug. Therefore, gene expression of an individual need only be assayed once. This single-gene expression profile can be harnessed to analyse the connection between genotype and phenotype for a large number of traits that manifest under many different conditions. Moreover, the response to a drug can be predicted before treatment, a critical feature for clinical application. Identifying a small number of predictive features from thousands of candidates is a well studied problem of high dimensional feature selection (Hastie et al, 2001). To avoid identifying features that match the training data by chance, our algorithm uses a combination of statistical tools including elastic net regularized regression (Zou and Hastie, 2005), non- parametric bootstrap (Efron, 1979) and tests designed to further select only those that are most likely causal. The selected features are then used to optimise a linear prediction function (see section Materials and methods). Our results demonstrate that Camelot can predict a strain’s response to a drug, for 87/94 drugs. The inclusion of gene expression data measured under unrelated (drug-free) condi- tions significantly contributes to Camelot’s accuracy in predicting drug response and in its ability to detect causal genes involved in this response. We experimentally confirmed 25/27 of Camelot’s predictions regarding the influence of a specific gene in the response to a specific drug. Our data demonstrate that Camelot is able to identify genes involved in drug resistance robustly. Results We used a data set containing information from 104 segregants that arose from the mating of two genetically diverse strains, ‘BY’ and ‘RM’ (Brem and Kruglyak, 2005). The data include the growth yield from each segregant grown in the presence of one of 94 chemicals (‘drugs’) (Perlstein et al, 2007), 526 processed markers denoting genotype (Lee et al, 2006) and 6189 gene expression profiles, measured in rich media, for each segregant (Brem and Kruglyak, 2005). Camelot outperforms association and linkage analysis in providing a set of features that yield significantly more accurate prediction of drug response (see Figure 1A–D). We found that Camelot’s predictions for growth in the test strains were more accurate for 88% of the conditions examined, compared with those obtained using standard linkage methods (Figure 1A), and in many cases led to dramatic improvement in the accuracy of prediction, for example, for clomiphene and haloperidol (Figure 1C and D). The BY and RM strains used in this study are genetically distant, with 0.5% sequence diversity between them. This genetic diversity manifests in significant phenotypic diversity. Not only do the strains differ in their response to drugs; each drug has a different set of fast- and slow-growing segregants (Box 1A). While Camelot’s statistically rigorous feature selection framework contributes to its success, so does the use of gene expression data, as evidenced when we compare our method with and without the use of expression data (Figure 1B–D). Note that the gene expression data were obtained from cells grown under nutrient-rich, non-perturbed conditions, whereas the growth data were measured in the presence of different Introduction We evaluated the performance of our approach using 10-fold cross-validation; we randomly split the segregants (strains) into training and test sets and completely withheld any data relating to the test strains during model selection. Camelot uses gene expression, genotype and drug response data from strains in the training set to build a model that both predicts growth for each condition ( þ drug) and identifies the genes responsible for the differences in phenotype between strains. Camelot was subsequently used to predict the drug response for the withheld test strains using only genotype and gene expression data measured under drug-free conditions (see section Materials and methods). These test strains simulate a situation in which Camelot is used to predict the phenotype of new, previously unobserved, strains. 2 Molecular Systems Biology 2009 & 2009 EMBO and Macmillan Publishers Limited Gene expression measured in the absence of drug helps predict drug response Our goal is to obtain baseline information about a strain, genotype and gene expression data measured from each 2 Molecular Systems Biology 2009 Identifying the genetic basis of drug resistance B-J Chen et al Totarol Bithionol Resveratrol SMP10 DFI Haloperidol Clotrimazole SK&F Tyrothricin Mepatricin 1 –0.4 1.5 –1.5 Phenome A B D (drug response) L (genotype) E (expression) Input: D, L and E Segregants Markers Transcripts LCamelot = i ECamelot = j, k + Output: Regression model D = LCamelot β + ECamelot β 3 Novel segregants + i j k Camelot feature selection i j k = – drug + drug i j k Prediction Training Post-analysis Marker i locus ORF Zoom-in score Causal potential Rank 1 Rank 2 Rank 3 Experimental validation ... ... Input C E C L β , C L β C E iversity of drug response and the outline of the Camelot algorithm 1 Diversity of drug response and the outline of the Camelot algorithm Box 1 Diversity of drug response and the outline of the Camelot algorithm Totarol Bithionol Resveratrol SMP10 DFI Haloperidol Clotrimazole SK&F Tyrothricin Mepatricin 1 –0.4 1.5 –1.5 Phenome A T B R S D H C S T M 1.5 –1.5 Phenome A A DFI Haloperidol Clotrimazole SK&F Tyrothricin Mepatricin B D (drug response) L (genotype) E (expression) Input: D, L and E Segregants Markers Transcripts LCamelot = i ECamelot = j, k + Output: Regression model D = LCamelot β + ECamelot β 3 Novel segregants + i j k Camelot feature selection i j k = – drug + drug i j k Prediction Training Post-analysis Marker i locus ORF Zoom-in score Causal potential Rank 1 Rank 2 Rank 3 Experimental validation ... ... Input C E C L β , C L β C E Box 1 (A) Growth in the presence of a subset of drugs is represented by the heat map on the left (blue corresponds to low growth yield and yellow to high growth yield). Each row represents the data for a single drug (SMP10 is 1,9-pyrazoloanthone, DFI is diphenyliodonium and SK&F is SK&F 96365) and each column represents a different strain/segregant. The red rectangle shows the response of a segregant to the set of drugs indicated, known as the ‘phenome’, of the strain. Gene expression measured in the absence of drug helps predict drug response Input C E C L β , C L β C E B Transcripts Post-analysis Marker i locus ORF Zoom-in score Causal potential Rank 1 Rank 2 Rank 3 Experimental validation ... ... Box 1 (A) Growth in the presence of a subset of drugs is represented by the heat map on the left (blue corresponds to low growth yield and yellow to high growth yield). Each row represents the data for a single drug (SMP10 is 1,9-pyrazoloanthone, DFI is diphenyliodonium and SK&F is SK&F 96365) and each column represents a different strain/segregant. The red rectangle shows the response of a segregant to the set of drugs indicated, known as the ‘phenome’, of the strain. The heat map on the right represents the correlation between the responses of the segregants to the drugs (Pearson’s correlation coefficient). The rows and columns are in the same order as the rows in the heat map on the left. The range in Pearson’s correlation coefficient demonstrates that there is considerable diversity in the response of the segregants to these drugs; the correlation ranges from strong positive correlation (r¼0.64) to strong anticorrelation (0.40). The same scale is used for all the figures. (B) Overview of Camelot. The input data include matched genotype (L) and gene expression (E) data for each segregant measured under standard conditions (no drug) and growth yield/drug response (D) measured in the presence of a drug. Each column represents a strain/segregant and each row represents a marker feature in the genotype matrix or a transcript feature in the gene expression matrix. Camelot outputs a predictive regression model with a small set of markers and gene expression features. In the training phase, Camelot takes genotype, gene expression and drug response as input and uses feature selection methods (elastic net, bootstrap, the triangle test and model revision) to choose a small set of marker and gene expression features that best predict the drug response that are enriched for features likely to have a causal influence on the phenotype. Selected sets of features are denoted by LCamelot and ECamelot, representing selected markers and transcripts, respectively. A linear regression model is then built on LCamelot and ECamelot. In the prediction stage, Camelot uses the model built on the training data (regression coefficients bLC and bEC) and the genotype and expression data for the held-out segregants to predict growth in the presence of drug. Gene expression measured in the absence of drug helps predict drug response The heat map on the right represents the correlation between the responses of the segregants to the drugs (Pearson’s correlation coefficient). The rows and columns are in the same order as the rows in the heat map on the left. The range in Pearson’s correlation coefficient demonstrates that there is considerable diversity in the response of the segregants to these drugs; the correlation ranges from strong positive correlation (r¼0.64) to strong anticorrelation (0.40). The same scale is used for all the figures. (B) Overview of Camelot. The input data include matched genotype (L) and gene expression (E) data for each segregant measured under standard conditions (no drug) and growth yield/drug response (D) measured in the presence of a drug. Each column represents a strain/segregant and each row represents a marker feature in the genotype matrix or a transcript feature in the gene expression matrix. Camelot outputs a predictive regression model with a small set of markers and gene expression features. In the training phase, Camelot takes genotype, gene expression and drug response as input and uses feature selection methods (elastic net, bootstrap, the triangle test and model revision) to choose a small set of marker and gene expression features that best predict the drug response that are enriched for features likely to have a causal influence on the phenotype. Selected sets of features are denoted by LCamelot and ECamelot, representing selected markers and transcripts, respectively. A linear regression model is then built on LCamelot and ECamelot. In the prediction stage, Camelot uses the model built on the training data (regression coefficients bLC and bEC) and the genotype and expression data for the held-out segregants to predict growth in the presence of drug. Following model selection, Camelot takes each selected marker (LCamelot) and uses the zoom-in score to prioritize the likelihood that each gene within the linked region is causal. B D (drug response) L (genotype) E (expression) Input: D, L and E Segregants Markers Transcripts LCamelot = i ECamelot = j, k + Output: Regression model D = LCamelot β + ECamelot β 3 Novel segregants + i j k Camelot feature selection i j k = – drug + drug i j k Prediction Training Post-analysis Marker i locus ORF Zoom-in score Causal potential Rank 1 Rank 2 Rank 3 Experimental validation ... ... Identifying the genetic basis of drug resistance B-J Chen et al Gene expression measured in the absence of drug helps predict drug response 4 B 0 0.3 0.6 0.9 0 0.3 0.6 0.9 Accuracy of elastic L Accuracy of Camelot ΔAcc<0 ΔAcc<0.2 ΔAcc<0.4 ΔAcc0.4 0 0.3 0.6 0.9 0 0.3 0.6 0.9 A B Accuracy of linkage analysis Accuracy of Camelot 0 0.3 0.6 0.9 0 0.3 0.6 0.9 Accuracy of elastic L Accuracy of Camelot B Elastic L Camelot Linkage r = 0.72 r = 0.45 r = 0.45 Haloperidol at 55 h Growth D Prediction Clomiphene at 80 h No linkage Elastic L Camelot Linkage r = 0.33 r = 0.69 Growth C Prediction C D Figure 1 Camelot has superior predictive ability. Comparison of prediction methods on held out test data from different models. (A) Classification accuracy (see section Materials and methods): Camelot compared with linkage analysis. Each dot represents a condition (growth yield in the presence of a drug), showing the fraction correctly predicted by Camelot (y-axis) and linkage analysis (x-axis). Dots above the diagonal indicate the superior performance of Camelot and are colour coded to indicate the degree of improvement. (B) As in panel A, but the classification accuracy by Camelot is compared with that of the elastic-net L model lacking transcript features (see section Materials and methods). This demonstrates that for many conditions the inclusion of gene expression features improves Camelot’s performance. (C) The top bar represents growth in the presence of clomiphene; each column is associated with a different segregant (matched horizontal positions within the panel) sorted by growth from low (blue) to high (yellow). The observed growth is compared with model prediction from linkage analysis, the elastic-net L model and Camelot. The bar marked elastic L represents predictions from bootstrapped elastic net regression using genotype alone, and the bottom bar represents prediction from Camelot. Prediction (on test data) improves from no detected linkage to most accurate for Camelot. The same scale is used for all the figures. (D) As in panel C, but for haloperidol. predictor (Pearl, 2000). When the feature correlated with growth is based on linkage to a DNA marker, the issue of causality is straightforward: the observed phenotype is likely influenced by genetic polymorphism within the linked region. Gene expression measured in the absence of drug helps predict drug response However, when the feature is based on correlation between the abundance of a transcript and the phenotype, three possibi- lities exist: (1) the transcript and phenotype correlate due to a common cause resulting from DNA variation (Figure 2C), (2) DNA variation exerts its effect on the phenotype through the gene, and hence the expression level serves as an indicator of the causal effect of the genetic differences on the phenotype (Figure 2D) or (3) growth rate influences the abundance of the transcript. The last option is not considered in this experi- mental design, as gene expression was measured in the absence of drugs. drugs and that the expression features chosen differed between the drugs. Therefore, the features selected are unlikely to represent genes whose expression merely corre- lates with rapid growth (Airoldi et al, 2009). The response of segregants to different conditions is heritable (Perlstein et al, 2006), so the boost in performance, over genotype alone, gained by using gene expression data (generated in the absence of drug) is counter-intuitive (Figure 1B). A factor that contributes to the accuracy is that transcript features chosen by Camelot typically correlate well with the measured growth yield in the presence of a drug. This success in prediction is similar to the success of gene-expression-based classifiers in predicting response to chemotherapy in cancer genomics (van’t Veer et al, 2002). However, correlation does not necessarily imply causality. For example, there are 123 genes whose expression correlates with growth in hydrogen peroxide with an absolute coefficient of 0.35 or greater. Of these, Camelot only chose one transcript feature, DHH1 (Figure 3A). We explain how Camelot goes beyond correlation to identify the most likely causal gene. First, Camelot limits the set of possible candidate transcript features to 854 transcripts that are not particular to any specific drug, yet are a priori more likely to be causal based on the functional classification of their cognate genes (see section Materials and methods). Camelot selects features using a bootstrap procedure on coefficients of regularized regression (see section Materials and methods). Systematic evaluation using synthetic data shows that bootstrapping of regression 4 Molecular Systems Biology 2009 Gene expression measured in the absence of drug helps predict drug response Following model selection, Camelot takes each selected marker (LCamelot) and uses the zoom-in score to prioritize the likelihood that each gene within the linked region is causal. Molecular Systems Biology 2009 3 & 2009 EMBO and Macmillan Publishers Limited Clomiphene at 80 h No linkage Elastic L Camelot Linkage r = 0.33 r = 0.69 Growth Elastic L Camelot Linkage r = 0.72 r = 0.45 r = 0.45 Haloperidol at 55 h Growth ΔAcc<0 ΔAcc<0.2 ΔAcc<0.4 ΔAcc0.4 0 0.3 0.6 0.9 0 0.3 0.6 0.9 A B C D Accuracy of linkage analysis Accuracy of Camelot 0 0.3 0.6 0.9 0 0.3 0.6 0.9 Accuracy of elastic L Accuracy of Camelot Prediction Prediction Figure 1 Camelot has superior predictive ability. Comparison of prediction methods on held out test data from different models. (A) Classification accuracy (see section Materials and methods): Camelot compared with linkage analysis. Each dot represents a condition (growth yield in the presence of a drug), showing the fraction correctly predicted by Camelot (y-axis) and linkage analysis (x-axis). Dots above the diagonal indicate the superior performance of Camelot and are colour coded to indicate the degree of improvement. (B) As in panel A, but the classification accuracy by Camelot is compared with that of the elastic-net L model lacking transcript features (see section Materials and methods). This demonstrates that for many conditions the inclusion of gene expression features improves Camelot’s performance. (C) The top bar represents growth in the presence of clomiphene; each column is associated with a different segregant (matched horizontal positions within the panel) sorted by growth from low (blue) to high (yellow). The observed growth is compared with model prediction from linkage analysis, the elastic-net L model and Camelot. The bar marked elastic L represents predictions from bootstrapped elastic net regression using genotype alone, and the bottom bar represents prediction from Camelot. Prediction (on test data) improves from no detected linkage to most accurate for Camelot. The same scale is used for all the figures. (D) As in panel C, but for haloperidol. & 2009 EMBO and Macmillan Publishers Limited Identifying features that actively influence the phenotype DHH1 was chosen as a candidate feature for H2O2 (r¼0.44) and passed the triangle test with P-value 1.6  105. significant confidence after bootstrapping. The permutation- based triangle test asks, ‘Is gene expression significantly predictive of the growth beyond the contribution of the linked genotype?’ (Figure 2B and section Materials and methods). We assume that the linked DNA marker is causative a priori and require that the transcript feature remains significantly predictive of growth even after the influence of the marker is controlled for. While this test does not guarantee that the transcript feature is indeed causal, it identifies transcript features that are more likely causal and enriches the final selection with causal features. For example, the abundance of the DHH1 transcript was selected by our bootstrap procedure as a feature that predicted the response to 10 different drugs. After administering the triangle test, DHH1 passed as causal for only six of these drugs. These were subsequently validated experimentally (Figure 3D). The variability in DHH1 expres- sion across segregants arises because of polymorphism in MKT1 (chromosome XIV) (Lee et al, 2009), although it is likely that other genetic factors also affect DHH1 expression. We believe that DHH1 expression is influenced by multiple genetic factors, that are individually too weak to detect, and that this dramatically increases Camelot’s precision in correctly pin- pointing the causal features that generate the phenotype, both compared with elastic net regression alone and the feature selection methods used by Schadt et al (2005) and Chen et al (2008) (Supplementary Figure 1). For the hydrogen peroxide response, GO-based filtering reduced the list of 123 candidate transcripts to the 15 genes shown in Figure 2A. Bootstrapping further reduced the list of expression features to a single gene, DHH1, that was subsequently experimentally validated (Figure 3C). dramatically increases Camelot’s precision in correctly pin- pointing the causal features that generate the phenotype, both compared with elastic net regression alone and the feature selection methods used by Schadt et al (2005) and Chen et al (2008) (Supplementary Figure 1). For the hydrogen peroxide response, GO-based filtering reduced the list of 123 candidate transcripts to the 15 genes shown in Figure 2A. Bootstrapping further reduced the list of expression features to a single gene, DHH1, that was subsequently experimentally validated (Figure 3C). g In the next stage, Camelot explicitly tests for causality. Identifying features that actively influence the phenotype The error bars represent the standard error of the mean for all growth yield data. These data confirm the causal effect of DHH1. (D) DHH1 is a hub passing the triangle test for six drugs (left column). Five of these were tested; validated causal effects are in green, with one false positive listed in red. To assess the drug specificity of DHH1-mediated effects, four negative controls were tested (right column); confirmed negative predictions are listed in green and one false negative in red. See Supplementary Figure 2 for drug response curves for each of the drugs tested, as represented in Figure 3C. Figure 2 Correlation versus causality. (A) Growth yield in the presence of hydrogen peroxide and correlated expression profiles for genes in the candidate pool (absolute Pearson correlation coefficients X0.36, Po2  104), showing that the expression of multiple genes correlates with growth. Each column is associated with a different segregant (matched horizontal position across panel) sorted by growth yield (as in Figure 1) and gene expression on a red–green scale. (B) The triangle test evaluates the likelihood that each transcript feature causally explains the phenotype (red edge). It distinguishes between causal chain (left, red edge) and co-regulation structures (right, grey edge) using permutation testing to evaluate the contribution of gene expression controlled for the genotype of L. That is, expression is permuted under the allele of the linked genotype (see section Materials and methods). Orange represents RM and blue BY for the genotype at the locus. Some notation for all the figures: Blue ovals represent the genotype of a marker; yellow ovals, drug response; green ovals, gene expression; red arrows, the driving edge; black arrows, causal relationships and grey arrows, relationships tested in the test. Red letters indicate the type of the selected feature (expression in this case). (C) Sequence variation at Chromosome XIV locus is the cause of variation in both DHH1 expression and the response to lycorine; however, in this situation DHH1 expression does not causally influence the drug response. DHH1 was a candidate feature for lycorine (correlation coefficient, r¼0.44), but failed the triangle test, showing that high correlation does not necessarily reflect causality. The heat maps show segregants ordered based on response to lycorine. (D) Example of a causal chain where polymorphisms at a Chromosome XIV locus lead to change in DHH1 expression that results in differences in cell growth in the presence of H2O2. Identifying features that actively influence the phenotype Camelot aims to find a model that is not only predictive, but also identifies genes that are responsible for the phenotypic variation. Identification of these genes provides insight into the biological processes and stresses involved in response to a drug, and has practical implications for identifying alternative drug targets in resistant strains. Care must be taken when attributing a causal interpretation to a correlated feature, even when the feature acts as a potent –3.5 –2.5 –1.5 –0.5 0.0 0.4 0.8 1.2 A C D B log [%] OD600 ERG6 Chr XIII H2O2 Chr XIV DHH1 H2O2 at 112 h r = 0.65 r = 0.41 r = 0.47 Linkage DHH1 Chr XIII Camelot Elastic (L) Totarol H2O2 Valinomycin Trifluoperazine Dequalinium Cl Benzethonium Cl Hexylresorcinol Lycorine Prediction Control Tamoxifen Hinokitiol Growth H2O2 BY4742 BY4742 dhh1Δ Prediction Figure 3 Causal role of DHH1. (A) Growth yield in the presence of H2O2 compared with model prediction from linkage analysis, elastic-net L model and Camelot, represented as in Figure 1C, demonstrating superior prediction by Camelot. Camelot chose a Chromosome XIII locus (227 254–243 624) and expression of DHH1 as features to predict the drug response; the values for each segregant are represented in the same order within the panel. (B) The full prediction function obtained from Camelot for response to H2O2. DHH1 is selected as a feature and confirmed by the triangle test; the Chromosome XIII marker is selected as a feature and the zoom-in score identifies ERG6 as the causal gene within the region, fitting with reports that overexpression of ERG6 leads to decreased resistance to hydrogen peroxide (Khoury et al, 2008). The Chromosome XIV locus is at position 449 639–486 861. Some notation for all the figures: Green rectangles (such as ERG6) represent expression of a gene within a linked region. (C) Averaged OD600 absorbance growth measurements of BY (red) and BY dhh1D mutant (blue) plotted against twofold dilution series of H2O2. The error bars represent the standard error of the mean for all growth yield data. These data confirm the causal effect of DHH1. (D) DHH1 is a hub passing the triangle test for six drugs (left column). Five of these were tested; validated causal effects are in green, with one false positive listed in red. Identifying features that actively influence the phenotype Five of these were tested; validated causal effects are in green, with one false positive listed in red. To assess the drug specificity of DHH1-mediated effects, four negative controls were tested (right column); confirmed negative predictions are listed in green and one false negative in red. See Supplementary Figure 2 for drug response curves for each of the drugs tested, as represented in Figure 3C. ? D L E ? Genotype B Expression Growth A H2O2 at 112 h r = 0.65 r = 0.41 r = 0.47 Linkage DHH1 Chr XIII Camelot Elastic (L) Growth Prediction B ERG6 Chr XIII H2O2 Chr XIV DHH1 B A H2O2 at 112 h NUP1 MSH2 NUP188 VPS1 ARR4 DHH1 SFB3 GCN20 RMD7 EMP24 KKQ8 KNS1 SIP2 EMI5 PPZ1 3 –3 G A B E G B A –3.5 –2.5 –1.5 –0.5 0.0 0.4 0.8 1.2 C D log [%] OD600 Totarol H2O2 Valinomycin Trifluoperazine Dequalinium Cl Benzethonium Cl Hexylresorcinol Lycorine Prediction Control Tamoxifen Hinokitiol H2O2 BY4742 BY4742 dhh1Δ D Totarol H2O2 Valinomycin Trifluoperazine Dequalinium Cl Benzethonium Cl Hexylresorcinol Lycorine Prediction Control Tamoxifen Hinokitiol –3.5 –2.5 –1.5 –0.5 0.0 0.4 0.8 1.2 C log [%] OD600 H2O2 BY4742 BY4742 dhh1Δ C D H2O2 Chr XIV DHH1 D Lycorine Chr XIV DHH1 C C C D Figure 3 Causal role of DHH1. (A) Growth yield in the presence of H2O2 compared with model prediction from linkage analysis, elastic-net L model and Camelot, represented as in Figure 1C, demonstrating superior prediction by Camelot. Camelot chose a Chromosome XIII locus (227 254–243 624) and expression of DHH1 as features to predict the drug response; the values for each segregant are represented in the same order within the panel. (B) The full prediction function obtained from Camelot for response to H2O2. DHH1 is selected as a feature and confirmed by the triangle test; the Chromosome XIII marker is selected as a feature and the zoom-in score identifies ERG6 as the causal gene within the region, fitting with reports that overexpression of ERG6 leads to decreased resistance to hydrogen peroxide (Khoury et al, 2008). The Chromosome XIV locus is at position 449 639–486 861. Some notation for all the figures: Green rectangles (such as ERG6) represent expression of a gene within a linked region. (C) Averaged OD600 absorbance growth measurements of BY (red) and BY dhh1D mutant (blue) plotted against twofold dilution series of H2O2. & 2009 EMBO and Macmillan Publishers Limited Identifying features that actively influence the phenotype DH selected as a feature and confirmed by the triangle test; the Chromosom marker is selected as a feature and the zoom-in score identifies ERG6 causal gene within the region, fitting with reports that overexpression of leads to decreased resistance to hydrogen peroxide (Khoury et al, 2008 Chromosome XIV locus is at position 449 639–486 861. Some notation for figures: Green rectangles (such as ERG6) represent expression of a gene a linked region. (C) Averaged OD600 absorbance growth measurements (red) and BY dhh1D mutant (blue) plotted against twofold dilution series of The error bars represent the standard error of the mean for all growth yield These data confirm the causal effect of DHH1. (D) DHH1 is a hub passi triangle test for six drugs (left column). Five of these were tested; validated effects are in green, with one false positive listed in red. To assess th specificity of DHH1-mediated effects, four negative controls were tested column); confirmed negative predictions are listed in green and one negative in red. See Supplementary Figure 2 for drug response curves fo of the drugs tested, as represented in Figure 3C. H2O2 at 112 h H2O2 Chr XIV DHH1 Lycorine Chr XIV DHH1 NUP1 MSH2 NUP188 VPS1 ARR4 DHH1 SFB3 GCN20 RMD7 EMP24 KKQ8 KNS1 SIP2 EMI5 PPZ1 3 –3 ? D L E ? Genotype A C D B Expression Growth Figure 2 Correlation versus causality. (A) Growth yield in the presence of hydrogen peroxide and correlated expression profiles for genes in the candidate pool (absolute Pearson correlation coefficients X0.36, Po2  104), showing that the expression of multiple genes correlates with growth. Each column is associated with a different segregant (matched horizontal position across panel) sorted by growth yield (as in Figure 1) and gene expression on a red–green scale. (B) The triangle test evaluates the likelihood that each transcript feature causally explains the phenotype (red edge). It distinguishes between causal chain (left, red edge) and co-regulation structures (right, grey edge) using permutation testing to evaluate the contribution of gene expression controlled for the genotype of L. That is, expression is permuted under the allele of the linked genotype (see section Materials and methods). Orange represents RM and blue BY for the genotype at the locus. Identifying features that actively influence the phenotype Some notation for all the figures: Blue ovals represent the genotype of a marker; yellow ovals, drug response; green ovals, gene expression; red arrows, the driving edge; black arrows, causal relationships and grey arrows, relationships tested in the test. Red letters indicate the type of the selected feature (expression in this case). (C) Sequence variation at Chromosome XIV locus is the cause of variation in both DHH1 expression and the response to lycorine; however, in this situation DHH1 expression does not causally influence the drug response. DHH1 was a candidate feature for lycorine (correlation coefficient, r¼0.44), but failed the triangle test, showing that high correlation does not necessarily reflect causality. The heat maps show segregants ordered based on response to lycorine. (D) Example of a causal chain where polymorphisms at a Chromosome XIV locus lead to change in DHH1 expression that results in differences in cell growth in the presence of H2O2. DHH1 was chosen as a candidate feature for H2O2 (r¼0.44) and passed the triangle test with P-value 1.6  105. significant confidence after bootstrapping. The permutation- based triangle test asks, ‘Is gene expression significantly predictive of the growth beyond the contribution of the linked H2O2 at 112 h H2O2 Chr XIV DHH1 Lycorine Chr XIV DHH1 NUP1 MSH2 NUP188 VPS1 ARR4 DHH1 SFB3 GCN20 RMD7 EMP24 KKQ8 KNS1 SIP2 EMI5 PPZ1 3 –3 ? D L E ? Genotype A C D B Expression Growth gure 2 Correlation versus causality. (A) Growth yield in the presence of drogen peroxide and correlated expression profiles for genes in the candidate ol (absolute Pearson correlation coefficients X0.36, Po2  104), showing at the expression of multiple genes correlates with growth. Each column is sociated with a different segregant (matched horizontal position across panel) rted by growth yield (as in Figure 1) and gene expression on a red–green scale. ) The triangle test evaluates the likelihood that each transcript feature causally plains the phenotype (red edge). It distinguishes between causal chain (left, d edge) and co-regulation structures (right, grey edge) using permutation sting to evaluate the contribution of gene expression controlled for the notype of L. That is, expression is permuted under the allele of the linked notype (see section Materials and methods). Orange represents RM and blue Y for the genotype at the locus. Identifying features that actively influence the phenotype Some notation for all the figures: Blue ovals present the genotype of a marker; yellow ovals, drug response; green ovals, ne expression; red arrows, the driving edge; black arrows, causal relationships d grey arrows, relationships tested in the test. Red letters indicate the type of e selected feature (expression in this case). (C) Sequence variation at romosome XIV locus is the cause of variation in both DHH1 expression and e response to lycorine; however, in this situation DHH1 expression does not usally influence the drug response. DHH1 was a candidate feature for lycorine orrelation coefficient, r¼0.44), but failed the triangle test, showing that high rrelation does not necessarily reflect causality The heat maps show –3.5 –2.5 –1.5 –0.5 0.0 0.4 0.8 1.2 A C D B log [%] OD600 ERG6 Chr XIII H2O2 Chr XIV DHH1 H2O2 at 112 h r = 0.65 r = 0.41 r = 0.47 Linkage DHH1 Chr XIII Camelot Elastic (L) Totarol H2O2 Valinomycin Trifluoperazine Dequalinium Cl Benzethonium Cl Hexylresorcinol Lycorine Prediction Control Tamoxifen Hinokitiol Growth H2O2 BY4742 BY4742 dhh1Δ Prediction Figure 3 Causal role of DHH1. (A) Growth yield in the presence of H2O2 compared with model prediction from linkage analysis, elastic-net L model and Camelot, represented as in Figure 1C, demonstrating superior prediction by Camelot. Camelot chose a Chromosome XIII locus (227 254–243 624) and expression of DHH1 as features to predict the drug response; the values for each segregant are represented in the same order within the panel. (B) The full prediction function obtained from Camelot for response to H2O2. DHH1 is selected as a feature and confirmed by the triangle test; the Chromosome XIII marker is selected as a feature and the zoom-in score identifies ERG6 as the causal gene within the region, fitting with reports that overexpression of ERG6 leads to decreased resistance to hydrogen peroxide (Khoury et al, 2008). The Chromosome XIV locus is at position 449 639–486 861. Some notation for all the figures: Green rectangles (such as ERG6) represent expression of a gene within a linked region. (C) Averaged OD600 absorbance growth measurements of BY (red) and BY dhh1D mutant (blue) plotted against twofold dilution series of H2O2. The error bars represent the standard error of the mean for all growth yield data. These data confirm the causal effect of DHH1. (D) DHH1 is a hub passing the triangle test for six drugs (left column). Identifying features that actively influence the phenotype To assess the drug specificity of DHH1-mediated effects, four negative controls were tested (right column); confirmed negative predictions are listed in green and one false negative in red. See Supplementary Figure 2 for drug response curves for each of the drugs tested, as represented in Figure 3C. Identifying the genetic basis of drug resistance B-J Chen et al Identifying the genetic basis of drug resistance B-J Chen et al dramatically increases Camelot’s precision in correctly pin- pointing the causal features that generate the phenotype, both compared with elastic net regression alone and the feature selection methods used by Schadt et al (2005) and Chen et al (2008) (Supplementary Figure 1). For the hydrogen peroxide response, GO-based filtering reduced the list of 123 candidate significant confidence after bootstrapping. The permuta based triangle test asks, ‘Is gene expression signific predictive of the growth beyond the contribution of the li genotype?’ (Figure 2B and section Materials and methods assume that the linked DNA marker is causative a prior require that the transcript feature remains signific predictive of growth even after the influence of the mark controlled for. While this test does not guarantee tha transcript feature is indeed causal, it identifies trans features that are more likely causal and enriches the selection with causal features. For example, the abundan the DHH1 transcript was selected by our bootstrap proce as a feature that predicted the response to 10 different d After administering the triangle test, DHH1 passed as c for only six of these drugs. These were subsequently valid H2O2 at 112 h H2O2 Chr XIV DHH1 Lycorine Chr XIV DHH1 NUP1 MSH2 NUP188 VPS1 ARR4 DHH1 SFB3 GCN20 RMD7 EMP24 KKQ8 KNS1 SIP2 EMI5 PPZ1 3 –3 ? D L E ? Genotype A C D B Expression Growth Figure 2 Correlation versus causality. (A) Growth yield in the presence of hydrogen peroxide and correlated expression profiles for genes in the candidate pool (absolute Pearson correlation coefficients X0.36, Po2  104), showing that the expression of multiple genes correlates with growth. Each column is associated with a different segregant (matched horizontal position across panel) sorted by growth yield (as in Figure 1) and gene expression on a red–green scale. (B) The triangle test evaluates the likelihood that each transcript feature causally explains the phenotype (red edge). Identifying features that actively influence the phenotype It distinguishes between causal chain (left, red edge) and co-regulation structures (right, grey edge) using permutation testing to evaluate the contribution of gene expression controlled for the genotype of L. That is, expression is permuted under the allele of the linked genotype (see section Materials and methods). Orange represents RM and blue BY for the genotype at the locus. Some notation for all the figures: Blue ovals represent the genotype of a marker; yellow ovals, drug response; green ovals, gene expression; red arrows, the driving edge; black arrows, causal relationships and grey arrows, relationships tested in the test. Red letters indicate the type of the selected feature (expression in this case). (C) Sequence variation at Chromosome XIV locus is the cause of variation in both DHH1 expression and the response to lycorine; however, in this situation DHH1 expression does not causally influence the drug response. DHH1 was a candidate feature for lycorine (correlation coefficient, r¼0.44), but failed the triangle test, showing that high correlation does not necessarily reflect causality. The heat maps show segregants ordered based on response to lycorine. (D) Example of a causal chain where polymorphisms at a Chromosome XIV locus lead to change in DHH1 expression that results in differences in cell growth in the presence of H2O2. DHH1 was chosen as a candidate feature for H2O2 (r¼0.44) and passed the triangle test with P-value 1.6  105. –3.5 –2.5 –1.5 –0.5 0.0 0.4 0.8 1.2 A C D B log [%] OD600 ERG Chr XIII H2O2 Chr XIV DHH1 H2O2 at 112 h r = 0.65 r = 0.41 r = 0.47 Linkage DHH1 Chr XIII Camelot Elastic (L) Totarol H2O2 Valinomycin Trifluoperazine Dequalinium Cl Benzethonium Cl Hexylreso Lycorine Prediction Control Tamoxifen Hinokitiol Growth H2O2 BY4742 BY4742 dhh1Δ Prediction Figure 3 Causal role of DHH1. (A) Growth yield in the presence of compared with model prediction from linkage analysis, elastic-net L mod Camelot, represented as in Figure 1C, demonstrating superior predict Camelot. Camelot chose a Chromosome XIII locus (227 254–243 624 expression of DHH1 as features to predict the drug response; the values fo segregant are represented in the same order within the panel. (B) T prediction function obtained from Camelot for response to H2O2. From prediction to mechanism The true value of gene expression comes to light when one focuses not on how resistant a strain is, but rather why it is so. Rather than being a black box predictor, transcript features can help shed light on the mechanisms underlying resistance. DHH1 was chosen as a feature for a large number of drugs, so we tested Camelot’s prediction that DHH1 plays a causal role in mediating resistance to these drugs. DHH1 expression is negatively correlated with growth in the presence of hydrogen peroxide (correlation coefficient r¼0.44), and we tested the prediction that DHH1 influences drug response by measuring the growth yield of wild-type and dhh1D strains in hydrogen peroxide (Figure 3C and section Materials and methods). The dhh1D strain grew better than the wild type, confirming that DHH1 negatively influences the phenotype. These examples illustrate the power of Camelot to identify genes that causally influence the response to multiple drugs, predict the mechanism of action of drugs and provide insight into the underlying biology. g This result complements the finding that Dhh1 colocalizes with the sequence-specific RNA-binding protein Puf3 and regulates the abundance of 153 Puf3-bound mRNAs (Lee et al, 2009). Puf3 is a factor that binds select nuclear-encoded genes involved in mitochondrial biogenesis and likely regulates the transport/translation/stability of these messages (Garcia- Rodriguez et al, 2007; Saint-Georges et al, 2008). These Puf3- bound, mitochondrial-related genes are significantly upregu- lated in dhh1D strains (Lee et al, 2009). As DHH1 is expressed at a higher level in the BYparent, this strain might have a lower capacity for detoxification of the reactive oxygen species produced on hydrogen-peroxide treatment and a lesser ability to withstand this insult. Genes annotated for mitochondria are upregulated in the RM strain (Litvin et al, 2009) and this strain is predisposed towards respiratory growth (Smith and Kruglyak, 2008). Identifying features that actively influence the phenotype We apply a causality test to all transcript features chosen with Molecular Systems Biology 2009 5 & 2009 EMBO and Macmillan Publishers Limited Identifying the genetic basis of drug resistance B-J Chen et al Identifying the genetic basis of drug resistance B-J Chen et al possible application of Camelot in predicting the mechanism of action of novel drugs. explains why gene expression is so potent in improving prediction accuracy. MGA2, a gene whose product is involved in fatty-acid metabolism (Chellappa et al, 2001; Jiang et al, 2002; Kandasamy et al, 2004), was identified as another transcript feature predictive of growth for six drugs. Three of these (cerulenin, ikarugamycin and tomatine) act by perturbing processes involved in fatty-acid and lipid synthesis and membrane permeability (Vance et al, 1972; Hasumi et al, 1992; Friedman, 2002). Unsaturated fatty acids (FA) are essential components of membranes and FA synthesis is effected by controlling the stability of OLE1 mRNA. Ole1 is required for the formation of monounsaturated FA precursors (Martin et al, 2007). Mga2 acts to stabilize or destabilize the OLE1 message depending on the conditions (Kandasamy et al, 2004). The gene expression data show that in the non- perturbed state MGA2 expression is negatively correlated with OLE1 expression (r¼0.54) and positively correlated with the drug response. Using gene expression to identify causal genes within a linked region Transcript features relate to a single gene and hence directly identify the involved gene. DNA marker features are better founded in their causal nature, but typically involve large chromosomal regions containing tens of genes. For these features, Camelot uses gene expression to help pinpoint the causal gene within the linked locus. The zoom-in score uses gene expression to prioritize the likelihood that each gene within the linked region is causal. Like the triangle test, the zoom-in score is a measure of how well gene expression predicts the phenotype. Linkage implies that the marker is driving the causality; therefore, the zoom-in score includes an additional measure for cis-linkage, how well the marker predicts the gene expression. The zoom-in score incorporates both of these qualities, as well as conservation of the protein sequence to prioritize genes within a locus (see Figure 4A and section Materials and methods). & 2009 EMBO and Macmillan Publishers Limited 6 Molecular Systems Biology 2009 Testing the causal role of transcript features –4.8 –4.2 –3.6 –3.0 0.0 0.4 0.8 1.2 A C D B log[M] OD600 Doxorubicin –3 –2 –6 –5 –4 0.0 0.4 0.8 1.2 log[M] OD600 Tunicamycin BY4722 PHO84-BY BY4722 PHO84-RM ORF Expression Figure 4 Causal role of PHO84. (A) The zoom-in score for each locus to drug association (red arrow) evaluates the likelihood, P(L, E, D), that each gene in the locus causally influences the growth of the strain in response to drug, based on its expression (each row represents a gene at the locus and each column a segregant; see section Materials and methods for details). (B) Validation of the ability of the zoom-in score to distinguish which drugs are influenced by PHO84. To the left are high- scoring drugs predicted to be influenced by PHO84; all six drugs were validated including two previously associated with PHO84 (Perlstein et al, 2007) (light green) and four new drugs associated with PHO84 (dark green). To the right are low-scoring drugs, not expected to be influenced by PHO84; PHO84 had no effect on the response for any of the three, validating the ability of the zoom-in score to make positive and negative predictions. (C) Averaged OD600 absorbance growth measurements of BY (red) and BY with an allele swap for PHO84-RM (blue) plotted against concentration of doxorubicin. See Supplementary Figure 3 for the response to each drug represented as in panel C. (D) As panel C, but for tunicamycin, showing that variation in the DNA sequence of PHO84 has little effect. P(L,E,D) Locus Growth D L E ? ? A ORF Expression Doxorubicin Hexylresorcinol Haloperidol Furoxan Pentachlorophenol TCPN Dichlorophene Prediction Control Tunicamycin Ebselen B B A D –3 –2 –6 –5 –4 0.0 0.4 0.8 1.2 log[M] OD600 Tunicamycin BY4722 PHO84-BY BY4722 PHO84-RM –4.8 –4.2 –3.6 –3.0 0.0 0.4 0.8 1.2 C log[M] OD600 Doxorubicin D C Figure 4 Causal role of PHO84. (A) The zoom-in score for each locus to drug association (red arrow) evaluates the likelihood, P(L, E, D), that each gene in the locus causally influences the growth of the strain in response to drug, based on its expression (each row represents a gene at the locus and each column a segregant; see section Materials and methods for details). (B) Validation of the ability of the zoom-in score to distinguish which drugs are influenced by PHO84. Testing the causal role of transcript features We confirmed our predictions for the influence of DHH1 on growth in totarol, valinomycin, hydrogen peroxide and trifluoperazine. Benzethoniumchloride was the only false positive among the drugs tested (Figure 3D and Supplemen- tary Figure 2). We included lycorine, hinokitiol, hexylresorci- nol and tamoxifen as negative controls to demonstrate that DHH1 activity is drug specific. Only growth in tamoxifen was influenced by DHH1; indeed tamoxifen perturbs mitochondrial function (Tuquet et al, 2000; Cardoso et al, 2001). This demonstrates the stringency of our approach, which is designed to minimize false positives and does not detect all genes that influence drug responsiveness or all drugs influenced by a gene. In summary, we confirmed 4/5 of the positive predictions tested and 3/4 of the negative predictions for DHH1, demonstrating the drug specificity of our predic- tions. Although the drugs linked to DHH1 are diverse and include an antibiotic (valinomycin) and an antipsychotic drug (trifluoperazine), they all affect mitochondrial function (Nicolson et al, 1999; Evans et al, 2000; Nulton-Persson and Szweda, 2001; Lee et al, 2005; Safiulina et al, 2006; Yip et al, 2006; Sancho et al, 2007; Lee et al, 2008). This suggests a Camelot chose two features for hydrogen peroxide, the DHH1 transcript and a region on chromosome XIII (locus 227 254–243 624) containing 88 genes (Figure 3B). The zoom- in score identified ERG6 as the causal gene within this region, that is, polymorphism in the ERG6 sequence between the BY and RM strains is likely responsible for the differences in the response to hydrogen peroxide between the parent strains. Overexpression of ERG6 leads to decreased resistance to hydrogen peroxide (Khoury et al, 2008), matching Camelot’s prediction (Figure 3B). These results demonstrate how the triangle test and zoom-in score combine to provide a better understanding of the cellular response to each drug. Similar to linkage analysis (Perlstein et al, 2007), Camelot identified the two largest marker hotspots, a region on chromosome XIII (locus 27 644–33 681), linked to 25 drugs, and a region on chromosome XIV (linked to 12 drugs). While 6 Molecular Systems Biology 2009 Identifying the genetic basis of drug resistance B-J Chen et al P(L,E,D) Locus Doxorubicin Hexylresorcinol Haloperidol Furoxan Pentachlorophenol TCPN Dichlorophene Prediction Control Tunicamycin Ebselen Growth D L E ? ? Testing the causal role of transcript features PHO84 was top scored for a number of additional drugs linking to the chromosome XIII hotspot, but scored poorly for other drug phenotypes linking to this hotspot. We used the zoom-in score to distinguish which drugs are causally influenced by PHO84 and validated these predictions by growing wild-type BY and allele-swapped (AS) strains (BY strain containing PHO84 with one amino-acid substitution, L259P, from the RM strain) individually in the presence of one of nine drugs. We included drugs with both positive and negative predictions. Camelot correctly predicted both positive and negative responses 9/9 times, demonstrating that the zoom-in score can be used to identify which of the Chromosome XIII-linked drug phenotypes are causally influ- enced by the PHO84 allele (Figure 4B–D and Supplementary Figure 3). We performed a similar analysis for the drugs linking to the Chromosome XIV region and identified three drugs likely to respond to MKT1 and three linked drugs that are unlikely to be affected by MKT1. Again Camelot correctly predicted the response to the drugs in an AS (BY MKT1-RM) strain 6/6 times (Supplementary Figure 4). These data validate our approach and demonstrate that Camelot is also able to capture factors accounting for phenotypic variation, using markers as features, for a number of causal genes. Testing the causal role of transcript features To the left are high- scoring drugs predicted to be influenced by PHO84; all six drugs were validated including two previously associated with PHO84 (Perlstein et al, 2007) (light green) and four new drugs associated with PHO84 (dark green). To the right are low-scoring drugs, not expected to be influenced by PHO84; PHO84 had no effect on the response for any of the three, validating the ability of the zoom-in score to make positive and negative predictions. (C) Averaged OD600 absorbance growth measurements of BY (red) and BY with an allele swap for PHO84-RM (blue) plotted against concentration of doxorubicin. See Supplementary Figure 3 for the response to each drug represented as in panel C. (D) As panel C, but for tunicamycin, showing that variation in the DNA sequence of PHO84 has little effect. linkage alone only detects large multi-gene loci in this data set, the zoom-in score further identified PHO84 (chromosome XIII), as the top-ranked causal variant for multiple drugs. Two of these drugs, tetrachloroisophthalonitrile and pentachlor- ophenol, were manually identified and verified previously (Perlstein et al, 2007). PHO84 was top scored for a number of additional drugs linking to the chromosome XIII hotspot, but scored poorly for other drug phenotypes linking to this hotspot. We used the zoom-in score to distinguish which drugs are causally influenced by PHO84 and validated these predictions by growing wild-type BY and allele-swapped (AS) strains (BY strain containing PHO84 with one amino-acid substitution, L259P, from the RM strain) individually in the presence of one of nine drugs. We included drugs with both positive and negative predictions. Camelot correctly predicted both positive and negative responses 9/9 times, demonstrating that the zoom-in score can be used to identify which of the Chromosome XIII-linked drug phenotypes are causally influ- enced by the PHO84 allele (Figure 4B–D and Supplementary Figure 3). We performed a similar analysis for the drugs linking to the Chromosome XIV region and identified three drugs likely to respond to MKT1 and three linked drugs that are unlikely to be affected by MKT1. Again Camelot correctly predicted the response to the drugs in an AS (BY MKT1-RM) linkage alone only detects large multi-gene loci in this data set, the zoom-in score further identified PHO84 (chromosome XIII), as the top-ranked causal variant for multiple drugs. Two of these drugs, tetrachloroisophthalonitrile and pentachlor- ophenol, were manually identified and verified previously (Perlstein et al, 2007). & 2009 EMBO and Macmillan Publishers Limited PHO84 gene expression and feedback The results show a large difference in drug sensitivity between BY and RM. The AS strain (BY GPB2-RM) grows at a rate similar to the RM strain. (B) Camelot identifies two loci (Chromosome I: 1–55 329 and Chromosome XIII: 27 644– 33 681) and causal genes encoded within these loci, GPB2 and PHO84, that are responsible for the response to haloperidol. (C) Analysis shows that GPB2 and PHO84 interact with each other to influence growth in the presence of haloperidol. Shown are the genotypes for PHO84 and GPB2, and growth in the presence of haloperidol. Segregants with both the PHO84-RM and GPB2-BY alleles have significantly better resistance (P-value from Wilcoxon rank-sum test) to haloperidol compared with other segregants. Figure 5 Causal role of GPB2 in response to drugs. (A) Strains were grown overnight in YPD medium, diluted to OD600B0.2 and plated with 10-fold dilution on YPD þ drug media (see section Materials and methods). The top three panels are photos of YPD plates containing DMSO (control), E6 berbamine or gliotoxin. The bottom panels are photos of YPD plates containing DMSO or haloperidol. The results show a large difference in drug sensitivity between BY and RM. The AS strain (BY GPB2-RM) grows at a rate similar to the RM strain. (B) Camelot identifies two loci (Chromosome I: 1–55 329 and Chromosome XIII: 27 644– 33 681) and causal genes encoded within these loci, GPB2 and PHO84, that are responsible for the response to haloperidol. (C) Analysis shows that GPB2 and PHO84 interact with each other to influence growth in the presence of haloperidol. Shown are the genotypes for PHO84 and GPB2, and growth in the presence of haloperidol. Segregants with both the PHO84-RM and GPB2-BY alleles have significantly better resistance (P-value from Wilcoxon rank-sum test) to haloperidol compared with other segregants. Although the AS strain contains BY cis- and trans-regulatory factors, the presence of the RM coding region alone (with one amino-acid substitution L259P) brought the expression of PHO84 in the AS strain down to that of the RM strain (Figure 6A). The difference in expression results from negative feedback that acts through the Pho84 protein under high- phosphate conditions (Figure 6B; Wykoff et al, 2007). To quantify the degree of negative feedback between strains, we used RT–PCR to measure PHO84 expression under both low and high-phosphate conditions. PHO84 gene expression and feedback As expected, PHO84 expression is significantly downregulated under high-phos- phate, relative to low phosphate, conditions in all three strains (Figure 6C). Nevertheless, the negative feedback is stronger in the RM and AS strains (817- and 170-fold change, respectively) relative to the BY strain that only goes down 11-fold. Under low-phosphate conditions, the gene expression for all three strains is similar, suggesting that the loop is not active (Supplementary Figure 8). This implies that the relative strength of the negative feedback differs between strains under the high-phosphate conditions that activate this loop. BY GPB2 coding region was replaced with that from the RM strain (see section Materials and methods) and experimentally validated Camelot’s prediction that GPB2 plays a causal role in response to these drugs by showing that the BY GPB2-RM strain is more sensitive to the presence of E6 berbamine, gliotoxin and haloperidol than the BY strain. Indeed, the AS strain is highly similar to the RM strain on E6 berbamine and haloperidol, suggesting that variation in the GPB2 sequence accounts for much of the difference in the response to these drugs (Figure 5A). Gpb2 is an effector of Ga protein Gpa2 and inhibits PKA downstream of Gpa2, which increases dependence on cAMP (Harashima et al, 2006; Peeters et al, 2006). Both gliotoxin and haloperidol affect the cAMP/PKA pathway. Gliotoxin is a fungicide that increases cAMP/PKA activity (Waring et al, 1997), whereas haloperidol, a clinical antidepressant (dopa- mine D2 receptor antagonist), increases cAMP/PKA activity in striatum (Kaneko et al, 1992; Turalba et al, 2004). These results support our finding that polymorphism in GPB2 has an effect on the response to these drugs, and suggest that the mechanism of action involves G-protein signalling. Our findings suggest that E6 berbamine, whose pharmacological effect remains unknown, may also have similar effect on the cAMP/PKA pathway. We used arsenate, a toxic non-metabolizable phosphate analogue, as an indicator of the relative affinity of Pho84 for phosphate. The RM and AS strains are significantly more sensitive to arsenate, suggesting that the RM version of PHO84 is a more efficient transporter of phosphate than the BY strain (Supplementary Figure 9). This effect is mediated by Pho84 as addition of methylphosphonate (an inhibitor of Pho84) reverses this phenotype (data not shown). It is likely that the differences in Pho84 function between BY and RM are responsible for the observed differences in drug sensitivity. GPB2 a new causal gene for multiple drugs Segregants with both the PHO84-RM and GPB2-BY alleles have significantly better resistance (P-value from Wilcoxon rank-sum test) to haloperidol compared with other segregants. Identifying the genetic basis of drug resistance B-J Chen et al PHO84 Chr XIII Haloperidol Chr I GPB2 statistically, using data from the segregants. Strains carrying both RM-PHO84 and BY-GPB2 grow better than strains with other combinations of alleles (Figure 5C), indicating that PHO84 and GPB2 may function through a common pathway. The involvement of Pho84 as a sensor and signalling molecule for phosphate-based activation of PKA (Giots et al, 2003) further implicates PKA function in the response to haloperidol. 8 Molecular Systems Biology 2009 GPB2 a new causal gene for multiple drugs Both PHO84 and MKT1 have previously been shown to influence phenotypic differences between BY and RM, although Camelot successfully linked four new phenotypes (response to drug) to PHO84 and three new phenotypes to MKT1. To further test Camelot, we assessed whether it could identify new genes, not previously implicated in the differ- ences between BY and RM. One of the strongest signals from our zoom-in analysis comes from the locus of Chromosome I: 1–55 329, which links to growth under a number of drugs including haloperidol, E6 berbamine and gliotoxin. Segregants bearing the RM allele are highly sensitive to these drugs. GPB2 is consistently the top-scored gene at this locus for all these drugs. Sequence alignment showed that GPB2 differs by 10 amino-acid substitutions between BY and RM and that one of them is highly conserved across fungal species (P269L, BY-GPB2 encodes proline and RM-GPB2 encodes leucine). We engineered an AS strain (BY GPB2-RM) in which the entire Molecular Systems Biology 2009 7 & 2009 EMBO and Macmillan Publishers Limited Identifying the genetic basis of drug resistance B-J Chen et al PHO84 Chr XIII Haloperidol Chr I GPB2 BY-GPB2RM E6 b. Gliotoxin Haloperidol BY RM BY-GPB2RM BY RM DMSO DMSO Chr XIII Chr I Haloperidol at 55 h P<10–6 P<2.7 x 10–7 PHO84RM PHO84BY GPB2RM GPB2BY Haloperidol at 72 h Figure 5 Causal role of GPB2 in response to drugs. (A) Strains were grown overnight in YPD medium, diluted to OD600B0.2 and plated with 10-fold dilution on YPD þ drug media (see section Materials and methods). The top three panels are photos of YPD plates containing DMSO (control), E6 berbamine or gliotoxin. The bottom panels are photos of YPD plates containing DMSO or haloperidol. The results show a large difference in drug sensitivity between BY and RM. The AS strain (BY GPB2-RM) grows at a rate similar to the RM strain. (B) Camelot identifies two loci (Chromosome I: 1–55 329 and Chromosome XIII: 27 644– 33 681) and causal genes encoded within these loci, GPB2 and PHO84, that are responsible for the response to haloperidol. (C) Analysis shows that GPB2 and PHO84 interact with each other to influence growth in the presence of haloperidol. Shown are the genotypes for PHO84 and GPB2, and growth in the presence of haloperidol. & 2009 EMBO and Macmillan Publishers Limited PHO84 gene expression and feedback In total, we validated 18/18 predictions made using the zoom- in score, including 9/9 for PHO84. Although PHO84 has two SNPs between BY and RM in its coding region, there is no genetic variation in regulatory regions such as the promoter or 30UTR. Moreover, the AS strain, containing only one amino- acid substitution (L259P) in the coding region of PHO84 in the BY background, recapitulated the growth rate of RM for many of the positive drugs tested. So it is surprising that expression of PHO84, generated in the absence of any drugs, could accurately distinguish between drugs that are affected by PHO84 and those that are not. To better understand why this information is encoded in the expression data, we carried out RT–PCR using strains grown in YPD media (no drug) to monitor PHO84 expression in the BY, RM and the AS (BY PHO84-RM) strains. Figure 5 Causal role of GPB2 in response to drugs. (A) Strains were grown overnight in YPD medium, diluted to OD600B0.2 and plated with 10-fold dilution on YPD þ drug media (see section Materials and methods). The top three panels are photos of YPD plates containing DMSO (control), E6 berbamine or gliotoxin. The bottom panels are photos of YPD plates containing DMSO or haloperidol. The results show a large difference in drug sensitivity between BY and RM. The AS strain (BY GPB2-RM) grows at a rate similar to the RM strain. (B) Camelot identifies two loci (Chromosome I: 1–55 329 and Chromosome XIII: 27 644– 33 681) and causal genes encoded within these loci, GPB2 and PHO84, that are responsible for the response to haloperidol. (C) Analysis shows that GPB2 and PHO84 interact with each other to influence growth in the presence of haloperidol. Shown are the genotypes for PHO84 and GPB2, and growth in the presence of haloperidol. Segregants with both the PHO84-RM and GPB2-BY alleles have significantly better resistance (P-value from Wilcoxon rank-sum test) to haloperidol compared with other segregants. Figure 5 Causal role of GPB2 in response to drugs. (A) Strains were grown overnight in YPD medium, diluted to OD600B0.2 and plated with 10-fold dilution on YPD þ drug media (see section Materials and methods). The top three panels are photos of YPD plates containing DMSO (control), E6 berbamine or gliotoxin. The bottom panels are photos of YPD plates containing DMSO or haloperidol. PHO84 gene expression and feedback BY A BY PHO84−RM RM −6 −3 0 log fold difference B Pho84 Intracellular Pi A B D NPP1 PHO85 PHO86 PHO87 PHO84 PHO84 GTR1 Chr III Chr X Chr XIII Chr XVI C BY BY PHO84−RM RM −9 −6 −3 0 log fold difference D D C Figure 6 Feedback in PHO84 expression. (A) Expression levels of PHO84 in the BY, RM and the PHO84-RM AS strains. The expression of PHO84 in the AS and RM strains is similar and significantly lower than in BY. The fold difference is calculated relative to the BY strain. Since the AS strain only differs from the BY strain in the PHO84 coding sequence, feedback regulation must act through the PHO84 gene itself. The error bars represent the s.d. of three replicates. All RT–PCR experiments were conducted independently at least three times. (B) A negative feedback loop regulates expression of Pho84 in response to the concentration of intracellular phosphate. When phosphate levels are low, Pho84 is expressed and transports inorganic phosphate into the cell; Pho84 is repressed as intracellular phosphate levels rise. (C) Expression of PHO84 in SC þ high-phosphate media compared with that in SC þ low-phosphate media for each strain. The cells were harvested 90 min after the addition of phosphate. The AS and RM strains are repressed to a greater extent than BY in response to the addition of phosphate. (D) Weak eQTL that influence the expression of PHO84. These loci are enriched in genes involved in phosphate metabolism and phosphate transport. PHO84 expression links to regions that contain GTR1, NPP1, PHO84, PHO85, PHO86 and PHO87. The width of arrows corresponds to the significance of linkage (P-value for each linkage o0.01; see section Materials and methods). The only region that links to PHO84 expression is its own. PHO84 has strong cis-linkage with P-value 6.3 105. We therefore asked why PHO84 expression might provide in- formation beyond that of the presence of the PHO84 allele. Removing the genome-wide correction for multiple testing in eQTL, we detect additional regions, each with very weak linkage (Supplementary Table V). These regions contain GTR1, NPP1, PHO85, PHO86 and PHO87, each involved in phosphate metabolism/transport, that contain multiple non-synonymous coding SNPs. This suggests that many genes associated with phosphate metabolism/transport (enrichment P-value 7.4 106; see section Materials and methods) weakly influence PHO84 and the expression data represent the combined influence of these factors (Figure 6D). PHO84 gene expression and feedback The models constructed by Camelot are not ‘black box’ predictors, but explain the variation in phenotype between the segregants by identifying the genes that influence the phenotype. We use gene expression data to pinpoint causal variants within large linked regions and to identify genes, outside linked regions, whose change in expression mediates the drug response. For each feature type (transcript and marker) we took the two largest hubs (i.e., a gene associated with many drugs) and systematically validated Camelot’s predictions. We also identified a new causal gene GPB2 and linked it to a number of drugs including the antidepressant haloperidol. Twenty-five out of 27 predictions of causal factors associated with response to a drug were confirmed, demon- strating that our method is robust. By incorporating signal from gene expression, Camelot not only identifies the causal genes driving the phenotype, but also provides insights into changes in the underlying regulatory network and the mechanisms involved. For example, the results from Camelot suggest a role for mitochondria in response to a number of drugs. & 2009 EMBO and Macmillan Publishers Limited Molecular Systems Biology 2009 9 PHO84 gene expression and feedback Variation in gene expression serves as an indicator of the variation in protein function, which acts through a feedback mechanism; the expression level itself is unlikely to be causal directly. The response to haloperidol is highly variable among segregants. Although the mechanism of action could not be established based on linkage to a large region alone, Camelot provided clues by zooming in on GPB2 and PHO84. These genes were subsequently validated as causal for the drug response phenotype (Figure 5B). We assessed the combined influence of both genes for growth under haloperidol Identifying the genetic basis of drug resistance B-J Chen et al BY A C D B BY PHO84−RM RM −6 −3 0 log fold difference BY BY PHO84−RM RM −9 −6 −3 0 log fold difference Pho84 Intracellular Pi NPP1 PHO85 PHO86 PHO87 PHO84 PHO84 GTR1 Chr III Chr X Chr XIII Chr XVI Figure 6 Feedback in PHO84 expression. (A) Expression levels of PHO84 in the BY, RM and the PHO84-RM AS strains. The expression of PHO84 in the AS and RM strains is similar and significantly lower than in BY. The fold difference is calculated relative to the BY strain. Since the AS strain only differs from the BY strain in the PHO84 coding sequence, feedback regulation must act through the PHO84 gene itself. The error bars represent the s.d. of three replicates. All RT–PCR experiments were conducted independently at least three times. (B) A negative feedback loop regulates expression of Pho84 in response to the concentration of intracellular phosphate. When phosphate levels are low, Pho84 is expressed and transports inorganic phosphate into the cell; Pho84 is repressed as intracellular phosphate levels rise. (C) Expression of PHO84 in SC þ high-phosphate media compared with that in SC þ low-phosphate media for each strain. The cells were harvested 90 min after the addition of phosphate. The AS and RM strains are repressed to a greater extent than BY in response to the addition of phosphate. (D) Weak eQTL that influence the expression of PHO84. These loci are enriched in genes involved in phosphate metabolism and phosphate transport. PHO84 expression links to regions that contain GTR1, NPP1, PHO84, PHO85, PHO86 and PHO87. The width of arrows corresponds to the significance of linkage (P-value for each linkage o0.01; see section Materials and methods). Data and pre-processing The strain, genotype and gene expression measurements used are those of Brem and Kruglyak (2005). Growth yields in the presence of chemicals (‘drug’), consisting of 313 growth conditions (different concentrations of chemicals and time points) and 94 different chemical molecules, were from Perlstein et al (2007). These include genotype, gene expression and drug response data for 104 strains. We merged adjacent, highly-correlated markers, to obtain a total of 526 markers (Lee et al, 2006). For our analysis, we normalized all data to have a mean of 0 and variance of 1. We compiled a list of candidate gene expression features based on two sources. One contained genes with potential regulatory effects, including transcription factors, signalling molecules, chromatin factors and RNA factors, as described by Lee et al (2006). The other list included genes involved in vacuolar transport, endosome, endosome transport and vesicle-mediated transport, since these functions, or cellular compartments, are enriched for multi-drug resistance genes (Hillenmeyer et al, 2008). We combined these two lists and filtered out genes with s.d.p0.2 in expression level, obtaining 854 expression profiles, which were used as candidate features for all our models. GO categories from http:// www.yeastgenome.org/ were used to associate genes with each category. Camelot uses gene expression data generated under control conditions to predict the phenotype under a new condition. The additional power gained from gene expression is remark- able given that the gene expression and genotype data used here were generated in the absence of drugs, two years before the generation of the growth (drug) data in another laboratory (Brem and Kruglyak, 2005; Perlstein et al, 2007). This shows that our results are based on a robust phenomenon and represent an inherent characteristic of the segregants. They are compatible with our work demonstrating that genetic variation alters cell state and predisposes the segregants towards different cellular responses (Litvin et al, 2009). We propose that gene expression is useful because it integrates information from multiple loci that are individually too weak to detect, but which, in combination, contribute significantly to the phenotype (Figure 6D). In this way, the combined influence of a large number of weak linkages (many of which are undetectable) can explain a large part of the heritable variation and as a consequence, gene expression data, generated under reference conditions, helps in predicting the response of segregants to new drugs. Discussion We systematically applied Camelot to predict growth of 104 yeast strains in the presence of one of a panel of 94 diverse drugs. Camelot consistently performed well and successfully built robust predictive models for 87/94 drugs. It is intriguing that a single gene expression profile measured in the absence of any drugs empowered the prediction of traits under novel conditions ( þ drugs) that are dramatically different from the perturbation-free conditions used for expression profiling. Identification of a transcript feature does not necessarily mean that the amount of transcript is responsible for the difference in phenotype between the strains. In the case of DHH1 (whose coding sequence is identical in BYand RM), it is likely that a difference in DHH1 expression accounts for variation in the regulation of mitochondrial biogenesis genes & 2009 EMBO and Macmillan Publishers Limited Molecular Systems Biology 2009 9 Identifying the genetic basis of drug resistance B-J Chen et al Camelot’s integration of genotype and gene expression not only enhances its ability to pinpoint causal genes, but it can also potentially identify the mechanism of action and the biological processes involved, thereby expanding the number of drug targets, for example, by identifying a connection between Dhh1 and mitochondria. Our method, therefore, has immedi- ate application for identifying alternative or novel drug targets, for example, in drug-resistant pathogens. Our approach is highly robust and is applicable to other phenotypes and species, including humans. For example, genotype and gene expression data generated from each patient in the non- perturbed (non-diseased or non-drugged) state prior to the onset of disease could be used to predict outcomes (positive or negative responses to a drug or adverse reactions) in response to the therapeutic interventions under consideration. A critical feature is that appropriate drugs/interventions could be predicted for the healthy individual before a drug is administered. While the statistical and algorithmic improve- ment required to accommodate a genome of greater scale and complexity carries a heavy statistical burden, Camelot provides another step towards the realization of personalized medicine, as well as highlighting the power to be gained by exploiting gene expression data for this application. between individual segregants, and that this influences the drug response. However, for PHO84, it is likely variation in Pho84 function that accounts for the differences in drug sensitivity and that gene expression varies through a feedback mechanism that ‘reports’ the difference in protein function. Generation of the GPB2RM AS strain The mating type of BY4724 was first switched to generate HCY413 using a plasmid that expresses HO from a GAL promoter. BY strains harbouring the GPB2 coding sequence from RM11-1a were generated using the Delitto Perfetto method of Storici and Resnick (Storici et al, 2003; Storici and Resnick, 2006). The GPB2 coding sequence and 50UTR were sequenced to confirm that the coding sequence of the AS strain matched that of RM, whereas the upstream region remained that of BY. Primers used in this study are listed in Supplementary Table II. Data and pre-processing Three explanations are likely; the gene expression data might reflect (i) whether the cell is ‘prepared’ to tolerate a particular type of insult (Tagkopoulos et al, 2008), (ii) genetic variation in the regulatory network and the manner in which it is perturbed in response to the conditions or (iii) genetic variation in protein function via feedback loops. We expect that one or more of these explanations describe the situation for distinct phenotypes, genes and conditions. Discussion We note that a large number of the detected linkages between BY and RM involve feedback loops, including AMN1, HAP1, HAP4 and ZAP1 (Ronald et al, 2005). This could explain why expression frequently helps in the identification of differences in protein function, including in human genetics, where strong cis-eQTLs have been identified for genes whose cognate proteins harbour functional variation associated with human disease, for example, SORT1 associated with lipid metabolism (Willer et al, 2008) and multiple genes associated with metabolic traits (Emilsson et al, 2008). Others have demonstrated the predictive value of gene expression towards classifying phenotype (Golub et al, 1999; Alizadeh et al, 2000; van’t Veer et al, 2002; Huang et al, 2007; Kutalik et al, 2008) and how integrating genotype and gene expression data could be used to better understand the relationship between genotype and phenotype in populations (Mehrabian et al, 2005; Schadt et al, 2005; Chen et al, 2008; Emilsson et al, 2008). However, to our knowledge, Camelot is the first approach to both quantitatively predict phenotype and identify genes that causally affect the phenotype. Central to Camelot is the interplay between causality and predictability; causal genes are better predictors and good predictors are more likely to be causal. Optimization of Camelot for both goals concurrently results in the model’s exceptionally robust performance across an unprecedented number of complex traits. 10 Molecular Systems Biology 2009 Statistical analysis Camelot, the elastic net L model and linkage analysis are evaluated with 10-fold cross-validation (n¼93–94). Elastic net L models are derived in the same way as Camelot models, except that only genotype features were allowed in regression. Linkage analysis is performed with Wilcoxon rank-sum test to scan the 526 merged markers for genome-wide significant linkages (FDR¼2%, Po5.6 105) (Perlstein et al, 2007). Linear regression models are built on significant linkages using robust regression (robustfit function in Matlab). Classification accuracy is used to evaluate predictions of models. Growth data are discretized into three classes according to their normalized values: resistant to the drug, no significant response and sensitive to the drug. Predictions of responses to drugs were made based on the predicted values from regression models. Classification accuracy (Acc) is defined as the number of correct classifications divided by the number of test data. However, the elastic net target function optimizes only for prediction error, which is a proxy for the goal of identifying underlying causal features. Not all predictive features are necessarily causal and indeed elastic net regression alone yields models with too many features (Supplementary Figure 5). We further reduce the number of selected features using non-parametric bootstrap (Efron, 1979). Indeed, our performance on synthetic data demonstrates that wrapping elastic net with bootstrapping enhances the precision with which we identify causal factors (Supplementary Figure 1). The elastic net and bootstrap procedures are used to generate an initial small set of high-quality candidate features. For each selected transcript feature ({E}), we use the triangle test for causality (see below) to refine our set of selected features. To improve the likelihood that the final feature set contains causal genes, transcript features that pass the triangle test are kept in the regression and their associated (genotype) markers are removed, whereas transcript features that fail the test are removed and replaced with their associated genotype markers. Once a final set of features is selected, regression coefficients predicting D (response to drug) are re-optimized. The significance of the interaction between PHO84 and GPB2 alleles is assessed by Wilcoxon rank-sum test, where segregants with both the PHO84-RM and GPB2-BYalleles are treated as one sample and the other segregants as another independent sample. Enrichment of phosphate metabolism/transport-related genes (GO annotation) in the linked regions shown in Figure 6D was calculated using the hypergeometric distribution. PðD; Eg; LgÞ ¼ PðDjLg; EgÞPðEgjLgÞPðLgÞ A biologically plausible model should have a small number of causal factors with a non-zero weight. To achieve this goal, we use the elastic net (Zou and Hastie, 2005) regression method to select only the most significant features. Briefly, we solve the optimization problem We calculate both P(D|Lg, Eg) and P(Eg|Lg) using least-square fitting regression and P(Lg) based on the conservation of the coding sequence (see Supplementary information for more details). The decomposed probability consists of three parts. The first term P(D|Lg, Eg) explains the phenotype with both genotype and expression profile of gene g, suggesting g has a causal effect. The second and third terms act as prior probabilities that the gene has a causal role, independent of the specific phenotype. ^b ¼ arg min b D  Xb j j2; subject to ð1  aÞ b j j1þa b j j2pt for some t; where D represents growth, X is the feature matrix (both D and X are standardized), b (^b, the solution) is the vector of coefficients and a and t are regularization parameters chosen using a 10-fold cross-validation procedure. The regularization terms reduce over-fitting the data. The constraint enforced by the l1 norm assures sparseness of selected features and l2-norm prevents arbitrary choice of only one out of several highly correlated features. The latter is especially important in the gene expression domain, which is abundant in large groups of highly correlated features. To compute the coefficients ^b, we used least angle regression (LARS) (Efron et al, 2004). Validation growth experiments Strains used in this study are listed in Supplementary Table I. The MKT1-SK1 (D55N) and PHO84 (L259P) AS strains are as described (Deutschbauer and Davis, 2005; Perlstein et al, 2007). The dhh1D & 2009 EMBO and Macmillan Publishers Limited & 2009 EMBO and Macmillan Publishers Limited Identifying the genetic basis of drug resistance B-J Chen et al strain was a gift from Liz Miller (Columbia University). MKT1, PHO84 and dhh1D growth yield experiments were performed in multi-well (96- or 384-well) plates as described by Perlstein et al (2007). Serial dilutions were carried out in replicate and the resulting growth yield and IC50 values generated using GraphPad Prism (v. 4.01). strain was a gift from Liz Miller (Columbia University). MKT1, PHO84 and dhh1D growth yield experiments were performed in multi-well (96- or 384-well) plates as described by Perlstein et al (2007). Serial dilutions were carried out in replicate and the resulting growth yield and IC50 values generated using GraphPad Prism (v. 4.01). Triangle test The triangle test is applied to every transcript feature selected and is used to evaluate the likelihood that the gene is significantly predictive of the response to a drug, beyond the contribution of the linked genotype. Assuming a transcript feature E is selected for phenotype D, we use permutation testing to evaluate the significance of causal edge E-D. This is carried out for all genetic loci L that link to E and is controlled for the influence of L-D. More specifically, we assess the significance of association between E and D by permuting E fixed under the genotype L. If gene expression remains significantly predictive (even when permuted while keeping the allele at L fixed), we determine that E holds additional information beyond that encoded in the marker L and is likely a causal factor. For plate assays, overnight cultures of cells were grown in YPD medium at 301C, diluted to OD600B0.1 and plated at 10-fold dilutions on YPD plates containing DMSO or DMSO þ drug. Plates were incubated at 301C or room temperature for 1–2 days for GPB2 or 5 days for the arsenate assay. Final concentrations of drugs were as described by Perlstein et al (2007). For GPB2: gliotoxin (15.3 mM), E6- berbamine (16.5 mM) and haloperidol (66.6 mM); for PHO84: arsenate was used at a final concentration of 2 mM and methylphosphonate at 10 mM as described by Mouillon and Persson (2005). & 2009 EMBO and Macmillan Publishers Limited Zoom-in score An outline of the Camelot algorithm, including the triangle test and zoom-in score, is provided here; see Supplementary information for technical details of the statistical procedures and computational steps. The zoom-in score is a Bayesian prioritization score that ranks all genes within a linked region, evaluating the likelihood that each gene is causal. It is used to pinpoint the causal gene variant responsible for creating the linkage signal, and is applied to each of the marker features selected. The method integrates three cues: ‘Is the gene expression level a good predictor of drug resistance’, that is, does the gene expression correlate with the drug resistance? ‘Is the gene ‘cis- linked’, that is, is the gene’s expression linked to its own locus?’ and ‘How well is the sequence of the gene conserved across 19 yeast species (Wapinski et al, 2007)?’, consistent with our intuition that deviations from the conserved sequence are more likely to have a causal influence. This allows us to prioritize genes within each linked genomic region for their potential effect on the phenotype D. As input, Camelot is given a matrix X of features by segregants for two types: (1) Genotypes of genomic markers, L, derived from SNP microarrays and (2) gene expression data, E, obtained using microarrays under standard conditions (no drug). Additionally, Camelot is given a target matrix Y of drugs by segregants; each row represents D, the response of 104 segregants in the presence of a drug at a particular dose and time point. For each drug response D, Camelot selects a linear regression model, DB{L} þ {E}, involving a small number of selected features ({L} and {E}). The objective is to select a model that is accurate in its prediction of D and whose features are likely to have a causal influence on D, that is, experimentally altering these features (by allele swap, deletion or overexpression) influences the drug response D. The Camelot algorithm progresses in three steps: feature selection, causality testing and model refinement. Let gene g reside in genotype Lg and have an expression profile Eg; we can decompose the joint probability P(D, Eg, Lg) as follows: PðD; Eg; LgÞ ¼ PðDjLg; EgÞPðEgjLgÞPðLgÞ PðD; Eg; LgÞ ¼ PðDjLg; EgÞPðEgjLgÞPðLgÞ Acknowledgements This research was supported by the National Institutes of Health Roadmap Initiative, NIH Director’s New Innovator Award Program, through Grant number 1-DP2-OD002414-01 and National Centers for Biomedical Computing Grant 1U54CA121852-01A1. DP holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund. NLG is supported by NIH G12 RR003037-24-2245476. We thank Ron Davis for the kind gift of YAD350 and Fred Winston for FY1333. We also wish to thank Oren Litvin, Itsik Pe’er, Aviv Regev, Eran Segal, Olga Troyanskaya, Lyle Ungar and Dennis Wykoff for valuable comments. Author contributions: BJC, HCC, NLG and DP designed research; BJC and DP designed the Camelot method; BJC implemented the Camelot method; BJC, HCC and DP analysed the data; EOP performed the drug validation for DHH1, PHO84 and MKT1; DM and HCC constructed the GPB2 allele swap; BJC and HCC performed all experiments related to PHO84 feedback and carried out the drug validation for GPB2; and BJC, HCC and DP wrote the paper. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, Mouy M, Steinthorsdottir V, Eiriksdottir GH, Bjornsdottir G, Reynisdottir I, Gudbjartsson D, Helgadottir A, Jonasdottir A, Styrkarsdottir U, Gretarsdottir S et al (2008) Genetics of gene expression and its effect on disease. Nature 452: 423–428 Evans GB, Furneaux RH, Gainsford GJ, Murphy MP (2000) The synthesis and antibacterial activity of totarol derivatives. Part 3: modification of ring-B. Bioorg Med Chem 8: 1663–1675 modification of ring-B. 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Total RNA was prepared using the Ambion RiboPure-Yeast kit according to the manufacturer’s instructions, with the exception that a 10 mg sample was digested twice each for 1 h at 371C with 2 U DNase I. cDNA was made using the Stratagene AffinityScript kit and random primers. RT–PCR was performed with a Chromo4 machine (BioRad) using iQ SYBR Green Supermix (BioRad) and primers listed in Supplementary Table II. Data were scaled to ERV25 (Pfaffl, 2001). Chellappa R, Kandasamy P, Oh CS, Jiang Y, Vemula M, Martin CE (2001) The membrane proteins, Spt23p and Mga2p, play distinct roles in the activation of Saccharomyces cerevisiae OLE1 gene expression. Fatty acid-mediated regulation of Mga2p activity is independent of its proteolytic processing into a soluble transcription activator. J Biol Chem 276: 43548–43556 For the low and high-phosphate conditions, overnight cultures were washed twice with sterile distilled water and used to inoculate SC medium containing low phosphate (250 mM). 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Oral supplementation with selected Lactobacillus acidophilus triggers IL-17-dependent innate defense response, activation of innate lymphoid cells type 3 and improves colitis
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www.nature.com/scientificreports OPEN Oral supplementation with selected Lactobacillus acidophilus triggers IL‑17‑dependent innate defense response, activation of innate lymphoid cells type 3 and improves colitis Jiří Hrdý1,6, Aurélie Couturier‑Maillard2, Denise Boutillier1, Carmen Lapadatescu3, Philippe Blanc3, Jan Procházka4, Bruno Pot1,7, Bernhard Ryffel2,5,9, Corinne Grangette1,9* & Mathias Chamaillard1,8,9* Live biotherapeutic products constitute an emerging therapeutic approach to prevent or treat inflammatory bowel diseases. Lactobacillus acidophilus is a constituent of the human microbiota with probiotic potential, that is illustrated by improvement of intestinal inflammation and antimicrobial activity against several pathogens. In this study, we evaluated the immunomodulatory properties of the L. acidophilus strain BIO5768 at steady state and upon acute inflammation. Supplementation of naïve mice with BIO5768 heightened the transcript level of some IL-17 target genes encoding for protein with microbicidal activity independently of NOD2 signaling. Of these, the BIO5768-induced expression of Angiogenin-4 was blunted in monocolonized mice that are deficient for the receptor of IL-17 (but not for NOD2). Interestingly, priming of bone marrow derived dendritic cells by BIO5768 enhanced their ability to support the secretion of IL-17 by ­CD4+ T cells. Equally of importance, the production of IL-22 by type 3 innate lymphoid cells is concomitantly heightened in response to BIO5768. When administered alone or in combination with Bifidobacterium animalis spp. lactis BIO5764 and Limosilactobacillus reuteri, BIO5768 was able to alleviate at least partially intestinal inflammation induced by Citrobacter rodentium infection. Furthermore, BIO5768 was also able to improve colitis induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS). In conclusion, we identify a new potential probiotic strain for the management of inflammatory bowel diseases, and provide some insights into its IL-17-dependent and independent mode of action. Crohn’s disease (CD) is traditionally characterized by impaired dendritic cells f­ unction1 and the development of transmural inflammatory lesions leading to progressive destruction of the intestinal wall. In Europe, the combined prevalence is about 250–300 cases per 100,000 inhabitants. Several epidemiological and experimental 1 Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d’Infection et d’Immunité de Lille, 59000 Lille, France. 2INEM‑UMR7355, Molecular Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), and Infectious Diseases, University and CNRS, Orléans, France. 3Bioprox, 7 rue Aristide Briand, 92300 Levallois‑Perret, France. 4Institute of Molecular Genetics, Czech Centre for Phenogenomics, Czech Academy of Sciences, 252 50 Vestec, Czech Republic. 5Division of Immunology and South African Medical Research Council (SAMRC) Immunology, Department of Clinical Immunology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925 Cape Town, RSA. 6Present address: Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic. 7Present address: Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium. 8Present address: Univ. Lille, Inserm, U1003, 59000 Lille, France. 9These authors jointly supervised this work: Bernhard Ryffel, Corinne Grangette and Mathias Chamaillard. *email: corinne.grangette@pasteur-lille.fr; mathias.chamaillard@inserm.fr Scientific Reports | (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 1 Vol.:(0123456789) www.nature.com/scientificreports/ evidences indicate that incidence rates in emerging countries are rising due to the influence of many geneenvironmental interactions, such as, amongst others, NOD2 signaling and tobacco ­smoking2,3. While the lifetime therapeutic management of the disease is far from optimal, CD alters patient’s ability to work and their social interaction in various ways. Invasive surgery and bowel resection is required in about two-thirds of CD patients, although it does not cure the disease. Consequently, the annual economic burden of medical care of CD patients ranges between 2.1 and 16.7 billion € in Europe with about 2.2 million people a­ ffected4. The gut microbiota plays a crucial role in many physiological processes from the earliest days of life, including the maturation of intestinal immunity. Recent progress in high-throughput sequencing revealed that lowered bacterial diversity is commonly observed in the gut microbiota of CD p ­ atients5,6. Specifically, a decreased prevalence of the anti-inflammatory Faecalibacterium prausnitzii was associated with a higher risk of postoperative recurrence of ileal ­CD7. Inappropriate interaction between F. prausnitzii and the mucosal immune system is thereby thought to progressively impairs the integrity of the intestinal barrier and subsequently influence disease initiation and p ­ rogression8,9. During the early postnatal period when the gut associated lymphoid tissue is developing, it has now been demonstrated that both interleukin-17 (IL-17) and interleukin-22 (IL-22) may shape the gut microbiota composition and promote the integrity of the intestinal b ­ arrier10. This said, both IL-17 and IL-22 needs to be tightly regulated to prevent unwarranted tissue damage and epithelial cell proliferation. At steady state, the major source of IL-17 and IL-22 are CD4-expressing T cells and the type 3 innate lymphoid cell (ILC3) respectively, defect of which may result in dysbiosis and increased susceptibility to intestinal i­ nflammation11–13. Under normal conditions, ILC3 is induced by bacterial metabolites such as SCFA or tryptophan metabolites. Pleiotropism in T ­ h17-associated responses may at least be attributed to IL-22. The aforementioned protective effect of IL-17 and IL-22 mainly relies on the downstream secretion of anti-microbial peptides (AMPs) by intestinal epithelial cells. Even if a matter of ongoing debate concerns the precise epithelial cell type that is targeted by IL-17 and IL-22, we and other postulated that the treatment of IBD may be improved with therapeutic agents that reinforce IL-17 and IL-22-mediated intestinal barrier function. Supplementation with health-promoting probiotics is becoming particularly attractive not only to reconstitute the diversity and the functionality of patient’s microbiome but also to counteract the exaggerated inflammatory responses. While probiotics showed successful impact against ulcerative colitis, none of the reported clinical trials with probiotics proved some efficacy in ­CD14–17. A possible explanation for such inefficiency is that their mode of action may rely on certain genes that are found mutated in CD patients. In agreement with this hypothesis, we provided evidence that the protective capacity of a selected strain of Ligilactobacillus salivarius Ls33 (formerly known as Lactobacillus salivarius Ls33) requires an intact nucleotide-binding oligomerization domain 2 (NOD2) ­signaling18, mutations of which occur in more than one third of CD patients in Europe and North America. We then performed a comprehensive screening of the Bioprox probiotic collection for identifying strains that are exhibiting anti-inflammatory and antimicrobial abilities independently of NOD2 signaling. This led us to identify a Lactobacillus acidophilus strain able to induce IL-17-dependent antimicrobial responses independently of NOD2. This rod-shaped strain BIO5768 that produces lactic acid through the fermentation of carbohydrates was originally isolated from the human gastrointestinal tract and is produced and commercialized as dietary supplements by the society Bioprox Healthcare. In the current study, we report that supplementation with L. acidophilus BIO5768 enhanced the activity of CD4-expressing T cells and type 3 innate lymphoid cells (ILC3), that are known to play an essential role in the maintenance of the barrier function and tissue ­repair16,19. ILC3 is a heterogeneous population consisting of three subpopulations: ­NCR+ ILC3, ­NCR- ILC3 and LTi. Specifically, we tested their capacity to modulate the expression of antimicrobial peptides (AMPs) and the secretion of IL-17 both in vitro and in vivo. Of these, the expression of Angiogenin 4 that is secreted by Paneth cells and Goblet cells into the gut lumen was enhanced in response to BIO5768 in an IL-17-dependent (but not NOD2-independent) manner. Equally of importance, its ability to induce the secretion of additional AMPs (such as Defa4, Defb2, Reg3b and Reg3g) was shown to be independent of IL-17. Given that BIO5768 exhibited a different mode of action than the previously studied strains Bifidobacterium animalis spp. lactis BIO5764 (referred herein as BlO5764) and Limosilactobacillus reuteri BIO5454 (formerly known as Lactobacillus reuteri BIO5454, referred herein as BIO5454)20, we compared its anti-inflammatory capacity in vivo when administered alone or in combination, by using a Citrobacter rodentium infection model. The anti-inflammatory property of BIO5768 was then confirmed by making use of a TNBS colitis model. Results L. acidophilus BIO5768 heightens IL‑22 production by type 3 innate lymphoid cells and maturation of dendritic cell that supports IL‑17 by CD4‑expressing T cells. We first evaluated the capacity of either freshly cultured (F) or lyophilized (L) BIO5768 to regulate the expression of Th17 cytokines and their antimicrobial target genes in the small and large intestine of mice. Oral supplementation with lyophilized (but not freshly cultured) BIO5768 significantly increased the expression of Il17a (p < 0.05) and to a lower extent of Il22 (p = 0.0519) in the small intestine Fig. 1A). In agreement, the expression of the Defb2 gene significantly correlated with its upstream regulator IL-22 (Spearman r 0.7637, P value two tailed = 0.0034). Similar results were observed in the colon, but the difference did not reach significance (Fig. 1B). These result suggested that BIO5768 may preferentially adhere to the small intestine for strengthening the activity of Th17 and ILC3 cells at steady state. This led us to evaluate the production of IL-17 and IL-22 by their major cellular sources within the draining mesenteric lymph nodes (MLN). In agreement with our qRT-PCR analysis, flow cytometry analysis revealed an increased number of IL-22-producing Natural Cytotoxicity Receptor negative (NCR-) ILC3 in the MLN of mice supplemented by BIO5768 (Fig. 1C and Figs. S1 and S2). By contrast, a similar frequency of either IL-17-producing CD4 T cells or IL-22-producing NCR + ILC3 cells was observed in the MLN of treated and untreated mice (Fig. S3). Furthermore, BIO5768 was not able to expand the number of regulatory T cells Scientific Reports | Vol:.(1234567890) (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 2 www.nature.com/scientificreports/ Figure 1.  Capacity of the L. acidophilus BIO5768 to induce the expression of antimicrobial genes downstream of IL-17 and IL-22 and to activate bone marrow derived dendritic cells (BMDC) for supporting production of IL-17- and IL-22. Gene expression by qRT-PCR analysis of Reg3g, Reg3b, Defa4, Defb2, Il22 and Il17a (A) in the small intestine or (B) in the proximal colon of BALB/c mice after 5 days of either fresh (F; n = 6) or lyophilized (L; n = 6) BIO5768 supplementation when compared to controls (n = 6). Results are expressed as relative gene expressions ­(2−∆∆ct) values, by comparing the PCR cycle thresholds (Ct) for the gene of interest and for the house keeping gene β-actin (bact), compared with control mice. (C) Percentage of IL-17-producing CD4 T cells and of IL-22 producing NCR- ILC3 within mesenteric lymph nodes of mice that were supplemented with BIO5768 (n = 7) when compared to control animals (n = 6), as determined by flow cytometry. (D) Measurement of IL17 production by ELISA in the supernatant collected after 24 h of coculture between untreated or BIO5768stimulated BMDCs and naïve CD4 T cells that were sorted by magnetic beads. (E) Comparison of MFI (Mean of Fluorescence Intensity) of activation markers MHCII, CD40 and CD86 in untreated or BIO5768-stimulated BMDCs. Representative results of 6 independent in vitro experiments are shown (bars represent mean ± SEM). * p < 0.05; **p < 0.01; ***p < 0.001. (Fig. S3). We then evaluated the capacity of the BIO5768 strain to induce the maturation of bone marrow derived dendritic cells (BMDCs) that play a key role in the induction of cellular immunity and polarization of protective T helper cell subsets. To this end, BMDCs from BALB/c mice were stimulated by BIO5768 for 24 h before being co-cultured with unfractionated naïve CD4-expressing T cells at a ratio of 1:10. In agreement, the secretion of IL-17 was significantly enhanced when BIO5768-primed BMDCs were cocultured with CD4 T cells (Fig. 1D). To get further insights, cell surface markers of DC activation were analyzed by flow cytometry. Clearly, BIO5768 significantly increased cell surface presence of MHCII (p < 0.01), CD40 (p < 0.05) and CD86 (p < 0.01), demonstrating a strong effect of BIO5768 on the maturation of DC (Fig. 1E). Collectively, these experiments revealed that BIO5768 support the capacity of DCs to induce the production of IL-17 and IL-22 by ­CD4+ T cells and type 3 innate lymphoid cells, respectively. IL‑17 signaling is required for induction of Angiogenin‑4 in response to L. acidophilus BIO5768 independently of NOD2. To test the possible dependence of NOD2 and IL-17 signaling on the induction IL-22-mediated immune response to BIO5768, germ-free (GF) mice deficient for Nod2 (Nod2−/−), for the receptor-Interacting Protein 2 (Rip2−/−) and for IL-17 Receptor A (IL17ra−/−) were mono-colonized or not by BIO5768 and compared to wild-type (WT) germ free (GF) animals. Thirty days after mono-colonization, BIO5768 significantly promoted gene expression of Defa4, Reg3g and Ang4 in both caecum and colon of mono-colonized WT mice when compared to GF animals (Fig. 2A and Fig. S4). The increase of Reg-3γ was also confirmed at the protein level after immunohistochemistry staining of small intestinal section of Balb/c mice that were supplemented (or not) with BIO5768 (Fig. S4). Of interest, the induction of Ang4 expression was blunted in the colon Scientific Reports | (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 3 Vol.:(0123456789) www.nature.com/scientificreports/ Figure 2.  The anti-microbial abilities of L. acidophilus BIO5768 in vivo is independent of NOD2 and IL-17 signaling. GF female WT (n = 9) or deficient for NOD2 (Nod2−/−; n = 5), RIP2 (Rip2−/−; n = 4), and IL-17 Receptor A (Il17Ra−/; n = 4) were mono-colonized with strain BIO5768 by a single administration (5 × ­108 CFU/ mice) and compared to untreated GF WT mice (n = 9). (A) After 30 days mono-association, gene expression by qRT-PCR analysis of Reg3g, Reg3b, Ang4, Defa4, Defb2, Il10, Il17a, Il17f and Il22 in the distal colon and caecum of monocolonized and GF mice. Results are expressed as means ± SEM by comparing the PCR cycle thresholds (Ct) for the gene of interest and for the house keeping gene Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) of mono-colonized animals compared with GF WT mice. (B) Impact of BIO5768 monocolonization on the percentage of IL-22 producing NCR + and NCR− ILC3 and C ­ D4+ T cells within colon and caecum, as determined by flow cytometry. Data represent means values of each group from one gnotobiotic experiment ± SEM. * p < 0.05; **p < 0.01; ***p < 0.001. of mono-colonized Il-17r−/− mice, while greater variability was noticed for either similarly treated Nod2- or Rip2-deficient mice (Fig. 2A). Even if we also observed some heterogeneity between Nod2-deficient mice, the supplementation with BIO5768 heightened the expression of the known Nod2-target gene Defa4 independently of IL-17 signaling (Fig. 2A). In agreement with our gene expression analysis depicted in Fig. 1, BIO5768 administration failed to induce colonic expression of Defb2, Il17a and Reg3b. On the other hand, BIO5768 induced gene expression of key immunoregulatory cytokine Il10 and Il17f in WT independently of NOD2 and IL-17 signaling (Fig. 2A). In line with this observation, Nod2 expression was dispensable for the ability of BIO5768 to promote the maturation of BMDCs (data not shown). Furthermore, administration of BIO5768 significantly lowered transcript level of Il22 in WT (p < 0.01), Nod2−/− (p = 0.057) and Rip2−/− (p < 0.01) to a similar extent as what observed with commensal bacteria belonging to class Clostridia that modulate retinoic acid concentration in the ­gut21. By contrast to what observed at the transcriptional level, FACS analysis of the large intestine and the caecum from GF and monocolonized mice revealed an enhanced proportion of IL-22-producing ILC3 and ­CD4+ T cells despite similar mean fluorescence intensity of IL-22 staining and numbers of either ILC3 or ­CD4+ T cells (Fig. 2B). Collectively, these results indicate that sensing of BIO5768 indirectly modulates accumulation of IL-22-producing ILC3 in an IL-17 dependent manner. L. acidophilus BIO5768 downregulates inflammatory responses induced by Citrobacter rodentium infection. A Citrobacter rodentium infection model in mice was used since both IL-17 and IL-22 are involved in host defense against this pathogenic bacterium. C. rodentium mimics the human situation in which enteropathogenic and enterohemorrhagic strains of Escherichia coli contribute to the development of intestinal diarrhea. We therefore evaluated the impact of the oral administration of BIO5768 on the prevention and/or limitation of transient colitis caused by this pathogenic bacterium. Despite no effect of BIO5768 on bacterial Scientific Reports | Vol:.(1234567890) (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 4 www.nature.com/scientificreports/ Figure 3.  Impact of L. acidophilus BIO5768 supplementation in a mouse model of C. rodentium infection. BIO5768 (5 × ­108 CFU) was daily administered to C57BL/6J mice 5 days prior to infection and after the infection until the day of sacrifice. Mice were orally inoculated with 1 × ­109 CFU C. rodentium DBS 120 K strain and sacrificed at either 4 or 9 days after infection. (A) Effect of BIO5768 on bacterial load of C. rodentium determined by plating over the course of the experiment, fecal samples dilution on Luria Bertani medium containing 50 µg/ml kanamycin and compared with control infected mice. (B) Effect of BIO5768 supplementation on the colon length. (C) Effect of BIO5768 supplementation on the crypt length. (D) qRT-PCR analysis of the expression of pro-inflammatory genes in the proximal colon of mice after 4 days post infection. (E) qRT-PCR analysis of the expression of pro-inflammatory genes in the distal colon of mice after 10 days post infection. Results are expressed as relative gene expressions (­ 2−∆∆ct) values, by comparing the PCR cycle thresholds (Ct) for the gene of interest and for the house keeping gene β-actin (bact), compared with control mice. Results of a representative experiment out of 2 are expressed as means ± SEM of uninfected control mice (n = 10) and infected mice that are supplemented (n = 5) or not (n = 10) with BI05768. * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001. burden (Fig. 3A), administration of BIO5768 improved the colon shortening that is caused by C. rodentium (Fig. 3B). By contrast, no effect of BIO5768 administration was observed on crypts hyperplasia measured at day 10 post-infection (Fig. 3C). C. rodentium infection significantly increased the colonic expression of genes encoding for TNF-α and IL-6 at day four post infection compared to non-infected mice (p < 0.05). Administration of BIO5768 significantly improved the transcript level of Il6 at the proximal colon of mice (p < 0.05) compared to group infected by C. rodentium without probiotic bacteria supplementation (Fig. 3D). After 9 days post infection, the expression of Tnfa (p < 0.001), Il6 (p < 0.0001), Il1b (p < 0.001) and Il10 (p < 0.05) was significantly heightened in the distal colon of infected mice, despite no difference on Foxp3, when compared to non-infected animals (Fig. 3E and Fig. S4). By contrast, the expression of these aforementioned pro-inflammatory markers in the colon of infected mice supplemented with BIO5768 was similar to the one of non-infected animals (Fig. 3E). Scientific Reports | (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 5 Vol.:(0123456789) www.nature.com/scientificreports/ Figure 4.  Capacity of the mixture to limit Citrobacter rodentium-induced colitis in C57BL/6J mice. (A) Experimental design. Mixture of three bacterial strains (5 × ­108 CFU/day/mice, all strains were present in equal amount in the mixture) was daily administered by intragastric preventive gavage for 5 days (n = 10 per group). (B) C. rodentium burden, (C) Colon lengths. (D) qRT-PCR analysis of the expression of pro-inflammatory genes in the proximal colon of mice after 4 days post infection when compared to non-infected animals. (E) qRT-PCR analysis of the expression of pro-inflammatory genes in the distal colon of mice after 10 days post infection when compared to non-infected animals. Results from one experiment are expressed as relative gene expressions ­(2−∆∆ct) by comparing the PCR cycle thresholds (Ct) for the gene of interest and for the house keeping gene β-actin (bact), compared with control mice. * p < 0.05; ** p < 0.01, *** p < 0.001. The mixture of BIO5768 with two other strains at least partially alleviated inflammation in the C. rodentium infection model and promotes accumulation of IL‑22‑producing type 3 innate lymphoid cells in a NOD2‑dependent manner. We evaluated the capacity of L. acidophilus BIO5768 in combination (referred as mixture) with the two other strains B. animalis spp. lactis BIO5764 and Li. reuteri BIO5454 that were previously shown to limit the severity of colitis caused by C. rodentium20. Mice were treated orally for five consecutive days by the mixture prior to C. rodentium infection (Fig. 4A). Similarly to single strain application (for BIO5764 and BIO5454 see ­reference20 and for BIO5768 see Fig. 3A), the mixture had no effect on neither the burden of C. rodentium (Fig. 4B) nor on the colon length (Fig. 4C). However, the mixture supplementation was able to significantly downregulate the gene expression of Il1b (p < 0.01—Fig. 4D) as what observed with single strain administration (Fig. 3D). By contrast, only moderate effect of the infection was measured on the colonic expression of either Cxcl2, Tnfa or Il6 at day 4 post-infection (Fig. 4D). After 9 days post-infection, the amplitude of the inflammatory response to the infection was significantly enhanced when compared to earlier time point (Fig. 4E). In addition, the induction of the aforementioned genes was not observed upon the supplementation of the mixture to the mice that were subsequently infected when compared to non-infected mice (Fig. 4E). As what observed with BIO5768 alone, the mixture was not able to increase significantly the abundance of C ­ D4+ ­CD25+ ­FoxP3+ Tregs in MLN (Fig. S6), as previously observed with B ­ IO546420. Daily administration of the mixture to WT mice modestly induced the transcript level of Il22 in a NOD2/ RIP2-dependent manner, although there was no change in expression of Defa4, which is a NOD2-induced antimicrobial peptides (Fig. S6A,B). The capacity of the mixture to promote accumulation of IL-22-producing ILC3 isolated from MLN was then confirmed by multiparameter flow cytometry analysis. As what observed with Scientific Reports | Vol:.(1234567890) (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 6 www.nature.com/scientificreports/ Figure 5.  Protective effect of L. acidophilus BIO5768 supplementation in a mouse model of TNBS-induced colitis. BIO5768 (5 × ­108 CFU of each) was administered to BALB/c mice for 5 consecutive days before and 1 day after TNBS induction (n = 10 mice per group). After 48 h, mice were sacrificed and the impact of BIO5768 was analyzed on (A) Body weight loss, (B) Macroscopic grading of inflammation according to Wallace score, (C) Histological analyses of colon tissue according to Ameho score. (D) Representative histological sections (E) Colon lengths. (F) Gene expression of pro-inflammatory markers as determined by qRT-PCR analysis. Results are expressed as relative gene expressions ­(2−∆∆ct) values, by comparing the PCR cycle thresholds (Ct) for the gene of interest and for the house keeping gene β-actin (bact), compared with control mice. Results correspond to means ± SEM of 10 mice per group of a representative experiment from 2 experiments. *p < 0.05. BIO5768 alone (Fig. 1D), the mixture significantly elevated IL-22 production by N ­ CR− ILC3 in WT mice but not in either Nod2-or Rip2-deficient mice (Fig. S6C). In agreement with our in vitro data that are depicted in Fig. 1, we failed to detect any change in the proportion of IL-17-producing CD4 T cells at steady state (Fig. S6D). Given that BIO5768 has the capacity to promote the accumulation of IL-22-producing ILC3 independently of NOD2, the Bifidobacterium strain BIO5764 that belongs to the phylum of Actinobacteria is likely responsible for the NOD2-dependent IL-22 response to the mixture. L. acidophilus BIO5768 ameliorates the severity of TNBS‑induced acute colitis in mice. The potential ability of the strain BIO5768 to limit the severity of colitis was first evaluated in an experimental murine model of TNBS-induced acute colitis. While we observed only a moderate effect of the bacterial oral supplementation on weight loss (Fig. 5A), BIO5768 administration dampened the severity of colitis as indicated by a significant decrease of the macroscopic Wallace score (Fig. 5B; p < 0.05), confirmed by the histological analyses Scientific Reports | (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 7 Vol.:(0123456789) www.nature.com/scientificreports/ of colon tissue indicated by a decreased Ameho score, albeit at the limit of significance (Fig. 5C,D; p = 0.06). Despite no differences in the colon lengths (Fig. 5E), the expression of genes encoding the pro-inflammatory markers Tnfa and Cxcl2 was also significantly (p < 0.05) downregulated in the BIO5738-treated group and to a lower extend also the gene encoding for Il6 (Fig. 5F). Discussion The anti-inflammatory potential of different Lactobacilli and Bifidobacteria strains in has been largely reported by use of either chemically -induced colitis or infectious ­colitis22–26. Given that we previously reported that the anti-inflammatory capacity of selected lactobacilli relied on an intact NOD2 ­signaling18, we postulated that the NOD2-dependent beneficial effect of probiotics could explain the failure of clinical trials using probiotics in CD. In agreement with our hypothesis, successful results were observed in ulcerative colitis, in which NOD2 plays a minor role if ­any14,17. Genome-wide association studies unveiled that NOD2 is the most important genetic factor linked to abnormal dendritic cell function and AMP production in ileal CD, which are a largely reported feature of the disease. Therefore the selection of probiotic strains able to exhibit protective effects in a NOD2independent manner is relevant to alleviate CD outcome in patients carrying NOD2 mutations. Lactobacillus acidophilus is one of the main commercial species of lactic acid bacteria available in different types of dairy products or dietary supplements with claimed probiotic e­ ffects25. Interestingly, L. acidophilus was reported to suppress the activation of the IL-23/Th17 axis associated with DSS-induced c­ olitis26. RORγt is involved in Th17 cell development, which produces the key effector cytokine IL-17, playing a dual role in IBD. Th17 cells have been shown to be capable of regulatory functions and to be crucial in maintaining mucosal immunity against specific pathogens by promoting mucosal barrier repair. In this report, we demonstrated the capacity of the strain L. acidophilus BIO5768 to improve the severity of inflammation in two experimental models of colitis. The beneficial effect of this facultative anaerobic bacterium was partly mediated by its capacity to promote the functional activity of NCR- subset of ILC3 to secrete IL-22. Furthermore, we demonstrate that BIO5768 may promote the maturation of dendritic cells for supporting the production of IL-17 by CD4 T cells. Consequently, the epithelial expression of transcripts encoding for IL-22 and downstream target gene was blunted in Il17ra−/− mice. This led us to provide evidence that the selected strain BIO5768 triggers IL-17-mediated AMP expression independently of NOD2 signaling. This potential probiotic strain could be of great interest for the treatment of CD patients with loss-of-function NOD2 polymorphisms. In agreement with our observation, neonatal and adulthood supplementation of mice by L. acidophilus also limited the severity of pathology induced by C. rodentium in ­mice16,27. Similarly, L. acidophilus NCFM was shown to be effective in inhibiting colitis induced by C. rodentium28 and other strains are also able to induce a sustained AMP production even if it remains to be determined whether it occurs independently of ­NOD229. Further studies on the efficacy of this bacterial strain in preclinical models of chronic colitis is now awaited, especially in models exhibiting NOD2 deficiency. Indeed, the NOD2fs mutation results in a loss-of-function phenotype in human myeloid dendritic cells in ­CD1. To confirm the efficacy of the strain to treat patients with NOD2 mutations, fate mapping studies are also needed to assess probiotic-induced trained immunity including the migration capacity of DC in vivo. A strain-dependent effect among probiotic species is well known, and differences among L. acidophilus strains in improving intestinal epithelial barrier function was reported ­recently30. Notably, the strain of L. acidophilus LA1 uniquely enhanced intestinal tight ­junction31 barrier function in a TLR2 dependent ­manner30. L. acidophilus was also reported to exhibit antioxidant and anti-inflammatory potential in an experimental model of ­arthritis32. The protective effect of L. acidophilus against experimental colitis was also shown to be dose-dependent, emphasizing the importance of selecting an optimal dosing r­ egimen33. A recent report also indicated that the antiinflammatory abilities of L. acidophilus LA-5 depend on the matrix in which the bacterium is delivered (capsules versus yogurt)34. Different Lactobacillus related taxa and especially Limosilactobacillus reuteri were also shown to activate IL-22 production by ­ILC335,36. Recently, a protective effect of Li. reuteri D8 on tissue repair has been documented in vitro using co-cultured system with lamina propria lymphocytes (LPLs) in an organoid ­model37. The authors demonstrated that the indole-3-aldehyde produced by the strain stimulated LPLs to produce IL-22 through Aryl hydrocarbon Receptor and subsequent phosphorylation of signal transducer and activator of transcription 3 (STAT3)37. Other studies have reported that supplementation with three Lactobacillus strains with high tryptophan-metabolizing activities were able to restore intestinal IL-22 ­production38,39. Lactobacilli were also reported to maintain healthy gut mucosa by producing L-ornithine able to increase the level of l-kynurenine and subsequent expansion of RORγt+ IL-22+ ILC3 c­ ells40. On the contrary, Kennedy et al.41 observed no effect of L. plantarum 299 on TNBS-induced colitis in rat experimental model. It suggests that probiotics may mediate their beneficial effect in a strain-dependent manner via distinct signaling pathways that overall remain poorly studied. Many studies reported improved performance of probiotic mixtures, compared to individual strains. A mixture containing L. acidophilus was shown to alleviate DSS-induced colitis, notably by increasing the expressions of tight junctions and by upregulating the number of ­Tregs42. We then evaluated its probiotic properties in combination with the two other strains B. animalis spp. lactis BIO5764 and Li. reuteri BIO5454, previously reported to exhibit anti-inflammatory abilities in experimentally induced colitis, albeit with different modes of a­ ction20. Indeed, strain BIO5454 efficiently triggered IL-22 secretion by ILC3 and C ­ D4+ T in vitro, and induced regulatory lymphocytes and NOD2-independent AMP expression. BIO5764 efficiently induced IL-17A and IL-22 in a NOD2-dependent manner, while having a minor impact on ­Tregs20. In the C. rodentium infectious colitis model, the mixture with the three strains was able to downregulate the expression of inflammatory genes, in a similar manner as the BIO5768 strain alone. Combining of this strain with two other dairy strains maintained not only the anti-inflammatory potential, but the mixture promoted the secretion of IL-22 by NCR-negative subset of ILC3 in a NOD2-dependent manner. Scientific Reports | Vol:.(1234567890) (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 8 www.nature.com/scientificreports/ Our results suggest that the selected BIO5768 strain alone could provide an interesting complementary therapy in maintaining remission and improving the quality of life of patients. It remains necessary to investigate their clinical efficacy and the safety of the strains even in CD patients bearing NOD2 mutations. Materials and methods Bacterial strains. The three bacterial strains were selected from the Bioprox collection: Limosilactobacillus reuteri BIO5454 (BIO5454), Lactobacillus acidophilus BIO5768 (BIO5768), Bifidobacterium animalis spp. lactis BIO5764 (BIO5764). Lactobacilli were grown at 37 °C in MRS broth (Difco, Detroit, USA). Bifidobacteria were cultured in MRS media supplemented with cysteine (0.5 µg/ml) under anaerobic condition. Bacteria were grown overnight, harvested by centrifugation (10 min at 4000 × g), washed twice with PBS buffer (pH 7.2). For in vitro stimulation, bacteria were resuspended in PBS containing 20% (v/v) glycerol to a final concentration of 2 × ­109 CFU/ml and stored at − 80 °C until used. For in vivo administration, fresh cultured bacteria were resuspended in PBS at 2.5 × ­109 CFU/ml and were intragastrically administrated to mice (5 × ­108 CFU in 200 µl) as described ­previously20. Mice. C57BL/6 and BALB/c female mice were purchased from Charles River (L´Arbresle, France) and were housed in specific pathogen-free condition in the animal facilities of the Institut Pasteur de Lille (accredited No. C59-350009). 7–8 week old mice were maintained in a temperature-controlled (20 ± 2 °C) facility with a strict 12-h dark/light cycle. Animal experiments were performed in compliance with European guidelines of laboratory animal care (number 86/609/CEE) and with French legislation (Government Act 87–848). The study was carried out in compliance with the ARRIVE guideline and was approved by local Animal Ethics Committees (Nord-Pas-de-Calais CEEA N_75, Lille, France) and the Ministère de l’Education Nationale, de l’Enseignement Supérieur et de la Recherche, France (accredited No. 201608251651940). For Citrobacter rodentium infection, experiments were performed in the biosafety level 2 facility as described ­previously20. Before experimentation, animals were provided a one-week acclimation period and were given ad libitum access to regular mouse chow and drinking water. GF that are deficient or not for Nod2 (Nod2−/−), for the receptor Interacting Protein 2 (Rip2−/−), and for IL-17 Receptor A (Il17ra−/−) were generated on a C57BL/6 background at TAMM/CNRS Orleans (TAAM agreement number: D-45-234-6) and were bred in isolators under strict GF conditions. Monocolonisation experiments were approved by national and local Animal Ethics Committees authorization number 1038. Preparation of bone marrow derived dendritic cells (BMDC). BMDC were generated from bone marrow progenitor cells as described p ­ reviously43. Briefly, progenitor cells were obtained by flushing tibia and femur from BALB/c mice and cultured at 37 °C under 5% ­CO2 in Iscove’s modified Dulbecco’s media supplemented by FCS (10%), gentamycin (50 µg/ml), glutamine (2 mM), β-mercaptoethanol (50 µM) and 10% of supernatant from a granulocyte–macrophage colony-stimulating factor (GM-CSF)-expressing J588 myeloma cell line for 10 days. On day 10, cells were stimulated by bacteria (ratio bacteria/cell: 10:1). After 24 h stimulation, BMDC were harvested, washed and stained using mAbs anti-CD11c PE-Cy7, CD40 PE, CD80 FITC, CD86 PE-Cy5, MHCII APC (eBioscience, San Diego, CA, USA) and acquired on BD FACS Canto II (Becton Dickinson). Preclinical model of TNBS‑induced colitis. TNBS-induced murine model of acute colitis was performed using BALB/c mice as described p ­ reviously20. Briefly, anesthetized mice received an intra-rectal administration of TNBS (Sigma-Aldrich Chemical, France; 110 mg/kg) dissolved in 0.9% NaCl/ethanol (50/50 v/v). The protective effect of the probiotic strain was evaluated by oral preventive administration (intragastric feeding) of bacteria (5 × ­108 CFU/mice) starting 5 days before colitis induction. Forty eight hours after colitis induction, mice were sacrificed and the severity of colitis was graded according to the macroscopic inflammation based on Wallace scoring m ­ ethod44. Histological analysis was performed on May-Grünwald-Giemsa stained 5 μm tissue sections from colon samples and inflammation was graded according to Ameho score. Immediately after sacrifice, colonic samples were taken and stored in RNAlater storage solution (Ambion, Austin, TX, USA) at − 80 °C until further processed. Preclinical model of infectious colitis. Citrobacter rodentium infection was performed using the kanamycin resistant DBS 120 K strain as described ­previously20. Briefly, a single colony of C. rodentium was cultured overnight in Luria Bertani broth containing 50 µg/ml kanamycin, under agitation. Bacteria suspension was centrifuged, washed, resuspended in PBS and adjusted to 5 × ­109 CFU/ml. Mice were infected by oral administration of C. rodentium ­(109 CFU per mice). The potential capacity of the selected probiotic strains to limit inflammation caused by C. rodentium was evaluated upon intragastric administration of the bacteria or the mixture (5 × ­108 CFU per mice, all strains were present in equal amount in the mixture) 5 days prior C. rodentium infection and daily following infection until termination of the experiment. Mice were sacrificed 9 days after infection. Level of infection was monitored as described p ­ reviously20. Histological analyses were performed on May-Grünwald-Giemsa stained 5 μm tissue sections from colon samples fixed in 10% formalin and embedded in paraffin and crypt length was measured using ZEN (Zeiss, Oberkochen, Germany). Immediately after sacrifice, proximal and distal colon segments were put in RNAlater® (Ambion, Life Technologies, Foster City, CA, USA) and frozen at − 80 °C until RNA extraction and qRT-PCR analysis. Scientific Reports | (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 9 Vol.:(0123456789) www.nature.com/scientificreports/ RNA extraction and analysis of gene expression using quantitative real‑time polymerase chain reaction (qRT‑PCR). Intestinal samples were removed at sacrifice and stored in RNAlater® storage solution (Ambion, Life Technologies, Foster City, CA, USA) at − 80 °C until qRT-PCR analysis. Tissue samples were homogenized using Lysing Matrix D (MPbio, Eschwege, Germany) and total RNA from samples was extracted as described ­previously20. Briefly, Macherey-Nagel NucleoSpin RNAII isolation kit (Düren, Germany) was used for RNA extraction according to the manufacturer’s recommendation. RNA quantity and quality were checked by Nanodrop (260/280 nm, 260/230 nm) and 1 µg RNA was reverse-transcribed using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Woolston Warrington, UK). Quantitative RT-PCR (qRT-PCR) was performed using the Power SYBR Green PCR Master Mix (Applied Biosystems) on ViiA 7 Real-Time PCR System (Applied Biosystems). Primers sequences can be available upon request. Results are expressed as relative gene expressions ­(2−∆∆ct) values, by comparing the PCR cycle thresholds (Ct) for the gene of interest and for the house keeping gene β-actin (bact) (or Glyceraldehyde-3-Phosphate Dehydrogenase, Gapdh for mono-associated mice) as described ­previously45. Supplementation of naive mice and characterization of IL‑22 and IL‑17‑producing cells and regulatory T cells in mesenteric lymph nodes and intestinal resection specimens by flow cytometry. Strains (5 × ­108 CFU/day/mice) were administered by intragastric gavage to WT conventional BALB/c mice for 5 days. Colon samples were removed at sacrifice and stored in RNAlater® storage solution (Ambion, Life Technologies, Foster City, CA, USA) at − 80 °C until qRT-PCR analysis. MLN and intestine were harvested and immediately processed for flow cytometry. Cell suspensions of MLN and intestine (3–5 × ­106 cells, in RPMI1640 supplemented by 10% FCS, 2 mM l-glutamine, 2 mM HEPES, 40 mg/ml gentamycine) were stimulated using the Leukocyte Activation Cocktail containing BD GolgiPlug (BD Biosciences) (1 μl/ml of cell suspension) for 5 h. Cells were stained by mAbs anti-mouse CD11c eFluor450, CD11b eFluor 450, B220 eFluor 450, CD3 eFluor 450, CD117 Alexa Fluor 700, NK1.1 PerCP-Cy5.5, NKp46 FITC (provided by eBioscience), CD4 APC-H7, CD90.2 BV 500; CD45RB BV 605, MHCII BV 650 (provided by BD Bioscience, san Jose, CA, USA). Subsequently, cells were permeabilized and fixed using the Transcription Factor Buffer Set (BD Bioscience), and intracellular staining was performed using mAbs anti-IL-17A eFluor450, anti-FOXP3 PE-Cy7, anti-IL-22 PE and RORgt APC (eBioscience). Flow cytometry data were analyzed using software FlowJo. Gating strategy and representative dot plots for control and BIO5768 treated mice are presented in Figs. S1 and S2. Monocolonisation of axenic mice with the BIO5768 strain. GF WT and Nod2−/−, Rip2−/−, and Il17ra−/− mice (9–13 weeks old, C57BL/6 background) were mono-associated with the BIO5768 strain by a single intragastric gavage (5 × ­108 CFU/mice). After 30 days of mono-association, colon samples were removed at sacrifice and stored in RNAlater® storage solution (Ambion, Life Technologies, Foster City, CA, USA) at − 80 °C until qRT-PCR analysis was performed. Cell suspensions of colon and caecum from mono-colonized mice were performed as described ­previously46. Cells (1 × ­105 cells) were stained by mAbs anti-mouse CD11c FITC (HL3 clone), CD11b FITC (M1/70 clone), B220 FITC (RA3-6B2 clone), CD3 FITC (145-2C11 clone), NK1.1 FITC (PK136 clone), CD4 V500/Amcyan (RM4-5 clone), CD117 APC-H7 (2B8 clone), NKp46 APC/eFluor 660 (29A1.4 clone), Il7ra V450/PB (SB/199 clone), CD90.2 PE-Cy7 (53-2.1 clone). Mouse IgG2a, k (G155-178 clone) and Goat IgG (Poly5164 clone) were used as isotype controls. Subsequently, cells were permeabilized and fixed using the Transcription Factor Buffer Set (BD Bioscience) and intracellular staining was performed using mAbs anti-IL-22 PE (1H8PWSR clone) and RORgt PerCP-Cy5.5 (Q31-378 clone). Statistics. GraphPad Prism was employed for graph preparation and statistical evaluation. 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Scientific Reports | (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 11 Vol.:(0123456789) www.nature.com/scientificreports/ Acknowledgements This work was supported by the ANR BiopaneX project (ANR-12-RPIB-0014), the Institut Pasteur de Lille, the “Institut National de la Santé et de la Recherche Médicale » (Inserm), the « Centre National de la Recherche Scientifique » (CNRS) The Region Centre Val de Loire (2003-00085470), the Conseil Général du Loiret, the European Regional Development Fund (FEDER No. 2016-00110366 and EX005756) and Charles University research program Cooperation IMMU 207032. The authors thank Anne Delanoye-Crespin, Emilie Floquet, Florence Savigny and Véronique Peucelle for their excellent technical help in mice experimentation, histological and/or qRT-PCR analysis. We are also grateful to the staff of the Centre de Dévelopement des Technologies Avancées (CDTA, Orleans, France), the animal facility of the Institut Pasteur de Lille and the BioImaging Center of Lille and to Nathalie Roudier for critical review of the manuscript. Author contributions C.G. and M.C. conceived and supervised the study. J.H. and A.C.-M. performed most of the experiments. J.H., D.B. and A.C.-M. did histology, qRT-PCR. A.C.-M. and B.R. contributed to studies on germ-free mice and monocolonized animals. J.H., A.C.-M., C.G. and D.B. performed the experiments on Citrobacter infection and Denise Boutillier and Corinne Grangette the bacterial culture and TNBS colitis experiments. J.P. performed immunochistochemistry on intestinal sections. J.H., C.G., M.C. and A.C.-M. analyzed the data and performed statistical analysis. J.H. and M.C. wrote the initial draft of the manuscript. C.L. and P.B. provided the strains. C.G., B.P., P.B. and C.L. participated to the writing of the manuscript and scientific discussions. Competing interests Carmen Lapadatescu was employed full time by the company Bioprox. Philippe Blanc is employed full time by the company Bioprox. Bruno Pot is employed by Yakult Europe. The other authors have no conflicts of interest to declare. Additional information Supplementary Information The online version contains supplementary material available at https://​doi.​org/​ 10.​1038/​s41598-​022-​21643-0. Correspondence and requests for materials should be addressed to C.G. or M.C. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. © The Author(s) 2022 Scientific Reports | Vol:.(1234567890) (2022) 12:17591 | https://doi.org/10.1038/s41598-022-21643-0 12
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Relationship between cognitive behavioral variables and mental health status among university students: A meta-analysis
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RESEARCH ARTICLE RESEARCH ARTICLE Relationship between cognitive behavioral variables and mental health status among university students: A meta-analysis Tomonari IrieID1,2*, Kengo Yokomitsu3, Yuji Sakano4 1 School of Education and Culture, Hokusho University, Hokkaido, Japan, 2 Graduate School of Psychological Science, Health Sciences University of Hokkaido, Hokkaido, Japan, 3 College of Comprehensive Psychology, Ritsumeikan University, Osaka, Japan, 4 School of Psychological Science, Health Sciences University of Hokkaido, Hokkaido, Japan a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 * tirie30000@gmail.com * tirie30000@gmail.com * tirie30000@gmail.com OPEN ACCESS Citation: Irie T, Yokomitsu K, Sakano Y (2019) Relationship between cognitive behavioral variables and mental health status among university students: A meta-analysis. PLoS ONE 14(9): e0223310. https://doi.org/10.1371/journal. pone.0223310 Editor: Marta Panzeri, Universita degli studi di Padova (Padua University), ITALY Received: January 22, 2019 Accepted: September 18, 2019 Published: September 27, 2019 Copyright: © 2019 Irie et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Editor: Marta Panzeri, Universita degli studi di Padova (Padua University), ITALY Editor: Marta Panzeri, Universita degli studi di Padova (Padua University), ITALY Received: January 22, 2019 Accepted: September 18, 2019 Published: September 27, 2019 Copyright: © 2019 Irie et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Introduction Mental health problems among university students is an important issue. Auerbach et al. ana- lyzed data on mental health problems of university students in each country using the World Mental Health Surveys [1]. The results indicated that university students suffering from psy- chiatric disorders were reluctant to attend university and were unable to receive appropriate treatment. Steptoe et al. investigated the extent of depressive symptoms in 17,348 university students between the ages of 17 and 30 in 23 countries [2]. They found that the prevalence of severe depressive symptoms was 38% in university students from East Asia (e.g., Japan, Korea), 13.9% for men and 17.1% for women from Western countries. Therefore, establishing and managing a support system in universities that focuses on mental health problems has become an important issue. Data Availability Statement: All data files are available from the OPEN ICPSR database (DOI 10. 3886/E108123V2.). Abstract Cognitive behavioral therapy is an effective treatment for improving mental health prob- lems among university students. However, intervention components have different effects on mental health problems. This paper is a meta-analysis of the data concerning the relationship between cognitive behavioral variables and mental health status among university students. A total of five electronic databases were reviewed, and 876 articles met the initial selection criteria. Reviewers applied standardized coding schemes to extract the correlational relationship between cognitive behavioral variables and mental health status. A total of 55 articles were included in the meta-analysis. Correlations were found for three cognitive behavioral variables (attention, thought, and behavior) across nine mental health domains (negative affect, positive affect, happiness, social function, stress response, psychological symptom, quality of life, well-being, and general health). Across each cognitive behavioral process and all mental health domains, the estimated mean correlation was medium (r = .32 - .46), and varied by the domain of mental health. Data Availability Statement: All data files are available from the OPEN ICPSR database (DOI 10. 3886/E108123V2.). Funding: This work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI grant number 17K13944. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Mental health problems among university students have negative influences on academic performance and social function. Richardson et al. conducted a meta-analysis of 217 studies Competing interests: The authors have declared that no competing interests exist. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 1 / 30 Relationship between cognitive behavioral variables and mental health status among university students that examined the relationship between mental health status and academic performance [3]. This analysis revealed that the intensity of general stress has a negative impact on academic performance. Weissman et al. investigated the influence of depressive and anxiety symptoms on daily life in adolescence and on social life throughout adulthood [4]. This study showed that depressive and anxiety symptoms in adolescence influenced their job turnover rate and the likelihood that they will remain unmarried. The WHO definition of health emphasizes not only the absence of illness but also positive aspects such as social functioning and well-being [5]. Keyes classified the positive aspects of mental health in terms of hedonia and positive functioning [6]. Specifically, hedonia includes “experiencing positive affect” and “avowing happiness or life satisfaction”; in addition, positive functioning includes “social acceptance,” “social actualization,” “social contribution,” “social coherence,” “social integration,” “personal growth,” “purpose in life,” “autonomy,” “environ- mental mastery,” “self-acceptance,” and “positive relationships with others.” Furthermore, showing “personal growth,” “purpose in life,” “autonomy,” “environmental mastery,” “self- acceptance,” and “positive relationships with others” are components of well-being [7]. There- fore, in order to measure mental health, it is necessary to assess not only the general health condition including psychological symptoms or stress responses related to mental illness indi- cated by WHO, but also affective state, happiness, social functioning, and well-being. Cognitive behavior therapy (CBT) is widely applied as a psychological approach to promote good mental health in university students. Charlesworth et al. examined the effect of relaxation training on state and trait anxiety in 18 college students [8]. The results indicated that relaxa- tion training reduces trait anxiety. Perna et al. (1998) examined the effect of cognitive behav- ioral stress management program on the mood states in 34 university students [9]. The results showed that cognitive behavioral stress management program reduces dysphoric mood states. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 Search strategy We identified relevant articles in multiple electronic databases (PsycINFO, PubMed, and CENTRAL). In addition, we used the SIGLE and PsyEXTRA databases to search grey litera- ture. The search included articles published in English from the earliest date available to June 11, 2019 in each database. The selected search terms were “universities,” “college,” “undergrad- uate,” “mental processes,” “adaptation, psychological,” “attitude,” “attention,” “psychology,” and “mental health.” After the database search, we also searched the reference sections of the articles for additional sources. Additionally, the Thesaurus of Psychological Index Terms, cre- ated by the American Psychological Association, can be used as a type of thesaurus search in PsycINFO. Therefore, we utilized this additional tool when searching PsycINFO to obtain all possible references in addition to the above-mentioned terminologies. Inclusion and exclusion criteria Studies included for meta-analysis met the following criteria: (1) written in English, (2) sam- ples were specifically college or junior college students, (3) assessed a bivariate relationship between mental health status and cognitive behavioral variables, (4) reported an effect size, or a statistic that can be calculated, measuring the bivariate association between cognitive behav- ioral variables and mental health status, and (5) published in a peer-reviewed journal. It also included baseline data for intervention studies. Studies were excluded if their samples were psychiatric patients. Data Availability Statement: All data files are available from the OPEN ICPSR database (DOI 10. 3886/E108123V2.). Rosenzweig et al. examined the effect of mindfulness training on mood states for 302 univer- sity students in their sophomore year [10]. They found that mindfulness training reduces dys- phoric mood states. Levin et al. examined the effect of web-based acceptance and commitment therapy on the academic concerns and well-being of 79 college students [11]. The results indi- cated that acceptance and commitment therapy improved concerns about academic learning and social well-being. CBT is an effective approach to improve mental health in university students. CBT includes many therapeutic components and outcome measures. Harvey et al. pointed out that there are five cognitive behavioral variables that can be applied to cognitive behavioral therapy (i.e., attention, memory, reasoning, thought, and behavior [12]). Attention includes variables such as selective attention and mindfulness. Memory includes variables such as overgeneral mem- ory and memory distrust. Reasoning includes variables such as interpretation and attribution. Thought includes variables such as rumination and belief. Behavior includes variables such as avoidance and coping. These five variables are not disorder specific, and are applied in the transdiagnostic approach [12]. Conley et al. conducted a systematic review on the effects of psychological interventions for promoting mental health in university students [13]. The results indicated that mindfulness training is more effective than CBT, relaxation training, and meditation. Furthermore, CBT was found to be more effective than relaxation training and meditation. Each component of psychological approaches to mental health problems of university stu- dents has a different effect. The outcome measures of cognitive behavioral variables that affect the mental health problems of university students have not been verified. Less than one in five adolescents who are in need of treatment receive appropriate psychological interventions [14]. To improve access to effective psychological interventions, it may be useful to develop a brief intervention [15]. In this way, the student counseling center at universities can offer PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 2 / 30 Relationship between cognitive behavioral variables and mental health status among university students psychological interventions during semester term [16,17]. Identifying cognitive behavioral var- iables that strongly influences mental health status is important for developing an effective protocol. In the present study, we aim to conduct an analysis to identify cognitive behavioral variables that influence mental health status in university students. Definition of terms First, we defined cognitive behavioral variables according to Harvey et al’s definition [12]. The definition is as follows: (1) attention, (2) memory, (3) reasoning, (4) thought, and (5) behavior. Second, we defined mental health according to WHO’s definition of health and Keyes’s defini- tion of positive aspects of mental health [5,6]. The definition is as follows: (1) negative affect, (2) positive affect, (3) happiness, (4) social function, (5) stress response, (6) psychological symptom, (7) quality of life (QOL), (8) well-being, and (9) general health. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 Screening procedures Based on the inclusion criteria, two independent raters evaluated “include,” “exclude,” and “unsure” for each article. The value of Kappa indicates fair agreement (κ = .47) [18]. Of the 876 articles extracted using the electronic search, we rejected 616 articles for which both the raters evaluated “exclude.” This resulted in 260 articles, of which 27 articles received the same “include” evaluation by both raters, 66 articles received the same “unsure” evaluation by both raters, and 167 articles were evaluated as either “include” or “unsure” by either rater. There were 18 duplicates among the 260 articles. Therefore, we searched the reference sections of the 242 articles. As a result of the reference section search, we extracted 38 new articles. Two raters independently read the full texts of the 280 articles and judged whether they should be subject to meta-analysis. The inter-rater disagreement were resolved by discussion between the raters once they reached a consensus. Furthermore, as defined above, cognitive behavioral measures PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 3 / 30 Relationship between cognitive behavioral variables and mental health status among university students were categorized as attention, memory, reasoning, thought, or behavior, mental health mea- sures were categorized as negative affect, positive affect, happiness, social function, stress response, psychological symptom, QOL, well-being, or general health. The inter-rater classifi- cation differences were resolved by discussions between raters based on the definition and a consensus was reached. A total of 55 articles were selected for the meta-analysis (Table 1). Fig 1 presents the procedure used to extract the articles. Meta-analytic procedures This study targeted investigations reporting on the bivariate relationship between cognitive behavioral variables and mental health status. Therefore, multivariable measures of associa- tion, such as regression coefficients, were excluded because they are not directly comparable to measures of bivariate association [74]. A meta-analysis was conducted for each combination of cognitive behavioral process and mental health status. When multiple outcomes were used in the study, the effect sizes were extracted for each combination of classifications if the combina- tion of classifications was different (e.g., combination of automatic thoughts and positive affect [thought and positive affect], and combination of automatic thoughts and depressive symp- toms [thought and psychological symptoms]). When the effect size was reported in the same combination, it was integrated into the research (e.g., combination of automatic thoughts and depressive symptoms [thought and psychological symptoms] and combination of automatic thoughts and anxiety symptoms [thought and psychological symptoms]). To integrate the effect size, we used Fisher’s z scale weighted for sample size. Cohen’s standard definition of small (.10), medium (.30), and large (.50) effect sizes were used to interpret the effect size find- ings [75]. In a meta-analysis, clinical and statistical heterogeneity are inevitable because sub- jects and areas differ depending on the study [76]. Therefore, we used the random effect model to calculate the effect size. Furthermore, we calculated I2 [76], and the statistical heterogeneity of the research included in the meta-analysis was confirmed. If we detected a large heterogene- ity, then we conducted a subgroup analysis based on the classification of mental health status (i.e., positive affect, negative affect etc.). To confirm publication bias, we examined the symme- try of the funnel plot using a linear regression test [77] and the trim and fill method [78]. For all analyses, we used the R version 3.4.1 [79]. We used the metafor package [80] to integrate effect size and examine the symmetry of the funnel plot. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 Relationship between cognitive behavioral variables and mental health status among university students Table 1. Characteristics of the included studies. Study N Nationality Cognitive behavioral variables Mental health Anderson & Arnoult (1989) [19] 159 USA Thought Negative affect, Psychological symptom Berking et al. (2012) [20] 151 Germany Attention, Thought, Behavior Psychological symptom Bettis et al. (2017) [21] 62 USA Behavior Stress response, Psychological Symptom Birks et al. (2009) [22] 289 England Behavior Stress response Bodenlos et al. (2015) [23] 310 USA Attention Social function, Stress response Bowlin & Baer (2012) [24] 280 USA Attention Negative affect, Stress response, Well-being Brittian et al. (2015) [25] 2315 USA Thought Psychological symptom Calogero & Pina (2011) [26] 225 USA Thought Negative affect, Psychological symptom Chen et al. (2014) [27] 113 USA Thought Psychological symptom Coffey et al. (2010) [28] 413 USA Attention, Thought, Behavior Psychological symptom Costa et al. (2013) [29] 1078 Spain, Mexico, Portugal, Brazil Attention, Thought, Behavior General health, Happiness Deng et al. (2011) [30] 263 China Attention Negative affect, Positive affect, QOL Disch et al. (2000) [31] 467 USA Attention Social function, Happiness Flett et al. (2016) [32] 214 Canada Attention, Thought Negative affect Gilbert & Christopher (2009) [33] 268 USA Attention, Thought Psychological symptom Griva & Anagnostopoulos (2010) [34] 268 Greece Behavior Psychological symptom Hintz et al. (2015) [35] 223 USA Thought Negative affect, Stress response Hipwell (2005) [36] 183 Scotland Behavior Psychological symptom Hovey & Seligman (2007) [37] 190 USA Behavior Psychological symptom Iwasaki (2003) [38] 85 Canada Behavior Well-being, General health Jayalakshmi & Magdalin (2015) [39] 125 India Behavior Well-being Khan et al. (2016) [40] 207 Pakistan Behavior Psychological symptom Kim et al. (2015) [41] 107 USA Behavior Well-being Kneeland & Dovidio (2019) [42] 97 New Zealand Thought Stress response, Psychological Symptom Koesten et al. (2009) [43] 395 USA Behavior General health Kraemer et al. (2016) [44] 452 USA Attention, Thought Negative affect Krafft et al. (2019) [45] 339 USA Thought Stress response Lihua et al (2017) [46] 330 China Behavior Psychological symptom Luo & Wang (2009) [47] 284 China Behavior Psychological symptom Mahmoud et al. (2012) [48] 508 USA Behavior Negative affect, Stress response Marino et al. (2016) [49] 795 Italy Attention Happiness Masuda & Tully (2012) [50] 494 USA Attention, Behavior Psychological symptom, General health Masuda & Wendell (2010) [51] 91 USA Attention, Thought Stress response, General health Masuda et al. Characteristics of included studies We extracted three categories of cognitive behavioral variables, “attention,” “thought,” and “behavior”, and all categories of mental health based on reading the full-text. The variables of “memory” and “reasoning” were not extracted. Table 1 presents the characteristics of the included studies. Furthermore, Table 2 presents the results of the classification, and Table 3 presents the scales used in each classification. As Table 2 indicates, “behavior” (29 studies, 48 effect sizes) is the most common cognitive behavioral variable related to mental health status. The second most common is “thought” (23 studies, 33 effect sizes) and the third is “attention” (20 studies, 36 effect sizes). “Psychological symptom” (32 studies, 41 effect sizes) is the most common mental health category related to the cognitive behavioral variables. Psychological symptoms included “depressive symptoms,” “anxiety symptoms,”“pathological worry,” “post-traumatic stress disorder symptoms,” and the like (details are shown in Table 3). The second most common is “stress response” (14 studies, 17 effect sizes) and the third is “negative affect” (13 studies, 17 effect sizes). Table 4 shows the meta-analysis results for each classification. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 4 / 30 Relationship between cognitive behavioral variables and mental health status among university students Table 1. (Continued) Study N Nationality Cognitive behavioral variables Mental health Sanchez et al. (2018b) [60] 211 USA Behavior Positive affect Sasaki & Yamasaki (2005) [61] 292 Japan Behavior Social function, Psychological symptom Shapiro et al. (2011) [62] 32 USA Attention Stress response, Well-being Su & Chen (2015) [63] 110 Taiwan Thought, Behavior Psychological symptom Thanoi & Klainin-Yobas (2015) [64] 747 Thailand Thought Negative affect, Stress response Tucker et al. (2016) [65] 123 USA Thought Psychological symptom Vand et al. (2014) [66] 400 Iran Attention, Thought Negative affect, Psychological symptom Wang et al. (2016) [67] 262 Taiwan Behavior Negative affect, Positive affect, Social function Wang et al. (2017) [68] 533 China Attention Psychological symptom Wong (2010) [69] 398 Singapore Thought Happiness, Psychological symptom Wong et al. (2014) [70] 160 USA Thought Psychological symptom Woodruff et al. (2013) [71] 147 USA Attention, Behavior Negative affect, Positive affect, Happiness, Psychological symptom, QOL Zawadzki et al. (2018) [72] 491 USA Thought Psychological symptom, General health Zhou et al. (2013) [73] 418 China Attention Psychological symptom https://doi org/10 1371/journal pone 0223310 t001 (2009) [52] 301 USA Attention, Behavior Stress response, General health Masuda et al. (2010) [53] 375 USA Thought, Behavior Stress response, General health Mayorga et al. (2018) [54] 448 USA Behavior Negative affect, Stress response, Psychological symptom Moeller & Seehuus (2019) [55] 2054 USA Behavior Psychological symptom Montes-Berges & Augusto (2007) [56] 119 Spain Attention, Behavior Psychological symptom de Oliveira et al. (2015) [57] 184 Brazil Thought Psychological symptom Ranjbar et al. (2013) [58] 369 Iran Behavior Social function, Psychological symptom, General health Sanchez et al. (2018a) [59] 308 USA Behavior Psychological symptom (Continued) Table 1. Characteristics of the included studies. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 5 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 Relationship between attention and mental health status Studies on attention measured the awareness of personal experiences such as body sensa- tion, thought, and emotion (e.g., mindfulness, metacognitive awareness). Table 4 and Fig 2 present a medium correlation between attention and mental health status (r = .34, 95% con- fidence interval [CI] = .30 to .38). Because we observed a large statistical heterogeneity (I2 = 91.8%), we conducted a subgroup analysis based on the classification of mental health status. Six studies reported a bivariate relationship between attention and negative affect. The results of this meta-analysis indicate a medium correlation between attention and negative affect (r = -.39, 95% CI = −.47 to −.31). Two studies reported a bivariate relationship between attention and positive affect. The results of this meta-analysis indicate a small or medium cor- relation between attention and positive affect (r = .23, 95% CI = .15 to .31). Four studies reported a bivariate relationship between attention and happiness. The results of this meta- analysis indicate a small or medium correlation between attention and happiness (r = .28, 95% CI = .15 to .41). Five studies reported a bivariate relationship between attention and stress response. The results of this meta-analysis indicate a medium correlation between attention and stress response (r = −.35, 95% CI = −.45 to −.25). Nine studies reported a bivariate rela- tionship between attention and psychological symptom. The results of this meta-analysis indicate a medium correlation between attention and psychological symptom (r = −.32, 95% CI = −.46 to −.18). Two studies reported a bivariate relationship between attention and QOL. The results of this meta-analysis indicate a medium correlation between attention and QOL (r = .32, 95% CI = .23 to .40). Three studies reported a bivariate relationship between attention and well-being. The results of this meta-analysis indicate a medium correlation between atten- tion and well-being (r = .39, 95% CI = .31 to .47). Four studies reported a bivariate relationship between attention and general health. The results of this meta-analysis indicate a medium cor- relation between attention and general health (r = .32, 95% CI = .17 to .48). We did not con- duct subgroup analysis because only one study reported a bivariate relationship between attention and social function. 6 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 Relationship between cognitive behavioral variables and mental health status among university students Fig 1. Flowchart of study selection. https://doi.org/10.1371/journal.pone.0223310.g001 Fig 1. Relationship between attention and mental health status Flowchart of study selection. 7 / 30 Relationship between cognitive behavioral variables and mental health status among university students Relationship between thought and mental health status Studies on thought measured thinking variables (e.g., automatic thoughts, irrational belief). Table 4 and Fig 3 present a medium or large correlation between thought and mental health status (r = .46, 95% CI = .39 to .53). Because we observed a large statistical heterogeneity (I2 = 96.5%), we conducted a subgroup analysis based on the classification of mental health status. ) g p y Seven studies reported a bivariate relationship between thought and negative affect. As a result of integrating the effect size, we found a medium or large correlation between thought and negative affect (r = .46, 95% CI = .35 to .58). Six studies reported a bivariate relationship between thought and stress response. As a result of integrating the effect size, we found a large correlation between thought and stress response (r = .54, 95% CI = .31 to .77). Fifteen studies reported a bivariate relationship between thought and psychological symptom. As a result of integrating the effect size, we found a medium or large correlation between thought and psy- chological symptom (r = .43, 95% CI = .32 to .54). Four studies reported a bivariate relation- ship between thought and general health. As a result of integrating the effect size, we found a medium correlation between thought and general health (r = −.36, 95% CI = −.40 to −.32). We did not conduct subgroup analysis because no studies or only one study reported a bivariate relationship between positive affect, happiness, social function, QOL, and well-being. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 https://doi.org/10.1371/journal.pone.0223310.t002 Relationship between behavior and mental health status Studies on behavior measured coping processes of external or internal experiences (e.g., prob- lem-solving coping, commitment). Table 4 and Fig 4 presents a medium correlation between behavior and mental health status (r = .33, 95% CI = .27 to .38). Because a large statistical het- erogeneity was observed (I2 = 95.2%), we conducted a subgroup analysis based on the classifi- cation of mental health status. Four studies reported a bivariate relationship between behavior and negative affect. As a result of integrating the effect size, we found a small or medium correlation between thought and negative affect (r = −.40, 95% CI = −.63 to −.17). Three studies reported a bivariate rela- tionship between behavior and positive affect. There is no significant correlation between behavior and positive affect as a result of integrating the effect size (r = .21, 95% CI = −.07 to .49). Three studies reported a bivariate relationship between behavior and happiness. As a Table 2. Classification of the included studies. Category Studies N Cognitive behavioral variables Attention 20 36 Thought 23 33 Behavior 29 48 Mental health Negative affect 13 17 Positive affect 4 5 Happiness 4 8 Social function 5 5 Stress response 14 17 Psychological symptoms 32 41 Quality of life 2 3 Well-being 5 6 General Health 9 15 https://doi.org/10.1371/journal.pone.0223310.t002 Table 2. Classification of the included studies. Category Studies N Cognitive behavioral variables Attention 20 36 Thought 23 33 Behavior 29 48 Mental health Negative affect 13 17 Positive affect 4 5 Happiness 4 8 Social function 5 5 Stress response 14 17 Psychological symptoms 32 41 Quality of life 2 3 Well-being 5 6 General Health 9 15 https://doi.org/10.1371/journal.pone.0223310.t002 PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 8 / 30 Relationship between cognitive behavioral variables and mental health status among university students Table 3. Measures used in each classification. Measure Psychometricsa Studies α rxx Attention Mindful Attention Awareness Scale .80 .81 Deng et al. (2011) [30] (Brown & Ryan, 2003) [81] Flett et al. (2016) [32] Gilbert & Christopher (2009) [33] Masuda & Tully (2012) [50] Masuda & Wendell (2010) [51] Masuda et al. (2009) [52] Shapiro et al. (2011) [62] Wang et al. (2017) [68] Woodruff et al. (2013) [71] Five Facet Mindfulness Questionnaire .75 - .91 - Bodenlos et al. (2015) [23] (Baer et al., 2006) [82] Bowlin & Baer (2012) [24] Coffey et al. (2010) [28] Woodruff et al. (2013) [71] Trait Meta-Mood Scale (subscale; Attention, Clarity) .86 - .90 - Coffey et al. (2010) [28] (Salovey et al., 1995) [83] Costa et al. (2013) [29] Montes-Berges & Augusto (2007) [56] Metacognition questionnaire .72 - .89 .76 - .94 Marino et al. (2016) [49] (Cartwright-Hatton & Wells, 1997) [84] Vand et al. (2014) [66] Emotion-Regulation Skills Questionnaire (subscale; Awareness) .90 .75 Berking et al. (2012) [20] (Berking & Znoj, 2008) [85] Cognitive and Affective Mindfulness Scale-Revised .74 - .77 - Kraemer et al. (2016) [44] (Feldman et al., 2007) [86] Self-Compassion Scale (subscale; Mindfulness) .81 .85 Zhou et al. (2013) [73] (Neff, 2003) [87] Lerning Styles Inventory (subscale; Deep cognitive processing) .82 .88 Disch et al. (2000) [31] (Schmeck, 1983) [88] Thought Objectified Body Consciousness Scale (subscale; Surveillance) .76 - .89 - Calogero & Pina (2011) [26] (McKinley & Hyde, 1996) [89] Dysfunctional Belief and Attitudes about Sleep Scale .69 - Vand et al. (2014) [66] (Morin, 1993) [90] Perceived Control Over Stressful Events Scale (subscale; Present control) .79 - .86 .48 - .59 Hintz et al. (2015) [35] (Frazier et al 2011) [91] Response Styles Questionnaire (subscale; Ruminative) - .80 Flett et al. (2016) [32] (Nolen-Hoeksema & Morrow, 1991) [92] Su & Chen (2015) [63] (Nolen-Hoeksema et al., 1994) [93] Thanoi & Klainin-Yobas (2015) [64] Intolerance of Uncertainty Scale .94 .74 Kraemer et al. (2016) [44] (Freeston et al., 1994 [94]; Buhr & Dugas, 2002 [95]) Mizes Anorectic Cognitions Questionnaire-Revised .90 - Masuda et al. (2010) [53] (Mizes et al., 2000) [96] Masuda & Wendell (2010) [51] (Continued) Table 3. Measures used in each classification. (Frazier et al 2011) [91] PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 9 / 30 Relationship between cognitive behavioral variables and mental health status among university students Table 3. (Continued) Measure Psychometricsa Studies α rxx Crandell Cognitions Inventory .95 - Gilbert & Christopher (2009) [33] (Crandell & Chambless, 1986) [97] Emotion-Regulation Skills Questionnaire (subscale; Tolerance, Readiness to confront distressing situations) .90 - .93 .75 - .78 Berking et al. (2012) [20] (Berking & Znoj, 2008) [85] Rumination Reflection Questionnaire .90 - .91 - Coffey et al. (2010) [28] (Trapnell & Campbell, 1999) [98] Cognitive Distortion Questionnaire .85 .87 de Oliveira et al. (2015) [57] (de Oliveira et al., 2015) [57] Automatic Thought Questionnaire-Negative .98 - Wong (2010) [69] (Hollon & Kendall, 1980) [99] Automatic Thought Questionnaire-Positive .97 - Wong (2010) [69] (Ingram & Wisnicki, 1988) [100] Scale of Ehinic Experience (subscale; Perceived discrimination) .83 - .91 .77 - .86 Brittian et al. (2015) [25] (Malcarne et al., 2006) [101] Tucker et al. (2016) [65] Acculturative Stress Scale for International Students (subscale; Perceived discrimination) .92 - Wong et al. (2014) [70] (Sandhu & Asrabadi, 1994) [102] Everyday Discrimination Scale .88 - Chen et al. (2014) [27] (Williams et al., 1997) [103] Ruminative Response Scale .90 .67 Kneeland & Dovidio (2019) [42] (Treynor et al., 2003) [104] White Bear Suppression Inventory .89 .69 Kneeland & Dovidio (2019) [42] (Wegner & Zanakos, 1994) [105] Zawadzki et al. (2018) [72] Thought Control Questionnaire .67-.79 .67-.83 Zawadzki et al. (2018) [72] (Wells & Davies, 1994) [106] Cognitive Fusion Questionnaire .88-.93 .80 Krafft et al. (2019) [45] (Gillanders et al., 2014) [107] Behavior Acceptance and Action Questionnaire .88 - .90 .72 Masuda & Tully (2012) [50] (Bond & Bunce, 2003) [108] Masuda et al. (2009) [52] Masuda et al. (2010) [53] Woodruff et al. (2013) [71] Dialectical Coping Scale .81 - Wang et al. (2016) [67] (Wang et al., 2016) [67] Brief COPE Inventory .81 - .88 - Mahmoud et al. (2012) [48] (Carver, 1997) [109] Emotional Intelligence Scale .87 - Birks et al. (2009) [22] (Schutte et al., 1998) [110] Jayalakshmi & Magdalin (2015) [39] General Coping Questionnaire (subscale; dispositional coping) .86 - .92 .63 - .86 Sasaki & Yamasaki (2005) [61] (Sasaki & Yamasaki, 2002) [111] Religious Coping Scale .97 - Hovey & Seligman (2007) [37] (Boudreaux et al., 1995) [112] (Continued) Table 3. (Continued) Table 3. (Continued) Table 3. (Continued) PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 10 / 30 Relationship between cognitive behavioral variables and mental health status among university students Table 3. (Continued) Measure Psychometricsa Studies α rxx Trait Meta-Mood Scale (subscale; Repair) .86 - .90 - Coffey et al. (2010) [28] (Salovey et al., 1995) [83] Costa et al. (2013) [29] Montes-Berges & Augusto (2007) [56] Trait Coping Style Questionnaire - - Luo & Wang (2009) [47] (Wang, 1999) [113] Difficulties in Emotion Regulation Scale .76 - .90 - Coffey et al. (2010) [28] (Gratz & Roemer, 2004) [114] Mayorga et al. (2018) [54] Proactive Coping Inventory .80 - .85 - Griva & Anagnostopoulos (2010) [34] (Greenglass, 2002) [115] Brief Religious Coping Scale .60 - .94 - Khan et al. (2016) [40] (Pargament et al., 2011) [116] Kim et al. (2015) [41] Cognitive Flexibility Scale .72 - .82 - Koesten et al. (2009) [43] (Martin & Rubin, 1995) [117] Social Problem-Solving Inventory-Revised .68 - .91 - Ranjbar et al. (2013) [58] (D’ Zurilla et al., 2011) [118] Coping Orientation for Problem Experiences .45 - .92 .46 - .86 Iwasaki (2003) [38] (Carver et al., 1989) [119] Social Skills Inventory .75-.88 .81-.96 Moeller & Seehuus (2019) [55] (Riggio, 1986) [120] Coping Strategies Inventory .71-.94 .67-.83 Sanchez et al. (2018a) [59] (Tobin et al., 1989) [121] Sanchez et al. (2018b) [60] Confucian Coping Scale .51-.77 - Lihua et al. (2017) [46] (Li & Hou, 2012) [122] Responses to Stress Questionnaire (subscale; engagement disengagement coping) .80-.92 .69-.81 Bettis et al. (2017) [21] (Connor-Smith et al., 2000) [123] Problem-Solving Questionnaire .51-.86 - Hipwell (2005) [36] (Cassidy & Long, 1996) [124] Negative affect Positive and Negative Affect Schedule (subscale; Negative affect) .84 - .87 .39 - .71 Anderson & Arnoult (1989) [19] (PANAS; Watson et al., 1988) [125] Deng et al. (2011) [30] Kraemer et al. (2016) [44] Wang et al. (2016) [67] Woodruff et al. (2013) [71] Mayorga et al. (2018) [54] Depression Anxiety Stress Scale (subscale; Depression, Anxiety) .90 - .95 - Bowlin & Baer (2012) [24] (DASS; Crawford, & Henry, 2003) [126] Flett et al. (2016) [32] Hintz et al. (2015) [35] Mahmoud et al. (2012) [48] (Continued) Table 3. (Continued) PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 11 / 30 Relationship between cognitive behavioral variables and mental health status among university students Table 3. (Continued) Measure Psychometricsa Studies α rxx Vand et al. (2014) [66] Moeller & Seehuus (2019) [55] Thought, Feeling, and Experience Questionnaire (subscale; Depression, Anxiety, Hopelessness) .90 - Thanoi & Klainin-Yobas (2015) [64] (TEFQ; Thanoi et al., 2011) [127] Objectified Body Consciousness Scale (subscale; Body shame) .72 - .89 .73 - .79 Calogero & Pina (2011) [26] (McKinley & Hyde, 1996) [89] Body Image Guilt and Shame Scale (subscale; Body guilt) .88 - .90 - Calogero & Pina (2011) [26] (Thompson et al., 2003) [128] Multiple Affect Adjective Check List .72 - .85 .31 - .68 Anderson & Arnoult (1989) [19] (Zuckerman, 1960) [129] Positive affect Positive and Negative Affect Schedule (subscale; Positive affect) .86 - .90 .47 - .68 Deng et al. (2011) [30] (PANAS; Watson et al., 1988) [125] Wang et al. (2016) [67] Woodruff et al. (2013) [71] Mental Health Inventory (subscale; positive affect) .81 - .96 - Sanchez et al. (2018b) [60] (Veit & Ware, 1983) [130] Happiness Satisfaction with Life Scale .87 .82 Costa et al. (2013) [29] (SWLS; Diener et al., 1985) [131] Wong (2010) [69] Woodruff et al. (2013) [71] Fordyce Emotion Questionnaire - .86 Woodruff et al. (2013) [71] (Fordyce, 1988) [132] Social and Emotional Health Surveys .92 - Marino et al. (2016) [49] (SEHS; Furlong et al., 2014) [133] Spiritual Well-Being Scale (subscale; Existential well-being) - - Disch et al. (2000) [31] (Ellison, 1983) [134] Oxford Happiness Questionnaire-Short .78 .86 Wong (2010) [69] (Hills & Aygyle, 2002) [135] Social function Medical Outcomes Study Short Form Sruvey (subscale; Social functioning) .80 - Bodenlos et al. (2015) [23]b (Ware & Sherbourne, 1992) [136] Interpersonal Relationship Harmony Inventory - - Wang et al. (2016) [67] (Kwan et al., 1997) [137] General Health Questionnaire (subscale; Social dysfunction) .70 - .90 - Koesten et al. (2009) [43] (Goldberg, 1978) [138] Ranjbar et al. (2013) [58] Sasaki & Yamasaki (2005) [61] Stress response Interpersonal Reactivity Index (subscale; Personal distress) .71 - .77 .62 - .71 Masuda & Wendell (2010) [51] (Davis, 1983) [139] Masuda et al. (2009) [52] Masuda et al. (2010) [53] (Continued) Table 3. (Continued) PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 12 / 30 Relationship between cognitive behavioral variables and mental health status among university students Table 3. (Continued) Measure Psychometricsa Studies α rxx Perceived Stress Scale .84 - .86 .85 Birks et al. (2009) [22] (Cohen et al., 1983) [140] Bodenlos et al. (2015) [23] Shapiro et al. (2011) [62] Kneeland & Dovidio (2019) [42] Bettis et al. (2017) [21] Depression Anxiety Stress Scale (subscale; Stress) .93 - Bowlin & Baer (2012) [24] (DASS; Crawford, & Henry, 2003) [126] Hintz et al. (2015) [35] Mahmoud et al. (2012) [48] Thought, Feeling, and Experience Questionnaire (subscale; Stress) .90 - Thanoi & Klainin-Yobas (2015) [64] (TEFQ; Thanoi et al., 2011) [127] Counseling Center Assessment of Psychological Symptoms-34 (subscale; distress) .76-.89 74-.87 Krafft et al. (2019) [45] (Locke et al., 2012) [141] The Social, Attitudinal, Familial, and Environmental Scale .89 - Mayorga et al. (2018) [54] (Mena et al., 1987) Responses to Stress Questionnaire (subscale; social stress) .80-.92 .69-.81 Bettis et al. (2017) [21] (Connor-Smith et al., 2000) [123] Psychological symptoms Beck Depression Inventory .86 - Anderson & Arnoult (1989) [19] (Beck et al., 1961) [142] Hovey & Seligman (2007) [37] de Oliveira et al. (2015) [57] Wong (2010) [69] Woodruff et al. (2013) [71] Kneeland & Dovidio (2019) [42] Lihua et al. (2017) [46] Beck Anxiety Inventory .92 .75 de Oliveira et al. (2015) [57] (Beck et al., 1988) [143] Wong (2010) [69] Woodruff et al. (2013) [71] Lihua et al. (2017) [46] Center for Epidemiologic Studies Depression Scale .85 .53 Brittian et al. (2015) [25] (Radloff, 1977) [144] Gilbert & Christopher (2009) [33] Tucker et al. (2016) [65] Medical Outcomes Study Short Form Sruvey (subscale; Mental health 5) .77 - Montes-Berges & Augusto (2007) [56] (Ware & Sherbourne, 1992) [136] Sanchez et al. (2018a) [59] Brief Symptom Inventory .74 - .89 - Berking et al. (2012) [20] (Derogatis & Spencer, 1982) [145] Coffey et al. (2010) [28] Masuda & Tully (2012) [50] Hopelessness Depression Symptom Questionnaire .93 - Zhou et al. (2013) [73] (Metalsky & Joiner, 1997) [146] Penn State Worry Questionnaire .88 .79 Vand et al. (2014) [66] (Meyer et al., 1990) [147] Eating Disorder Examination Questionnaire .84 - .85 .81 Calogero & Pina (2011) [26] (Mond et al., 2006) [148] Three Dichotomous Items - - Su & Chen (2015) [63] (Continued) Table 3. (Continued) PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 13 / 30 https://doi.org/10.1371/journal.pone.0223310.t004 Relationship between cognitive behavioral variables and mental health status among university students Table 3. (Continued) Measure Psychometricsa Studies α rxx (Rost et al., 1993) [149] Posttraumatic Diagnostic Scale .92 .83 Su & Chen (2015) [63] (Foa et al., 1997) [150] Hopkins Symptom Checklist-21-item version .90 - Wong et al. (2014) [70] (Green et al., 1988) [151] Patient Health Questionnaire-9 Scale .89 - Chen et al. (2014) [27] (Kroenke et al., 2001) [152] Bettis et al. (2017) [21] Generalized Anxiety Disorder 7-item .92 .83 Chen et al. (2014) [27] (Spitzer et al., 2006) [153] Bettis et al. (2017) [21] General Health Questionnaire (subscale; Depression) .70 - .90 - Ranjbar et al. (2013) [58] (Goldberg, 1978) [138] Sasaki & Yamasaki (2005) [61] SCL-90 Symptom checklist .62 - .96 - Luo & Wang (2009) [47] (Derogatis, 1994) [154] Wang et al. (2017) [68] State-Trait Anxiety Inventory (subscale; Trait scale) .92 - Griva & Anagnostopoulos (2010) [34] (Spielberger et al., 1970) [155] Personality Assessment Inventory (subscale; Anxiety) .90 - Hovey & Seligman (2007) [37] (Morey, 1991) [156] Scale for Measuring Depression and Anxiety .74 - Khan et al. (2016) [40] (Costello & Comrey, 1967) [157] PTSD Checklist .97 .96 Zawadzki et al. (2018) [72] (Weathers et al., 1993) [158] Inventory of Depression and Anxiety Symptoms .77-.89 .72-.83 Mayorga et al. (2018) [54] (Watson et al., 2007) [159] Quality of life World Health Organization Quality of Life-BREF .68 - .82 - Deng et al. (2011) [30] (Skevington et al., 2004) [160] Woodruff et al. (2013) [71] Well-being Subjective Well-Being .90 - Shapiro et al. (2011) [62] (Diener, 1984) [161] Scale of Psychological Well-Being .86 - .93 .81 - .85 Bowlin & Baer (2012) [24] (Ryff, 1989) [7] Iwasaki (2003) [38] Medical Outcomes Study Short Form Sruvey (subscale; Emotional well-being) .80 - Bodenlos et al. (2015) [23] (Ware & Sherbourne, 1992) [136] Warwick-Edinburgh Mental Well-being Scale .89 - .91 .83 Jayalakshmi & Magdalin (2015) [39] (Tennant et al., 2007) [162] Mental Health Inventory (subscale; psychological well-being) .81 - .96 - Kim et al. (2015) [41] (Veit & Ware, 1983) [130] General Health General Health Questionnaire .70 - .90 - Costa et al. (2013) [29] (Goldberg, 1978) [138] Koesten et al. (2009) [43] Masuda & Tully (2012) [50] (Continued) Table 3. (Continued) Table 3. (Continued) 14 / 30 Relationship between cognitive behavioral variables and mental health status among university students result of integrating the effect size, we found a medium correlation between behavior and hap- piness (r = .39, 95% CI = .23 to .56). Four studies reported a bivariate relationship between behavior and social function. As a result of integrating the effect size, we found a small correla- tion between behavior and social function (r = .19, 95% CI = .07 to .31). Six studies reported a Table 3. (Continued) Measure Psychometricsa Studies α rxx Masuda & Wendell (2010) [51] Masuda et al. (2009) [52] Masuda et al. (2010) [53] Ranjbar et al. (2013) [58] Zawadzki et al. (2018) [72] Mental Health Inventory .81 - .96 - Iwasaki (2003) [38] (MHI; Veit and Ware, 1983) [130] aThe psychometrics include measures of internal consistency (α) and test re-test reliability (r xx). https://doi.org/10.1371/journal.pone.0223310.t003 Relationship between cognitive behavioral variables and mental health status among university students result of integrating the effect size, we found a medium correlation between behavior and hap- piness (r = .39, 95% CI = .23 to .56). Four studies reported a bivariate relationship between behavior and social function. As a result of integrating the effect size, we found a small correla- tion between behavior and social function (r = .19, 95% CI = .07 to .31). Six studies reported a Table 3. (Continued) Measure Psychometricsa Studies α rxx Masuda & Wendell (2010) [51] Masuda et al. (2009) [52] Masuda et al. (2010) [53] Ranjbar et al. (2013) [58] Zawadzki et al. (2018) [72] Mental Health Inventory .81 - .96 - Iwasaki (2003) [38] (MHI; Veit and Ware, 1983) [130] aThe psychometrics include measures of internal consistency (α) and test re-test reliability (r xx). https://doi.org/10.1371/journal.pone.0223310.t003 Relationship between cognitive behavioral variables and mental health status among university students Table 3. (Continued) result of integrating the effect size, we found a medium correlation between behavior and hap- piness (r = .39, 95% CI = .23 to .56). Four studies reported a bivariate relationship between behavior and social function. As a result of integrating the effect size, we found a small correla- tion between behavior and social function (r = .19, 95% CI = .07 to .31). Six studies reported a result of integrating the effect size, we found a medium correlation between behavior and hap- piness (r = .39, 95% CI = .23 to .56). aN = number of studies bBased on Trim and Fill method N = number of studies bBased on Trim and Fill method Four studies reported a bivariate relationship between behavior and social function. As a result of integrating the effect size, we found a small correla- tion between behavior and social function (r = .19, 95% CI = .07 to .31). Six studies reported a Table 4. Estimated associations between cognitive behavioral variables and mental health. Classification of mental health Attention Thought Behavior r Na Sample size I2 r N Sample size I2 r N Sample size I2 [95% CI] (n) (%) [95% CI] (n) (%) [95% CI] (n) (%) Negative affect -.39 6 5,275 84.5 .46 7 9,696 94.7 -.40 4 1,873 95.1 [-.47, -.31] [.35, .58] [-.63, -.17] Positive affect .23 2 557 0.0 - 0 - - .21 3 1,093 94.8 [.15, .31] [-.07, .49] Happiness .28 4 19,111 96.9 - 1 1,592 - .39 3 1,634 88.7 [.15, .41] [.23, .56] Social function - 1 1,860 - - 0 - - .19 4 5,628 94.5 [.16, .46] Stress response -.35 5 3,684 80.9 .54 6 3,463 96.7 -.47 6 2,293 73.1 [-.45, -.25] [.31, .77] [-.55, -.39] Psychological symptom -.32 9 7,883 96.6 .43 15 8,615 95.8 -.29 17 18,041 97.7 [-.46, -.18] [.32, .54] [-.40, -.19] Quality of life .32 2 557 0.0 - 0 - - - 1 147 - [.23, .40] Well-being .39 3 3,292 69.5 - 0 - - .23 3 1,189 0.1 [.31, .47] [.17, .29] General health .32 4 3,042 90.9 -.36 4 2,035 0.0 .38 7 6,128 91.3 [.17, .48] [-.40, -.32] [.29, .47] Overall .34 36 45,261 91.8 .46 33 26,802 96.5 .33 48 37,901 96.0 [.30, .38] [.39, .53] [.27, .38] .32a [.28, .36]b aN = number of studies Table 4. Estimated associations between cognitive behavioral variables and mental health. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 15 / 30 Relationship between cognitive behavioral variables and mental health status among university students and mental health. 9 16 / 30 Fig 2. Forest plot of the relationship between attention and mental health. https://doi.org/10.1371/journal.pone.0223310.g002 oi.org/10.1371/journal.pone.0223310 September 27, 2019 16 / 30 ationship between attention and mental health. 16 / 30 Relationship between cognitive behavioral variables and mental health status among university students bivariate relationship between behavior and stress response. As a result of integrating the effect size, we found a medium or large correlation between behavior and stress response (r = −.47, 95% CI = −.55 to −.39). Seventeen studies reported a bivariate relationship between behavior and psychological symptom. As a result of integrating the effect size, we found a medium cor- relation between behavior and psychological symptom (r = −.29, 95% CI = −.40 to −.19). Three studies reported a bivariate relationship between behavior and well-being. As a result of integrating the effect size, we found a small or medium correlation between behavior and well- being (r = .23, 95% CI = .17 to .29). Seven studies reported a bivariate relationship between behavior and general health. As a result of integrating the effect size, we found a medium cor- relation between behavior and general health (r = .38, 95% CI = .29 to .47). We did not conduct a subgroup analysis because only one study reported a bivariate relationship between behavior and QOL. Reporting bias We assessed the risk of reporting bias through visual inspection and linear regression tests of funnel plots [77]. Because it has been argued that the test for funnel plot asymmetry should be used only when there are at least 10 studies [18], we only conducted a linear regression test when there were over 10 studies. With the linear regression test, asymmetry of the funnel plot was detected in studies that reported bivariate relations between attention and mental health status (p < .001). Based on the trim and fill method, the uncorrected effect size (before adding the possible missing studies) is .34 (95% CI = .30 to .38), and the corrected effect size (after adding six possible missing studies) is .32 (95% CI = .28 to .36). Although there is evidence of publication bias, its effect is not significant (Fig 5). PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 Discussion This study is the first meta-analysis of the relationship between cognitive behavior variables and mental health status in university students. We found that the overall correlation coeffi- cients between cognitive behavioral variables and mental health status were medium (atten- tion: r = .32; thought: r = .46; behavior: r = .33). However, we detected a large heterogeneity (attention: I2 = 91.8%; thought: I2 = 96.5%; behavior: I2 = 96.0%), which means that the effect sizes likely depend on mental health status, while cognitive behavioral variables are related to mental health status. Therefore, we classified mental health as “negative affect,” “positive affect,” “happiness,” “social function,” “stress response,” “psychological symptom,” “QOL,” “well-being,” and “general health” and conducted a meta-analysis on them. As Table 4 shows, attention has larger effect sizes than behavior in relation to well-being. For positive affect and QOL, attention shows significant effect sizes, but thought and behavior do not. Thought has larger effect sizes than attention and behavior on negative affect, stress response, and psychological symptom. In social function, behavior shows significant effect sizes, but attention and thought do not. These findings suggest that attention is related to the positive aspects of mental health such as well-being, and thought is related to the negative aspects of mental health such as negative affect. Behavior is related to social function, but attention and thought are not. As mentioned above, this study identifies cognitive behavioral variables that are strongly related to the mental health status in university students. Next, we review how these cognitive behavioral variables have been used in existing psychotherapy. To develop effective psycholog- ical intervention methods, we will consider what kind of future research is necessary. These results support previous studies that examined the effects of psychological treatment. First, the classification of attention in this study includes mindfulness and metacognitive PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 17 / 30 17 / 30 Relationship between cognitive behavioral variables and mental health status among university students PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 18 / 30 Relationship between cognitive behavioral variables and mental health status among university students PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 Fig 3. Forest plot of the relationship between thought and mental health. https://doi.org/10.1371/journal.pone.0223310.g003 awareness (e.g., Mindful Attention Awareness Scale [81], Metacognition Questionnaire [84]). As techniques to promote mindfulness and metacognitive awareness, mindfulness-based psy- chotherapy [163], attention training [164], and computer-based training to train attention [165] are available [12]. Mindfulness-based psychotherapy is the most frequently reported and effec- tive technique by clinical trials and meta-analyses [166–168]. Mindfulness is defined as “paying attention in a particular way: on purpose, in the present moment, and nonjudgmentally” [169]. Several clinical trials and meta-analyses report that mindfulness-based psychotherapy is effec- tive when it creates positive aspects in mental health [170,171]. Furthermore, integrating 23 meta-analyses that reported on the effectiveness of mindfulness-based psychotherapy revealed that mindfulness-based psychotherapy not only improved depressive symptoms (standard mean difference (SMD) = −.37) and anxiety symptoms (SMD = −.48) but also promoted QOL (SMD = −.39) [172]. In previous research, while the subjects were not purely university stu- dents, mindfulness-based psychotherapy not only improved the negative aspects of mental health but also promoted the positive aspects. In addition, in the present study, the attention process was correlated with positive aspects of mental health in university students [25,26,28], suggesting that psychological interventions targeting the attention process may be effective when promoting positive mental health in this population. Second, the classification of thought in this study includes automatic thoughts and dysfunc- tional belief (e.g., Automatic Thought Questionnaire-Negative [99], Dysfunctional Belief and Attitudes about Sleep Scale [90]). Cognitive therapy is a technique to improve automatic thoughts and dysfunctional belief [12]. Cognitive therapy is a psychological treatment focused on thought that improves depressive symptoms and supports clients by observing and consid- ering the thought processes [173]. The Society of Clinical Psychology reported that cognitive therapy is an effective treatment for depression [174]. A meta-analysis suggests that the cogni- tive therapy treatment of depression has a higher remission rate as opposed to no intervention (Odds Ratio = 0.42) [175]. Another meta-analysis shows that cognitive therapy improves gen- eralized anxiety and social anxiety [176,177]. In previous research, while subjects were not purely university students, cognitive therapy improved the negative aspects of mental health. In the present study, the thought process was correlated with the negative aspects of mental health in university students [33,57]; so psychological interventions targeting the thought pro- cess may be effective treatments for the negative aspects of mental health in this population. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 Fig 3. Forest plot of the relationship between thought and mental health. https://doi.org/10.1371/journal.pone.0223310.g003 Third, the classification of behavior in this study included coping and commitment (e.g., Brief COPE Inventory [109], Acceptance and Action Questionnaire [108]). As techniques to promote coping and commitment, behavioral activation and acceptance and commitment therapy are available [12]. Behavioral activation is a psychological treatment that focuses on increased engagement in adaptive activities, decreased engagement in activities that maintain depression or increased risk of depression, and solving problems that limit access to rewards or that maintain or increase aversive control [178]. Acceptance and commitment therapy is a psychological treatment that focuses on decreasing experiential avoidance and increasing action along the valued direction [179]. Behavioral activation and acceptance and commitment therapy are effective in improving social dysfunctions because they aim to resolve problems by Third, the classification of behavior in this study included coping and commitment (e.g., Brief COPE Inventory [109], Acceptance and Action Questionnaire [108]). As techniques to promote coping and commitment, behavioral activation and acceptance and commitment therapy are available [12]. Behavioral activation is a psychological treatment that focuses on increased engagement in adaptive activities, decreased engagement in activities that maintain depression or increased risk of depression, and solving problems that limit access to rewards or that maintain or increase aversive control [178]. Acceptance and commitment therapy is a psychological treatment that focuses on decreasing experiential avoidance and increasing action along the valued direction [179]. Behavioral activation and acceptance and commitment therapy are effective in improving social dysfunctions because they aim to resolve problems by focusing on real-life behavior. In randomized controlled trials, behavioral activation and acceptance and commitment therapy are shown to be effective against social dysfunction (behavioral activation: d = 1.21 [180]; acceptance and commitment therapy: partial η2 = .22 [181]). In previous research, while subjects were not purely university students, behavior acti- vation and acceptance and commitment therapy improved social dysfunction. In the present (behavioral activation: d = 1.21 [180]; acceptance and commitment therapy: partial η2 = .22 [181]). In previous research, while subjects were not purely university students, behavior acti- vation and acceptance and commitment therapy improved social dysfunction. Fig 3. Forest plot of the relationship between thought and mental health. https://doi.org/10.1371/journal.pone.0223310.g003 In the present PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 19 / 30 Relationship between cognitive behavioral variables and mental health status among university students Relationship between cognitive behavioral variables and mental health status among university students org/10.1371/journal.pone.0223310 September 27, 2019 20 / 30 /10 1371/j l 0223310 S t b 27 2019 20 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 20 / 30 Relationship between cognitive behavioral variables and mental health status among university students Relationship between cognitive behavioral variables and mental health status among university students study, the behavior process was correlated with the social function in university students [43,58], therefore, psychological interventions that target the behavior process may be effective when it comes to social dysfunction in university students. As mentioned above, when provid- ing psychological interventions to university students, it would be best to provide psychother- apy that focuses on the attention, thought, and behavior variables that target mental health problems. Fig 4. Forest plot of the relationship between behavior and mental health. https://doi.org/10.1371/journal.pone.0223310.g004 Fig 4. Forest plot of the relationship between behavior and mental health. https://doi.org/10.1371/journal.pone.0223310.g004 Fig 4. Forest plot of the relationship between behavior and mental health. https://doi.org/10.1371/journal.pone.0223310.g004 study, the behavior process was correlated with the social function in university students [43,58], therefore, psychological interventions that target the behavior process may be effective when it comes to social dysfunction in university students. As mentioned above, when provid- ing psychological interventions to university students, it would be best to provide psychother- apy that focuses on the attention, thought, and behavior variables that target mental health problems. /10.1371/journal.pone.0223310.g004 study, the behavior process was correlated with the social function in university students [43,58], therefore, psychological interventions that target the behavior process may be effective when it comes to social dysfunction in university students. As mentioned above, when provid- ing psychological interventions to university students, it would be best to provide psychother- apy that focuses on the attention, thought, and behavior variables that target mental health problems. Fig 5. Funnel plot of the relationship between attention and mental health. Black circles: included studies, White circles: added possible missing studies using Trim and Fill methods. https://doi.org/10.1371/journal.pone.0223310.g005 Fig 5. Funnel plot of the relationship between attention and mental health. Black circles: included studies, White circles: added possible missing studies using Trim and Fill methods. https://doi.org/10.1371/journal.pone.0223310.g005 between attention and mental health. Fig 3. Forest plot of the relationship between thought and mental health. https://doi.org/10.1371/journal.pone.0223310.g003 Black circles: included studies, White circles: added possible missing studies using Trim Fig 5. Funnel plot of the relationship between attention and mental health. Black circles: included studies, White circles: added possible missing studies using Trim and Fill methods. Fig 5. Funnel plot of the relationship between attention and mental health. Black circles: included studies, White circles: added possible missing studies using Trim and Fill methods. https://doi.org/10.1371/journal.pone.0223310.g005 21 / 30 Relationship between cognitive behavioral variables and mental health status among university students This meta-analysis is not without limitations. First, we detected a large heterogeneity in the studies included in the meta-analysis. The heterogeneity did not affect the results of the present study because this meta-analysis used the random effect model. However, future studies must consider heterogeneities among university students. Studies focusing on university students have at times taken into consideration several demographic variables, such as a student’s major [182]. In contrast, some studies were conducted without considering the differences in demographics [183]. These differences in demographics may affect the results of the analysis [22]. In addition, because the present study extracted only English articles, which is an interna- tional language, the influence of the cultural background could not be verified. In the future, it is necessary to analyze the data pertaining to each demographic, including cultural back- ground, and accumulate the findings. Furthermore, we could not conduct a meta-analysis on some of the classifications because we could not extract the required amount of data. There- fore, some relationships between cognitive behavioral variables and mental health status were unclear (e.g., thought and positive aspects of mental health [positive affect, happiness, QOL, and well-being]); it will be necessary to try and resolve this issue in the future. Conclusion The present study is the first to examine the relationship between cognitive behavioral vari- ables and mental health status among university students using meta-analysis. The findings reveal that cognitive behavioral variables are overall correlated with mental health status. Therefore, psychological treatment based on CBT is effective for solving mental health prob- lems among university students. Psychological treatment, including thought process, can be effective in treating the negative aspects of mental health, and the attention process can be effective in treating the positive aspects of mental health. However, this meta-analysis could not reveal some of the relationships between cognitive behavioral variables and mental health status. In summary, psychological treatment based on CBT is effective in solving mental health problems among university students. However, outcomes vary, and several factors influence them. Therefore, when examining the effects of psychological treatment on university stu- dents, various outcomes should be included. PLOS ONE | https://doi.org/10.1371/journal.pone.0223310 September 27, 2019 References 1. 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Phytochemical and Pharmacological Role of Liquiritigenin and Isoliquiritigenin From Radix Glycyrrhizae in Human Health and Disease Models
Frontiers in aging neuroscience
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REVIEW REVIEW published: 01 November 2018 doi: 10.3389/fnagi.2018.00348 Mahesh Ramalingam1, Hyojung Kim2, Yunjong Lee2* and Yun-Il Lee1,3* Mahesh Ramalingam1, Hyojung Kim2, Yunjong Lee2* and Yun-Il Lee1,3* 1 Well Aging Research Center, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea, 2 Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, South Korea, 3 Companion Diagnostics and Medical Technology Research Group, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea The increasing lifespan in developed countries results in age-associated chronic diseases. Biological aging is a complex process associated with accumulated cellular damage by environmental or genetic factors with increasing age. Aging results in marked changes in brain structure and function. Age-related neurodegenerative diseases and disorders (NDDs) represent an ever-growing socioeconomic challenge and lead to an overall reduction in quality of life around the world. Alzheimer’s disease (AD) and Parkinson’s disease (PD) are most common degenerative neurological disorders of the central nervous system (CNS) in aging process. The low levels of acetylcholine and dopamine are major neuropathological feature of NDDs in addition to oxidative stress, intracellular calcium ion imbalance, mitochondrial dysfunction, ubiquitin-proteasome system impairment and endoplasmic reticulum stress. Current treatments minimally influence these diseases and are ineffective in curing the multifunctional pathological mechanisms. Synthetic neuroprotective agents sometimes have negative reactions as an adverse effect in humans. Recently, numerous ethnobotanical studies have reported that herbal medicines for the treatment or prevention of NDDs are significantly better than synthetic drug treatment. Medicinal herbs have traditionally been used around the world for centuries. Radix Glycyrrhizae (RG) is the dried roots and rhizomes of Glycyrrhiza uralensis or G. glabra or G. inflata from the Leguminosae/Fabaceae family. It has been used for centuries in traditional medicine as a life enhancer, for the treatment of coughs and influenza, and for detoxification. Diverse chemical constituents from RG have reported including flavanones, chalcones, triterpenoid saponins, coumarines, and other glycosides. Among them, flavanone liquiritigenin (LG) and its precursor and isomer chalcone isoliquiritigenin (ILG) are the main bioactive constituents of RG. In the present review, we summarize evidence in the literature on the structure and phytochemical properties and pharmacological applications of LG and ILG in age-related diseases to establish new therapeutics to improve human health and lifespan. Keywords: isoliquiritigenin, liquiritigenin, memory, Parkinson’s disease, Radix Glycyrrhizae Edited by: Seung-Nam Kim, Dongguk University Seoul, South Korea Reviewed by: Youngmin Bu, Kyuung Hee University, South Korea Seung-Mann Paek, Gyeongsang National University, South Korea *Correspondence: Yunjong Lee ylee69@skku.edu Yun-Il Lee ylee56@dgist.ac.kr Received: 26 June 2018 Accepted: 15 October 2018 Published: 01 November 2018 Glycyrrhiza uralensis Fisch. Glycyrrhiza uralensis, commonly known as licorice (or liquorice), is one of the most popular herbal medicines, used as antitussive, expectorant, and antipyretic in traditional prescriptions, foods, beverages, brewing, tobacco, and cosmetics for its effects of relieving cough, pharyngitis, bronchitis, and bronchial asthma (Cao et al., 2004; Kao et al., 2014). It is a perennial glandular herb, 30–100 cm high, with an erect stem with short whitish hairs and echinate glandular hairs; the lower part of the stem is woody. Leaves are alternate and imparipinnate, with 7–17 leaflets. Leaves are ovate-elliptical in shape and 2–5.5 cm long by 1– 3 cm wide (WHO, 1999). The apex is obtuse-rounded and the base is rounded and both surfaces are covered with glandular hairs and short hairs. Stipules are lanceolate and inflorescence is an axillary cluster. Flowers are purplish and papilionaceous with villous calyx. The fruit is a flat oblong pod, 6–9 mm wide, that is sometimes falcate and is densely covered with brownish echinate glandular hairs. Each pod contains 2–8 seeds. The root is cylindrical, fibrous, flexible, 20–22 cm long and 15 mm in diameter, with or without cork, which is reddish, furrowed, and light yellow inside (WHO, 1999). Alzheimer’s disease (AD) and Parkinson’s disease (PD) are most common age-related neurological disorders of the central nervous system (CNS). AD is characterized by insoluble extracellular β-amyloid peptide (Aβ) forming senile plaques deposition, intraneuronal tau accumulation and hyperphosphorylated microtubule-associated fibrillary tangles. It may contribute to progressive neuronal degeneration with memory loss and cognitive impairment in brain during normal aging (Dickson et al., 1988). PD is characterized by loss of dopamine(DA)-rgic neurons and the presence of intracytoplasmic aggregated α-synuclein Lewy bodies in the substantia nigra pars compacta of the brain eventually leads to bradykinesia, rigidity, slowing of movement and postural instability (Gibb and Lees, 1988). In addition, low levels of brain neurotransmitter acetylcholine (ACh) (Houghton and Howes, 2005), oxidative stress, intracellular calcium ion imbalance, mitochondrial dysfunction, ubiquitin-proteasome system impairment and endoplasmic reticulum stress are involved in the pathogenesis of NDDs (Ramalingam and Kim, 2016b). Aging enables the development of chronic diseases, and anti- aging mechanisms not only increase lifespan but also preserve function resembling a more youthful state (Fontana, 2009). Therefore, there is a focus on developing novel multi-disease preventative and therapeutic approaches (Kennedy et al., 2014). At present, there are no cures for NDDs. INTRODUCTION have widespread interest and their active ingredients may help to identify new multi-functional therapeutic agents. Numerous plant-based natural and their manufactured synthetic neuroprotective drugs have been permitted by the U.S. Food and Drug Administration (FDA) over the past 30 years (Kumar et al., 2012; Cragg and Newman, 2013). Plants have been used for many centuries in traditional medicines to treat NDDs (Abushouk et al., 2017). Dietary compounds present in daily foods such as fruits, seeds, vegetables, and beverages have been reported for neuroprotective by various signaling pathways against NDDs (Asthana et al., 2016). Although there are many medicinal plants documented in pharmacopeias, only a few have been extensively studied to understanding their potential effectiveness in the treatment of NDDs (Vijayakumar et al., 2016). The average life expectancy at birth in developed countries was about 47 years at the beginning of the 20th century and increased to 77.8 years in the beginning of the 21st century (Oeppen and Vaupel, 2002). Senescence or biological aging is neither irreversible nor inevitable fate of all organisms and significantly delayed (da Costa et al., 2016). The rate of dying prematurely has decreased, whereas the rate of death from aging-associated chronic diseases such as diabetes mellitus, cancer, and heart, kidney, and neurological diseases has increased (Fontana, 2009). The aging process in biological systems is complex (Gottfries, 1990) and is proving to be a major risk factor for all of the common chronic and lethal conditions. Aging results in marked changes in brain structure and function (Cole and Franke, 2017). Age-related neurodegenerative disorders (NDDs) represent an ever-growing socioeconomic challenge and lead to an overall reduction in quality of life around the world (Tarailo-Graovac et al., 2016). Citation: Ramalingam M, Kim H, Lee Y and Lee Y-I (2018) Phytochemical and Pharmacological Role of Liquiritigenin and Isoliquiritigenin From Radix Glycyrrhizae in Human Health and Disease Models. Front. Aging Neurosci. 10:348. doi: 10.3389/fnagi.2018.00348 November 2018 | Volume 10 | Article 348 1 Frontiers in Aging Neuroscience | www.frontiersin.org The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. Glycyrrhiza uralensis Fisch. The existing therapies are focused on increasing the amount of ACh and DA by inhibiting acetylcholinesterase and monoamine oxidase (MAO) inhibition, respectively or elevating the concentration of the precursor levodopa (L-DOPA) (Houghton and Howes, 2005). Classification Kingdom: Plantae (Plants) Subkingdom: Tracheobionta (Vascular Plants) Superdivision: Spermatophyta (Seed Plants) Division: Magnoliophyta (Flowering Plants) Class: Magnoliopsida (Dicotyledons) Subclass: Rosidae Order: Fabales Family: Leguminosae/Fabaceae Genus: Glycyrrhiza Species: G. uralensis Fisch. Binomial: Glycyrrhiza uralensis Fisch. Ex DC. (Theplantlist, 201 Wikipedia, 2018) The brain is the body’s most complex organ and not all drugs are sanctioned for the treatment of age-related NDDs. The currently available treatments have proven ineffective in curing the multi-functional pathological conditions of NDDs (Vijayakumar et al., 2016). Synthetically manufactured drugs have certain side effects, such as dry mouth, tiredness, sleepiness, sluggishness, drowsiness, anxiety, tension, nervousness, and trouble with balance in humans (Phani Kumar et al., 2015). Recently, increasing scientific researches on medicinal plants Frontiers in Aging Neuroscience | www.frontiersin.org RADIX GLYCYRRHIZAE The chemical ingredients may change during the extraction process of the herbs due to the solvents interaction or heating process is considered for their altered pharmacological effects (Wang et al., 2013). RG combined with Sargassum, Herba Cirsii Japonici, Euphorbia Kansui, and Flos Genkwa might cause cardiac toxicity (Huang et al., 2001). In contrast, RG reduces the toxicity of hydroxysafflor yellow A from Flos Carthami, strychnine and brucine from Semen Strychni, and aconite from Radix Aconiti Lateralis Praeparata (Wang et al., 2013). Therefore, systematic safety evaluation of prolonged use or overdose of compounds and potential drug–drug interactions is needed before the use of herbal medicine as a nutritional supplement and/or therapeutic drugs. Radix Glycyrrhizae (RG) is the dried roots and rhizomes of three Glycyrrhiza species—G. uralensis Fisch. ex DC., G. glabra L, and G. inflata Batalin—that is prescribed as licorice in Pharmacopeias (Liu et al., 2013; Wang et al., 2015). Among these species, G. uralensis is the most frequently used species for RG in Korea, China and Japan that constitutes 90% of total licorice production around the world (Zhang and Ye, 2009). Moreover, G. uralensis known as Far East Asian licorice and G. glabra as Western licorice (Davis and Morris, 1991), this review is limited to G. uralensis. The roots and rhizomes are cylindrical, fibrous, flexible, 20–100 cm long and 0.6–3.5 cm in diameter, with or without cork. Roots are externally reddish brown or grayish brown, longitudinally wrinkled, furrowed, and lenticellate, with sparse rootlet scars (WHO, 1999). The texture is compact and slightly fibrous, and the interior is yellowish white and starchy. The cambium ring is distinct and the rays radiate, some with clefts. Rhizomes are cylindrical with external bud scars, and pith is present in the center of the fracture (WHO, 1999). ISOLIQUIRITIGENIN AND LIQUIRITIGENIN The medicinal plants lies in their chemical constituents to produce physiological actions to have various health benefits in the human body (Sharma et al., 2018). As a result of genetic, ecological, and environmental differences, herbal medicines generally vary in their quality and chemical constituents (Bopana and Saxena, 2007). RG contains at least 400 different chemical constituents including triterpenoid saponins, flavanones, chalcones, coumarines, and their glycosides (Fujii et al., 2014; Kao et al., 2014). As there are many phytochemicals present in each plant, it is necessary to identify a single phytochemical that might be useful in the treatment of human health and diseases (Ramalingam and Kim, 2016a). However, little is known about the effective chemical constituents responsible for biological activities isolated from RG (Ji et al., 2016). More than 25% of the components in RG have been identified as active constituents through oral bioavailability, virtual screening and drug-likeness (Liu et al., 2013). RG is one of the most commonly used and oldest herbal medicines documented in the pharmacopeias (Liu et al., 2013). The earliest Chinese written literature Shennong’s Classic of Materia Medica describing the use of licorice dates from 2100 BC for its life-enhancing properties (Wang et al., 2015). Its clinical practice against cough, influenza, liver damage and for detoxification values has received considerable attention throughout the world (Ji et al., 2016). Recent researches revealed its antioxidant, anti-inflammatory, anti-viral, anti- diabetic, cytotoxic, skin-whitening and cholinergic activities (Mae et al., 2003; Isbrucker and Burdock, 2006; Nassiri and Hossein, 2008; Ahn et al., 2010). It is used as a natural sweetener and food additive in snacks, candies, cookies, seasoning sauce, soy sauce, and drinks (Kitagawa, 2002). Synonyms Glycyrrhiza asperrima var. desertorum Regel Glycyrrhiza asperrima var. uralensis Regel Glycyrrhiza glandulifera Ledeb. (Theplantlist, 2013) November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org 2 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. Vernacular Names Chinese : Gan Cao ( ) Korean : Gam Cho ( ) Japanese : Uraru-kanzou ( ) present in all three species, is a sweet-tasting saponin that can cause hypertension, sodium salt and water retention, and reduced potassium ion levels (WHO, 1999; Farag et al., 2012), but the aqueous extract has less negative effects compared to glycyrrhizin pure compound (Bernardi et al., 1994; Cantelli-Forti et al., 1994). High doses of glycyrrhizic acid (400 mg/day) have risk of side effects, such as cardiac dysfunction, edema, and hypertension (Størmer et al., 1993). ( ) Japanese : Uraru-kanzou ( ) Frontiers in Aging Neuroscience | www.frontiersin.org QUALITY AND SAFETY Particulars ILG LG Chemical properties Structure IUPAC name (E)-1-(2,4-dihydroxyphenyl)-3-(4- hydroxyphenyl)prop-2-en-1-one (2S)-7-hydroxy-2-(4-hydroxyphenyl)- 2,3-dihydrochromen-4-one MeSH entry term 2′,4′,4-trihydroxychalcone 7,4′-dihydroxyflavanone CAS number 961-29-5 578-86-9 Molecular formula C15H12O4 C15H12O4 Molecular weight 256.257 g/mol 256.257 g/mol Hydrogen bond donor count 3 2 Hydrogen bond acceptor count 4 4 Classification Flavonoids →chalcones Flavonoids →flavanones Interchangeable properties Neutral pH1,2 ILG LG Acidic pH1,2 ILG LG Basic pH3,4 ILG LG DMEM or RPMI16405 (37◦C, 5% CO2, pH 7.4) ILG LG PBS(0–4◦C, pH 7.4)5 ILG LG ILG, isoliquiritigenin; LG, liquiritigenin; DMEM, Dulbecco’s modified Eagle’s medium; RPMI 1640, Roswell Park Memorial Institute 1640 medium. 1(Cisak and Mielczarek, 1992); 2(Furlong and Nudelman, 1988); 3(Nudelman and Furlong, 1991); 4(Andújar et al., 2003); 5(Simmler et al., 2013). TABLE 1 | Chemical and interchangeable properties of ILG and LG. LG ILG ILG, isoliquiritigenin; LG, liquiritigenin; DMEM, Dulbecco’s modified Eagle’s medium; RPMI 1640, Roswell Park Memorial Institute 1640 medium. 1(Cisak and Mielczarek, 1992); 2(Furlong and Nudelman, 1988); 3(Nudelman and Furlong, 1991); 4(Andújar et al., 2003); 5(Simmler et al., 2013). as inflammation. Unpredictable chronic mild stress (UCMS) has been used as a model for chronic anxiety/depressive-like behavior. Male ICR mice were pretreated with LG at 7.5 and 15 mg/kg intragastrically for 7 days followed by subcutaneous injection of 0.5 mg/kg LPS. LG pretreatment significantly reduced the LPS-induced significant increase in immobility duration in forced swimming and tail suspension tests. Moreover, levels of the pro-inflammatory cytokines interleukin (IL)-6 (IL-6) and tumor necrosis factor-α (TNF-α) in serum and hippocampus were decreased in the LG group compared with the control LPS group. LG also decreased the expression of p-p65NF-κB, p-IκBα, brain-derived neurotrophic factor (BDNF), and p-TrkB (tropomyosin receptor kinase B). These results indicated that the antidepressant and antianxiety activities of LG might be associated with anti-inflammatory and BDNF/TrkB pathways (Su et al., 2016). undergo rapid cyclization into flavanones at neutral and lower acidic pH whereas flavones isomers undergo a reversible reaction to their chalcones at basic pH. This interconversion between chalcone and flavanone represents temperature dependent isomerization and racemization of these active compounds (Furlong and Nudelman, 1988; Miles and Main, 1989; Nudelman and Furlong, 1991; Cisak and Mielczarek, 1992; Yamín et al., 1997; Andújar et al., 2003). Interestingly, these chemical conditions match the cell culture-based assays also. QUALITY AND SAFETY The chalcone isoliquiritigenin (ILG; 2′,4,4′- trihydroxychalcone) is biosynthetically and structurally interrelated to the flavanone liquiritigenin (LG; 4′,7- dihydroxyflavanone) (Simmler et al., 2013). These two polyphenols are the main bioactive constituents of RG (Table 1). ILG is the isomeric precursor of LG (Jayaprakasam et al., 2009). In flavonoid biosynthesis, chalcone isomerase (CHI) promotes enzymatic isomerization through which the ionized 2′- hydroxychalcones (e.g., ILG) is stereochemically converted to 2-S flavanone (e.g., LG). During this process, the ionized chalcone interacts with amino acid side chains in the CHI active site to produce flavanone by high enantioselectivity (Jez et al., 2000; Jez and Noel, 2002). Moreover, studies have reported that ILG and LG are interchangeable by pH and temperature. Chalcones The chalcone isoliquiritigenin (ILG; 2′,4,4′- trihydroxychalcone) is biosynthetically and structurally interrelated to the flavanone liquiritigenin (LG; 4′,7- dihydroxyflavanone) (Simmler et al., 2013). These two polyphenols are the main bioactive constituents of RG (Table 1). ILG is the isomeric precursor of LG (Jayaprakasam et al., 2009). In flavonoid biosynthesis, chalcone isomerase (CHI) promotes enzymatic isomerization through which the ionized 2′- hydroxychalcones (e.g., ILG) is stereochemically converted to 2-S flavanone (e.g., LG). During this process, the ionized chalcone interacts with amino acid side chains in the CHI active site to produce flavanone by high enantioselectivity (Jez et al., 2000; Jez and Noel, 2002). Moreover, studies have reported that ILG and LG are interchangeable by pH and temperature. Chalcones Use of herbal medicines is an important tradition in rural communities for health and disease prevention (Fennell et al., 2004). However, there is always a risk of ineffectiveness, side effects, or misadministration of toxic plants. Identification, collection, processing, storage and contaminants in the natural plant products have also contributed to the deleterious effect in human body (Street et al., 2008). Quality, safety, and efficacy are the main concerns that must be evaluated in crude or fractionated extracts and their individual compounds and documented before they are prescribed for use as herbal medicines and botanical dietary supplements. Licorice species have a unique profile of secondary metabolites and distinct biological activities (Li et al., 2016). Glycyrrhizin, November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org 3 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. TABLE 1 | Chemical and interchangeable properties of ILG and LG. QUALITY AND SAFETY LG and ILG were incubated in cell culture mediums such as RPMI 1640 or DMEM/F12 supplemented with 5 or 10% heat-inactivated fetal bovine serum maintained at pH around 7.4 in 5% CO2 at 37◦C (with or without MCF-7 cells). ILG began isomerization and reached interconversion ratio of 10.4% ILG and 89.6% LG after 96 h. It suggests that LG and ILG have interconnected biological activities and the biological activity of ILG can be linked to its flavanone LG (Simmler et al., 2013). For the chronic type of anxiety, mice were exposed to UCMS for 6 weeks and intragastrically treated with LG (7.5 and 15 mg/kg) from the third week. LG-treated mice showed a reduced immobility time in forced swimming test (FST) and tail suspension test (TST) and a reduction in sucrose preference test (SPT). There were no significant changes in spontaneous locomotor activities. Levels of pro- inflammatory cytokines IL-6, IL-1β, and TNF-α in serum and hippocampus were downregulated by LG treatment. The elevated concentrations of glucocorticoids (GC) in plasma and serum malondialdehyde (MDA) were decreased, together with improved superoxide dismutase (SOD) and catalase (CAT) activity and glutathione (GSH) content. LG also upregulated the concentrations of 5-hydroxytryptamine (serotonin; 5-HT) and PHARMACOLOGICAL ACTIVITIES AGAINST NDDs Studies on bioactivities revealed that LG and ILG have some valuable pharmacological activities against NDDs. Anti-psychostimulant Activities These data suggest that ILG might be a potential agent against cocaine-induced neuronal cell injury and death (Jeon et al., 2008). g Treatment of dopaminergic neuronal SN4741 cells with ILG at 0.1, 0.5, and 1 µM did not affect cell viability. Pretreatment with ILG (1 µM) attenuated 6-hydroxydopamine (6-OHDA)– induced cell death. ILG pretreatment significantly inhibited 6-OHDA–induced nuclear condensation, fragmentation and apoptosis, in accordance with inhibition of caspase-3 activation. ILG pretreatment completely attenuated generation of ROS and reactive nitrogen species (RNS), in addition to suppressing mitochondrial membrane potential (MMP) dissipation and cytochrome c in the cytosol. The protective effects of ILG appear to be mediated through attenuation of c-Jun N-terminal kinase (JNK), p38, and Akt by modulating the Bcl-2/Bax ratio, whereas the extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway is not affected. ILG significantly enhanced production of BDNF, a neurotrophic factor, and reduced the downregulation of BDNF release that increases the survival and the morphological differentiation of dopaminergic neurons (Hwang and Chun, 2012). ILG (1 µM) pretreatment for 20 h followed for 24-h treatment with rotenone (3 µM) or sodium nitroprusside (SNP; 0.4 mM) in PC12 cells significantly improved MMP, adenosine triphosphate (ATP) level, and cell viability as well as cell proliferation (Denzer et al., 2016). Activation of dopamine neurons by continued cocaine drug abuse that originate in the ventral tegmental area cause D1 and D2 DA receptor signaling dysfunction then leads to upregulation of c-Fos in the nucleus accumbens and prefrontal cortex (Bardo, 1998; Anderson and Pierce, 2005). Oral administration of ILG for 1 h prior to an injection of cocaine (20 mg/kg, i.p.) in male Sprague-Dawley rats suppressed the extracellular DA level in the nucleus accumbens in a dose-dependent manner and attenuated the expression of c-Fos. Gamma-aminobutyric acid (GABA)-β receptors attenuate the reinforcing effect of drugs. These effects of ILG were entirely stopped by a GABAβ receptor antagonist SCH 80911. These results suggest that ILG might be effective by modulating the GABAβ receptor to block the cocaine effects, and may be used in pharmacotherapy for drug addiction (Jang et al., 2008). An E3 ubiquitin ligase, RNF146 recognizes its substrates through poly(ADP-ribosyl)ation (PARsylation) of proteins mediated by poly(ADP-ribose) polymerases (PARPs) (Kang et al., 2011; Zhou et al., 2011; Fatokun et al., 2014; DaRosa et al., 2015). RNF146 can disturb PARP1-regulated cellular processes and has neuroprotective activity against N-methyl- D-aspartate (NMDA)–induced excitotoxicity, DNA damage, and stroke. Anti-psychostimulant Activities Anti-psychostimulant Activities Dopamine (DA) is a neurotransmitter in the CNS activated by drugs of abuse and psychostimulants such as cocaine (Jang et al., 2008; Jeon et al., 2008). It increases extracellular DA levels from dopaminergic neurons, resulting in spontaneous hyperlocomotion and other neurobehavioral changes. ILG inhibited cocaine-induced DA release in the nucleus accumbens of rat brain (Jeon et al., 2008). In addition, ILG caused alterations of a protooncogene protein c-Fos expression in cocaine-treated rat brain (White and Gall, 1987; Jang et al., 2008). Moreover, ILG treatment was associated with differences in gene expression patterns for 56 proteins including gamma enolase, glial fibrillary acidic protein (GFAP), and ubiquitin carboxyl-terminal hydrolase isozyme L1. These data suggest that ILG might be a potential agent against cocaine-induced neuronal cell injury and death (Jeon et al., 2008). Activation of dopamine neurons by continued cocaine drug abuse that originate in the ventral tegmental area cause D1 and D2 DA receptor signaling dysfunction then leads to upregulation of c-Fos in the nucleus accumbens and prefrontal cortex (Bardo, 1998; Anderson and Pierce, 2005). Oral administration of ILG for 1 h prior to an injection of cocaine (20 mg/kg, i.p.) in male Sprague-Dawley rats suppressed the extracellular DA level in the nucleus accumbens in a dose-dependent manner and attenuated the expression of c-Fos. Gamma-aminobutyric acid (GABA)-β receptors attenuate the reinforcing effect of drugs. These effects of ILG were entirely stopped by a GABAβ receptor antagonist SCH 80911. These results suggest that ILG might be effective by modulating the GABAβ receptor to block the cocaine effects, and may be used in pharmacotherapy for drug addiction (Jang et al., 2008). p y Dopamine (DA) is a neurotransmitter in the CNS activated by drugs of abuse and psychostimulants such as cocaine (Jang et al., 2008; Jeon et al., 2008). It increases extracellular DA levels from dopaminergic neurons, resulting in spontaneous hyperlocomotion and other neurobehavioral changes. ILG inhibited cocaine-induced DA release in the nucleus accumbens of rat brain (Jeon et al., 2008). In addition, ILG caused alterations of a protooncogene protein c-Fos expression in cocaine-treated rat brain (White and Gall, 1987; Jang et al., 2008). Moreover, ILG treatment was associated with differences in gene expression patterns for 56 proteins including gamma enolase, glial fibrillary acidic protein (GFAP), and ubiquitin carboxyl-terminal hydrolase isozyme L1. Anti-psychostimulant Activities LG treatment at 10 µM increased 3-fold of RNF146 mRNA and protein expressions in SH-SY5Y cells and caused a nuclear translocation of endogenous estrogen receptor β (ERβ). Tamoxifen, an ER antagonist, blocked the LG-induced increase in RNF146 expression, indicating that ER activation was responsible for RNF146 induction. In addition, LG failed to induce RNF146 expression in an ERβ deletion model (Kim et al., 2017). Antidepressant and Antianxiety Activities Major depression is a severe life-threatening disorder caused by a complex pathophysiological process related to a person’s knowledge (Su et al., 2016; Tao et al., 2016). Lipopolysaccharide (LPS) has been used to cause acute depressive behavior as well November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org 4 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. and useful for the treatment of anxiety and depression and the treatment and prevention of PD. norepinephrine (NE) in hippocampus of mice. Different degrees of attenuation in BDNF and phosphorylated phosphoinositide 3-kinase (PI3K), protein kinase B (Akt), mammalian target of rapamycin (mTOR), and TrkB were observed. Collectively, these data showed that LG could alleviate depressive-like symptoms, possibly through regulation of the PI3K/Akt/mTOR–mediated BDNF/TrkB pathway in the hippocampus (Tao et al., 2016). Activities Against Parkinson’s Disease PD is a progressive NDD described by the selective loss of dopaminergic (DArgic) neurons and formation of intracellular Lewy bodies such as α-synuclein (α-syn) within the substantia nigra. The α-syn monomers misfold into toxic oligomers of α-syn aggregates that subsequently increase the reactive oxygen species (ROS) level and induce apoptosis, resulting in dopaminergic neuronal injury in PD. G. uralensis is one of the main herbs in approximately 40% of traditional medical prescriptions described in pharmacopeias for the treatment of PD. ILG showed inhibitory effects against membrane toxicity in in vitro aggregated α-syn and disaggregated preformed mature fibrils in a transgenic Caenorhabditis elegans PD model (Liao et al., 2016). Anti-Alzheimer’s Activities Alzheimer’s disease is a chronic NDD and most common cause of dementia characterized by the increasing age-related impairment of learning and memory (Weon et al., 2016). The pathological hallmarks of AD are amyloid beta (Aβ) accumulation, senile plaques, neurofibrillary tangles, dystrophic neurites, and neuronal loss (Lin et al., 2012; Ko et al., 2017). LG in the dose range of 0.2–2 µM to rat hippocampal neurons prevented Aβ25−35-induced cell death as shown by 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and lactate dehydrogenase (LDH) detection assays. LG blocked the significant increase in [Ca2+]i and ROS accumulation induced by Aβ25−35. LG also exerted an anti-apoptotic role against Aβ25−35 toxicity by increasing the Bcl-2 expression LG probably has some neurotropic actions, including increasing the expression of nuclear respiratory factor 3 (Ntf-3) at both the gene and protein levels. LG downregulated Aβ A4 precursor protein- binding family B member 1 (Apbb-1), a peptide that forms the extracellular amyloid fibrils, explaining the mechanism of inhibited Aβ accumulation in rat primary hippocampal neurons (Liu et al., 2009). As previously reported, LG can penetrate into the brain and exert neuroprotective activity (Yang E.J. et al., 2013). Intraperitoneal administration of LG to mice for 3 consecutive days resulted an increased levels of RNF146 mRNA and protein expressions in ventral midbrain, striatum, and cerebellum. In a 6-OHDA–induced PD-like model, LG pretreatment markedly enhanced tyrosine hydroxylase (TH)-positive DArgic neurons and almost completely inhibited PARP1 activity. Moreover, LG was shown to selectively activate ERβ, but not ERα, thus avoiding aberrant tumor growth in vivo (Mersereau et al., 2008) and improving the safety profile of long-term LG treatment for NDDs (Kim et al., 2017). Therefore, ILG and LG are potential candidates against PD in in vitro and in vivo models and their working mechanisms are diagrammatically represented in Figure 1. Multiple factors can be attributed to the learning and memory deficiency in AD. LG (2.3, 7, and 21 mg/kg/day) effectively attenuated Aβ-induced learning and memory impairment in Wistar rats determined by Morris water maze and shuttle box test. Treatment with LG had no effect on Aβ expression caused by injection of Aβ25−35. LG treatment markedly attenuated the CA1 hippocampal neuronal loss in AD model rats as indicated by microtubule-associated protein 2 (MAP2) immunostaining and Nissl’s staining. Moreover, Notch signaling affects CNS, inhibits neuronal differentiation and triggers downstream reactions. Anti-Alzheimer’s Activities The expression of Notch-2 mRNA and protein levels in the AD model rat brains were inhibited by LG treatment (Liu et al., 2010a). Study suggest that LG may serve as a NeuroSERM, an molecule that acts on estrogen mechanisms in the brain while avoiding peripheral estrogen receptors (Liu et al., 2009). Inhibitory Activities Against Monoamine Oxidases The monoamine oxidases (MAOA and MAOB) catalyze the oxidative deamination of monoamines in the CNS and peripheral nervous system (PNS). MAO inhibitors are used in therapy for disorders of the CNS (Kanazawa, 1994). Licorice extracts (30 µg/ml) from different specimens were showed inhibitory effects on MAO without characterization of their active constituents (Hatano et al., 1991). LG (IC50: 32 µM) and ILG (IC50: 13.9 µM) inhibited the activity of MAOA in a dose- dependent manner, but non-competitively with the positive control clorgyline (IC50: 0.198 µM). The IC50 values for MAOB inhibition for LG, ILG, and positive control deprenyl were 104.6, 47.2, and 0.251 µM, respectively (Pan et al., 2000). These reports indicate that LG and ILG might be major MAO inhibitors in RG LG up to a concentration of 100 µM did not affect the viability of SH-SY5Y cells. In addition, LG completely eliminated the hydrogen peroxide (H2O2)–induced oxidative injury in SH-SY5Y cells. LG treatment (10 µM, 48 h) showed substantial protective effects on cell viability against PD-associated toxins 6-OHDA November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org 5 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. (70 µM, 24 h) and rotenone (20 µM, 24 h). In a model of H2O2 toxicity, primary mouse cortical neurons exposed to LG showed a 4-fold increase in RNF146 expression and reversed cellular ATP content and mitochondrial membrane potential. H2O2 induces robust PARP1 activation, which was largely abolished by LG treatment (Kim et al., 2017). AIMP2, a parkin substrate, enhances cell toxicity, and the levels of PAR-conjugated proteins were significantly reduced by LG-induced RNF146 expression. These effects collectively indicate that LG has various cytoprotective abilities against multiple PARP1-activating stimuli. shRNA- mediated silencing of RNF146 expression annihilated the LG- mediated cytoprotection against H2O2 injury in SH-SY5Y cells. Moreover, the shRNA-RNF146 expression knocked down the endogenous RNF146 expression by more than 80% and resulted in a sustained increase in PAR activity and depletion of ATP following H2O2 toxicity. Similarly, CRISPR-Cas9–mediated ERβ ablation eliminated the LG-induced neuroprotection against H2O2 toxicity. Taken together, these data indicate that LG- induced activations of ERβ and RNF146 inhibit PARP1 and confer neuroprotection (Kim et al., 2017). (70 µM, 24 h) and rotenone (20 µM, 24 h). Inhibitory Activities Against Monoamine Oxidases In a model of H2O2 toxicity, primary mouse cortical neurons exposed to LG showed a 4-fold increase in RNF146 expression and reversed cellular ATP content and mitochondrial membrane potential. H2O2 induces robust PARP1 activation, which was largely abolished by LG treatment (Kim et al., 2017). AIMP2, a parkin substrate, enhances cell toxicity, and the levels of PAR-conjugated proteins were significantly reduced by LG-induced RNF146 expression. These effects collectively indicate that LG has various cytoprotective abilities against multiple PARP1-activating stimuli. shRNA- mediated silencing of RNF146 expression annihilated the LG- mediated cytoprotection against H2O2 injury in SH-SY5Y cells. Moreover, the shRNA-RNF146 expression knocked down the endogenous RNF146 expression by more than 80% and resulted in a sustained increase in PAR activity and depletion of ATP following H2O2 toxicity. Similarly, CRISPR-Cas9–mediated ERβ ablation eliminated the LG-induced neuroprotection against H2O2 toxicity. Taken together, these data indicate that LG- induced activations of ERβ and RNF146 inhibit PARP1 and confer neuroprotection (Kim et al., 2017). maze task. ILG also ameliorated the HFD-induced peripheral insulin resistance, which may results to neuronal damage and cognitive deficits, as measured by decreased plasma insulin and glucose levels. ILG treatment decreased the expression of TNF-α, p-JNK, IL-1β, p-IRSSer307 to reverse inflammation and insulin resistance (Ma et al., 2015). This suggests that ILG has protective activity against the HFD caused learning and memory deficits through inhibition of the TNF-α/JNK/IRS pathway. Based on these findings, LG might be used to enhance cognitive performance in neurological disorders such as AD. Frontiers in Aging Neuroscience | www.frontiersin.org Memory Enhancing Activities AD related pathways include amyloid plaque formation and AChE (acetylcholine esterase). Other pathological processes are related to both AD and PD, thus could be therapeutic targets by ILG or LG. The scheme was generated by using Pathway Builder Tool. FIGURE 1 | Diagrammatic representation of pathological phenotypes (depression, dementia, inflammation, oxidative stress, amyloid plaque, neurotransmitter deficits, Lewy aggregation, ER stress, mitochondrial deficits, and cell death) and underlying molecular pathways that could be involved in Alzheimer’s and Parkinson’s disease. Pathways regulated by isoliquiritigenin (ILG) and liquiritigenin (LG) were labeled as green and red lines, respectively. Pathways targeted by both ILG and LG were colored as black line. Arrows (↓) denote stimulation and bars (⊥) denote inhibition by ILG (green), LG (red), and both (black). PD related pathways include MAO (monoamine oxidase), and Lewy aggregation. AD related pathways include amyloid plaque formation and AChE (acetylcholine esterase). Other pathological processes are related to both AD and PD, thus could be therapeutic targets by ILG or LG. The scheme was generated by using Pathway Builder Tool. fragment of Notch-2IC were significantly decreased in LQ-treated Tg2576 mice (Liu et al., 2011). These data suggest that LG treatment might be a best therapeutic strategy against mitochondrial dysfunction (Jo et al., 2016). Mitochondria are powerhouses that continuously undergo fusion, fission, transport, and degradation for regulation of their functions. Mitochondrial fission is controlled by dynamin-related protein-1 (DRP-1) while fusion is regulated by mitofuscin 1 and 2 (Mfn1/2) and optic atrophy protein 1 (Opa1). LG treatment of SK-N-MC cells stably expressing YFP resulted in highly elongated and aggregated mitochondria, suggesting that LG induces mitochondrial fusion in a dose- and time-dependent manner (Jo et al., 2016). Pretreatment with LG effectively restored mitochondrial fragmentation in Mfn1 and Mfn2 knockout MEF cells, but had no effect on Opa1 knockout cells. Treatment of SK-N-MC/mito-YFP with LG inhibited Aβ-induced mitochondrial fragmentation. Sopolamine is a muscarinic cholinergic receptor antagonist that causes disturbances in the cholinergic system in association with cognitive decline (Haider et al., 2016) by formation of ROS and free radicals (El-Sherbiny et al., 2003). The scopolamine- induced spontaneous alternation behavior, cognitive deficit, and discrimination index of recognition memory were significantly reversed by LG at 20 mg/kg in 4-week-old male CD-1 mice. Scopoamine significantly increased the level of acetylcholinesterase (AChE) and MDA whereas treatment with LG inhibited these increases, suggesting that LG improves cognitive dysfunction. Memory Enhancing Activities N-methyl-D-aspartic acid receptors (NMDARs) in the CNS have been allied to learning and memory (Nakazawa et al., 2004). Administration of LG at 20 mg/kg to ICR mice resulted in an increased level of spontaneous alternation behavior without an alternation in the number of arm entries. LG also significantly improved longer step-through latency time in a passive avoidance test. Regarding cognitive enhancement, LG influenced on hippocampal NMDAR subunits 1, 2A, and 2B expressions in ICR mice. For NMDAR downstream targets, LG significantly increased PSD-95 expression and phosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII), ERK, and cAMP response element binding protein (CREB) in the hippocampus (Ko et al., 2018). LG promotes neurogenesis within the CNS via Notch-2 signaling pathway inhibition by ERβ dependent learning and memory. LG inhibits expression of Notch-2 mRNA and protein in progenitor cells, which may explain the high number of neurons with overexpression of ERβ (Liu et al., 2010b). Treatment of Tg2576 mice with LG at 30 mg/kg showed a greater improvement in learning and memory than doses of 3 and 10 mg/kg in Morris water maze and shuttle box test. LG did not alter the levels of amyloid precursor protein (APP); however, levels of an oligomeric form of Aβ protein in Tg2576 mice were significantly reduced in a dose-dependent manner. GFAP levels by immunostaining and immunoblotting were decreased significantly by treatment with 10 and 30 mg/kg LG compared with vehicle treatment in Tg2576 mice. Levels of the active Treatment of ICR mice fed a high-fat diet (HFD) with ILG at 30 and 60 mg/kg/day increased the time spent in the target quadrant where the platform was located in a Morris water November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org 6 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. FIGURE 1 | Diagrammatic representation of pathological phenotypes (depression, dementia, inflammation, oxidative stress, amyloid plaque, neurotransmitter deficits, Lewy aggregation, ER stress, mitochondrial deficits, and cell death) and underlying molecular pathways that could be involved in Alzheimer’s and Parkinson’s disease. Pathways regulated by isoliquiritigenin (ILG) and liquiritigenin (LG) were labeled as green and red lines, respectively. Pathways targeted by both ILG and LG were colored as black line. Arrows (↓) denote stimulation and bars (⊥) denote inhibition by ILG (green), LG (red), and both (black). PD related pathways include MAO (monoamine oxidase), and Lewy aggregation. Memory Enhancing Activities Moreover, LG treatment ameliorated the scopolamine-induced hippocampal expression of BDNF, ERK, and CREB related to cognitive function. Therefore, LG may have November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org Frontiers in Aging Neuroscience | www.frontiersin.org 7 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. potential learning and memory enhancement effects in mice (Ko et al., 2017). The above reports show that the ERβ agonist LG has a promising future as a principal active constituent for the treatment of AD. the function of LG (Liu et al., 2015). These results suggest that the ERβ agonist LG significantly inhibits the PI3K/Akt/mTOR pathways representing a possible therapy for TMZ susceptibility in gliomas. Neuroprotection Against Glutamate-Induced Toxicity g HIV-1 in CNS results in an array of deficits known as HIV-1-associated neurocognitive disorders (HAND) allied with dendritic simplification and synaptic loss (Antinori et al., 2007). Treatment with HIV-1 transactivating protein (Tat) at 50 nM for 24 h resulted in a significant reduction of F-actin-labeled dendritic puncta and loss of dendrites in brain primary neuronal cultures. LG treatment against Tat 1-86B toxicity protects cell viability, prevents cumulative injury to the dendritic network, and aids recovery from HAND (Bertrand et al., 2014). Results suggest that LG acts via an ERβ-dependent mechanism to avert synaptodendritic damage induced by HIV-1 Tat 1-86B (Bertrand et al., 2014). High concentrations of neurotransmitter glutamate can persuade neuronal cell death by receptor-induced cytotoxicity or ROS-mediated oxidative stress, leading to the learning and memory deficits in NDDs (Yang E.J. et al., 2013). Oxidative stress can be induced by 5 mM glutamate in the mouse hippocampal neuronal cell line, HT22, which lacks ionotropic glutamate receptors. Glutamate concentrations greater than millimolar levels can cause oxidative stress through inhibition of cysteine uptake, leading to glutathione reduction in the cells (Murphy et al., 1989). Pretreatment with LG (10 and 50 µM) and ILG (5 and 10 µM) for 12 h showed protective efficacy against cell cytotoxicity and ROS production induced by 12-h treatment with glutamate. LG effectively recovered the glutamate and calcium chloride (CaCl2) toxicity in a concentration-dependent manner (Yang E.J. et al., 2013). The Bid level was increased and phosphorylation of mitogen-activated protein kinases (MAPKs) upon glutamate induction was decreased by 50 µM LG or 5 µM ILG (Yang E.J. et al., 2013; Yang et al., 2016). These results showed that LG and ILG effectively prevented glutamate-induced toxicity by attenuation of mitochondrial dysfunction, and may help to prevent NDDs. Neuroprotection Against Stroke p g Stroke, with predominant clinical manifestations of ischemia of the brain and hemorrhagic injury, is a major cause of mortality worldwide (Li et al., 2015). The blood-brain barrier (BBB) is a diffusion barrier that selectively blocks influx and efflux of most compounds between blood and brain (Ballabh et al., 2004). However, following a stroke the BBB is disrupted and LG and ILG were detected in plasma and brain tissue with the onset of reperfusion in male Sprague-Dawley rats, suggesting that LG and ILG are able to penetrate the BBB and become distributed in the brain tissue, where they exhibit a protective effect (Li et al., 2015). Zhan and Yang demonstrated that ILG exerted protective effects against rat model of transient middle cerebral artery occlusion (MCAO)-induced focal cerebral ischemia (Zhan and Yang, 2006). Anti-nociception Activities Transient receptor potential melastatin 3 (TRPM3) is a calcium- permeable nonselective cation channel member of the large superfamily of TRP ion channels (Straub et al., 2013) expressed in sensory neurons of trigeminal and dorsal root ganglia (DRG). Activation of TRPM3 by the neurosteroid pregnenolone sulfate (PregS) and heat is linked to neuronal myelination (Hoffmann et al., 2010). Incubation of human embryonic kidney 293 (HEK293) cells stably expressing TRPM3 (HEKmTRPM3) with LG at 25 µM abrogated PregS (35 µM)-induced [Ca2+]i entry. LG elicited a half-maximal block with an IC50 of 500 nM. Moreover, LG had no impact on capsaicin (2 µM)-induced transient receptor potential vanilloid-related (TRPV)1 activation, but concentration dependently inhibited allyl isothiocyanate (AITC)- induced TRPA1 activation. In addition, TRPM7-dependent inward or outward currents were affected by LG (20 µM) treatment in HEK293 cells without impairing cell proliferation and viability. Moreover, activation of TRPM3 in DRG neurons is linked to thermosensation. LG at 10 µM strongly counteracted the PregS-induced calcium entry in rat DRG neurons, suggesting that its TRP channel-inhibiting properties and/or TRPM3 inhibition may be useful in the development of novel and tolerable analgesic therapies (Straub et al., 2013). Neurogenesis Activities Recent studies focused on the identification of compounds such as phytoestrogens that are neuro-selective estrogen receptor agonists (NeuroSERMs) (Zhao et al., 2005) and mimic the actions of estrogen in the brain but have insignificant effects on non-neuronal estrogen-responsive tissues (Zhao et al., 2002). ERβ is also reported for learning and memory functions (Liu et al., 2008; Walf et al., 2008). Liu et al. (2010a) reported the effects of LG on newborn Sparague-Dawley rat brain-derived progenitor cells. Study reported that stem and progenitor cells were differentiated into mature neurons by inhibition of Notch proteins (Woo et al., 2009). Decreased Notch-2 mRNA and Neuroprotection Against Brain Glioma p g Gliomas are the most common and extremely serious type of primary intracranial neoplasm results in higher mortality and morbidity (Lacroix et al., 2001). The loss of ERβ expression in high-grade glioma tumors suggests the potential tumor suppressor role of ERβ. Treatment of temozolomide (TMZ)- resistant U138 glioma cells with LG significantly increased ERβ expression and synergistically inhibited the U138 glioma cells to TMZ-induced proliferation. In addition, ERβ knockdown or activation of the PI3K/Akt/mTOR pathway by IGF-1 eradicated November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org 8 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. and macrophages play a vital role in the inflammatory response (Iontcheva et al., 2004). ILG and LG significantly inhibited nitric oxide (NO) production in RAW 264.7 macrophages. LG (30 µM) and ILG (1.6 µM) almost completely suppressed the LPS (1 µg/ml)-induced inducible nitric oxide synthase (iNOS) expression by inhibiting NF-κB/IκBa activation in RAW264.7 macrophages in a dose-dependent manner (Kim J.Y. et al., 2008; Kim Y.W. et al., 2008). In addition, ILG suppressed the LPS-induced phosphorylation of ERK and P38 MAPK, but not JNK1/2 (Kim J.Y. et al., 2008). Treatment of rats with LG (50 mg/kg/day for 3 days p.o. or 15 mg/kg/day for 2 days i.v.) significantly reduced paw swelling induced by carrageenan (Kim Y.W. et al., 2008). These results suggest that LG and ILG have been considered as possible anti-inflammatory agents. protein expression in progenitor cells after LG treatment explains the increased neurogenesis and higher number of neurons. In addition, LG promotes neurogenesis by ERβ dependent Notch- 2 protein inhibition in SH-SY5Y cells. ERβ gene silencing using RNAi indicated the relationships between Notch receptors, ERs, and neurogenesis (Liu et al., 2010b). Anti-periodontitis Activities Periodontal diseases (gum disease) and dental caries (tooth decay) are the most common human oral infections. Mutans streptococci such as Streptococcus mutans and Streptococcus sobrinus are associated with dental caries through their aciduric, acidogenic, and adhesion properties (Liljemark and Bloomquist, 1996). Different concentrations of ILG and LG were used to determine the MICs for P. gingivalis, F. nucleatum, P. intermedia, S. mutans, and S. sobrinus. ILG and LG displayed significant growth inhibition in gram-negative periodontal bacteria, but had no effect on gram-positive streptococci. ILG was found to be a effective inhibitor of P. gingivalis collagenase and MMP- 9 compared with LG. ILG also suppressed dimerization of the inflammatory mediator toll-like receptor 4 (TLR4), which correlated with NF-κB p65 inhibition, activator protein-1 (AP-1) activation and subsequently reduced expression of cytokines in LPS-induced inflammation (Feldman et al., 2011). Anti-asthmatic Effects Asthma is a common long-term inflammatory airway disease characterized by the polarized Th2 cell secretion of Th2 cytokines (Yang E.J. et al., 2013). G. uralensis was reported for its protective responsiveness in asthma patients (Wang et al., 1998). An anti-asthma formula, ASHMITM, containing G. uralensis, has been reported for improvement in lung function and reduced airway hyperresponsiveness in allergic asthma (Wen et al., 2005). In addition, LG and ILG had high ability in eotaxin secretion suppression compared to glycyrrhizin (Jayaprakasam et al., 2009). Yang N. et al. (2013) reported that the ASHMI OTHER PHARMACOLOGICAL ACTIVITIES In addition to the neuropharmacological activities of ILG and LG mentioned above, numerous studies have revealed additional potential therapeutic effects such as radical scavenging, anti- microbial, anti-inflammatory, and antitumor activities. The anti-inflammatory properties of LG were studied in a LPS- stimulated BV-2 microglial cell model and tert-butyl hydrogen peroxide (t-BHP)-treated ICR male mice model. LG (25, 50, and 100 µM) inhibited LPS-stimulated NO levels in a dose-dependent manner. LG inhibited expressions of iNOS, Cox-2, and pro- inflammatory genes IL-1β and IL-6, but had no effect on TNF- α expression. t-BHP toxicity induced a significant increase in alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels in serum and TNF-α, IL-1β, IL-6 mRNA expression in the liver of mice, whereas these levels were diminished by LG treatment (Yu et al., 2015). These results suggest that LG inhibits various inflammatory mediators and suppresses inflammation in the liver. Radical Scavenging Activities Reactive oxygen species induced by oxidative stress result in damage to cellular proteins, lipids, and nucleic acids. RG extract G9315 containing six flavonoids showed good radical scavenging activity against superoxide (O2·−), hydroxyl (·OH), H2O2, and singlet oxygen (1O2) species (Fu and Liu, 1995). In structure- activity relationship studies ILG showed higher activity than LG (Zhang et al., 2012). The ·OH and ·OOH radical scavenging activity of ILG was by radical adduct formation and that of LG was through hydrogen atom transfer methods. ILG showed more efficient radical scavenging activity than LG because of its nearly planar conjugated conformation (Wang et al., 2017). LG at 100 µM showed the potential to scavenge 2,2-diphenyl-1- picrylhydrazyl (DPPH) free radicals (Yu et al., 2015). gen Receptor Signaling Activities Estrogen Receptor Signaling Activities The ERα and ERβ are nuclear transcription factors that regulate the transcription of target genes (Paterni et al., 2015). LG in RG shows 20-fold greater affinity for ERβ than ERα determined by competitive binding assays. Although LG binds ERα, it induced minimal transcriptional activation of receptor genes at higher concentration of 2.5 µM. From above results, steroid receptor coactivator-2 (SRC-2) engaged to ER target genes proposing that transcriptional potency and ligand binding are not interrelated after LG treatment (Mersereau et al., 2008). In another study, LG treatment to luciferase reporter plasmid transfected MCF-7 and T47D cells induced a higher differentiation at 5 × 10−7 M (Lecomte et al., 2017). Antibacterial Activities The antibacterial activity of ILG and LG have similar minimal inhibitory concentration (MIC) at 25 µg/ml against Mycobacterium tuberculosis (Chokchaisiri et al., 2009). ILG inhibited growth of Mycobacterium bovis at 50 µg/ml (Brown et al., 2007), whereas 250 µg/ml was needed for growth inhibition of Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus hemolyticus (de Barros Machado et al., 2005). Anti-diabetic Activities Diabetes is a major metabolic disease with a rapidly increasing prevalence worldwide. In type 2 diabetes, a chronic increase in lipotoxicity and insulin deficiency contributes to increased beta- cell dysfunction and death (Oh, 2015). LG treatment (5 µM) to rat INS-1 insulinoma cells showed increased cell viability and insulin secretion. LG also increased cell viability and decreased apoptosis associated with palmitate (PA)-induced lipotoxicity. In addition, LG suppressed PA-induced endoplasmic reticulum stress markers such as C/EBP homologous protein (CHOP), eukaryotic initiation factor 2α (eIF-2α) and protein kinase RNA- like endoplasmic reticulum kinase (PERK), but had no effect on X-box binding protein (XBP), JNK and activating transcription factor 6 (ATF-6). In addition, LG activated phosphorylation of Akt by ER and subsequently inactivated the PERK pathway, highlighting its therapeutic value in the prevention of diabetes progression (Bae et al., 2018). Nitric oxide, an inflammatory mediator, plays a pathophysiological role in various diseases (Colasanti and Suzuki, 2000). Treatment of primary hepatocytes isolated from the liver of male Wistar rats with RG extract and its constituents ILG and LG significantly blocked NO levels in the presence of IL-1β without cytotoxicity. ILG showed an IC50 of 11.9 µM. Furthermore, ILG and LG reduced the levels of both iNOS mRNA and protein in primary rat hepatocytes. Moreover, TNF-α and IL-6 mRNA levels were downregulated by ILG and LG, supporting anti-inflammatory effects in hepatocytes (Tanemoto et al., 2015). Diabetes is characterized by abnormally high blood glucose levels. Oral administration of ILG (10 and 20 mg/kg) to streptozotocin (STZ)-induced diabetic rats for 2 weeks or 2.5 and 5 µM to glucose (30 mM)-insulted N2a cells significantly caused an activation of sirutin (SIRT1, a metabolic sensor of the cellular NAD+/NADH ratio) in a dose-dependent manner. In addition, ILG mimics the effects of PGC-1α-mediated mitochondrial biogenesis, calorie restriction, 5′ AMP-activated protein kinase (AMPK)–mediated autophagy and Forkhead box O3a (FOXO3a) mediated stress resistance to counteract experimental diabetic neuropathy (Yerra et al., 2017). The toxicity of acetaminophen, mostly used as analgesic and antipyretic agent, results in massive hepatic necrosis and causes major morbidity and mortality (Zakin and Boyer, 1990). Sprague- Dawley rats were orally administered LG dissolved in 40% PEG administered and then given a single oral dose of acetaminophen in 40% PEG (1.2 g/kg b.w.). LG treatment at 50 mg/kg/day p.o. for 4 days or 15 mg/kg i.v. Hepatoprotective Activities Cadmium (Cd), an environmental heavy metal, largely accumulates in the liver and kidney and induces pulmonary, hepatic, and renal tubular diseases. LG (10–100 µM) treatment to Cd (10 µM) or Cd (1 µM) + buthionine sulfoximine (BSO; 50 µM) exposed H4IIE rat-derived hepatocyte cells showed more active in protecting cells than ILG (0.1–10 µM) treatment. LG also prevented the GSH content reduction induced by BSO, suggesting that LG, but not ILG, have cytoprotection in Cd-induced cellular damages (Kim et al., 2004). Anti-inflammatory Activities Inflammation is an immune system response against harmful stimuli and is characterized by redness, swelling, heat, and pain November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org 9 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. formula contains LG, ILG, and 7,4′-DHF. These flavonoids suppress CA-stimulated synthesis of Th2 cytokine and levels of IL-4 and IL-5 in D10 cell culture media supernatants in a concentration-dependent manner without affecting cell viabilities (Yang N. et al., 2013). 4 µM) (Choi, 2012). These data suggest that LG may act as a potential therapeutic candidate against oxidative stress-induced dysfunction in osteoblasts. Anti-diabetic Activities In addition, ILG induces UGT1A1, GCLC, and MRP2 in Nrf2 WT mice but not in Nrf2 KO mice, concluding that ILG has Nrf2-dependent protective activities (Gong et al., 2015). Anti-diabetic Activities for 2 days significantly reduced the plasma ALT, improved plasma LDH, and ameliorated liver necrosis induced by acetaminophen. LQ administered i.v. had greater protective effects than p.o. against acetaminophen toxicity (Kim et al., 2006). In addition, LG showed a choleretic effect by increased hepatic bile flow, phase II enzymes and hepatic transporters against in a GalN/LPS-induced rat hepatitis model (Kim et al., 2009). ILG was found to be effective at 100 mg/kg b.w. after 120 min in an oral glucose tolerance test (OGTT), but LG was inefficient in lowering blood glucose levels in the STZ-induced diabetic mice model. In the glucose tolerance test, improvement was observed for ILG at 200 mg/kg b.w. post-administered after 15, 30, 60, 90, and 120 min. Hyperglycemic albino mice treated with 200 mg/kg b.w. of ILG for 14 days showed significant (53%) recovery of random blood glucose level and significant modification of liver glycogen content to 49.92% (Gaur et al., 2014). Phase II drug metabolism enzymes, nuclear receptors and other transcription factors in liver stimulates the toxic substances detoxification and excretion processes. Nuclear factor erythroid 2–related factor 2 (Nrf2) plays major role in drug disposition and phase II drug metabolism enzymes (Zollner et al., 2010). Nrf2 dissociates from Keap1 and translocates into the nucleus leading to expression of target genes under stress conditions. ILG significantly induces Nrf2, UGT1A1, BSEB, MRP2 and GCLS in HepG2 cells. In addition, ILG induces UGT1A1, GCLC, and MRP2 in Nrf2 WT mice but not in Nrf2 KO mice, concluding that ILG has Nrf2-dependent protective activities (Gong et al., 2015). Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with low recovery rates, and currently available conventional and modified therapies are rarely effective (Kern et al., 2002). Treatment of the human hepatocarcinoma cell line SMMC-7721 with LG resulted in a concentration-dependent decrease in cell viability and apoptosis. The free radical scavenger, N-acetyl-cysteine (NAC), Phase II drug metabolism enzymes, nuclear receptors and other transcription factors in liver stimulates the toxic substances detoxification and excretion processes. Nuclear factor erythroid 2–related factor 2 (Nrf2) plays major role in drug disposition and phase II drug metabolism enzymes (Zollner et al., 2010). Nrf2 dissociates from Keap1 and translocates into the nucleus leading to expression of target genes under stress conditions. ILG significantly induces Nrf2, UGT1A1, BSEB, MRP2 and GCLS in HepG2 cells. Frontiers in Aging Neuroscience | www.frontiersin.org Anti-osteoporosis Activities Osteoporosis is a disease results from altered bone mass have impact on life expectancy and the quality of life (Lane and Kelman, 2003). Osteoblasts can markedly enhance bone formation (Choi, 2012). LG stimulated cell growth of MC3T3- E1 cells in addition to increasing calcium ion deposition, ALP activity and collagen content, suggesting that LG may induce early and later phases of osteogenic differentiation. The increased osteoblast function was also associated with LG-induced GSH content. In osteoblastic MC3T3-E1 cells, antimycin A (70 µM)– induced production of ROS, cytokines TNF-α and IL-6 and receptor activator of nuclear factor kappa-B ligand (RANKL) was significantly inhibited by treatment with LG (0.04, 0.4, and Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with low recovery rates, and currently available conventional and modified therapies are rarely effective (Kern et al., 2002). Treatment of the human hepatocarcinoma cell line SMMC-7721 with LG resulted in a concentration-dependent decrease in cell viability and apoptosis. The free radical scavenger, N-acetyl-cysteine (NAC), November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org Frontiers in Aging Neuroscience | www.frontiersin.org 10 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. FIGURE 2 | Diagrammatic representation of various pharmacological activities of isoliquiritigenin (ILG) and liquiritigenin (LG). FIGURE 2 | Diagrammatic representation of various pharmacological activities of isoliquiritigenin (ILG) and liquiritigenin (LG). (Paterni et al., 2015). LG also showed an IC50 of 88.3 µM in vitro in glioma U87 cells and in an in vivo study of U87 glioma cells induced nude mice xenografts (Paterni et al., 2015). ILG treatment blocked the cell growth and induced apoptosis on mouse RCN-9 and human COLO-320DM colon cancer cells (Takahashi et al., 2004). Furthermore, ILG treated at 15 ppm at libitum to azoxymethane (AOM; 10 mg/kg b.w. s.c.)-induced colon carcinogenesis in ddY mice inhibited the preneoplastic aberrant crypt foci (ACF) induction (Baba et al., 2002). ILG mixed at 100 ppm in diet fed against AOM (15 mg/kg b.w., 3 times/weekly) induced for 3 weeks effectively reduced the ACF in the colon of male F344 rats (Takahashi et al., 2004). suppressed both LG-induced apoptosis and ROS production. Expression of caspase-3, the principal caspase associated with apoptotic nuclear changes, significantly increased in a time-dependent manner, with a 7-fold induction at 72 h after LG (0.4 mM) treatment. Anti-osteoporosis Activities Furthermore, LG treatment increased tumor suppressor p53 protein and decreased anti-apoptotic Bcl-2 protein through ROS production and mitochondrial membrane potential loss, in agreement with decreased activities of antioxidant enzymes SOD, GSH, and glutathione peroxidase (GPx) in SMMC-7721 cells. These effects have been proven to be cell-specific as LG at 0.4 mM did not cause significant cell death in human hepatic L-02 cells (Zhang et al., 2009). REFERENCES Bopana, N., and Saxena, S. (2007). Asparagus racemosus–ethnopharmacological evaluation and conservation needs. J. Ethnopharmacol. 110, 1–15. doi: 10.1016/ j.jep.2007.01.001 Abushouk, A. I., Negida, A., Ahmed, H., and Abdel-Daim, M. M. (2017). 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This work was also supported by Samsung Research Funding & Incubation Center for Future Technology (SRFC-IT1701-10). Anti-mutagenic and Anti-cancer Activities Aging process is considered major risk factor for age-related diseases such as AD and PD become main concerns in the challenge to improve health. Aging effects cause a cascade of stressors that weaken energy metabolism, mitochondrial functions, and gene expression. The current synthetic drugs treatments to multi-functional age-related NDDs have proven ineffective in curing and have certain side effects. On the other hand, botanical drugs are multicomponent complex systems that might interact with multiple signaling pathways and targets in the human body. This new era on botanical research has provide many opportunities to develop new therapies for patients with age-related diseases. RG have been used widely in traditional medicines throughout the world because of its rich components such as triterpenoids, flavanones, chalcones, coumarines and their glycosides. These active components suggest that RG may be an effective herb for the treatment of different The human osteosarcoma U2OS cell line (which does not express endogenous ERs), human breast MCF-7 cancer cell line (which express ERα), and human cervical HeLa cancer cell line were treated with different doses of LG (0.5, 1, 2, and 2.5 µM). LG treatment at 2 µM stimulated the ERE-tk- luciferase, and ER regulatory elements CECR6, NKG2E, and NKD in ERβ transfected cells due to its greater selectivity, but not with ERα transfected cells. LG (2 mg; 2.5 µl/h) infused for 30 days to nude mice did not involve in uterine enlargement or MCF-7 breast cancer cells induced xenograft (Mersereau et al., 2008). RG extract G9315 containing ILG and LG significantly inhibited the Cytoxan induced mouse bone- marrow micronuclei formation suggesting an antimutagenic activity (Fu and Liu, 1995). LG was shown to inhibit breast (MDA-MB-231, MCF7, SKBR3) and colon (LoVo, HCT) cancer cells proliferation November 2018 | Volume 10 | Article 348 Frontiers in Aging Neuroscience | www.frontiersin.org Frontiers in Aging Neuroscience | www.frontiersin.org 11 The Role of Liquiritigenin and Isoliquiritigenin Ramalingam et al. AUTHOR CONTRIBUTIONS kinds of disease. The main bioactive constituents ILG and LG showed prominent effects in AD, PD and other NDDs models by numerous in vitro and in vivo experimental studies. The various pharmacological abilities of ILG and LG clearly establish a protective role in human health and disease model(s) (Figure 2). 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Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. White, J. D., and Gall, C. M. (1987). Differential regulation of neuropeptide and proto-oncogene mRNA content in the hippocampus following recurrent seizures. Brain Res. 427, 21–29. doi: 10.1016/0169-328X(87) 90040-4 Copyright © 2018 Ramalingam, Kim, Lee and Lee. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. WHO (ed.). 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Evaluation of the efficacy of palonosetron for prevention of chemotherapy-induced nausea and vomiting in patients with gastric cancer treated with S-1 plus cisplatin
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Int J Clin Oncol (2016) 21:483–490 DOI 10.1007/s10147-015-0916-2 ORIGINAL ARTICLE Evaluation of the efficacy of palonosetron for prevention of chemotherapy‑induced nausea and vomiting in patients with gastric cancer treated with S‑1 plus cisplatin Katsunobu Oyama1 · Sachio Fushida1 · Masahide Kaji2 · Toshiya Takeda3 · Kazuhisa Yabushita4 · Hideaki Nezuka5 · Shinichi Kinami6 · Naotaka Kadoya7 · Yuki Takai8 · Yuji Tsukioka9 · Shigekazu Ohyama10 · Kunihiro Tsuji11 · Tomoya Tsukada1 · Jun Kinoshita1 · Takashi Fujimura1 · Tetsuo Ohta1 Received: 19 August 2015 / Accepted: 13 October 2015 / Published online: 27 October 2015 © The Author(s) 2015. This article is published with open access at Springerlink.com our previous study, which used granisetron, aprepitant, and dexamethasone, to assess the relative effectiveness of palonosetron versus granisetron in combination antiemetic therapy. * Sachio Fushida fushida@staff.kanazawa‑u.ac.jp 6 Department of General and Digestive Surgery, Kanazawa Medical University, Uchinada, Japan 7 Department of Surgery, Toyama Rosai Hospital, Uozu, Japan 8 Department of Gastroenterology, Keiju Medical Center, Nanao, Japan 9 Department of Surgery, Toyama City Hospital, Toyama, Japan 10 Department of Surgery, National Hospital Organization Kanazawa Medical Center, Kanazawa, Japan 11 Department of Gastroenterology, Ishikawa Prefectural Central Hospital, Kanazawa, Japan Digestive Disease Support Organization (DDSO) 35-1 Yonemaru- machi, Kanazawa, Ishikawa 921-8004, Japan. Introduction Chemotherapy-induced nausea and vomiting (CINV) is a common adverse event observed in patients with cancer who receive chemotherapy [1] and is one of the greatest fears of patients receiving chemotherapy [2, 3]. Inadequate control of CINV can lead to dehydration, nutritional defi- ciencies, and electrolyte imbalances, which may impair functional and mental activities and quality of life (QOL), increase the use of healthcare resources, and occasionally cause treatment delay or discontinuation [4–6]. Gener- ally, CINV persists for approximately 5 days after admin- istration of emetogenic antitumor agents. CINV occurring within the first 24  h has been defined as acute and that occurring after >24 h as delayed [7]. Palonosetron is a new generation 5-HT3RA, differing from first generation 5-HT3RAs in its pharmacokinetic and pharmacodynamic profiles, and may be uniquely suited to treat both early and delayed CINV. Four phase III clinical trials found that CINV prevention rates were higher with palonosetron than with first-generation 5-HT3RAs [16–19]. Palonosetron has a longer elimination half-life (t½) and a greater receptor-binding affinity than first-generation 5-HT3RAs [20]. Moreover, it has been shown to trigger 5-HT3 receptor internalization and prolong inhibition of receptor function [21]. Moreover, mechanistic studies using palonosetron and an NK1RA suggest interactions between the 5-HT3 receptor and NK1 receptor neurotransmitter pathways [22]. Corticosteroids have long been used as antiemetic agents to treat CINV [8], being effective for both acute and delayed emesis. The introduction of selective serotonin [5-hydroxy- tryptamine-3 (5-HT3)] receptor antagonists (RAs), such as ondansetron, dolasetron, and granisetron revolutionized the control of CINV. 5-HT3RAs are used to treat patients receiving moderate to highly emetogenic chemotherapy, with protective effects mainly in acute emesis. Although combinations of corticosteroids and 5-HT3RA have been standard for the management of CINV, >50 % of patients continue to vomit in response to highly emetogenic chemo- therapy, such as high-dose cisplatin [9], suggesting that this combination antiemetic therapy prevents vomiting in the acute phase, but not in the delayed phase [10–12]. Delayed nausea also tends to be more severe and less responsive to antiemetic therapy than acute nausea. When compared with other 5-HT3RAs, palonosetron was found to significantly reduce subjective sensations of nausea [23]. A pooled analysis of phase III clinical trials comparing palonosetron with first-generation 5-HT3RAs found that palonosetron was superior in controlling nausea [24] and may therefore be superior in controlling delayed nausea. Abstract Purpose  The purpose of our study was to evaluate the efficacy of a new combination antiemetic therapy consist- ing of palonosetron, aprepitant, and dexamethasone in gas- tric cancer patients undergoing chemotherapy with S-1 plus cisplatin. Results  Of the 72 included patients, 66 (91.6  %), 70 (97.2 %), and 50 (69.1 %) achieved CR, and 48 (66.7 %), 61 (84.7  %) and 49 (68.1  %) achieved CP during in the overall, acute, and delayed phases of cisplatin adminis- tration, respectively. Approximately half of the patients had some degree of anorexia. FLIE results indicated that 78.6  % of patients maintained their quality of life. Palo- nosetron was not superior to granisetron in combination antiemetic therapy. Methods  This prospective, multi-institutional observa- tional study assessed patient-reported nausea, vomiting, use of rescue therapy, change of dietary intake, and Func- tional Living Index-Emesis (FLIE) questionnaire results. The percentages of patients showing complete response (CR; no emesis and non-use of any rescue antiemetics) and complete protection (CP; no significant nausea and non- use of any rescue antiemetics), change of dietary intake, and impact of chemotherapy-induced nausea and vomit- ing on daily life during the overall (0–120 h after cisplatin administration), acute (0–24  h), and delayed (24–120  h) phases were examined. These findings were compared with Conclusions  Three-drug combination antiemetic therapy with palonosetron, aprepitant, and dexamethasone was tol- erable in gastric cancer patients undergoing treatment with S-1 plus cisplatin. The predominance of palonosetron to granisetron was not demonstrated in this study. Digestive Disease Support Organization (DDSO) 35-1 Yonemaru- machi, Kanazawa, Ishikawa 921-8004, Japan. Abstract 1 Department of Gastroenterological Surgery, Kanazawa University, 13‑1 Takara‑machi, Kanazawa, Ishikawa 920‑8641, Japan 2 Department of Surgery, Toyama Prefectural Central Hospital, Toyama, Japan 3 Department of Surgery, Public Central Hospital of Matto Ishikawa, Hakusan, Japan 10 Department of Surgery, National Hospital Organization Kanazawa Medical Center, Kanazawa, Japan 4 Department of Surgery, Takaoka City Hospital, Takaoka, Japan 11 Department of Gastroenterology, Ishikawa Prefectural Central Hospital, Kanazawa, Japan 5 Department of Surgery, Yatsuo General City Hospital, Toyama, Japan 1 3 Int J Clin Oncol (2016) 21:483–490 484 Keywords  Palonosetron · Gastric cancer · CINV · Anorexia · QOL that complete response (CR; no emesis and non-use of any rescue antiemetics) rates overall and during the acute and delayed phases of chemotherapy administration were 88.7, 98.1, and 88.7 %, respectively, and complete protec- tion (CP; no significant nausea and non-use of any rescue antiemetics) rates during the three phases of chemotherapy were 67.9, 96.2, and 67.9 %, respectively [14]. Similarly, a study of triplet antiemetic treatment with a corticoster- oid, a first generation 5-HT3RA and NK1RA reported that this largely alleviated acute and some delayed emesis, but found that delayed nausea rates were unacceptably high [15]. Introduction This prospective observational study assessed the antiemetic efficacy and tolerability of palonosetron, com- bined with dexamethasone and aprepitant, in patients with advanced gastric cancer receiving S-1 plus cisplatin chem- otherapy. By performing this study in patients similar to those who received triplet antiemetic therapy with grani- setron, dexamethasone and aprepitant [14], we were able to compare the relative effectiveness of palonosetron and granisetron in combination antiemetic therapy for patients with gastric cancer. Gastric cancer is one of the major causes of cancer deaths worldwide, and chemotherapy is the main treatment option for patients with advanced stage disease. A stand- ard chemotherapeutic regimen for advanced gastric cancer consists of a combination of cisplatin plus fluoropyrimi- dine, which induces CINV. A large phase III trial of S-1, an orally administrated 5-fluorouracil analog, plus cisplatin in patients with advanced gastric cancer who received com- binations of corticosteroids and 5-HT3RAs for manage- ment of CINV found that emesis occurred in 36 % of these patients and nausea in 67 % [13]. Methods Recently, two novel anti-CINV agents have become available, the neurokinin-1 (NK1) RA aprepitant and the new generation 5-HT3RA palonosetron, both of which were found to prevent delayed-phase CINV. An observa- tional study testing the combination of aprepitant, grani- setron and dexamethasone in patients receiving chemo- therapy with S-1 plus cisplatin for gastric cancer found 1 3 Response definitions the study protocol was approved by the institutional review board at each participating center. Moreover, the study was performed in accordance with the prin- ciples of the Declaration of Helsinki (Clinical trial ID: UMIN000009016). The observation period was divided into three distinct phases after injection of cisplatin—acute (0–24 h), delayed (24–120  h), and overall (0–120  h). During each 120-h assessment period, patients were required to maintain a diary and record the number and timing of any episodes of vomiting or retching; the frequency and timing of use of rescue antiemetics; and the degree of nausea using a 4-point categorical scale (0, none; 1, mild; 2, moderate; 3, severe). Changes in dietary intake were recorded by patients every day on days 1–5 as percent volume of diet after initiation of chemotherapy compared with before. Patients also com- pleted the FLIE questionnaire once per day from days 1–5; this questionnaire captured information about the effect of CINV on their daily lives. Chemotherapy All patients received S-1 plus cisplatin therapy as described in the SPIRITS trial [13], the standard chemotherapeu- tic regimen for advanced gastric cancer in Japan. S-1 (80 mg/m2) was administered orally twice daily for the first 3 weeks of each 5-week cycle. Cisplatin was administered as an intravenous infusion of 60 mg/m2 on day 8 of each cycle. The primary endpoint was the proportion of patients achieving CR during the overall study phase. No vomit- ing was defined as no vomiting, retching, or dry heaves. Secondary endpoints included the rate of CP. No signifi- cant nausea was defined as nausea scores of 0 and 1, and as nausea that does not interfere with normal patient activi- ties; changes in dietary intake; absence of vomiting and no nausea; and the impact of CINV on daily life, as meas- ured by the FLIE, during the overall, acute, and delayed phases. Safety was evaluated based on physical examina- tions, including vital signs, routine clinical laboratory tests, and adverse event reporting. Toxicity grades were assessed using the NCI Common Terminology Criteria for Adverse Events (NCI-CTCAE) v4.0. (http://ctep.cancer.gov/forms/ CTCAEv4.pdf). Any adverse events were determined by the investigator to be possibly, probably, or definitively related to the study drug. Eligibility criteria The study involved high or moderately emetogenic, chem- otherapy-naive patients scheduled to receive their first course of chemotherapy with S-1 (80  mg/m2) and cispl- atin (60 mg/m2) for pathologically confirmed gastric can- cer. All patients were aged ≥20 years and had an Eastern Cooperative Oncology Group (ECOG) Performance Sta- tus of 0–2. Patients with any vomiting, retching, or nau- sea [National Cancer Institute (NCI) ≥grade I] in the 24 h before the start of chemotherapy and those using any drug with potential antiemetic efficacy 48 h before chemother- apy were excluded. In addition, patients receiving radia- tion therapy to the abdomen or pelvis less than 1  week before treatment, those with a symptomatic primary or metastatic central nervous system malignancy, those at risk of vomiting for other reasons (e.g., epilepsy, active peptic ulcer, and gastrointestinal obstruction), and those with any uncontrolled disease other than malignancy that may pose an unwarranted risk, as determined by the inves- tigator, were also excluded. The FLIE is a patient-completed multidimensional ques- tionnaire that evaluates the QOL [26]. The Japanese ver- sion of the FLIE, which was used in this study, has been reported useful in assessing the impact of CINV on the QOL of Japanese patients [27]. The FLIE questionnaire contains a validated 18-item visual analog scale (VAS)- based, patient-reported outcome measure that captures information about the effect of CINV on the daily lives of the patients. FLIE has separate domains for the impact of nausea and vomiting on the daily function of patients. Each item is scored from 7 (not at all) to 1 (a great deal). Cut-offs for a minimal or no impact of CINV on daily life included an average score of >6 points, a total score of >108 of the maximum possible 126 points, and a score on each domain of >54. Antiemetic treatment Patients received the combination of antiemetics recom- mended in the 2010 Japanese Society of Clinical Oncol- ogy (JSCO) Guidelines for Antiemetics in Oncology [25]. On day 1, all patients received oral aprepitant 125  mg 60  min before cisplatin infusion plus intravenous dexa- methasone 9.9 mg and intravenous palonosetron 0.75 mg 30 min before cisplatin infusion. On days 2 and 3, patients received oral aprepitant 80  mg once daily each morning and oral dexamethasone 8 mg bid, and on day 4 patients received oral dexamethasone 8 mg bid. Patients were also prescribed a rescue antiemetic, to be used only when nau- sea and vomiting developed during the 120-h observation period. Design This was a multi-institutional, prospective, observa- tional, non-comparative study involving 20 institutions of the Digestive Disease Support Organization (DDSO). All patients provided written informed consent, and 1 3 1 3 485 Int J Clin Oncol (2016) 21:483–490 Statistical analysis In our previous study, CR was observed in 88.7  % and CP in 67.9 % of patients. To realize an equivalent 1 3 1 3 Int J Clin Oncol (2016) 21:483–490 486 Table 1   Patient demographic and clinical characteristics Characteristics No. of patients All 72 Age (years; 50–81, median 65) ≤65:≥66 34:38 Gender Male:female 58:14 ECOG performance status 0:1 47:25 Clinical stage of gastric cancer (TNM) II:III:IV:recurrence 0:20:37:15 Alcoholic drinks None:seldom:almost daily 49:4:19 History of chemotherapy Negative:positive 7:65 History of CINV Negative:positive 72:0 History of morning sick- ness Negative:positive 71:1 History of motion sick- ness Negative:positive 71:1 20 40 60 80 100 0 66.7% 91.6% overall (0-120 h) acute (0-24 h) delayed (24 -120 h) 84.7% 97.2% 68.1% 91.6% complete response complete protecon % of paents Fig. 1   Percentage of patients with complete response (CR) and com- plete protection (CP). CR for the overall, acute, and delayed phases was achieved in 91.6, 97.2, and 91.6 % of patients, respectively. CP rates for the overall, acute, and delayed phases were 66.7, 84.7, and 68.1 %, respectively Table 1   Patient demographic and clinical characteristics Characteristics No. of patients All 72 Age (years; 50–81, median 65) ≤65:≥66 34:38 Gender Male:female 58:14 ECOG performance status 0:1 47:25 Clinical stage of gastric cancer (TNM) II:III:IV:recurrence 0:20:37:15 Alcoholic drinks None:seldom:almost daily 49:4:19 History of chemotherapy Negative:positive 7:65 History of CINV Negative:positive 72:0 History of morning sick- ness Negative:positive 71:1 History of motion sick- ness Negative:positive 71:1 20 40 60 80 100 0 66.7% 91.6% overall (0-120 h) acute (0-24 h) delayed (24 -120 h) 84.7% 97.2% 68.1% 91.6% complete response complete protecon % of paents Fig. 1   Percentage of patients with complete response (CR) and com- plete protection (CP). CR for the overall, acute, and delayed phases was achieved in 91.6, 97.2, and 91.6 % of patients, respectively. CP rates for the overall, acute, and delayed phases were 66.7, 84.7, and 68.1 %, respectively Table 2   Percentage of patients achieving efficacy endpoints Overall (0–120 h) Acute (0–24 h) Delayed (24–120 h) Table 1   Patient demographic and clinical characteristics antiemetic effect with palonosetron, the expected CR rate was set at 89 %, the threshold CR rate at 77 % and the expected CP rate at 80 %. Antiemetic outcomes Antiemetic outcomes are shown in Fig. 1 and Table 2. CR during the overall, acute, and delayed phases of cisplatin administration was achieved by 66 (91.6 %), 70 (97.2 %) and 66 (91.6 %) patients, respectively, and CP during these phases was achieved by 48 (66.7 %), 61 (84.7 %), and 49 patients (68.1 %), respectively. Patient characteristics 20 40 60 80 100 0 66.7% 91.6% overall (0-120 h) acute (0-24 h) delayed (24 -120 h) 84.7% 97.2% 68.1% 91.6% complete response complete protecon % of paents Fig. 1   Percentage of patients with complete response (CR) and com- plete protection (CP). CR for the overall, acute, and delayed phases was achieved in 91.6, 97.2, and 91.6 % of patients, respectively. CP rates for the overall, acute, and delayed phases were 66.7, 84.7, and 68.1 %, respectively Between November 2012 and May 2014, 75 patients were enrolled at 14 centers in Japan. Of these, 72 satisfied the eligibility criteria; the three patients who were excluded did not receive cisplatin injections. The baseline demographic and clinical characteristics of the patients are described in Table 1. Of the 72 patients, 58 (80.6 %) were male, and the median age of the patients was 65 years. 20 40 60 80 100 0 66.7% 91.6% overall (0-120 h) acute (0-24 h) delayed (24 -120 h) 84.7% 97.2% 68.1% 91.6% complete response complete protecon % of paents Statistical analysis Using these parameters, we calculated that an estimated sample size of 63 sub- jects was required to provide a power of 80 %, assuming a normal equation method and an overall significance level of 0.05. Assuming that approximately 15 % of sub- jects would be withdrawn or drop out, the target sample size was set at 75 subjects. Rates of CR and CP, food intake and impact on daily life in this study were com- pared with those in our previous [14] using chi-squared tests. All statistical analyses were performed using the Statistical Package for Social Sciences (SPSS) software version 11.0. Safety Overall, antiemetic therapy was well tolerated. Adverse events considered by the investigator to be possibly, prob- ably, or definitely related to the study drug included ano- rexia in nine (12.5 %) patients, diarrhea in six (8.3 %), and hiccups and constipation in one (1.4 %) each. No serious adverse events appeared related to the study drug. Assessment of the QOL Of the 72 eligible patients, 70 completed the FLIE ques- tionnaires (Table  3). Over the 5  day study period, 55 patients (78.6 %) had total FLIE scores of >108, with 54 (77.1  %) having a nausea domain score of >54 and 64 (91.4  %) having a vomiting domain score of >54, indi- cating that CINV had minimal or no impact on daily life. During the acute phase, 62 patients (88.6  %) had total FLIE scores, 63 (90.0 %) had nausea domain scores and 68 (97.2  %) had vomiting domain scores indicating that CINV had minimal or no impact on daily life. During the delayed phase, 55 patients (78.6 %) had total FLIE scores, 54 (77.1 %) had nausea domain scores and 66 (94.3 %) had vomiting domain scores indicating that CINV had minimal or no impact on daily life. Fig. 1   Percentage of patients with complete response (CR) and com- plete protection (CP). CR for the overall, acute, and delayed phases was achieved in 91.6, 97.2, and 91.6 % of patients, respectively. CP rates for the overall, acute, and delayed phases were 66.7, 84.7, and 68.1 %, respectively Table 2   Percentage of patients achieving efficacy endpoints Overall (0–120 h) Acute (0–24 h) Delayed (24–120 h) Complete response (%) 91.6 97.2 91.6 Complete protection (%) 66.7 84.7 68.1 Table 2   Percentage of patients achieving efficacy endpoints 1 3 3 487 Int J Clin Oncol (2016) 21:483–490 Table 3   QOL assessment based on FLIE questionnaire NIDL no or minimal impact on daily life, defined as domain FLIE score of >54 and total FLIE score of >108 FLIE item Overall (0–120 h) Acute (0–24 h) Delayed (24–120 h) No. of patients % No. of patients % No. of patients % Total NIDL Total NIDL Total NIDL FLIE total score 70 55 78.6 70 62 88.6 70 55 78.6 Nausea domain total score 70 54 77.1 70 63 90.0 70 54 77.1 Vomiting domain total score 70 64 91.4 70 68 97.2 70 66 94.3 Table 3   QOL assessment based on FLIE questionnaire Table 4   Comparison of efficacy outcomes with those of a previous study assessing the combination of granisetron, aprepitant, and dexa- methasone a  From Ref. Assessment of the QOL [14] Present study (palonosetron/aprepitant/ granisetron) (%) Previous studya (granisetron/aprepitant/ granisetron) (%) Complete response  Acute 97.2 98.1  Delayed 91.6 88.7  Overall 91.6 88.7 Complete protection  Acute 84.7 96.2  Delayed 68.1 67.9  Overall 66.7 67.9 Reduction of diet intake  Acute 20.9 18.8  Delayed 55.6 54.0  Overall 55.6 54.0 Impact on daily life (FLIE)  Acute 88.6 98.0  Delayed 78.6 79.5  Overall 78.6 79.5 Table 4   Comparison of efficacy outcomes with those of a previous study assessing the combination of granisetron, aprepitant, and dexa- methasone 70-100% 30-69% 1-29% 0% 20 40 60 80 100 0 day 3 day 4 % of paents 79.1% 15.3% 5.6% 70.8% 16.7% 1.4% 11.1% 66.1% 25.0% 1.4% 12.5% 48.6% 27.8% 2.8% 20.8% 44.4% 26.4% 5.6% 23.6% day 2 day 1 day 5 Fig. 2   Decrease of diet intake compared with before chemotherapy period. Approximately half of the patients experienced some degree of anorexia; the decrease in oral intake was predominant in the delayed phase % of paents Fig. 2   Decrease of diet intake compared with before chemotherapy period. Approximately half of the patients experienced some degree of anorexia; the decrease in oral intake was predominant in the delayed phase Comparison between these results and those of our previous study A comparison of CR, CP, diet intake and impact on daily life in this study and that of our previous study evaluating the combination of aprepitant, granisetron and dexametha- sone as an antiemetic in advanced cancer patients treated with cisplatin and S-1 showed no significant differences in any of these parameters (Table 4). Dietary intake Approximately half of the patients had some degree of anorexia, with the decrease in oral intake being more pre- dominant during the delayed phase (Fig. 2). The volume of dietary intake was reduced by half in 30 % of patients. Additionally, 5 % of these patients could not consume any food or beverage during the delayed phase. Discussion Moreover, palono- setron was found to be superior to ondansetron in patient receiving highly emetogenic chemotherapy [17]. The most noteworthy differences between palonosetron and first- generation 5-HT3RAs occurred during the delayed phase. Although the latter two trials allowed dexamethasone pre- treatment at the investigator’s discretion, only one of these trials [17] found that concomitant dexamethasone was associated with antiemetic effects. A phase III trial compar- ing the anti-CINV effects of palonosetron plus dexametha- sone versus granisetron plus dexamethasone in patients receiving highly emetogenic chemotherapy found that palonosetron was non-inferior to granisetron during the acute phase and superior to granisetron during the delayed phase [18]. A pooled-analysis of phase III trials comparing palonosetron with first-generation 5-HT3RAs in combina- tion with corticosteroid showed that palonosetron was asso- ciated with higher rates of CR, CP, and absence of emesis and nausea [28]. Nevertheless, another meta-analysis found that the superiority of palonosetron was unclear in trials in which patients were administered dexamethasone [29]. At present, therefore, the superiority of palonosetron when combined with corticosteroid remains unclear. with granisetron plus aprepitant plus dexamethasone [33]. The trial described here found that triple combination antiemetic therapy with palonosetron, aprepitant and dexa- methasone for delayed emesis was well tolerated, but that the addition of palonosetron to aprepitant and dexametha- sone was no more effective than the addition of granisetron to aprepitant and dexamethasone. However, the prolonged antiemetic effect of palonosetron may have been masked when administered with other antiemetic agents, including an NK1RA. The discrepancy between our results and those of the TRIPLE trial may be due to the efficacy of previous tri- plet therapy with granisetron, dexamethasone and aprepi- tant being sufficient for gastric cancer patients treated with S-1 plus cisplatin, masking any additional effects of palonosetron. In fact, the CINV control rates in our studies were superior to those of other studies in patients with dif- ferent types of cancer receiving several chemotherapeutic regimens. Medical economics is an important issue in clinical practice and must be balanced with the results of evidence- based medicine. The drug costs of antiemetics including palonosetron was JPY 27.653 and JPY 16,808 with grani- setron per course of chemotherapy. In the present study, the drug replacement from granisetron to palonosetron is not worth the cost. This study had several limitations. First, the study cohort was limited to patients with gastric cancer receiving an initial course of S-1 plus cisplatin chemotherapy. Discussion Palonosetron, a new 5-HT3RA, first became available in 2003, the same year as aprepitant. Standard antiemetic therapy with corticosteroid and a first-generation 5-HT3RA 1 3 3 Int J Clin Oncol (2016) 21:483–490 488 provided significant advances in controlling acute eme- sis, but provided minimal benefit against delayed emesis. Palonosetron has a stronger binding affinity to its receptor and a longer plasma-elimination half-time than first gen- eration 5-HT3RAs. As CINV can persist for several days, a longer acting 5-HT3RA may be valuable in its treatment. Clinical trials have shown that palonosetron was effective in preventing both acute and delayed CINV [15–18]. Two phase III randomized trials in patients receiving moderately emetogenic chemotherapy showed that monotherapy with palonosetron better prevented delayed phase emesis than ondansetron [15] or dolasetron [16]. Moreover, palono- setron was found to be superior to ondansetron in patient receiving highly emetogenic chemotherapy [17]. The most noteworthy differences between palonosetron and first- generation 5-HT3RAs occurred during the delayed phase. Although the latter two trials allowed dexamethasone pre- treatment at the investigator’s discretion, only one of these trials [17] found that concomitant dexamethasone was associated with antiemetic effects. A phase III trial compar- ing the anti-CINV effects of palonosetron plus dexametha- sone versus granisetron plus dexamethasone in patients receiving highly emetogenic chemotherapy found that palonosetron was non-inferior to granisetron during the acute phase and superior to granisetron during the delayed phase [18]. A pooled-analysis of phase III trials comparing palonosetron with first-generation 5-HT3RAs in combina- tion with corticosteroid showed that palonosetron was asso- ciated with higher rates of CR, CP, and absence of emesis and nausea [28]. Nevertheless, another meta-analysis found that the superiority of palonosetron was unclear in trials in which patients were administered dexamethasone [29]. At present, therefore, the superiority of palonosetron when combined with corticosteroid remains unclear. provided significant advances in controlling acute eme- sis, but provided minimal benefit against delayed emesis. Palonosetron has a stronger binding affinity to its receptor and a longer plasma-elimination half-time than first gen- eration 5-HT3RAs. As CINV can persist for several days, a longer acting 5-HT3RA may be valuable in its treatment. Clinical trials have shown that palonosetron was effective in preventing both acute and delayed CINV [15–18]. Two phase III randomized trials in patients receiving moderately emetogenic chemotherapy showed that monotherapy with palonosetron better prevented delayed phase emesis than ondansetron [15] or dolasetron [16]. References 1. Bender CM, McDaniel RW, Murphy-Ende K et  al (2002) Chemotherapy-induced nausea and vomiting. Clin J Oncol Nurs 6:94–102 18. Aapro M, Grunberg S, Manikhas G et  al (2006) A phase III, double-blind, randomized trial of palonosetron compared with ondansetron in preventing chemotherapy-induced nausea and vomiting following highly emetogenic chemotherapy. Ann Oncol 17:1441–1449 2. de Boer-Dennert M, de Wit R, Schmitz PI et al (1997) Patient perceptions of the sideeffects of chemotherapy: the influence of 5HT3 antagonists. Br J Cancer 76:1055–1061 19. Saito M, Aogi K, Sekine I et al (2009) Palonosetron plus dexa- methasone versus granisetron plus dexamethasone for prevention of nausea and vomiting during chemotherapy: a double-blind, double-dummy, randomised, comparative phase III trial. Lancet Oncol 10:115–124 3. Hickok JT, Roscoe JA, Morrow GR et  al (2003) Nausea and emesis remain significant problems of chemotherapy despite prophylaxis with 5-hydroxytryptamine-3 antiemetics: a Uni- versity of Rochester James P. Wilmot cancer center community clinical oncology program study of 360 cancer patients treated in the community. Cancer 97:2880–2886 20. Rojas C, Stathis M, Thomas AG et  al (2008) Palonosetron exhibits unique molecular interactions with the 5-HT3 receptor. Anesth Analg 107:469–478 4. Lindley CM, Hirsch JD, O’Neill CV et al (1992) Quality of life consequences of chemotherapy-induced emesis. Qual Life Res 1:331–340 21. Rojas C, Thomas AG, Alt J et  al (2010) Palonosetron triggers 5-HT(3) receptor internalization and causes prolonged inhibition of receptor function. Eur J Pharmacol 626:193–199 5. Bloechl-Daum B, Deuson RR, Mavros P et al (2006) Delayed nausea and vomiting continue to reduce patients’ quality of life after highly and moderately emetogenic chemotherapy despite antiemetic treatment. J Clin Oncol 24:4472–4478i 22. Rojas C, Slusher BS (2012) Pharmacological mechanisms of 5-HT3 and tachykinin NK1 receptor antagonism to prevent chemotherapyinduced nausea and vomiting. Eur J Pharmacol 684:1–7 6. Ihbe-Heffinger A, Ehlken B, Bernard R et al (2004) The impact of delayed chemotherapy-induced nausea and vomiting on patients, health resource utilization and costs in German cancer centers. Ann Oncol 15:526–536 23. Decker GM, DeMeyer ES, Kisko DL (2006) Measuring the maintenance of daily life activities using the functional liv- ing index-emesis (FLIE) in patients receiving moderately eme- togenic chemotherapy. J Support Oncol 4(35–41):52 7. Tavorath R, Hesketh PJ (1996) Drug treatment of chemotherapy- induced delayed emesis. Drugs 52:639–648 24. Discussion Patients with other types of cancer receiving other chemotherapeu- tic regimens may differ in response to triple antiemetic regimens that include palonosetron. Second, the number of enrolled patients was relatively small, and the percent- ages of female (14/72) and younger (median age 65 years old) patients were low. This is important as female sex and younger age are risk factors for emesis. Third, our study was an observational study, such that patients and caregiv- ers were not blinded to the therapeutic regimens. Rand- omized controlled trials with a greater number of subjects are required to verify the findings presented here. Triplet antiemetic therapy, involving a 5-HT3RA, a cor- ticosteroid and an NK1RA, is now standard for patients receiving highly emetogenic chemotherapy. It is unclear, however, whether palonosetron is more effective against delayed emesis when administered with an NK1RA. Sev- eral single-arm studies found that palonosetron had addi- tional antiemetic efficacy when added to aprepitant and dexamethasone in patients with gynecological, head/neck and lung cancer [29–31]. Only one phase III trial, the TRI- PLE study, compared granisetron and palonosetron added to basal antiemetic therapy with NK1RA and corticos- teroid, finding that palonosetron was superior to granise- tron in preventing delayed emesis and nausea [32]. It also remains unclear whether palonosetron and NK1RA act synergistically. In a recent report with gynecological can- cer patients treated with moderately emetogenic chemo- therapy including paclitaxel and carboplatin, the antiemetic effect of triplet therapy with palonosetron plus aprepitant plus dexamethasone was equivalent with triplet therapy In conclusion, the tolerability of triple combination antiemetic therapy with palonosetron, aprepitant and dex- amethasone was satisfactory. Nevertheless, we did not observe an additional effect of palonosetron in patients with gastric cancer treated initially with S-1 plus cisplatin. The optimal antiemetic therapy may differ in different types of cancer and in patients receiving different chemotherapeu- tic regimens. New strategies are needed to further improve nausea and loss of appetite in cancer patients receiving chemotherapy. Acknowledgments  We would like to thank all of the investiga- tors who participated in this study. Study participants—Drs. Masato 3 489 Int J Clin Oncol (2016) 21:483–490 Kiriyama (Kurobe City Hospital, Toyama, Japan); Hironobu Kimura (Keiju Kanazawa Hospital, Ishikawa, Japan); Koji Nishijima (Red Cross Kanazawa Hospital, Ishikawa, Japan). 13. Compliance with ethical standards Conflict of interest  The authors declare that they have no conflict of interest. 15. Feyer P, Jordan K (2011) Update and new trends in antiemetic therapy: the continuing need for novel therapies. Ann Oncol 22:30–38 Open Access  This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://crea- tivecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 16. Gralla R, Lichinitser M, Van der Vegt S et  al (2003) Palono- setron improves prevention of chemotherapy-induced nausea and vomiting following moderately emetogenic chemotherapy: results of a double-blind randomized phase III trial compar- ing single doses of palonosetron with ondansetron. Ann Oncol 14:1570–1577 17. Eisenberg P, Figueroa-Vadillo J, Zamora R, 99–04 Palonosetron Study Group et  al (2003) Improved prevention of moderately emetogenic chemotherapy-induced nausea and vomiting with palonosetron, a pharmacologically novel 5-HT3 receptor antag- onist: results of a phase III, single-dose trial versus dolasetron. Cancer 98:2473–2482 Discussion Koizumi W, Narahara H, Hara T et al (2008) S-1 plus cisplatin versus S-1 alone for first-line treatment of advanced gastric can- cer (SPIRITS trial): a phase III trial. Lancet Oncol 9:215–221 14. Oyama K, Fushida S, Kaji M et al (2013) Aprepitant plus grani- setron and dexamethasone for prevention of chemotherapy- induced nausea and vomiting in patients with gastric cancer treated with S-1 plus cisplatin. J Gastroenterol 48:1234–1241 References Schwartzberg L, Barbour SY, Morrow GR et al (2014) Pooled analysis of phase III clinical studies of palonosetron versus ondansetron, dolasetron, and granisetron in the prevention of chemotherapy-induced nausea and vomiting (CINV). Support Care Cancer 22:469–477 8. Aapro MS, Alberts DS (1981) High-dose dexamethasone for pre- vention of cisplatin-induced vomiting. Cancer Chemother Phar- macol 7:11–14 9. Gralla RJ, Osoba D, Kris MG et al (1999) Recommendations for the use of antiemetics: evidence-based, clinical practice guide- lines. J Clin Oncol 17:2971–2994 25. Japan Society of Clinical Oncology (2010) Guidelines for antiemetics in oncology, 1st edn. Kanahara shuppann, Tokyo 10. Jantunen IT, Kataja VV, Muhonen TT (1997) An overview of randomised studies comparing 5-HT3 receptor antagonists to conventional anti-emetics in the prophylaxis of acute chemother- apy-induced vomiting. Eur J Cancer 33:66–74 26. Martin AR, Pearson JD, Cai B et al (2003) Assessing the impact of chemotherapy-induced nausea and vomiting on patients’ daily lives: a modified version of the Functional Living Index-Emesis (FLIE) with 5-day recall. Support Care Cancer 11:522–527 11. Latreille J, Pater J, Johnston D et al (1998) Use of dexamethasone and granisetron in the control of delayed emesis for patients who receive highly emetogenic chemotherapy. National Cancer Insti- tute of Canada Clinical Trials Group. J Clin Oncol 16:1174–1178 27. Satou A, Yamazaki T, Nukariya N et  al (2002) Development of a Japanese version of the FLIE. Gan To Kagaku Ryoho 29:281–291 28. Popovic M, Warr DG, Deangelis C et  al (2014) Efficacy and safety of palonosetron for the prophylaxis of chemotherapy- induced nausea and vomiting (CINV): a systematic review and meta-analysis of randomized controlled trials. Support Care Cancer 22:1685–1697 12. Tsukada H, Hirose T, Yokoyama A et  al (2001) Randomized comparison of ondansetron plus dexamethasone with dexameth- asone alone for the control of delayed cisplatin-induced emesis. Eur J Cancer 37:2398–2404 1 3 3 490 Int J Clin Oncol (2016) 21:483–490 29. Kitazaki TL, Fukuda Y, Fukahori S et al (2015) Usefulness of antiemetic therapy with aprepitant, palonosetron, and dexameth- asone for lung cancer patients on cisplatin-based or carboplatin- based chemotherapy. Support Care Cancer 23:185–190 32. Hashimoto H, Yamanaka T, Shimada Y et  al (2013) Palonose- tron (PALO) versus granisetron (GRA) in the triplet regimen with dexamethasone (DEX) and aprepitant (APR) for preventing chemotherapy-induced nausea and vomiting (CINV) in patients (pts) receiving highly emetogenic chemotherapy (HEC) with cisplatin (CDDP): A randomized, double-blind, phase III trial. ASCO2013 Annual Meeting abstr #9621. http://meetinglibrary. References asco.org/content/111042-132. Accessed 8 Aug 2013 30. Takeshima N, Matoda M, Abe M et al (2014) Efficacy and safety of triple therapy with aprepitant, palonosetron, and dexametha- sone for preventing nausea and vomiting induced by cisplatin- based chemotherapy for gynecological cancer: kCOG-G1003 phase II trial. Support Care Cancer 22:2891–2898 g g 33. Fujiwara S, Terai Y, Tsunetoh S et al (2015) Palonosetron versus granisetron in combination with aprepitant for the prevention of chemotherapy-induced nausea and vomiting in a population with gynecologic malignancy treated with moderately emetic chemo- therapy. J Gynecol Oncol. [Epub ahead of print] g g 33. Fujiwara S, Terai Y, Tsunetoh S et al (2015) Palonosetron versus granisetron in combination with aprepitant for the prevention of chemotherapy-induced nausea and vomiting in a population with gynecologic malignancy treated with moderately emetic chemo- therapy. J Gynecol Oncol. [Epub ahead of print] 31. Tsukahara K, Nakamura K, Motohashi R et al (2014) Antiemetic therapy of fosaprepitant, palonosetron, and dexamethasone com- bined with cisplatin-based chemotherapy for head and neck car- cinomas. Acta Otolaryngol 134:1198–1204 1 3 3
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Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México
Salud colectiva
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Artículo / Article Artículo / Article 247 4Licenciada en Oceanología. Doctora en Medio Ambiente y Desarrollo. Profesora- Investigadora, Universidad Autónoma de Baja California, México. evarista.arellano@uabc.edu.mx 3Licenciada en Lingüística. Magíster en Antropología. Profesora-Investigadora, Universidad Autónoma de Baja California, México. conmar@uabc.edu.mx evarista.arellano@uabc.edu.mx INTRODUCCIÓN proceso productivo, de un producto a otro, y para elevar progresivamente la productividad (3-6). A pesar de las largas horas de trabajo con pos­ turas corporales incómodas, pocas horas de des­ canso, la falta de protección en el lugar del trabajo, los riesgos y enfermedades a las que están expuestas, estas mujeres continúan empleándose en el campo ya que cuentan con pocas alternativas para resolver su subsistencia. Uno de los mayores riesgos a los que se enfrentan las jornaleras es la exposición a los agroquímicos –altamente tóxicos, solubles y persis­ tentes–, al estar trabajando en el campo mientras los fumigadores asperjan. Otros riesgos referidos por algunos autores son accidentes, enfermedades respi­ ratorias, afecciones cutáneas, gastrointestinales, ocu­ lares, insolación y picaduras de animales (3,7). En este texto se discute cómo un grupo de mujeres indígenas jornaleras perciben los riesgos inherentes a las condiciones laborales en las que se encuentran inmersas en un municipio en el no­ roeste de México. La investigación se centró en mujeres jornaleras ya que, a pesar de su partici­ pación creciente en labores agrícolas, hay pocos estudios sobre las percepciones de los riesgos re­ lacionados a su trabajo. El objetivo principal fue caracterizar las exigencias del trabajo agrícola y conocer las percepciones de este grupo sobre los riesgos de salud a los que están expuestas en su trabajo. Se consideró importante identificar las prácticas y percepciones desde el punto de vista de las actoras, dado que ello puede proporcionar elementos para ampliar el conocimiento sobre la problemática que viven las mujeres indígenas jor­ naleras en México. De acuerdo a algunos autores, las condi­ ciones de trabajo perjudiciales, los riesgos la­ borales y los problemas de salud originados por estos, arrojan indicadores más negativos entre los trabajadores manuales, las mujeres y los trabaja­ dores temporales (4,8,9). En particular los trabaja­ dores agrícolas están expuestos a un gran número de riesgos de trabajo; sin embargo, el impacto de estos riesgos laborales sobre la salud son poco vi­ sibles tanto para las instancias gubernamentales como para los productores agrícolas y los mismos trabajadores. La familiaridad y la cotidianeidad del trabajo jornalero reduce la percepción de la peli­ grosidad de los riesgos laborales inmediatos y los daños a su salud a largo plazo. El estudio se llevó a cabo en un valle agrícola del municipio de Ensenada, Baja California, ubicado en el noroeste de la República Mexicana. Occupational risks and health: perceptions of indigenous female agricultural workers in Northwestern Mexico Camarena Ojinaga L, von Glascoe C, Martínez Valdés C, Arellano García E. 248 Occupational risks and health: perceptions of indigenous female agricultural workers in Northwestern Mexico Camarena Ojinaga, Lourdes1; von Glascoe, Christine2; Martínez Valdés, Concepción3; Arellano García, Evarista4 Camarena Ojinaga, Lourdes1; von Glascoe, Christine2; Martínez Valdés, Concepción3; Arellano García, Evarista4 RESUMEN El objetivo de este estudio fue conocer las percepciones de las mujeres indíge­ nas jornaleras sobre los riesgos del trabajo relacionados con su salud, a partir de la caracte­ rización que ellas mismas realizaron sobre las exigencias del trabajo agrícola. Se considera el concepto de riesgo del trabajo como un constructo maleable en el cual se relacionan las condiciones de trabajo con las distintas percepciones y vivencias de los actores. A partir de un modelo microestructural se explican y relacionan los riesgos del trabajo con las desigualdades sociales y su impacto en la salud. La metodología fue de corte cualitativo; se emplearon la observación no participante, talleres participativos y entrevistas grupales en los años 2011 y 2012. El grupo que participó en este estudio fue de 60 mujeres indígenas. Entre los resultados destaca que su percepción acerca de los riesgos laborales se va cons­ truyendo sobre la base de las prácticas cotidianas en el lugar de trabajo y que gran parte de las actividades laborales que realizan las coloca en situaciones de riesgo. 1Licenciada en Psicología. Doctora en Ciencias Sociales. Profesora-Investigadora, Universidad Autónoma de Baja California, México. lcamarena@uabc.edu.mx 2Licenciada en Antropología y Medicina. Doctora en Ciencias Sociales. Profesora- Investigadora, El Colegio de la Frontera Norte, México. cglascoe@colef.mx 3Licenciada en Lingüística. Magíster en Antropología. Profesora-Investigadora, Universidad Autónoma de Baja California, México. conmar@uabc.edu.mx PALABRAS CLAVES Condiciones de Trabajo; Población Indígena; Percepción; México. ABSTRACT The objective of this study was to learn the perceptions of indigenous female day laborers regarding health-related risks in the workplace, based on their own characterization of the requirements of agricultural work. The concept of occupational risk is understood as a flexible construct in which work conditions and the different perceptions and lived experiences of social actors are interrelated. A microstructural model is employed to explain the occupational risks and their relationship to social inequalities and impacts in health. The methodology used was qualitative, employing non-participant observation, participatory workshops and group interviews during 2011-2012. Sixty indigenous women participated in the study. Results reveal that their perception regarding occupational risks is constructed from everyday practices in their place of work and that most of their work activities place them in situations of risk. KEY WORDS Working Conditions; Indigenous Population; Perception; Mexico. Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México 249 errada o correcta, sino entender por qué y cómo se forman dichas representaciones y cómo el sentido común evoluciona a partir de estas. Algunos autores han empleado el concepto de percepción como un elemento importante para es­ tudiar la salud desde la subjetividad de los actores, a través de modelos fenomenológicos (13,14). Berube (15) define la percepción del riesgo como el juicio subjetivo que hacen las personas sobre las características y severidad de un riesgo, principal­ mente con referencia a peligros naturales y ame­ nazas al medioambiente o la salud. Por otra parte, desde la década de 1950 ha habido un creciente in­ terés por estudiar la percepción del riesgo, en parti­ cular, el contraste de la percepción del riesgo entre las personas legas y los expertos. Para clarificar este contraste, se empleó una perspectiva psicométrica, que se convirtió en la estrategia metodológica más influyente (16-18). Los estudios efectuados bajo este enfoque parten de que la percepción del riesgo se puede estimar. Por ejemplo, Kahneman et al. (16) señalan que los individuos tienden a evaluar las probabilidades de quedar afectados por un riesgo particular y esto los lleva a formular juicios y tomar decisiones. A la vez, Finucane y Slovic incorporan a estos instrumentos las emociones y los afectos para medir cómo los individuos evalúan y enfrentan los riesgos (17). Otros autores, desde una perspectiva cognitiva, desarrollaron el Modelo de Creencias de Salud para explicar cómo los sujetos evalúan los riesgos a la salud sobre la base de criterios y valo­ raciones subjetivas (19). El modelo básico ha sido criticado por la falta de correspondencia entre las creencias de un individuo y su comportamiento con relación a un problema de salud que lo amenaza (20,21). Sin embargo, Rodríguez-Marín y Neipp López (21) indican que el modelo puede ser apro­ piado para explicar las conductas preventivas. Hay otros autores, como Janz y Becker (22), que consi­ deran que el modelo básico debe ampliarse, incor­ porando variables demográficas, sociopsicológicas y estructurales que pueden afectar la percepción del individuo y por consiguiente influenciar sus conductas. Todos estos enfoques resultan hasta cierto El objetivo del trabajo de investigación que aquí se presenta fue conocer las percepciones de las mujeres migrantes jornaleras sobre los riesgos de salud relacionados con su trabajo a partir de la caracterización que ellas mismas realizaron sobre las exigencias del trabajo agrícola. INTRODUCCIÓN El norte de México constituye un polo de atracción para los trabajadores del sur del país: cuenta con mejores condiciones de vida y mayores oportunidades de trabajo. El estado de Baja California es uno de los estados del norte que, en parte por su dinámica económica y por su ubicación geográfica cercana al mercado estadounidense, ha atraído mano de obra mestiza y principalmente indígena (1). Entre las actividades económicas primarias se encuentra la agricultura, con dos grandes zonas de pro­ ducción: el Valle de Mexicali y la Zona Costa. Las actividades agrícolas son de tipo intensivo; sobre­ salen la producción de trigo, algodón y alfalfa por la superficie sembrada, así como el tomate, la fresa y el cebollín por su alto valor de comercialización (2). La cercanía con EE.UU. representa una ventaja competitiva para la producción de hortalizas mexi­ canas debido a la baja remuneración salarial de los jornaleros, principalmente en los estados con mayor producción de hortalizas frescas (1). La percepción se forma por el contexto y la circunstancia social y, por lo tanto, esta se re­ laciona con la cultura de pertenencia y la clase social (10). Desde la perspectiva iniciada por la obra germinal de Douglas y Wildavsky, las autoras Arizpe, Paz y Velázquez (11) consideran que las percepciones están enmarcadas culturalmente y bajo una dinámica de construcción social, me­ diante la interacción entre los individuos. Por consiguiente, es a través de la percepción que se concibe la realidad, la cual es aprendida y re­ producida por los sujetos sociales. De la misma manera Morín asevera que El flujo de trabajadores migrantes se ha in­ crementado durante las últimas décadas en todo México y, en particular, el número de mujeres jor­ naleras. La feminización del trabajo agrícola se ha dado, entre otros factores, por la “flexibilidad” de las mujeres para pasar de una etapa a otra en el …la cultura es co-productora de la realidad percibida y concebida por cada uno. Nuestras percepciones están bajo control, no solo de las constantes fisiológicas, sino también de las variables culturales e históricas. (12 p.80) Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México Se trabajó bajo el supuesto de que la percepción del riesgo im­ plica un proceso que se va construyendo con base en las prácticas cotidianas en el lugar de trabajo, desde sus propias experiencias y las compartidas con sus compañeras jornaleras. Lo que se presenta en este trabajo forma parte de una investigación que se ha venido desarro­ llando a lo largo de tres años, la cual se ha en­ focado en estudiar las condiciones de vida de las mujeres indígenas, calidad de vida, riesgos y exi­ gencias laborales, derechos laborales y de salud. La temática que aquí se discute se centra en los riesgos en el trabajo y de salud. Se tomó como marco teórico el propuesto por Benach y Muntaner (8) que se compone de dos modelos que forman un marco teórico integral: el modelo macroestruc­ tural, que sitúa las relaciones de trabajo dentro de un contexto institucional más amplio determinado por relaciones sociales y relaciones de poder, y el modelo microestructural que relaciona las con­ diciones de trabajo, que incluyen la exposición a riesgos físicos o químicos así como la intensifi­ cación del trabajo con las desigualdades en salud. Desde esta perspectiva teórica, la organización del trabajo incluye las condiciones laborales como las exposiciones, daños y factores de riesgos tales como los físicos, químicos, biológicos, ergonó­ micos y psicosociales. Se considera que …cada factor de riesgo puede provocar efec­ tos distintos a la salud a través de diversos me­ canismos [donde] ejes como la clase social, el género y la etnia constituyen mecanismos relacionales clave que explican por qué los trabajadores y a menudo sus familias están expuestos a múltiples riesgos. (8 p.38) Todos estos enfoques resultan hasta cierto punto fragmentados, ya que carecen de una visión holística. Al respecto, Joffe (23) enfatiza que se re­ quiere una visión más integradora, como la teoría de las representaciones sociales que recupera la especificidad y la complejidad contenida en el pensamiento del sentido común, con relación a riesgos específicos. El interés de esta teoría no es tanto discernir si una respuesta ante un riesgo es Este modelo guía el modo en el que las au­ toras de este trabajo conciben los riesgos laborales, en particular, la articulación entre los riesgos del trabajo jornalero al que las mujeres sujetos de este 50 Camarena Ojinaga L, von Glascoe C, Martínez Valdés C, Arellano García E. Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México 250 estudio se encuentran expuestas y cómo ellas lo perciben. Se analiza también la consecuencia que estos riesgos de trabajo tienen a corto y largo plazo en su salud. En este sentido, se asume el concepto de riesgo laboral como un constructo maleable en el cual se relacionan las condiciones de trabajo con las distintas percepciones y vivencias de los actores. Como menciona Lazos, “los riesgos no solo se perciben y valoran sino también se viven” (24 p.83). participantes se seleccionaron a partir de dos condiciones: ser bilingüe y ser jornalera (tanto si su ingreso al trabajo agrícola era reciente, como si había trabajado durante un periodo largo de tiempo). Cada taller tuvo una duración de aproxi­ madamente cuatro horas, con una asistencia de 20 personas en promedio. Durante los talleres se identificaron a las par­ ticipantes con mayor experiencia laboral y mayor disponibilidad para continuar participando y rea­ lizar las entrevistas grupales. Se realizaron seis entrevistas grupales, de dos horas de duración, que tuvieron como objetivo profundizar en sus condiciones de vida y de trabajo, así como en su trayectoria de vida. En cada uno de los encuentros participaron entre cuatro y cinco mujeres. METODOLOGÍA La metodología utilizada fue de corte cua­ litativo: se emplearon la observación no partici­ pante, talleres participativos y entrevistas grupales. Durante el año 2011 y 2012, se realizaron 24 vi­ sitas en fines de semana debido al tiempo dispo­ nible de las mujeres sujetas de estudio dado que, durante la semana, se encontraban trabajando. Respecto a las observaciones, fueron realizadas por las cuatro autoras quienes tomaron registro en notas de campo y fotografías. Se observaron las condiciones en las que viven en sus domicilios, su desenvolvimiento en reuniones comunitarias y en los campos agrícolas. Aspectos éticos El protocolo de investigación fue aprobado por el Comité de Ética de la Facultad de Medicina de la Universidad Autónoma de Baja California. A todas las participantes se les proporcionó un formato de consentimiento informado en el cual se detallaron tanto los objetivos de investigación como la confidencialidad y el anonimato de las participantes. Con relación a los talleres, se emplearon dos técnicas: la primera fue enlistar las actividades laborales que les causaban molestias o enferme­ dades a través de la técnica de listado libre y la segunda técnica fue la categorización de las acti­ vidades según el tipo de enfermedad o molestia. El propósito de este ejercicio fue identificar la serie de actividades que realizan las mujeres en un día laboral, la intensidad y cantidad de tareas que cubren a lo largo de la jornada y la forma en que ellas viven y perciben sus condiciones de trabajo. Estas técnicas permiten acceder al uni­ verso de significaciones de los actores y a sus “realidades”, para conocer los significados que ellos dan a su experiencia, en otras palabras, apreciar las cosas desde el punto de vista de los actores. Estos talleres participativos se realizaron con mujeres indígenas jornaleras de diferentes edades que fluctuaron entre los 17 y 70 años, pertenecientes a dos grupos étnicos (mixteco y triqui), de seis colonias del Valle de San Quintín seleccionadas por índice de marginación. Las Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México 251 Además de ser difíciles sus condiciones de trabajo, son peligrosas. Pueden caerse y lastimarse por la presión de llenar el máximo número de botes en el tiempo asignado. No tienen opciones de decidir qué tareas realizar. En palabras de una mujer jornalera de 69 años: En el contexto descrito en el párrafo anterior, las mujeres expresaron sus condiciones de trabajo como difíciles por el horario, puesto que están fuera de sus casas a veces hasta 13 horas diarias; por otro lado, tienen que madrugar para tomar el transporte a los campos agrícolas, realizan sus faenas que pueden ser incluso de más de ocho horas, después esperan a que les paguen el día y regresan ya tarde a sus hogares. Las tareas domés­ ticas las realizan por la noche cuando deberían estar descansando. Se presentan algunos frag­ mentos para ilustrar el punto de vista de las mu­ jeres indígenas jornaleras en sus propias palabras: Yo me caí de la escalera del carrito donde se sube la gente, ya no quise subir, le dije yo al mayordomo porque como ya estoy grande ya no voy a subir; otro trabajo me das, le dije yo. No me quiso dar y me salí tres meses. Cuando vamos más lejos nos paramos a las tres y a esa hora hacemos el lonche e irnos rápido a la carretera para podernos ir a allá, porque allá sale el carro temprano depen­ diendo del lugar a donde va a las cinco. Las exigencias del trabajo obligan a las mu­ jeres a comer rápido, a un lado de los surcos, lo cual dificulta la interacción social entre ellas; asi­ mismo favorece que se contaminen los alimentos por el polvo y los agroquímicos. También están expuestas a cambios de temperatura y al polvo. Como han dicho algunas de ellas: …ahí madruga uno mucho. Me levantaba yo a las tres de la mañana. A las cuatro tiene uno que estar en el parque para salir porque esos carros van lejos; viene uno llegando a las nueve de la noche porque para pagar se tardan ellos mucho y entonces viene uno lle­ gando a las nueve. RESULTADOS Más de dos terceras partes del total de partici­ pantes en el estudio había trabajado en el campo entre 10 y 30 años; las más jóvenes, habían tra­ bajado entre uno y nueve años. El salario fluctúa entre 100 y 120 pesos mexicanos (entre nueve y diez dólares) por jornada laboral con una duración que oscila entre seis y diez horas. El trabajo, pagado a destajo también en la temporada de cosecha, se mide por el número de botes de plástico de 20 litros llenos hasta el tope de frutos. Cada bote se paga entre uno y cinco pesos (entre ocho y cuarenta cen­ tavos de dólar). Por lo regular, trabajan entre tres y seis días a la semana en los meses de mayor ac­ tividad y gran parte del año. Algunas permanecen trabajando con el mismo productor durante varios años y otras suelen ocuparse en diferentes campos de cultivo a lo largo del año. Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México Una vez vine llegando a las once de la noche a la casa; a mitad de camino se descompuso el carro y pues a esa hora estaba uno deteniéndose allá, hasta que lo compusieron; viene uno llegando a la casa a esas horas. A esas horas me puse a bañar, a las once de la noche y como no nos pagaron ese día al otro día salir tempranito porque si no, no me pagan al otro día si no voy. …cuando anda uno pizcando [recolección de los frutos de una cosecha] nos sacan a comer, pero no duramos ni veinte minutos, apenas va uno por el primer taco y vámonos. Si no come uno bien por eso se enferma. …en el trabajo da sed, da hambre, pero no se come igual como en su casa, sino que cami­ nando comiendo, trabajando comiendo… Hablaron de los riesgos de accidente en su trabajo y de la falta de seguridad social la cual im­ plica en México la atención a la salud, cobertura de accidentes de trabajo, incapacidades, vivienda, jubilación y otras prestaciones: En cuanto a las condiciones de trabajo, en ciertos campos tienen que llevar sus propias herra­ mientas (pala, azadón, tijeras), así como llevar su propio material de protección, como un “paliacate” (pañoleta) para cubrir la nariz y la boca, guantes y sombreros o “cachuchas” (gorra de visera): …cuando iba al tomate me resbalé porque había mucho lodo […] siempre pasan muchos accidentes en el trabajo, porque se resbala uno, porque se tropieza, no está limpio, hay mucha vara, hierba o agua y se resbala uno y se va uno de paso hasta el suelo. Para deshojar antes daban tijeras para recor­ tar uno la hoja del tomate y ahora no, ahora pura mano y no quieren guantes. Un cuchillo, tú tienes que llevar un cuchillo para cortar el hilo cuando se amarre y tijeras. A veces guan­ tes, a veces azadón. Se accidenta en el trabajo y no nos mandan al seguro, nos mandan a descansar mejor y pues esos días de descanso no son pagados. Nos mandan a la casa. Camarena Ojinaga L, von Glascoe C, Martínez Valdés C, Arellano García E. Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México 252 La exposición a agroquímicos es un riesgo para estas mujeres, aunque ellas no realizan tareas de fumigación; sin embargo, sí aplican herbicida a las hojas de las plantas a lo que ellas le llaman “pintar las matas enfermas”. Las mujeres jornaleras prácticamente son asperjadas ya que ellas perma­ necen en el campo de cultivo durante las etapas de aplicación, sin importar que algunas estén embarazadas. Relatan que, aunque algunos pa­ trones las cuidan, otros no se hacen responsables y culpan a las mujeres por no hacerse a un lado cuando se fumiga. esqueléticos a largo plazo. Aquellas actividades que consideraron que pueden causar mayor daño a su salud fueron: subirse a la escalera, lo cual les puede ocasionar fracturas por caídas; el uso de navajas y tijeras, que las expone a heridas punzo­ cortantes; deshojar sin protección, que les causa irritaciones de piel y de ojos (a). En general, lo que convierte a estas actividades en más perjudiciales es la presión que se ejerce sobre las mujeres para realizar en forma rápida las tareas asignadas. Con relación a las actividades que las mu­ jeres entrevistadas consideraron que dañan direc­ tamente su salud, mencionaron el contacto con plaguicidas a los cuales denominan “líquidos”. Las actividades que desde su punto de vista las exponen más a los agroquímicos son “pintar con líquido” (b) las hojas de las plantas; abrir y cerrar el acolchado de plástico (c) de los surcos para per­ mitir el rociado del plaguicida; quitar y poner el anillo a la mata del tomate (d), el corte de las hor­ talizas, el deshoje de las plántulas y las actividades de deshierbe. Cabe resaltar que es común que las jornaleras trabajen donde recientemente se ha fu­ migado o cuando se está fumigando y que en la mayoría de los campos agrícolas no se les propor­ ciona material ni equipo de protección. Sí, si estamos, pasan con líquido, fumigan la planta y está uno ahí por eso a mí me ha brotado granos en la cara porque es el líquido muy fuerte. Una vez pues sí me hizo daño, porque en todo mi pie cayó grano, en todo mi pie me salieron ronchas y granos. Me hizo daño el líquido porque ahí estaba yo y pasó el líquido muy fuerte. El líquido hace daño. DISCUSIÓN Diversos estudios enfatizan los efectos no­ civos de los riesgos laborales en el sector agrícola en la salud de los trabajadores. De acuerdo a la Organización Internacional del Trabajo (OIT) el sector agrícola es uno de los más peligrosos para la salud de los trabajadores (25 p.5, 26,27). Además, es una de las actividades en las que se presenta de manera más acentuada la situación deficiente y precaria de las condiciones laborales y el grave impacto a la salud sobre todo de las mujeres jornaleras (28). Contrario a lo expuesto por este autor, las jor­ naleras, aunque no conocen los nombres técnicos de las sustancias, sí tienen una aproximación bas­ tante clara de su peligrosidad y si bien, la mayoría de las trabajadoras no expresan estar capacitadas en cuanto al manejo de los plaguicidas, en las entrevistas grupales estas mujeres revelaron tener un conocimiento bastante completo acerca de las medidas de protección contra la exposición a los agroquímicos e incluso reconocieron claramente la sintomatología de las intoxicaciones agudas por exposición a las sustancias. Dada la creciente feminización en el sector agrícola, cobra importancia relacionar las condi­ ciones laborales con la salud ocupacional de las mujeres jornaleras. En los estudios realizados por Lu, en Filipinas, se enfatiza que la salud de las mu­ jeres en la producción agrícola debe relacionarse con los riesgos y peligros que presenta el trabajo agrícola (29,30). Tal y como argumentan estos es­ tudios, los hallazgos del presente trabajo muestran que en este grupo de mujeres jornaleras las condi­ ciones laborales y de salud están interrelacionadas ya que la mayor parte de las actividades que rea­ lizan son físicamente demandantes y riesgosas para su salud. Algunas mujeres mencionan que intentan tomar medidas para no enfermarse en el trabajo, pero también la mayoría coincide en percibir que son las mismas exigencias y condiciones del trabajo jornalero lo que les impide cuidarse para no enfermarse. Por la forma en la que se establece la relación laboral cuando se enferman no se atienden de manera oportuna, ya que faltar al trabajo implica una sanción económica por parte del patrón. En México, el trabajo agrícola suele estar ín­ timamente asociado a situaciones de precariedad y caracterizado por la inseguridad en el trabajo que se deriva de la inestabilidad, la falta de pro­ tección social y los bajos niveles salariales. Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México 253 es inevitable. Es ampliamente reconocido que los daños inmediatos y a largo plazo para la salud causados por la exposición a agroquímicos cons­ tituyen uno de los principales riesgos que corren los trabajadores agrícolas (31,32). De acuerdo al estudio realizado por Roa et al. (31), cualquier persona de una unidad doméstica jornalera puede estar en riesgo por exposición a agroquímicos ya que los trabajadores agrícolas pueden llevar a sus casas residuos de plaguicidas en su piel, en su ropa, zapatos o herramientas y pueden afectar la salud de cualquiera de los miembros de la unidad familiar. En este mismo estudio se encontró que las mujeres de familias jornaleras, además de tener un conocimiento fragmentado y parcial sobre pla­ guicidas y los riesgos que presenta la exposición a estos, suelen tener la creencia que solo quienes trabajan directamente con estas sustancias corren algún riesgo; y se observó también que las mujeres no distinguían entre los síntomas y los efectos de la exposición a plaguicidas. de efectos agudos en la salud, no ocurre lo mismo con los efectos a largo plazo como las enferme­ dades crónicas que no se reconocen como con­ secuencia de la exposición a riesgos laborales. El costo en el deterioro de la salud, y los cuidados que requieren cuando presentan padecimientos derivados de su trabajo, no se ve compensado por el precario salario que actualmente reciben las jornaleras. Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México Está mal eso de que uno ande trabajando y ellos metan a sus gentes a fumigar la planta. Hace mucho daño […] de­ berían fumigar en esta y en las otras que nos metan a cortar. Las mujeres entrevistadas comentaron que suelen padecer de irritaciones, comezón, ronchas y manchas en la piel por su exposición a los plaguicidas: …siempre le hace daño a uno el líquido. Ahí dolor de cabeza agarra cuando pasa el fumi­ gador. A ellos no les importa. …intoxicación leve y hasta grave ha habido. Hace más o menos seis meses, yo sufrí una infección muy fuerte de la piel, más de una semana no salí de mi casa […] estaba yo tra­ bajando y pasaron fumigando, entonces me empezó a dar comezón en la cara y se me hizo toda la cara muy dura, una piel muy fea como de elefante y me duró mucho para que se me quitara la infección y era una comezón bien fuerte como si fuera una sarna severa. Las actividades que más realizan en su trabajo son la cosecha, el deshierbe, la siembra, cargar botes, enredar guías y limpiar el suelo en cultivos de fresa, pepino, calabacita y tomate, que son los principales cultivos de las empresas agrícolas y ranchos particulares. A partir de las actividades laborales, las mujeres entrevistadas identificaron aquellas que estimaron pueden afectar de manera general su salud y las actividades que son perjudi­ ciales por dañar su salud. Señalan que la actividad de deshojar puede resultar en cefalea debido a la cantidad de polvo y “líquido” a que están expuestas. Estar en los in­ vernaderos les provoca vómito y cefalea ya que están respirando el “líquido” que se aplicó en los surcos. Reconocen que los malestares de vómito y cefalea están asociados a los plaguicidas y que estos son veneno. Si bien perciben las condiciones Las actividades laborales que consideraron que pueden afectar de manera general su salud fueron cargar botes pesados, no comer bien o comer demasiado rápido, estar trabajando en el polvo y permanecer en posturas incómodas por largo tiempo. Cortar, empacar y usar la pala para quitar el plástico de los surcos son posiciones que originan dolor y pueden causar daños músculo- DISCUSIÓN En este sentido, un estudio reciente de Lara (6) señala que no solo el trabajo es precario sino también lo son las condiciones de vida de quienes trabajan en situaciones precarias, ya que las desventajas labo­ rales se suman a las desventajas sociales y generan una “espiral de precariedad” que se traduce en vulnerabilidad y exclusión. La atención a la salud se presta a partir de la afiliación a instituciones a través del lugar del trabajo, pero para la población que no cuenta con trabajo formal se realiza a través de los servicios que proporciona la Secretaría de Salud y la medicina privada. Sin embargo, existen Como la alta tecnificación de la agroindustria requiere de grandes volúmenes de agroquímicos, la exposición de las jornaleras a estos xenobióticos 54 Camarena Ojinaga L, von Glascoe C, Martínez Valdés C, Arellano García E. 254 grandes brechas entre los distintos grupos de po­ blación respecto de la cantidad y calidad de los servicios que reciben. En el ámbito nacional, el 49,8% de la población no tiene cobertura en salud. Este porcentaje aumenta notablemente en la población indígena (33). En el caso de las jor­ naleras, gran parte de los empleadores evaden la obligación de inscribirlas en la seguridad social, quedando desprotegidas en caso de accidentes y/o enfermedad, y las mandan a sus casas sin cubrirles el pago de ese día o días mientras estén inhabi­ litadas para trabajar. Estas mujeres, al no poseer un contrato formal de trabajo y trabajar en condi­ ciones desprovistas de protecciones mínimas y sin seguridad social, quedan expuestas a una mayor precarización del trabajo. Lo anteriormente pre­ sentado permite vislumbrar que las consecuencias del deterioro de la salud de las trabajadoras no son asumidas por el sector salud, por los productores agrícolas ni por las autoridades gubernamentales. trabajo. Esta creencia anclada en la subjetividad, les ha permitido dar un sentido y un significado al trabajo que realizan. La mayoría coincide en percibir que las mismas exigencias del trabajo jornalero son las que les impide cuidarse para no enfermarse. Sin embargo, las mujeres ingenian maneras de tolerar o enfrentar las condiciones, exigencias y riesgos laborales, ya que como ellas dicen “no nos queda de otra”, pues tienen un res­ tringido campo de alternativas ocupacionales. DISCUSIÓN Las mujeres internalizan los riesgos a través de ciertos esquemas culturales y prácticas sociales como la sumisión y la abnegación, esquemas que son afirmados, en general, por la subordinación estructural de los indígenas en México. Aunado a esto, las mujeres que participaron en este estudio mostraron una tendencia a minimizar los riesgos laborales de manera que esto les permite, por un lado, verlos como parte “natural” del trabajo, lo que a su vez las lleva a una autoexigencia para elevar su productividad y con ello aumentar su ingreso diario. Por otro, es posible que la mini­ mización de los riesgos provenga de cómo ellas a su vez perciben las exigencias laborales. Desde su propia experiencia saben que sus condiciones laborales favorecen su explotación, y saben que es difícil conseguir otro tipo de empleo; sin em­ bargo, las relaciones sociales desiguales a las que están expuestas como mujeres indígenas explican por qué este sector de la población nacional tiene menos oportunidades laborales e ingresos econó­ micos menores. AGRADECIMIENTOS Esta investigación obtuvo financiamiento por parte de la Comisión Nacional para el Desarrollo de los Pueblos Indígenas (código de aprobación DFCI/219/11) y la Universidad Autónoma de Baja California (código de aprobación 414/4/C/8/15). 9. Espelt A, Borrell C, Rodríguez-Sanz M, Mun­ taner C, Pasarín MI, Benach J, Schaap M, Kunst AE, Navarro V. Inequalities in health by social class dimensions in European countries of di­ fferent political traditions. International Journal of Epidemiology. 2008;37(5):1095-1105. Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México 255 NOTAS FINALES c. El acolchado es una técnica en la que se utiliza plástico para envolver los cultivos con el fin de man­ tener el grado adecuado de humedad y temperatura y evitar la competencia con malezas. c. El acolchado es una técnica en la que se utiliza plástico para envolver los cultivos con el fin de man­ tener el grado adecuado de humedad y temperatura y evitar la competencia con malezas. a. Hay ciertas hortalizas y frutas cuyas hojas pre­ sentan vellosidades que al contacto con la piel causan irritación. a. Hay ciertas hortalizas y frutas cuyas hojas pre­ sentan vellosidades que al contacto con la piel causan irritación. d. También llamado anillo plástico o clip para tutor. Cada anillo está diseñado para sujetar el tallo del cultivo que se desea tutorear y se utiliza para aumentar la producción del cultivo y disminuir el espacio requerido por planta. b. Las mujeres emplean un pincel para cubrir las hojas de las plantas con el fungicida clorotalonil que se aplica de manera preventiva antes de que ocurra la infección, por ser un fungicida de acción multisitio. CONCLUSIONES Este estudio delinea la interacción que existe entre las condiciones y exigencias del trabajo, con los riesgos a la salud percibidos por las mu­ jeres indígenas jornaleras. Se abordaron las per­ cepciones que ellas tienen sobre las condiciones y exigencias laborales que enfrentan, a partir de la posibilidad de enfermarse por su trabajo y del riesgo de enfermar gravemente. Las mujeres de este estudio coincidieron en que la mayor parte de las actividades que realizan son físicamente demandantes e intensas y que las tareas diversas que realizan las colocan en situaciones de riesgo en cuanto a accidentes de trabajo y exposición a agroquímicos. En resumen, conocer las percepciones de las mujeres migrantes jornaleras sobre los riesgos de salud relacionados con su trabajo y la caracteri­ zación que ellas mismas hicieron sobre las exi­ gencias de este, permitió adentrarse en el proceso de construcción de una parte de la vida laboral de estas mujeres. La intención de este estudio fue aproximarse a la construcción subjetiva de lo que las mujeres indígenas jornaleras perciben y saben sobre los riesgos laborales que enfrentan de forma continua en los campos agrícolas y cómo los vin­ culan con daños a su salud. Se encontró que su percepción acerca de los riesgos laborales y de salud se va construyendo con base en las prác­ ticas cotidianas en el lugar de trabajo, desde sus propias experiencias y las compartidas con sus compañeras jornaleras. Saben que las posturas corporales que su trabajo requiere, las pocas horas de descanso, la falta de protecciones en el lugar del trabajo y estar expuestas a los agroquímicos, afectan su salud. A pesar de este conocimiento, persiste en ellas una propensión a minimizar la gravedad de los síntomas como las náuseas, los dolores de cabeza y las irritaciones dérmicas que padecen, ya que estas molestias son incorporadas a su coti­ dianeidad como consecuencias ineludibles de su REFERENCIAS BIBLIOGRÁFICAS 1. Massieu Y. Impactos de la biotecnología en la producción de hortalizas en México. Aportes. 2004;9(26):41-63. 2. Gobierno del Estado de Baja California. Plan Estatal de Desarrollo 2008-2013. Mexicali: GEBC; 2008. 10. Douglas M, Wildavsky A. Risk and culture: an essay on the selection of technologian and envi­ ronmental dangers. Berkeley: University of Cali­ fornia Press; 1982. 3. Moret J, Cosío C. Los jornaleros agrícolas de México. México DF: Universidad Autónoma de Chapingo-Diana; 2004. 11. Arizpe L, Fernández P, Velázquez M. Cultura y cambio global: Percepciones sociales sobre la deforestación de la Selva Lacandona. México DF: Editorial Miguel Ángel Porrúa; 1993. 4. Lara S. Análisis del mercado rural en México en un contexto de flexibilización. En: Giarraca N. Una nueva ruralidad en América Latina. Buenos Aires: CLACSO; 2001. 12. Morín E. Cultura y conocimiento. En: Watzlawick P, Krieg P. El ojo observador: Contribuciones al cons­ truccionismo. Barcelona: Gedisa; 1998. 5. Lara S. Violencia y contrapoder: una ventana al mundo de las mujeres indígenas migrantes en México. Revista de Estudios Femeninos. 2003;11(2):381-397. 13. Menéndez E. El punto de vista del actor: Ho­ mogeneidad, diferencia e historicidad. Relaciones. 2007;18(69):239-270. 6. Lara S. ¿Es posible hablar de un trabajo decente en la agricultura moderno-empresarial en México? El Cotidiano. 2008;23(147):25-33. 14. Mercado F. Entre el infierno y la gloria: La expe­ riencia de la enfermedad crónica en un barrio urbano. Guadalajara: Universidad de Guadalajara; 1996. 7. Camarena L, von Glascoe C, Arellano E, Mar­ tínez C. Apectos laborales y de salud de jornaleras indígenas migrantes en Baja California. En: Sanín LH. Género, ambiente y salud laboral. Chihuahua: Universidad Autónoma de Chihuahua; 2011. 15. Berube D. Intuitive Toxicology: The public perception of nanoscience. En: Allhoff F, Lin P. Na­ notechnology and society: Current and emerging ethical issues. Dordrecht: Springer; 2008. 16. Kahneman D, Slovic P. Judgement unter un­ certainty: Heuristics and biases. Cambridge: Cam­ bridge University Press; 1982. 8. Benach J, Muntaner C. Empleo, trabajo y des­ igualdades en salud: una visión global. Barcelona: Icaria Editorial; 2010. Camarena Ojinaga L, von Glascoe C, Martínez Valdés C, Arellano García E. 256 17. Slovic P. The perception of the risk: Reflec­ tions on the psychometric paradigm. En: Krimsk S, Golding D. Social theories of risk. New York: Praeger; 1992. p. 11-152. Disponible en: http://www.ifpri.org/sites/default/ files/publications/focus13_08.pdf. 27. International Labour Organization, Food and Agriculture Organisation. ILO-FAO working to­ gether: Safety and Health [Internet]. c2013 [citado 2 feb 2013]. Camarena Ojinaga L, von Glascoe C, Martínez Valdés C, Arellano García E. Riesgos del trabajo y salud: percepción de mujeres indígenas jornaleras en el noroeste de México. Salud Colectiva. 2013;9(2):247-256. REFERENCIAS BIBLIOGRÁFICAS Disponible en: http://www.fao-ilo. org/more/fao-ilo-safety/en/. 18. Slovic P. The perception of risk. 5a ed. London: Earthscan Publications; 2006. 19. Moreno E, Roales-Nieto J. 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Environmental Justice. 2002;110(2):233-240. 25. Organización Internacional del Trabajo. Pro­ grama de Actividades Sectoriales: Repertorio de recomendaciones prácticas sobre seguridad y salud en la agricultura. Ginebra: OIT; 2010. 33. Instituto Nacional de Salud Pública. Encuesta de salud y derechos de las mujeres indígenas. Cuernavaca: Instituto Nacional de Salud Pública; 2008. 26. Cole D. Occupational health hazards of agri­ culture: Understanding the links between agriculture and health [Internet]. 2006 [citado 2 feb 2013]. 26. Cole D. Occupational health hazards of agri­ culture: Understanding the links between agriculture and health [Internet]. 2006 [citado 2 feb 2013]. Recibido el 8 de noviembre de 2012 Versión final presentada el 20 de junio de 2013 Aprobado 1 de julio de 2013 Forma de citar Camarena Ojinaga L, von Glascoe C, Martínez Valdés C, Arellano García E. Riesgos del trabajo y salud: percepció de mujeres indígenas jornaleras en el noroeste de México. Salud Colectiva. 2013;9(2):247-256. Recibido el 8 de noviembre de 2012 Versión final presentada el 20 de junio de 2013 Aprobado 1 de julio de 2013
https://openalex.org/W3159040851
https://jaclinicalreports.springeropen.com/track/pdf/10.1186/s40981-021-00436-w
English
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Safety of perioperative period in robot-assisted atrial septal defect repair under hyperkalemic arrest
JA clinical reports
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* Correspondence: kmiyata0410@gmail.com 1Department of Anesthesia, New Heart Watanabe Institute, Hamadayama 3-19-11, Suginami-ku, Tokyo, Japan Full list of author information is available at the end of the article © The Author(s). 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Abstract Background: Various attempts have been made to meet patient desires, especially among younger and otherwise healthy individuals, for cosmetically satisfying incision with atrial septal defect (ASD) repair. One of procedures was a robotic-assisted totally endoscopic ASD repair via only two ports under hyperkalemic arrest without aortic cross- clamping. This study investigated perioperative management and safety for robotic-assisted total endoscopic ASD repair surgery under hyperkalemic arrest. Methods: We retrospectively reviewed perioperative management of thirty patients who underwent total endoscopic robot-assisted ASD repair under hyperkalemic arrest. All procedures were performed under general anesthesia using robotic-assisted total endoscopic for ASD repair via two or three ports under hyperkalemic arrest without aortic cross-clamping. Results: A total of 30 patients (mean age 45 ± 17 years, 8 male, 22 female) underwent successful ASD repair with the total endoscopic robotic-assisted procedures under hyperkalemic arrest. Hyperkalemic arrest was achieved and maintained by intravenous administration of mean potassium dose of 91±32 mEq (1.4±0.6 mEq/kg) with the lowest bladder temperature was 31.9±1.4 °C during hyperkalemic arrest. In all cases, serum potassium concentration was <5.0 mEq/L after weaning from cardiopulmonary bypass, although two cases who developed hyperkalemia >6 mEq/L after operation. At other time points, no patient exceeded 6 mEq/L of serum potassium concentration. At admission to the intensive care unit, mean serum creatine phosphokinase-MB level was 32±7mg/dL. There were no cases of arrhythmia or other cardiac complications during recovery. Conclusions: Perioperative management of robotic-assisted total endoscopic ASD repair under hyperkalemic arrest is safe and is not associated with fatal arrhythmia due to hyperkalemia. Keywords: Ultra-minimally invasive, Cardiac surgery, Robotic-assisted atrial septal defect repair, Hyp minimally invasive, Cardiac surgery, Robotic-assisted atrial septal defect repair, Hyperkalemic arrest reasons. We are performing robot-assisted totally endo- scopic ASD repair (TER-ASD repair) via only two ports under hyperkalemic cardiac arrest without aortic cross- clamping [3]. Although this method has several advan- tages including no risk of aorta and left atrial appendage injury due to aortic cross-clamp as well as excellent cos- metic results with the reduced number of ports, there are only few reports evaluating the safety of surgery under hyperkalemic arrest [4]. Moreover, possible com- plications such as changes in perioperative potassium Miyata et al. JA Clinical Reports (2021) 7:41 https://doi.org/10.1186/s40981-021-00436-w Open Access Background In the field of cardiac surgery, robot-assisted techniques have been developed for coronary artery bypass, mitral valve repair, and for atrial septal defect (ASD) repair [1, 2]. For ASD repair, sub-mammary incisions or lateral thoracotomies are commonly used because of cosmetic Safety of perioperative period in robot- assisted atrial septal defect repair under hyperkalemic arrest Kazuto Miyata1*, Tatsuya Tarui2, Sayaka Shigematsu1, Norihiko Ishikawa2 and Go Watanabe2 Results A transesophageal echocardiography (TEE) probe was inserted. A central venous catheter was placed in the left internal jugular vein and a 14−16 Fr venous cannula was inserted through the right internal jugular vein as drain- age for the superior vena cava. The femoral arteries were usually cannulated with a 16-22 Fr arterial cannula; if the diameters of the arteries were narrow, both arteries were cannulated with a 12 Fr cannula. A 22−28 Fr ven- ous cannula was inserted via the femoral vein and infer- ior vena cava, with its tip located in the right atrium. Patients’ demographic data are shown in Table 1. Mean duration of surgery and anesthesia were 131 ± 32 and 243 ± 41 min, respectively; duration of cardiac arrest and CPB was 10 ± 4 and 56 ± 18 min, respectively. Robot-assisted surgery completed successfully in all pa- tients without changing the surgical procedure such as median sternotomy and blood transfusion. There were no cases who developed SpO2 < 90% or ETco2 > 45 mmHg during one-lung ventilation. Cardiac arrest was induced by potassium 1 mEq/kg or > 1 mEq/kg in 8 or 22 cases, respectively. The mean dose of potassium injected during hyperkalemic arrest was 91 ± 32 mEq (1.4 ± 0.6 mEq/kg), with the maximum dose of 170 mEq (2.8 mEq/kg). The lowest bladder temperature was 31.9 Patients This is a retrospective data view of a single institute. After obtaining approval from The New Heart Watanabe Institute ethics committee (6 April 2020 and No. 2020- 1), the authors examined the medical records of all pa- tients received TER-ASD repair under hyperkalemic car- diac arrest from June 14, 2014, to February 9, 2018. Exclusion criteria were patients < 20 years, with the American Society of Anesthesiologist Physical Status (ASA-PS) ≥3, reduced cardiac function (ejection frac- tion <50%), histories of coronary artery, peripheral artery and lung diseases, renal dysfunction eGFR<60 ml/min/ 1.73 m2 and previous cardiac surgery. Outcome measurement Postoperative cardiac function was evaluated by creatine kinase MB (CK-MB) at ICU admission and 1 day after operation. At 5 days after operation, we evaluated car- diac function and residual shunt of ASD using transtho- racic echocardiography. Data are expressed as mean ± standard deviation. Anesthesia General anesthesia was induced with midazolam 0.1 mg/ kg, remifentanil 0.3−0.5 μg/kg/min, and rocuronium 0.9 mg/kg, followed by insertion of a left-sided, double lumen endotracheal tube. A normal endotracheal tube was used with a bronchial blocker in one patient in whom a double lumen endotracheal tube could not be intubated because of a small trachea. Anesthesia was maintained with sevoflurane (1−2%) and remifentanil (0.3−0.5 μg/kg/min) except the period of cardiopulmo- nary bypass (CPB), during which propofol (3−4 mg/kg/ h) and remifentanil (0.2−0.3 μg/kg/min) were used. The lungs were ventilated with a pressure control mode dur- ing both one-lung and bilateral lung ventilation. Respira- tory rate and peak plateau pressure (≤20 mmHg) were adjusted to maintain end-tidal carbon dioxide tension (ETco2) value below 45 mmHg. Bilateral lung ventilation was attempted if SpO2 decreased < 90%. Page 2 of 5 Miyata et al. JA Clinical Reports (2021) 7:41 Page 2 of 5 concentration, including fatal hyperkalemia, insufficient myocardial protection remains unsolved. The aim of this study is to investigate the safety of TER-ASD repair under hyperkalemic arrest from the points of potassium concentration and myocardial protection. temperature decreases to 30-32 °C and ventricular fibril- lation occurs, followed by infusion of potassium 1 mEq/ kg to induce cardiac arrest. Additional potassium was injected if required for inducing cardiac arrest. Aortic cross-clamps were not placed. ASD was directly closed using polytetra-fluoroethylene (Gore-Tex suture, W.L. Gore & Associates, Inc., Flag- staff, AZ, USA) after the right atrium was opened. De- airing was performed using left lung inflation before knotting the ASD defect. Serum potassium was filtered and removed out of the CPB using a hemodialyzer (PES- 210Ex, NIPRO Inc., Osaka, Japan) after ASD was closed. Defibrillation (150 J) was used for ventricular fibrillation after ASD closure. The patient was weaned off the CPB after rewarming to 36.0 °C and serum potassium con- centration < 5 mEq/L, followed by confirming absence of a residual ASD by TEE, administration of protamine, and removal of the cannulas in the right internal jugular vein and femoral vessels. In addition, we routinely ad- minister loop diuretics at a dose of 20 mg at CPB wean- ing. If potassium levels exceed 5 mEq/L after CPB weaning, calcium gluconate and sodium bicarbonate (1 mEq/kg) are administered. If potassium levels remain above 5 mEq/L, a glucose-insulin solution (glucose 5 g/ insulin 1U) is administered. The patient was then trans- ferred to the intensive care unit (ICU) after changing the double-lumen endobronchial tube to a single-lumen tube. We measured potassium concentration using blood gas analyzer (GEM 3500 premier, Instrumentation Laboratory Inc., Massachusetts, USA) Surgical procedures Two or three ports at the level of the fourth intercostal space in the left semi-lateral position were created. After establishing CPB, hypothermia was induced until bladder Page 3 of 5 Page 3 of 5 Miyata et al. JA Clinical Reports (2021) 7:41 Page 3 of 5 Table 1 Patients’ characteristics Age (years) 45±17 Height (cm) 158±21 Body weight (kg) 60±12 Gender (Male/Female) 8/22 ASA classification 1/2 25/5 Serum creatinine (mg/dl) 0.67±0.16 AST (U/L) 20±7 ALT (U/L) 22±21 T-Bil (mg/dl) 0.8±0.5 EF (%) 67±7 Qp/Qs (%) 2.4±0.9 (Mean ±SD) Table 1 Patients’ characteristics safely with good clinical results and excellent cosmetic outcomes. Recently, robotic technology has progressed to provide cardiac surgeons with assistance that improves precision and accuracy. Moreover, as robotic-assisted cardiac sur- gery is ultra-minimally invasive, cosmetic concerns in ASD patients, especially those who are young and fe- male, are resolved [3]. In terms of anesthetic management, robotic-assisted cardiac surgery has several concerns. One important concern is respiratory care during general anesthesia. Utilization of thoracoscopic ports requires the initiation of one-lung ventilation for adequate visualization of the cardiac structures. Moreover, insufflation of the left hemithorax with carbon dioxide is performed during ro- botic cardiac surgical procedures for adequate exposure of the heart and great vessels. In these condition, pa- tients may experience arterial oxygen desaturation and hypercapnia because of one-lung ventilation and left artificial pneumothorax due to carbon dioxide. As hyp- oxemia and hypercapnia induce increased pulmonary ar- tery vasoconstriction, right ventricular dysfunction may be caused by volumetric and pressure overload in pa- tients with ASD. However, despite these concerns, in our series, there were no cases of desaturation as SPO2 below 90% and hypercarbia as ETCO2 above 50 mmHg, and no cases of right ventricular dysfunction. ± 1.4 °C during cardiac arrest. The maximum potassium concentration exceeded the measurable level, i.e., 10 mEq/L, using continuous blood gas analysis (CDI 500 systems, TERUMO Inc. Tokyo, Japan) during CPB. Peri- operative potassium concentration is shown in Fig. 1. After ASD closure, thirteen patients (43%) experienced ventricular fibrillation, and 12 of these patients needed a single defibrillation to return from ventricular fibrillation to sinus rhythm, only one case needed the second single defibrillation to return to sinus rhythm. The rest of cases (57%) returned to spontaneous circulation naturally. After weaning from the CPB, there were no cases of re- sidual ASD shunt and biventricular cardiac dysfunction. Surgical procedures All cases were easily weaned from CPB under adminis- tration of dopamine 3 μg/kg/min. There are several approaches to achieve myocardial protection without aortic clamping and cardioplegia, such as deep hypothermic cardiac arrest and hyperkale- mic arrest [4–6]. Hyperkalemic cardiac arrest has been reported in reoperation for aortic valve replacement in a patient with a previous left internal thoracic artery to left arterial descending coronary artery bypass graft [4]. Compared to hypothermic cardiac arrest, hyperkalemia cardiac arrest is associated with decreased myocardial adenosine triphosphate levels [7]. In our series, serum CK-MB at ICU admission was slightly increased com- pared with the normal level. In all cases, 1 day after op- eration, serum CK-MB was decreased within normal levels which indicated that our hyperkalemia cardiac ar- rest technique provided efficient myocardial protection. Serum potassium level after CPB was > 6.0 mEq/L in two cases; > 5.5 and ≤6.0 mEq/L in four cases, although the mean potassium level was < 5.0 mEq/L after weaning off the CPB. It was < 6 mEq/L in all patients thereafter (Fig. 1). There were no cases of arrhythmia or bradycar- dia due to the hyperkalemia during recovery. Mean serum CK-MB was 32 ± 7 mg/dL and 13 ± 9 mg/dl on admission to the ICU and 1 day after surgery, respect- ively which returned to normal level in all cases. Trans- thoracic echocardiography 5 days after surgery revealed no residual ASD shunt and normal cardiac dysfunction with ejection fraction (EF) of 66 ± 4%. Duration from ICU admission to extubation was 5.0 ± 3.9 h. No patient required reintubation. There were no neurological com- plications, such as brain infarction and hemorrhage and no deaths. In our method, potassium was infused for cardiac ar- rest after inducing hypothermia. Hypokalemia caused by influx of extracellular potassium to intracellular com- partments is frequently observed during hypothermia after cardiac arrest [8, 9]. In turn, intracellular potassium is moved to the extracellular compartment during rewarming, suggesting that hyperkalemia is caused by administered potassium as well as by transport from the intracellular compartment and its effective removal is crucially important. Discussion In our case series, TER-ASD repair under hyperkalemic arrest was performed with no episodes of fatal hyperka- lemia and arrhythmia or organ dysfunction during the postoperative period. This procedure was performed To prevent postoperative fatal arrhythmia due to hyperkalemia, the most important procedure is to Page 4 of 5 Miyata et al. JA Clinical Reports (2021) 7:41 (2021) 7:41 Miyata et al. JA Clinical Reports institution. It would be difficult to generalize the results of this study to the general patient population. institution. It would be difficult to generalize the results of this study to the general patient population. Fig. 1 Potassium level after CPB weaning. T1, after administration of protamine; T2, ICU admission; T3, 1 h after ICU admission; T4, 3 h after ICU admission. The potassium level at T1 was 4.9±0.7 mEq/L, including two cases with levels exceeding 6 mEq/L. After ICU admission, the potassium level gradually decreased. Three hours after ICU admission, the potassium level was 3.7±0.3 mEq/L Availability of data and materials Availability of data and materials Not applicable Authors’ contributions KM anesthetized the patient, collected data from the cases, and drafted the manuscript. TT performed the operation in the operating room and co-wrote the paper. SS anesthetized the patient in the operating room and collected data from the cases. NI and GW performed the operation in the operating room. The authors read and approved the final manuscript. p g The authors declare that they have no competing interests. q If potassium levels exceed 5 mEq/L after CPB weaning, calcium gluconate and sodium bicarbonate (1 mEq/kg) are administered. Indeed, two patients showed potas- sium concentration > 6.0 mEq/L and required calcium gluconate and sodium bicarbonate. If potassium levels remain above 5 mEq/L, a glucose-insulin solution (glu- cose 5 g/insulin 1U) is administered. Although calcium gluconate stabilizes the cardiac cell membrane against undesirable depolarization and sodium bicarbonate and glucose-insulin solution induce potassium shift back into the intracellular component, these effects are transient and the potassium cannot be removed in vivo. Thus, we routinely administer loop diuretics at a dose of 20 mg at CPB weaning. In our series, urine output has been suffi- cient after CPB weaning and there were no cases with hyperkalemia exceeding 6 mEq/L from ICU admission onward. Conclusions In conclusion, perioperative management of TER-ASD repair under hypokalemic arrest is safe and is not associ- ated with fatal arrhythmia due to hyperkalemia. Author details 1 1Department of Anesthesia, New Heart Watanabe Institute, Hamadayama 3-19-11, Suginami-ku, Tokyo, Japan. 2Department of Cardiac Surgery, New Heart Watanabe Institute, Hamadayama 3-19-11, Suginami-ku, Tokyo, Japan. 1Department of Anesthesia, New Heart Watanabe Institute, Hamadayama 3-19-11, Suginami-ku, Tokyo, Japan. 2Department of Cardiac Surgery, New Heart Watanabe Institute, Hamadayama 3-19-11, Suginami-ku, Tokyo, Japan. Received: 10 January 2021 Revised: 30 March 2021 Received: 10 January 2021 Revised: 30 March 2021 Accepted: 3 April 2021 Accepted: 3 April 2021 Accepted: 3 April 2021 Abbreviations ASD: Atrial septal defect; TER-ASD repair: Totally endoscopic robot-assisted ASD repair; CPB: Cardiopulmonary bypass; ETCO2: End-tidal CO2; ICU: Intensive care unit; CPK-MB: Creatine kinase-MB ASD: Atrial septal defect; TER-ASD repair: Totally endoscopic robot-assisted ASD repair; CPB: Cardiopulmonary bypass; ETCO2: End-tidal CO2; ICU: Intensive care unit; CPK-MB: Creatine kinase-MB Competing interests Competing interests The authors declare that they have no competing interests. Competing interests The authors declare that they have no competing interests. Consent for publication Consent for publication We had obtained the consent to publish from the patient. Funding l Not applicable remove excessive serum potassium during CPB. In our series, the methods of reducing serum potassium levels included a dialyzer instead of a hemoconcentrator dur- ing CPB. The surface area of the dialyzer is 2.5 m2 com- pared with that of the hemoconcentrator, which is 1.2 m2. Serum potassium levels can be lowered more quickly using the dialyzer. However, compared with hyperkale- mic arrest time, CPB time was much longer, due to the longer time required to reduce the potassium level below 5 mEq/L. Declarations Ethics approval and consent to participate Not applicable Ethics approval and consent to participate Not applicable References 1. Argenziano M, Oz MC, DeRose JJ Jr, et al. Totally endoscopic atrial septal defect repair with robotic assistance. Heart Surg Forum. 2002;5(3):294–300. 1. Argenziano M, Oz MC, DeRose JJ Jr, et al. Totally endoscopic atrial septal defect repair with robotic assistance. Heart Surg Forum. 2002;5(3):294–300. g 2. Glower DD. Surgical approaches to mitral regurgitation. J Am Coll Cardiol. 2012;60(15):1315–22. https://doi.org/10.1016/j.jacc.2011.11.081. 3. Ishikawa N, Watanabe G, Tarui T, Kiuchi R, Ohtake H, Tomita S, et al. Two- port robotic cardiac surgery (TROCS) for atrial septal defect (ASD) using cross-arm technique - TROCS ASD Repair. Circ J. 2015;79(10):2271–3. https:// doi.org/10.1253/circj.CJ-15-0678. 4. Fujita T, Kobayashi J, Nakajima Hm, Toda K Systemic hyperkalemia and mild hypothermia for valve surgery in patients with patent internal mammary artery graft. Interact Cardiovasc Thorac Surg 2010;11:3-5, 1, DOI: https://doi. org/10.1510/icvts.2010.233262. 5. Byrne JG, Karavas AN, Filsoufi F, Mihaljevic T, Aklog L, Adams DH, et al. Aortic valve surgery after previous coronary artery bypass grafting with functioning internal mammary artery grafts. Ann Thorac Surg. 2002;73(3): 779–84. https://doi.org/10.1016/S0003-4975(01)03456-7. This study has some limitations. The patients were carefully selected to meet specific criteria. Patients did not have reduced cardiac function, coronary artery dis- ease, peripheral artery disease, lung disease, renal dys- function, or previous cardiac surgery. Another limitation is that this study was a retrospective analysis at a single 6. Tarui T, Watanabe G, Ishikawa N, Kiuchi R. Hyperkalemic arrest and the aortic no-touch technique in minimally invasive atrial septal defect closure in adults. Interact Cardiovasc Thorac Surg. 2017;24(5):799–801. https://doi. org/10.1093/icvts/ivw384. Page 5 of 5 Page 5 of 5 Miyata et al. JA Clinical Reports (2021) 7:41 Miyata et al. JA Clinical Reports (2021) 7:41 7. Chambers DJ. Mechanisms and alternative methods of achieving cardiac arrest. Ann Thorac Surg. 2003;75(2):S661–S66. https://doi.org/10.1016/ S0003-4975(02)04688-X. 8. Nielsen N, Sunde K, Hovdenes J, Riker RR, Rubertsson S, Stammet P, et al. Adverse events and their relation to mortality in out-of-hospital cardiac arrest patients treated with therapeutic hypothermia. Crit Care Med. 2011; 39(1):57–64. https://doi.org/10.1097/CCM.0b013e3181fa4301. 9. Xiao G, Guo Q, Shu M, Xie X, Deng J, Zhu Y, et al. Safety profile and outcome of mild therapeutic hypothermia in patients following cardiac arrest: systematic review and meta-analysis. Emerg Med J. 2013;30(2):91–100. https://doi.org/10.1136/emermed-2012-201120. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
https://openalex.org/W4283278264
http://palrap.pitt.edu/ojs/index.php/palrap/article/download/268/893
English
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In the PaLRaP Spotlight: Tanya Fischer, MEd, MSLIS (she/her)
Pennsylvania libraries
2,022
cc-by
1,448
Interview In the PaLRaP Spotlight: Tanya Fischer, MEd, MSLIS (she/her) Medical Writer, Patient Information National Comprehensive Cancer Network® (NCCN®) – Plymouth Meeting, PA Interview by Stephanie Campbell Stephanie Campbell is Library Acquisitions & Outreach Specialist at Pennsylvania College of Technology, sac4@pct.edu Tell us a little about yourself, your career trajectory, what led you to librarianship, and specifically medical librarianship? I really expected to be a public librarian. I was - and still am - excited by how public libraries build social capital. But sometimes you can’t predict the path your career will take. I spent many years as a self-employed artist ( ith t th t l i i i Bl k i h d Bi B Th th ) d dj t f t t Interview by Stephanie Campbell Stephanie Campbell is Library Acquisitions & Outreach Specialist at Pennsylvania College of Te Interview by Stephanie Campbell mpbell is Library Acquisitions & Outreach Specialist at Pennsylvania College of Technology, sac4@pct.edu Tell us a little about yourself, your career trajectory, what led you to librarianship, and specifically medical librarianship? I really expected to be a public librarian. I was - and still am - excited by how public libraries build social capital. But sometimes you can’t predict the path your career will take. I spent many years as a self-employed artist (with art on the television series Black-ish and Big Bang Theory among others) and as an adjunct professor at two community colleges in Arizona. Then, after five years in Pennsylvania public libraries, I pursued an MSLIS and participated in ILEAD USA in order to advance my library career. After completing my degree, I took a patient education consultant position at a local hospital in their Department of Education. Since the patient education team fell Vol. 10, No. 1 (Spring 2022) DOI 10.5195/palrap.2022.268 1 New articles in this journal are under a Creative Commons Attribution 4.0 United States License. This journal is published by the University Library System of the University of Pittsburgh as part of its D-Scribe Digital Publishing Program and is cosponsored by the University of Pittsburgh Press. New articles in this journal are under a Creative Commons Attribution 4.0 United States License. This journal is published by the University Library System of the University of Pittsburgh as part of its D-Scribe Digital Publishing Program and is cosponsored by the University of Pittsburgh Press. According to the NCCN website1, the National Comprehensive Cancer Network is a not-for-profit alliance of leading cancer centers who share information and expertise to improve cancer care for patients and practitioners worldwide. Please explain your role. According to the NCCN website1, the National Comprehensive Cancer Network is a not-for-profit alliance of leading cancer centers who share information and expertise to improve cancer care for patients and practitioners worldwide. Please explain your role. The National Comprehensive Cancer Network (NCCN) is an alliance of 32 leading cancer centers devoted to patient care, research, and education. Its core resource, NCCN Clinical Practice Guidelines in Oncology®, are the standard for cancer care. Clinical practice guidelines are decision tools created by multidisciplinary teams of experts from across NCCN Member Institutions to determine the best way to treat a patient, depending on their diagnosis, disease stage, and other factors, such as age. NCCN Guidelines for Patients are the patient-friendly versions of these guidelines. We currently have over 60 books in our library, plus animations, webinars, and numerous translations. My role as a patient information medical writer is to take an NCCN Clinical Practice Guideline (CPG) and write a new or update an existing NCCN patient guideline based on the treatment pathways or algorithms found within the CPG. The NCCN Guidelines for Patients are based on the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines). They explain the same options for cancer care but are written in plain language using health literacy and numeracy principles and apply Americans with Disabilities Act (ADA) design principles. Every patient book contains a chapter on shared decision-making with “Questions to Ask Your Doctor.” Images and illustrations reflect a diverse range of races, ages, and ethnicities. Gender-neutral and age-sensitive language is used throughout. NCCN Guidelines are the standard of cancer care and basis for insurance coverage in the United States. They are the most thorough and most frequently updated clinical practice guidelines available in any area of medicine and are used worldwide. We currently have 83 CPGs featuring 218 algorithms that apply to 97% of cancer cases in the United States. DOI 10.5195/palrap.2022.268 New articles in this journal are under a Creative Commons Attribution 4.0 United States License. This journal is published by the University Librar System of the University of Pittsburgh as part of its D-Scribe Digital Publishing Program and is cosponsored by the University of Pittsburgh Press. Pennsylvania Libraries: Research & Practice In the PaLRaP Spotlight: Tanya Fischer, MEd, MSLIS (she/her) palrap.org under library services, I also worked in the medical library. I wrote and reviewed in-patient education materials including patient handouts, videos for the patient channel, and other media, while creating LibGuides and conducting literature searches for the medical library. I have been a medical writer for patient information at National Comprehensive Cancer Network (NCCN) for three years. At NCCN, I write, review, and consult on NCCN Guidelines for Patients®, Know What Your Doctors Know patient webinars, animations, and other NCCN products. librarian. A typical day is spent writing about cancer – helping those with cancer understand their disease, prepare for testing and treatment, and engage in shared decision-making. The process starts with attending panel meetings and learning the disease, how it is diagnosed and treated. Currently, I am updating the breast cancer series which includes ductal carcinoma in situ (DCIS), invasive and inflammatory breast cancer, and metastatic breast cancer (MBC). All three books are in various stages of development. DCIS is in copyediting, invasive is in final layout, and MBC is in medical review. While working on MBC, I moderated a kidney cancer patient webinar and attended weekly animation meetings to review script and storyboard edits for new MBC animations. Do you have a physical library location or is it strictly online? What kind of resources to you provide? We do not have a physical library. All of our resources are available free online through our website (NCCN.org) or our mobile apps (NCCN.org/guidelines/nccn-mobile-app). Access to the clinical practice guidelines requires registration, but this information is only used to track global downloads. No registration is needed to access the patient resources (NCCN.org/patients). A selection of NCCN resources include:  NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines)  NCCN Drugs & Biologics Compendium (NCCN Compendium®)  NCCN Biomarkers Compendium®  NCCN Chemotherapy Order Templates (NCCN Templates®)  International Adaptations & Translations of the NCCN Clinical Practice Guidelines in Oncology Vol. 10, No. 1 (Spring 2022) DOI 10.5195/palrap.2022.268 2 Pennsylvania Libraries: Research & Practice In the PaLRaP Spotlight: Tanya Fischer, MEd, MSLIS (she/her) Pennsylvania Libraries: Research & Practice In the PaLRaP Spotlight: Tanya Fischer, MEd, MSLIS (she/her) palrap.org  NCCN Framework for Resource Stratification of NCCN Guidelines (NCCN Framework™)  NCCN Harmonized Guidelines™  NCCN Radiation Therapy Compendium™  JNCCN—Journal of the National Comprehensive Cancer Network  NCCN Guidelines for Patients  NCCN Framework for Resource Stratification of NCCN Guidelines (NCCN Framework™)  NCCN Harmonized Guidelines™  NCCN Radiation Therapy Compendium™  JNCCN—Journal of the National Comprehensive Cancer Network  NCCN Guidelines for Patients  NCCN Framework for Resource Stratification of NCCN Guidelines (NCCN Framework™)  NCCN Harmonized Guidelines™  NCCN Radiation Therapy Compendium™  JNCCN—Journal of the National Comprehensive Cancer Network  NCCN Guidelines for Patients  NCCN Framework for Resource Stratification of NCCN Guidelines (NCCN Framework™) Finally, can you tell us why you do what you do? I do what I do because I think every person has the right to the best care after receiving a cancer diagnosis. Everyone with cancer should have access to the evidence-based information regarding the preferred standard of care for their specific subtype of cancer. Information is power. Having this information ensures that no matter where you are being treated, you are getting the best care. A person with cancer should know what to expect from treatment, understand the likely course their cancer will take, advocate for the treatment options that will ensure the best quality and quantity of life, and engage in share decision-making with their care team. And as information professionals, it is our responsibility to contribute by providing access to these free, authoritative cancer resources to our communities. NCCN Guidelines for Patients can be added to any ILS. Feel free to contact Tanya at fischer@nccn.org for more information. 1 https://www.nccn.org/home/about Notes 1 https://www.nccn.org/home/about Vol. 10, No. 1 (Spring 2022) DOI 10.5195/palrap.2022.268 3
https://openalex.org/W4391228347
https://www.frontiersin.org/articles/10.3389/fpsyt.2024.1337030/pdf?isPublishedV2=False
English
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The relationship of social support to posttraumatic growth in COVID-19 among college students after experiencing campus lockdown: the effects of belief in a just world and meaning in life
Frontiers in psychiatry
2,024
cc-by
7,837
TYPE Original Research PUBLISHED 25 January 2024 DOI 10.3389/fpsyt.2024.1337030 TYPE Original Research PUBLISHED 25 January 2024 DOI 10.3389/fpsyt.2024.1337030 KEYWORDS COVID-19, campus lockdown, social support, belief in a just world, meaning in life, PTG COVID-19, campus lockdown, social support, belief in a just world, meaning in life, PTG The relationship of social support to posttraumatic growth in COVID-19 among college students after experiencing campus lockdown: the effects of belief in a just world and meaning in life The relationship of social support to posttraumatic growth in COVID-19 among college students after experiencing campus lockdown: the effects of belief in a just world and meaning in life OPEN ACCESS EDITED BY Gabriele Nibbio, University of Brescia, Italy REVIEWED BY Dan-Cristian Dabija, Babes¸-Bolyai University, Romania Dong Yang, Krirk University, Thailand Ana Moreira, University Institute of Psychological, Social and Life Sciences (ISPA), Portugal Hui Xu, McMaster University, Canada *CORRESPONDENCE Aoyu Wu w.ay@foxmail.com RECEIVED 12 November 2023 ACCEPTED 08 January 2024 PUBLISHED 25 January 2024 OPEN ACCESS EDITED BY Gabriele Nibbio, University of Brescia, Italy REVIEWED BY Dan-Cristian Dabija, Babes¸-Bolyai University, Romania Dong Yang, Krirk University, Thailand Ana Moreira, University Institute of Psychological, Social and Life Sciences (ISPA), Portugal Hui Xu, McMaster University, Canada KEYWORDS Introduction that social support can not only promote individuals to discover their potentials to cope with difficulties, but also help them reflect on crisis events and construct their cognition actively, discover the meaning behind traumatic events, and achieve post-traumatic growth. Besides, from the perspective of Resource Conservation Theory (16), social support is a social resource owned by individuals that provides material security and enables individuals to obtain psychological support when under pressure, thereby promoting posttraumatic growth. Numerous studies have shown that social support can predict posttraumatic growth significantly (17–19). On this basis, this study proposes H1: Social support positively predicts posttraumatic growth among college students. The global outbreak of COVID-19 in 2020 has had a major impact on people’s lives, not only threatening the physical health of individuals, but also impacting people’s mental health (1–6). The COVID-19 is considered as a new type of collective trauma (7). Research found that insomnia and posttraumatic stress symptoms are very common among college students, 31.33% and 16.36% of college students are found having depression and anxiety symptoms (8). Changes in living environment and learning patterns, unable to participate in social activities normally, and especially having COVID-19-related viral panic and contagious fear about the epidemic have impacted the mental health of college students greatly (9, 10). In addition to causing negative psychological effects on individuals, traumatic events may also lead to positive changes in their worldview, values, attitudes towards themselves and others, leading to posttraumatic growth (PTG) (11), which is a positive psychological change experienced by individuals after fighting against traumatic events (12). Many researches are currently focused on the negative effects of the pandemic on mental health, however, in the post-pandemic era, it is very relevant for researchers to turn their attention to the potential growth opportunities presented by adversity. Moreover, for the sake of college students’ health and well-being, lockdown orders were issued to prevent the epidemic on campus at the beginning of the Fall semester of 2022 in China. Little research is done in the context of campus lockdown, considering the distinctiveness of this policy, it is necessary to conduct research on college students who have experienced campus lockdowns. The mediating role of belief in a just world The theory of belief in a just world holds that people need to believe that the world they live in is stable and orderly, with predictable outcomes, and that they will be treated fairly without becoming victims of unforeseeable disasters. This provides people with a sense of security and control. Only under this premise can people have confidence in the future and pursue long-term goals with the belief that they will eventually get what they deserve (20). Therefore, researchers consider belief in a just world to be an important psychological resource. During the COVID-19 epidemic, quarantine became the most common coping measure, and social deprivation would affect individuals’ belief in a just world significantly (21). At this time, effective social support could provide individuals with a safe environment and coping resources (19, 22–24), and buffer the psychological impact of the epidemic, increasing individuals’ belief in a just world level (18, 25, 26). Individuals with high belief in a just world have strong emotional regulation abilities (21, 27), which helps to maintain a good level of mental health and improve well-being in life. According to the Posttraumatic Growth Model (12), an individual’s perception of the world is an important predictor of posttraumatic growth. After experiencing disaster events, individuals’ beliefs in a just world often change (28). Individuals with high belief in a just world tend to have higher levels of trust in interpersonal and social organizational relationships mostly and have a more positive attitude towards the future (29). Positive perceptions of the world can increase confidence in the face of injustice (27), and buffer the negative effects of traumatic events, which promotes posttraumatic growth (28). Therefore, we hypothesize that the belief in a just world may have a mediating effect between social support and posttraumatic growth accordingly. On this basis, this study proposes H2: Belief in a just world plays a mediating role between social support and posttraumatic growth among college students. “What doesn’t kill you makes you stronger”, thus spoke Nietzsche. Seizing opportunities in times of crisis and promoting growth is a desirable vision for people, but turning danger into opportunity requires certain conditions. Posttraumatic growth (PTG) refers to the positive psychological changes that individuals experience after experiencing traumatic situations or events (12). Aoyu Wu* Aoyu Wu* Department of Civil Engineering, Hebei Jiaotong Vocational and Technical College, Shijiazhuang, China Background: Campus lockdown orders were issued for the purpose of preventing and controlling COVID-19, which resulted in psychological problems among college students. However, the experiences they have during the pandemic may also lead to positive personal changes, including posttraumatic growth (PTG). The current study examined the mediating role of belief in a just world and meaning in life in social support and PTG during the COVID-19 campus lockdown. CITATION Wu A (2024) The relationship of social support to posttraumatic growth in COVID- 19 among college students after experiencing campus lockdown: the effects of belief in a just world and meaning in life. Front. Psychiatry 15:1337030. doi: 10.3389/fpsyt.2024.1337030 © 2024 Wu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Method: An online survey was conducted on 1711 college students in Hebei Province, China. Based on the survey results, a structural equation model was established. Results: Social support positively predicted PTG. Furthermore, belief in a just world and meaning in life played a mediating role between social support and PTG respectively. Besides, social support could also predict PTG through the multiple serial mediating effect of belief in a just world and meaning in life. Conclusion: These results indicated mechanisms by which social support influenced PTG, and this provided insights into how to promote post- traumatic growth among university students in the post-pandemic period. COVID-19, campus lockdown, social support, belief in a just world, meaning in life, PTG 01 01 Frontiers in Psychiatry frontiersin.org 10.3389/fpsyt.2024.1337030 Wu Introduction During the pandemic, whether it is the destruction caused by the epidemic in media reports or the experience of infection, individuals are more likely to reflect on themselves actively, e.g., interpersonal relationships, work, and life status, and think about the meaning of life, which will stimulate the occurrence of posttraumatic growth. The purpose of the present study is to explore the mechanism of social support on PTG in the context of COVID-19 epidemic by establishing a structural equation model to examine the mediating role of belief in a just world and meaning in life in the relationship between social support and PTG. Frontiers in Psychiatry The mediating role of meaning in life the core schema interpreting life experiences which are an important foundation to develop unique and stable life meaning experiences for individuals. Beliefs in a just world can guide people to conduct more positive self-evaluation and provide internal motivations to pursue long-term goals, helping them experience a higher sense of meaning in life (41) (42). When individuals witness or experience severe injustice, such that they are unable to maintain their belief in a just world, they may believe that the world is fundamentally random, and nothing goes around comes around. This may lead them to give up on long-term goals and seek immediate short-term goals, or simply giving them all up (20), reducing the sense of meaning in life. In addition, meaning of life enables individuals to recognize the value of their own existence, have a higher sense of self-efficacy, maintain a positive attitude in the face of difficulties (43), and strive to achieve goals in adversity. These positive changes in worldview, values, and attitudes about self and interpersonal relationships may indicate one’s posttraumatic growth in the face of adversity. Therefore, we can infer that social support may have a positive effect on the belief in a just world when facing difficulties, and individuals with a higher belief in a just world have a higher sense of life meaning by rethinking themselves and the world, which is conducive to the formation of posttraumatic growth. On this basis, this study proposes H4: Belief in a just world and meaning in life mediate the relationship between social support and posttraumatic growth among college students through their chain mediating effect. Meaning in life refers to an individual’s perception and awareness of human beings and the nature of their existence, as well as those things that they consider important, including the two dimensions of presence of meaning and search for meaning (30). According to the Shattered Assumptions Theory of Posttraumatic Growth (31) traumatic events can shatter assumptions about oneself and the world, making it necessary to rethink the meaning of life. When the meaning in life is reconstructed, individuals would form a new understanding of themselves and the world, and the new hypothesis towards the world begins to emerge. After experiencing a traumatic event, support and encouragement from others are important sources of meaning in life (32). The mediating role of meaning in life Social support helps to reconstruct the meaning of traumatic events, and view adversity from a positive perspective, through which individuals could explore psychological resources to cope with difficulties and establish a basic understanding of themselves and the world. What’s more, new life goals that individuals striving for will be set (33). Research has shown that social support provides a warm and receptive psychological atmosphere that allows people to confide in others when they are in pain, thereby promoting their sense of meaning and hope facing adversity (34). Therefore, social support is positively correlated with meaning in life significantly (32, 35). Moreover, individuals who experience the meaning of life in the face of difficulties are more likely to experience posttraumatic growth (36–39). In view with the above, we hypothesize that social support may influence posttraumatic growth through meaning in life. On this basis, this study proposes H3: Meaning in life plays a mediating role between social support and posttraumatic growth among college students. To sum up, this study proposes the following hypothesis, and the conceptual model is presented in Figure 1: H1: Social support positively predicts posttraumatic growth among college students. H2: Belief in a just world plays a mediating role between social support and posttraumatic growth among college students. The mediating role of belief in a just world The Theory of Crises and Personal Growth (13) believes that environmental factors are the key affecting whether individuals could gain growth or not after trauma, and social support, which refers to the material and spiritual assistance a person gained from social relationships such as family, relatives, friends, and organizations (14), is an important environmental factor. The Model of Thriving Through Relationships (15) believes that the reason for individuals to experience Posttraumatic Growth is due to having a strong social support system. Good interpersonal relationships can provide individuals with a safe atmosphere, facilitate the expression of negative emotions, and enable them to be accepted and comforted promptly, which is beneficial for individuals to devote more energy to coping with crisis events, encouraging individuals to actively think about traumatic events and reduce psychological distress. Therefore, this theory believes Frontiers in Psychiatry 02 frontiersin.org 10.3389/fpsyt.2024.1337030 Wu Participants The present study used the Meaning in Life Questionnaire (MLQ) compiled by Steger, Frazier, Oishi, and Kaler (30) and translated by Liu and Gan (47). The questionnaire consists of two subscales: the search for meaning and the presence of meaning with a total of nine items. Participants respond to the items on a 7-point Likert scale ranging from 1 (absolutely untrue) to 7 (absolutely true). Greater score indicates higher presence and search, and the Cronbach’s alpha was 0.86 for the total scale in the current study. Factor loading of every item is > 0.4, and AMOS was used to conducted CFA on the questionnaire and the results showed that the model fit is well, indicating the validity of the tools is acceptable: c²/df = 1.91, CFI = 0.92, TLI = 0.91, RMSEA = 0.069, SRMR = 0.06. AVE and CR on search for meaning are 0.45 and 0.78, and AVE and CR on presence of meaning are 0.51 and 0.79 respectively, indicating the validity of the tools is acceptable. An online questionnaire survey was conducted on 1711 college students (mean age = 19.89 years old, SD = 2.36, range = 18-24 years old), among which 1047 males (61.2%) and 664 females (38.8%) participated, including undergraduate and vocational colleges with 51 majors offered, in Hebei Province between March 7th and 15th, 2023. There were 847 freshmen (51.1%), 697 sophomores (40.7%), 73 juniors (4.3%), and 67 seniors (4.0%) participated in the survey. It is worth mentioning that the students were all quarantined at school during the fall semester of 2022. Perceived social support scale The Perceived Social Support Scale (PSSS) was compiled by Zimet et al. (44) and the Chinese version was revised by Jiang Qianjin (45). The revised scale consists of 12 items arising from three groups, namely family, friend, and significant others. Participants answered these using a 7-point Likert scale ranging from 1 (completely disagree) to 7 (completely agree). The total score reflects the overall level of social support perceived by the individual, and greater score indicates a higher level of perceived social support. The Cronbach’s alpha was 0.96 in the present study. Factor loading of every item is > 0.4, and AMOS was used to conducted Confirmatory Factor Analysis (CFA) on the questionnaire and the results showed that the model fit is well, indicating the validity of the tools is acceptable: c²/df = 1.92, CFI = 0.91, TLI = 0.92, RMSEA = 0.069, SRMR = 0.06. The original data was organized in Stata/MP13.1, and average variance extracted (AVE) and composite reliability (CR) are calculated using Excel 2013 (46). AVE and CR on family support are 0.49 and 0.7, AVE and CR on friend support are 0.55 and 0.83, and AVE and CR on other support are 0.48 and 0.79, indicating the validity of the tools is acceptable. Posttraumatic growth inventory PTG was assessed using the Posttraumatic Growth Inventory (PTGI) developed by Tedeschi and Calhoun (11) and revised by Wang and Wu (48). There are a total of 22 items, including five subscales, namely personal strength, new possibilities, relating to others, appreciation of life, and spiritual change. It was scored on a 6- point Likert scale from 0 (no change) to 5 (experienced this change to a very great degree). The Cronbach’s alpha was 0.97 for this scale in our sample. Factor loading of every item is > 0.4, and AMOS was used to conducted CFA on the questionnaire and the results showed that the model fit is well, indicating the validity of the tools is acceptable: c²/df = 1.94, CFI = 0.95, TLI = 0.93, RMSEA = 0.06, SRMR = 0.06. AVE and CR on personal strength are 0.51 and 0.79 respectively, AVE and CR on new possibilities are 0.47 and 0.78 respectively, AVE and CR on relating to others are 0.45 and 0.76 respectively, AVE and CR on appreciation of life are 0.55 and 0.83 respectively, AVE and CR spiritual change are 0.49 and 0.79 respectively, indicating the validity of the tools is acceptable. Belief in a just world scale Belief in a just world scale developed by Zhou Chunyan (20) was used. The scale consists of 17 items, including two lie detection items, which were rated on a 6-point Likert scale ranging from 1 (completely disagree) to 6 (completely agree). The total score reflects the level of belief in a just world, and greater score indicates a higher level of belief in a just world. The Cronbach’s alpha for the total scale was 0.94 in the present study. Factor loading of every item is > 0.4, and AMOS was used to conducted CFA on the questionnaire and the results showed that the model fit is well, indicating the validity of the tools is acceptable: c²/df = 2.05, CFI = 0.91, TLI = 0.90, RMSEA = 0.075, SRMR = 0.08. The original data was organized in Stata/MP13.1, and average variance extracted (AVE) and composite reliability (CR) are calculated using Excel 2013 (46). AVE and CR on self-present are 0.44 and 0.67, AVE and CR on others-future are 0.45 and 0.67, AVE and CR on other-present are 0.36 and 0.61, and AVE and CR on self- future are 0.47 and 0.78 respectively, indicating the validity of the tools is acceptable. The multiple serial mediating role of belief in a just world and meaning in life H3: Meaning in life plays a mediating role between social support and posttraumatic growth among college students. H4: Belief in a just world and meaning in life mediate the relationship between social support and posttraumatic growth among college students through their chain mediating effect. An effective social support system provides people with a safe psychological atmosphere, alleviates psychological impact when facing difficulties, and helps maintain a high belief in a just world. According to the Meaning-Making Model (40), beliefs constitute H4: Belief in a just world and meaning in life mediate the relationship between social support and posttraumatic growth among college students through their chain mediating effect. FIGURE 1 Conceptual model; SS, social support; BJW, belief in a just world; MiL, meaning in life. FIGURE 1 Conceptual model; SS, social support; BJW, belief in a just world; MiL, meaning in life. 03 03 Frontiers in Psychiatry frontiersin.org 10.3389/fpsyt.2024.1337030 Wu Results CI: 0.111, 0.194). And the mediating effect is partial. To be specific, belief in a just world played a mediating role between social support and PTG (indirect effect = 0.08; 95% CI: 0.040, 0.114); meaning in life played a mediating role between social support and PTG (indirect effect = 0.03, 95% CI: 0.019, 0.048); belief in a just world and meaning in life played a serial mediating role between social support and PTG (indirect effect = 0.04, 95% CI: 0.028, 0.060). None of the bootstrapped 95% CI includes zero, confirming the mediating effect of belief in a just world and meaning in life. Furthermore, in the relationship between social support and PTG, the mediating effect of belief in a just world was significantly greater than that of meaning in life (the mediating effect of belief in a just world minus the mediating effect of meaning in life = 0.05; 95% CI: 0.003, 0.100). These results illustrate that belief in a just world and meaning in life play a mediating role between social support and PTG. Moreover, compared to meaning in life, belief in a just world had a more substantial relation on social support to PTG of college students after COVID-19 campus lockdown. Discrepancy test and correlation analysis of various variables The results show that there was no significant difference in grade and whether the only child or not among the variables. Tables 1, 2 show the differences in gender, origin, and income level among the variables. From Table 1, the gender difference in the belief in a just world and post traumatic growth is significant, with female students having significantly higher scores in the belief in a just world than male students; and the posttraumatic growth score of males is significantly higher than that of females. In addition, there were significant differences in social support, belief in a just world, and sense of life significance among students from different regions of origin. College students from urban areas scored significantly higher on these three variables than college students from rural areas. There are significant differences in social support, belief in a just world, and meaning in life at the income level. Students from middle-income families have significantly higher scores in social support, belief in a just world, and meaning in life than students from low and high income families. Discussion The purpose of the present study is to explore the mechanism of social support on PTG in the context of COVID-19 epidemic by establishing a structural equation model to examine the mediating role of belief in a just world and meaning in life in the relationship between social support and PTG. Table 3 shows the mean scores, standard deviations, and correlation matrices for each variable. The Pearson correlation analysis indicates that social support, belief in a just world, meaning in life, and posttraumatic growth are positively inter- correlated among one another. The results of the study showed that social support could positively predict PTG, which was consistent with previous studies (18, 19, 25). From the perspective of the Model of Thriving through Relationships, social support, as an important personal resource, provides individuals with a safe atmosphere and creates an environment to alleviate negative emotions facing difficulties, which is beneficial to view the current adversity from a positive perspective, thereby promoting the development of PTG. The study further investigated the mediating effect between social support and PTG and found that both the belief in a just world and meaning in life can play a mediating role. Procedure and date analysis The statistical analyses were performed using SPSS 24.0 and Amos 24.0. Firstly, we used Harman’s single factor test to determine if there is a common method bias (49). Factor analysis was conducted on all items, and a total of 7 factors with eigenvalues > 1 were selected. The variation explained by the first factor was 30.2%, less than the critical value of 40%, indicating that there was no significant common method bias in this study. Afterwards, descriptive and correlation analysis were conducted. On this basis, a structural equation modeling method (50) was used to examine the mediating role of belief in a just world and meaning in life between social support and posttraumatic growth, after controlling gender, place of origin, and income as covariates. 04 Frontiers in Psychiatry frontiersin.org Wu 10.3389/fpsyt.2024.1337030 Wu p<0.05,**p<0.01,***p<0.001; SS, social support; BJW, belief in a just world; MiL, meaning in life. Testing for the mediation effects The PROCESS v4.2 macro program was used for the mediation analysis, repeated sampling 5000 times from the original date to calculate the 95% CI. If the 95% CI of the standardized path coefficient does not contain 0, it indicates that the mediating effect is significant (51). The results show that after controlling for gender, place of origin, and income level, the overall fit model fit is within an acceptable range (c2/df = 8.63, CFI = 0.98,TLI = 0.97, RMSEA = 0.067), and the model is presented in Figure 2. We found that social support could promote post-traumatic growth by positively predicting the belief in a just world, which was consistent with previous research (18, 52–54). As a public health emergency of international concern, the COVID-19 disrupted people’s routines. Continuous quarantine and isolation have The results show that the effect of social support on PTG was significant (direct effect = 0.31, 95% CI: 0.267, 0.356), while that on belief in a just world and meaning in life were significant mediators between social support and PTG (total indirect effect = 0.15, 95% TABLE 1 Analysis of differences in gender and origin among various variables. Gender Origin Male Female Urban Rural (n=1047) (n=664) t (n=434) (n=1277) t SS 5.23 ± 1.68 5.23 ± 1.08 0.89 5.38 ± 1.17 5.18 ± 1.12 3.13*** BJW 4.11 ± 0.98 4.25 ± 0.76 3.33** 4.24 ± 0.92 4.13 ± 0.89 2.18* MiL 4.98 ± 1.10 4.89 ± 0.97 1.71 5.04 ± 1.08 4.92 ± 1.04 2.15* PTG 4.25 ± 1.02 4.12 ± 0.95 2.56** 4.22 ± 1.04 4.20 ± 0.98 0.32 l b l f ld l f 05 frontiersin.org 10.3389/fpsyt.2024.1337030 Wu TABLE 2 Analysis of differences in income levels among various variables. Income levels Low-income (n=1369) Middle-income (n=277) High-income (n=65) F SS 5.18 ± 1.12 5.44 ± 1.14 5.38 ± 1.30 6.57** BJW 4.12 ± 0.89 4.33 ± 0.89 4.17 ± 1.51 5.95** MiL 4.91 ± 1.03 5.12 ± 1.04 4.92 ± 1.39 4.38** PTG 4.18 ± 0.98 4.31 ± 0.96 4.28 ± 1.30 2.01 **p<0.01; SS, social support; BJW, belief in a just world; MiL, meaning in life. TABLE 3 Descriptive results and correlation analysis between variables. TABLE 3 Descriptive results and correlation analysis between variables. Variables M SD 1 2 3 4 1. SS 5.23 1.14 2. BJW 4.16 0.90 0.63** 3. MiL 4.95 1.05 0.47** 0.55** 4. Testing for the mediation effects PTG 4.20 0.99 0.43** 0.46** 0.43** n=1711; **p<0.01; SS, social support; BJW, belief in a just world; MiL, meaning in life. Nowadays, in the post-pandemic era, the order of life is gradually being restored and college students value interpersonal relationships even more (58). With a good social support system, college students begin to reconstruct their understanding of the world. Moreover, normal social interaction makes college students feel supported and cared for by others, which helps to maintain and improve the quality of existing interpersonal relationships, thereby obtaining a higher sense of social support (59). To sum up, in warm and receptive psychological environment like this, the psychological impact of the epidemic on college students can be alleviated, which helps to rebuild belief in a just world. The positive understanding of the world can promote the development of PTG. This result validates the Posttraumatic Growth Model (12). reduced the sense of control and security that individuals felt. As for college students in their youth who cannot have a normal campus life, the deprivation of interpersonal relations reduced their belief in a just world. To prevent the epidemic on campus, China had adopted measures of lockdowns even in campus without outbreaks. This measure had protected the safety of staff’s lives, but it had also harmed the psychological well-being of students to some extent (55). Strict lockdowns prevented college students from engaging in normal social interactions with people outside of their own school (56), and they may feel treated unjustly. People were unable to control their own lives. The sense of absurdity when order was broken could easily make people feel that life is meaningless, and their sense of meaning was reduced (57). Afterwards, China had adjusted its policies in a timely manner based on the development of COVID-19, and no longer imposed strict lockdowns on campus. Staff were able to come in and go out of schools normally. The restoration of social interaction and life order allowed people to rebuild meaning in life, which facilitate PTG (19). Moreover, the study showed that social support could promote PTG by enhancing meaning in life of college students. Specifically, encouragement and support from others are important sources for individuals to have higher level of meaning in life when experiencing difficulties. Previous studies have also found that maintaining the FIGURE 2 Proposed mediation model. ***p<0.001. FIGURE 2 Proposed mediation model. ***p<0.001. Acknowledgments We would like to thank all participants. Conclusions Through the research on the relationship between social support, belief in a just world, meaning in life and posttraumatic growth of college students who had experienced school lockdown during COVID-19 pandemic, the following conclusions are drawn: Social support can not only directly promote PTG, but also through belief in a just world and the meaning in life. It can also be promoted through the serial mediation effect of belief in a just world and meaning in life. Funding The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article. Ethics statement The studies involving humans were approved by The ethics committee of Hebei Jiaotong Vocational and Technical College. The studies were conducted in accordance with the local legislation and institutional requirements. The participants provided their written informed consent to participate in this study. Written informed consent was obtained from the individual(s) for the publication of any potentially identifiable images or data included in this article. In all, through this study, we found that the impact of social support on PTG can be achieved through the belief in a just world and meaning of life. The research integrated the Model of Thriving Through Relationships (15) and the Shatter Assumptions Theory (31) effectively, which has enlightening significance for the study of the mechanism of PTG. In addition, this study also provided some inspiration for the well-being of college students after the epidemic. To promote PTG of college students who have experienced adversity in real life, social support should be provided to individuals. For example, during school lockdown and quarantine, school staff should provide enough help to college students. And timely attention ought to be paid to college students with prominent emotional fluctuations. In particular, staff need to help students establish trust in themselves and the world and make them realize the meaning of life to avoid losing faith in life during adversity. What’s more, this study suggests that except for focusing on alleviating negative psychological problems among college students affected by the epidemic, a positive belief in the world should be established as well. To maintain the meaning in life and people’s well-being, the policy makers should take people’s need for the belief in a just world into account. To achieve PTG, college students ought to master the ability to explore the strength faced with problems and learn to overcome difficulties. Author contributions AW: Conceptualization, Data curation, Formal Analysis, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing. Frontiers in Psychiatry Testing for the mediation effects 06 06 Frontiers in Psychiatry frontiersin.org 10.3389/fpsyt.2024.1337030 Wu meaning in life in adversity helps individuals face challenges with a more positive mindset. During the pandemic, meaning in life felt by college students played a crucial role in their psychological growth. According to the Shattered Assumptions Theory of Posttraumatic Growth, the things that happened pandemic may break college students’ original understanding of the world, causing them to lose the sense of control over themselves, others, or the world, and even the meaning in life as a result (60). In the post pandemic era, normal social interactions enable college students to feel that they have more social support. And the warm interpersonal environment can divert their attention from past negative experiences, encouraging individuals to pay attention to positive information. In this way, college students gradually regain a sense of control over their lives, so they set and strive for new goals, which will reshape their meaning in life. Besides, the meaning in life can also help college students discover the positive connotations behind disasters, which enables them to gain hope and face life with a grateful attitude. From the past experiences, college students learn to explore their potential when facing difficulties, thereby achieving PTG. future research can follow-up this group to further confirm incidence of PTG and the long-term mechanism of social support on it. Besides, compared to other countries, China’s policies had their own distinctive characteristics, so the experiences of Chinese college students during the epidemic is unique as well, and it is necessary to verify the model’s generalizability in cross-cultural scenarios. Data availability statement Our results also confirmed that social support played a positive role in predicting PTG through a chain mediating effect of belief in a just world and meaning in life. In the post-pandemic period, college students with high social support experience more psychological warmth, providing a safe environment and coping resources, which enables them to have a high belief in a just world even in a disordered life. The strength that college students leads them to recognize and reassess the difficult situation they are facing actively, through which helps them construct meaning in life, and see adversity as an opportunity to stimulate their own growth, namely PTG. The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation. Conflict of interest However, this study also has some limitations. This study adopted a cross-sectional study design and cannot discuss the changes and causal relationships between variables over time. Some researchers believe that PTG can be individual’ coping strategies when facing traumatic events, which may fade after a period (61). 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The Janus face of self-perceived growth: Toward a two- component model of posttraumatic growth. Psychol Inq (2004) 15(1):41–8. doi: 10.1016/j.paid.2020.110349 09 09 Frontiers in Psychiatry Frontiers in Psychiatry frontiersin.org
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Protocol for a transdiagnostic study of children with problems of attention, learning and memory (CALM)
BMC pediatrics
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© The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Abstract Background: A substantial proportion of the school-age population experience cognitive-related learning difficulties. Not all children who struggle at school receive a diagnosis, yet their problems are sufficient to warrant additional support. Understanding the causes of learning difficulties is the key to developing effective prevention and intervention strategies for struggling learners. The aim of this project is to apply a transdiagnostic approach to children with cognitive developmental difficulties related to learning to discover the underpinning mechanisms of learning problems. Methods: A cohort of 1000 children aged 5 to 18 years is being recruited. The sample consists of 800 children with problems in attention, learning and / memory, as identified by a health or educational professional, and 200 typically- developing children recruited from the same schools as those with difficulties. All children are completing assessments of cognition, including tests of phonological processing, short-term and working memory, attention, executive function and processing speed. Their parents/ carers are completing questionnaires about the child’s family history, communication skills, mental health and behaviour. Children are invited for an optional MRI brain scan and are asked to provide an optional DNA sample (saliva). Hypothesis-free data-driven methods will be used to identify the cognitive, behavioural and neural dimensions of learning difficulties. Machine-learning approaches will be used to map the multi-dimensional space of the cognitive, neural and behavioural measures to identify clusters of children with shared profiles. Finally, group comparisons will be used to test theories of development and disorder. Discussion: Our multi-systems approach to identifying the causes of learning difficulties in a heterogeneous sample of struggling learners provides a novel way to enhance our understanding of the common and complex needs of the majority of children who struggle at school. Our broad recruitment criteria targeting all children with cognitive learning problems, irrespective of diagnoses and comorbidities, are novel and make our sample unique. Our dataset will also provide a valuable resource of genetic, imaging and cognitive developmental data for the scientific community. Keywords: Learning difficulties, Transdiagnostic, Reading, Maths, Mental health, School progress, ADHD Protocol for a transdiagnostic study of children with problems of attention, learning and memory (CALM) Joni Holmes* , Annie Bryant, the CALM Team and Susan Elizabeth Gathercole Joni Holmes* , Annie Bryant, the CALM Team and Susan Elizabeth Gathercole Background through education services within the school setting. Others also receive specialist interventions through health services including CAMHS (for ADHD) and speech and language therapy services. The long-term economic and social outcomes of this common and highly heteroge- neous group of struggling learners include low rates of employment [12, 18, 37, 47] and increased risks of mental health and behavioural problems [17]. Understanding the underlying causes of these problems provides the key to advancing the development of targeted intervention and prevention strategies and ameliorating these ad- verse outcomes. Up to 15% of the school population are recognised as having special educational needs [14]. This group have problems that vary from difficulties in mastering language, reading and mathematics through to attention deficit hyperactivity disorder (ADHD), and many children have multiple areas of difficulty. For most children who are struggling academically, additional support is provided * Correspondence: joni.holmes@mrc-cbu.cam.ac.uk MRC Cognition and Brain Sciences Unit, University of Cambridge, 15 Chaucer Road, Cambridge CB2 7EF, England * Correspondence: joni.holmes@mrc-cbu.cam.ac.uk MRC Cognition and Brain Sciences Unit, University of Cambridge, 15 Chaucer Road, Cambridge CB2 7EF, England Holmes et al. BMC Pediatrics (2019) 19:10 https://doi.org/10.1186/s12887-018-1385-3 Holmes et al. BMC Pediatrics (2019) 19:10 https://doi.org/10.1186/s12887-018-1385-3 [7]) and common cognitive deficits (for example, in phonological skills, working memory (WM), and executive functions (EFs) extend across disorders of reading, maths and language (e.g. [3, 32, 39, 43, 44]). DNA samples will allow us to extend the dimensional analyses to the genetic level. This will be achieved pri- marily through participation in genetic consortia com- bining genotype data from developmental cohorts for genome-wide screening of speech, language and reading skills. Existing gene expression data (www.brainmap.org) will be combined with neural data from the CALM sample to identify broad gene groups whose regional expression profile matches important brain organizational features within the sample. These will be used to derive polygenic risk scores to explore how underlying genetic mechanisms might relate to differences in brain organization and in turn be associated with specific pat- terns of cognitive impairment. g g g ( g [ ]) The aim of this study is to apply a transdiagnostic ap- proach to children with cognitive developmental disor- ders related to learning, with the aim of discovering the underpinning mechanisms of disorder. The plan is to re- cruit a broad sample of children with problems of atten- tion, learning and/or memory (CALM, n = 800) and a school-matched group of children who are developing typically (TD, n = 200). Recruitment of the CALM group began in 2014 and will be completed by the end of 2018. These children have been recruited through health and education professionals supporting children who meet the inclusion criteria. Formal diagnoses are not required and no exclusions are made on the basis of comorbid psychiatric, psychological or physical health conditions. Exclusionary criteria are non-native English speakers, uncorrected sensory impairments and the confirmed presence of genetic or neurological conditions known to affect cognition. Recruitment of the TD group will be via schools attended by multiple children in the CALM group and will commence in autumn 2018. g p Although the primary statistical approach to be adopted in the study is hypothesis-free, the dataset will provide rich opportunities to test theories of development and dis- order, as the following two examples show. First, the large sample of children at educational risk provide high levels of power that can be used to tease apart the cognitive pathways that contribute to different aspects of academic learning. Page 2 of 11 Page 2 of 11 Holmes et al. BMC Pediatrics (2019) 19:10 Holmes et al. BMC Pediatrics (2019) 19:10 The current study adopts a transdiagnostic approach to identifying the cognitive, behavioural, neural and genetic mechanisms underpinning learning difficulties. It moves away from investigating tightly-defined deficits related to highly specific developmental impairments of cognition to- wards studying multiple levels the mechanisms and dimen- sions of disorder in a heterogeneous population. This approach is strongly endorsed by the RDoC NIMH project, in which the primary focus to date has been on psychiatric conditions including mood disorders and psychoses [11, 15]. It is now widely recognised as equally valuable for cognitive developmental disorders in which there are also high levels of comorbidity, high variability in symptoms for individuals with specific diagnoses and high-levels of co-occurrence of symptoms across different areas of learn- ing difficulty [6, 41, 49]. In putting aside singular diagnostic categories, the aim is to understand and characterise the (possibly multiple) dimensions of disorder at the level of the individual child, guiding effective choice of intervention. offered an optional MRI brain scan and asked to provide an optional saliva DNA sample. Parents / carers complete multiple questionnaires about family history and the child’s behaviour, mental health and communi- cation skills. The breath of the recruitment criteria, the scale of the study and the multiple levels of assessment across behaviour, cognition, the brain, and genes make this study a unique resource for understanding the mechanisms of learning difficulties in childhood. The dataset will be made open to the scientific community within 6 months of the completion of data collection and cleaning. We anticipate that this will be in 2020. The primary aim of this study is to use data-driven, hypothesis-free methods to identify dimensions that characterise children based on cognition, behaviour and brain. Adopting a systems neuroscience approach, we will map between these different levels of explanation. Secondary aims are to define groups of children with common cognitive, neural and behavioural profiles and to map dimensions and data-defined groups against traditional diagnostic categories. Levels of comorbidity across different aspects of learn- ing difficulties are high. Reading difficulties are estimated to co-occur up to 50% of the time with maths [33] or lan- guage problems [30]. Symptom variability is high within disorders (e.g. Recruitment and procedure Two groups of children aged 5 to 18 years are being re- cruited. The CALM group (n = 800) are referred via health and education practitioners. These include school Special Educational Needs Coordinators (SENCos), paediatricians, speech and language therapists (SaLTs), or psychiatrists and psychologists working in Child and Adolescent Men- tal Health Services (CAMHS). The majority of referrers work in the South East of England. Referrers are asked to pass an information pack to families with children who they judge in their professional opinion to have problems in the areas of attention, learning and / or memory. Fam- ilies send an expression of interest form to CALM if they would like to participate in the study. The research team then contacts the referrer to discuss the child’s problems and asks the referrer to describe the child’s primary reason for referral from a choice of attention, literacy, maths, lan- guage, memory problems or general poor educational pro- gress. If the child meets the inclusion criteria a CALM clinic appointment letter is sent to the family. Table 1 shows the likely referral profile for n = 800 based on the first n = 650 children attending the clinic. The assessment protocol has two scheduled breaks. During the first, the child is invited to provide an optional DNA (saliva) sample. Families are asked to provide separ- ate consent and assent for providing optional DNA sam- ples. The child’s height and weight is also measured in this break. During the second break the family is given the op- portunity to try a mock MRI scanner. The researcher ex- plains how an MRI scan works and gives the child the opportunity to practice going inside and laying still the mock scanner. At the end of the cognitive testing session, families are invited for an additional visit for the child to have an optional MRI scan. Expressions of interest for scanning are taken at this time and followed up with a telephone call to make a separate appointment and ensure the child is suitable for scanning. Consent and assent for scanning are obtained prior to the MRI scan. All families are asked to provide optional consent to be contacted re- garding future research projects. g The TD group will be 200 children who are typically developing. They will be recruited from schools attended by 1 or more children in the CALM group. Design This is a cohort study collecting individual differences measures of cognition and behaviour alongside MRI and DNA data. Recruitment and procedure School SEN- Cos who have referred children with difficulties to CALM will provide a point of contact within schools. All children on the school register with exception of those who have already been referred to CALM, those with sensory impairments and those who are non-native English speakers will be invited to participate. Children will be given an information pack in school to take home to their parents / carers, which will contain an expres- sion of interest form to be returned to CALM. Appoint- ments for assessments at the CALM clinic will be made upon receipt of expression of interest forms. Following the cognitive and behavioural assessment a report summarising the child’s strengths and weaknesses is sent to referrers of children in the CALM group (n = 800) to be used by the referrer to guide their ongoing support for the child. Methods sample size, an a priori power analysis was run for a simple linear regression model. Target recruitment was 995 partici- pants, yielding power of .95 to detect a small effect size, f2 = .02 or Cohen’s d = .2, with linear regression. Ethical approval was granted by the National Health Ser- vice (NHS) Health Research Authority NRES Committee East of England, REC approval reference 13/EE/0157, IRAS 127675. g All families attend the CALM clinic at the MRC Cogni- tion and Brain Sciences Unit, University of Cambridge, U.K., for the cognitive and behavioural assessments. At the beginning of the session written consent is obtained from the parent/ carer and verbal assent is taken for the child. The assessment takes approximately 3.5 h. Families are instructed to administer medication as normal if their child has a prescription, and wear glasses / hearing aids as normal if necessary. Cognitive and learning tasks, plus the child questionnaires, take place one-to-one between the examiner and the child in a dedicated testing room. Families sit in a waiting room outside the testing room and are asked to complete behaviour, family history and mental health ques- tionnaires about the child. For younger children sticker charts are used to motivate the child during the session. All children are awarded a small prize at the end of the session and families are reimbursed for their time and travel. For example, the data can distinguish whether working memory plays a unique role in supporting learn- ing [21, 42] or instead that its links with academic achievement are mediated by core domain-specific skills [5, 34, 43]. Second, data collected from the CALM group include substantial numbers of children both with and without ADHD who have learning difficulties. This will enable us to test whether in the children with ADHD, the learning problems have the same cognitive origins as the children with no ADHD or are at least in part are the disruptive consequences of the hyperactive and impulsive behavior distinguishing this group [31, 40]. All children complete a broad set of assessments of cognitive abilities known to be impaired in children with learning difficulties including tests of phonological pro- cessing, STM and working memory, executive function, attention and fluid reasoning (IQ). They are also given a set of learning measures assessing maths, language and literacy skills. At the time of the clinic visit, children are Page 3 of 11 Holmes et al. BMC Pediatrics (2019) 19:10 Holmes et al. BMC Pediatrics Recruitment phases The children (N = 1000) are being recruited in four phases. Diagnostic information supplied by referrers for children recruited in each Phase up to n = 650 is pro- vided in Table 2. A CONSORT flow diagram summaris- ing recruitment up to n = 650 is provided in Fig. 1. There are many possible ways of analysing the data to ex- plore the associations between learning, cognition, the brain and genetics. These include using regression models (e.g. to predict learning outcomes), and factor reduction and cluster- ing methods to identify underlying dimensions or groups of children with similar profiles. For the purpose of calculating Phase 1 Between October 2014 and February 2016 chil- dren aged between 5 and 18 years who were considered Holmes et al. BMC Pediatrics (2019) 19:10 Page 4 of 11 Holmes et al. BMC Pediatrics Table 1 Number of children by referral route and primary reason for referral (n female) for first 650 children attending CALM Category Attention problems Literacy problems Maths problems Language difficulties Poor educational progress Memory problems Total Education 86 (21) 52 (18) 12 (4) 38 (8) 138 (51) 57 (29) 383 (131) CAMHS1 & Paediatrics 134 (33) 5 (1) 4 (2) 19 (3) 58 (15) 5 (1) 225 (55) Speech & language therapy 3 (0) 2 (1) 0 18 (8) 2 (1) 6 (4) 31 (14) Total 223 (54) 59 (20) 16 (6) 75 (19) 198 (67) 68 (34) 639 (200) route and primary reason for referral (n female) for first 650 children attending CALM by a health or educational professional to have one or more difficulties in attention, memory, language, literacy and/or maths were recruited. The number of children assessed during Phase 1 was 322 (113 female). seen an ADHD nurse practitioner and under assessment for a diagnosis by a clinician; ii) those with speech and language problems, defined as having received support from a speech and language therapist within the last two years, or iii) those who have obsessive compulsive disorder (OCD), are on a waiting list to be assessed for OCD, or are currently receiving therapy for OCD traits. The recruitment age was narrowed to 6–12 years of age. The number of children assessed during Phase 2 was 215 (50 female). Recruitment phases Phase 2 Due to the high number of children recruited in Phase 1 without diagnoses priority for referrals in Phase 2 between March 2016 and August 2017 was given to: i) chil- dren with ADHD or probable ADHD, classed as having Table 2 Diagnostic status of children referred in phases one, two and three for first 650 children attending CALM (n female) Phase One Two Three (ongoing) Total ADD 5 (3) 6 (3) 0 11 (6) ADHD 24 (4) 83 (11) 30 (10) 137 (25) Possible ADHD 5 (1) 40 (13) 10 (3) 55 (17) Hyperactivity 1 (0) 0 0 1 (0) Dyslexia 22 (8) 9 (3) 4 (1) 35 (12) Dyspraxia 10 (4) 5 (0) 2 (0) 17 (4) Dysgraphia 1 (0) 0 0 1 (0) Dyscalculia 0 0 1 (1) 1 (1) FASD 4 (3) 1 (0) 1 (1) 6 (4) Generalised/global delay 4 (2) 3 (1) 0 7 (3) Social anxiety 1 (1) 0 0 1 (1) Depression 2 (2) 0 1 (1) 3 (3) Autism 15 (1) 19 (2) 8 (1) 42 (4) PDA 0 1 (1) 0 1 (1) Tourettes 2 (0) 2 (1) 1 (0) 5 (1) DAMP 3 (1) 1 (0) 0 4 (1) Anxiety 0 3 (0) 3 (1) 6 (1) OCD 1 (1) 2 (1) 1 (1) 4 (3) Sensory processing disorder 0 1 (0) 0 1 (0) Known genetic condition 1 (0) 1 (0) 4 (1) 6 (1) Language disorder 0 1 (1) 1 (0) 1 (1) Conduct disorder 0 1 (0) 0 1 (0) ODD 0 1 (0) 2 (0) 3 (0) Epilepsy 2 (1) 1 (0) 1 (0) 4 (1) Speech & language therapy support 18 (9) 91 (23) 14 (4) 123 (36) No diagnosis 242 (87) 103 (28) 62 (24) 407 (139) Page 5 of 11 Holmes et al. BMC Pediatrics (2019) 19:10 Holmes et al. BMC Pediatrics (2019) 19:10 Fig. 1 CONSORT flow diagram for first 650 children in the CALM sample Measures Cognition Phase 3 Having recruited a large number of children with ADHD and many who were receiving support from SaLTs in Phase 2, the Phase 1 recruitment criteria were reinstated in Phase 3 in September 2017. This phase is continuing to recruit until the total n = 800 CALM children across Phases 1, 2, and 3 is reached. Phase 3 Having recruited a large number of children with ADHD and many who were receiving support from SaLTs in Phase 2, the Phase 1 recruitment criteria were reinstated in Phase 3 in September 2017. This phase is continuing to recruit until the total n = 800 CALM children across Phases 1, 2, and 3 is reached. Phonological processing Two subtests from the Phono- logical Assessment Battery (PhAB), [20]) are administered. The Naming Speed subtest assesses speed of phonological production. Children are asked to name aloud five drawings of common objects: ball, hat, door, table, and box. They are then presented with a card showing many of these objects and are asked to name them aloud as quickly and accur- ately as possible. Children complete two trials (cards) and the total completion time in seconds is combined from both trials to give a naming speed raw score. Scores from children who make more than three uncorrected errors per card are treated with caution. The Alliteration subtest mea- sures the ability to isolate initial sounds of simple words. In a series of trials children are presented with three spoken single syllable words and asked to identify which two begin with the same sound. If the children fail to identify correct answers in the three practice trials a supplementary Alliter- ation Test with Pictures is administered. There are ten tri- als. Raw scores are the total number of trials correct. Raw scores from both PhAB subtests are converted to standard scores (M = 100, SD = 15). Phase 4 From autumn 2018, 200 TD children aged 5 to 18 years will be recruited through schools attended by children in the first three phases. Recruitment criteria Inclusion criteria for both groups are aged 5 to 18 years and native English speakers (the first language learned and the main language used in the home). All children with cognitive and / or learning problems, as identified by a professional working with them, are accepted into the CALM group irrespective of diagnosis or comorbidi- ties. Children in the TD group will be accepted if they attend the same school as a child in the CALM group and have not been referred to the CALM clinic. Exclusion criteria for both groups are significant uncorrected problems of hearing or vision, pre-existing neurological conditions for which cognitive difficulties are known possible symptoms, and not being a native English speaker. The Children’s Test of Nonword Repetition (CNRep, [22]) is also given. This assesses phonological processing and short-term memory. Forty unfamiliar non-words ran- ging in syllable length from 1 to 4 syllables are spoken Page 6 of 11 Page 6 of 11 Holmes et al. BMC Pediatrics (2019) 19:10 Holmes et al. BMC Pediatrics that vary in length but not in lexical complexity. A span-type procedure is employed in which the length of the instruction sequence increases systematically. Each span consists of a block of six trials. Testing starts at one action (e.g., Touch the red ruler), increases by one action per block (e.g., touch the red ruler and then pick up the yellow pencil), and is terminated after three incorrect trials in one block. The object array is in view at all times. Par- ticipants listen to the instructions and are restricted from manipulating any of the objects. At the end of the presen- tation, participants are asked to perform the actions in se- quence. Responses are recorded as accurate if all elements of the individual action phrase—action, object, and colour—are correctly recalled in their original serial pos- ition in the instruction sequence. The number of correct features (colour), objects (item such as pencil / pen etc) and actions (touch pick up) are also recorded. aloud one at a time. The child is asked to repeat each word immediately after presentation. Correct scores are given for non-words pronounced correctly. Raw scores out of a possible total of 40 are recorded. The CNRep test was not administered to the first 300 children attending the CALM clinic. Recruitment criteria Processing speed The Visual Scanning and Motor Speed subtests of the Delis Kaplan Executive Function System [13] are administered. Motor speed involves tra- cing a dotted line to connect circles as quickly as pos- sible. The visual scanning test requires children to cross out all the number threes on a response page of num- bers and letters. Errors and time taken to complete the tasks are recorded, and completion times are converted to scaled scores (M = 10, SD = 3). Short-term and working memory Four subtests from the Automated Working Memory Assessment (AWMA, [1]) are administered. All are span tasks, with 6 trials at each span length. Tasks automatically progress up a span level if there are four or more correct answers within a block and discontinue following three or more incorrect responses. Trials correct are converted to standard scores for each task (M = 100, SD = 15). Digit Recall (verbal STM) involves immediate serial recall of sequences of spoken digits. The maximum list length is nine digits. Backward Digit Recall (verbal WM) follows the same pro- cedure except children attempt to recall the memory items in reverse sequence. Maximum list length is set to seven digits. The Dot Matrix subtest (visuo-spatial STM) requires children to recall the locations of a series of dots presented one at a time in a four by four matrix. Up to nine dots can be presented in a sequence. In Mr. X (visuo-spatial WM) the child must first decide whether the two Mr. X figures are holding a ball in the same hand as each other. The Mr. X figure on the left is upright, while the Mr. X on the right can be rotated to one of seven positions. The child is asked to remember the loca- tion of the ball held by the Mr. X on the right, and after successive displays of pairs of Mr. Xs the child attempts serial recall of positions in which the ball was held. This task increases up to a maximum of span length of 7. Episodic memory The Stories subtest of the Children’s Memory Scale [9] is used to assess language skills and episodic memory. The child hears two stories (the pairs of stories presented depend on the age of the child). Recruitment criteria Raw scores for all three subtests are converted to standard scores (M = 100, SD = 3). Attention The Test of Everyday Attention for Children 2 (TEA-Ch2 [28]), is administered. Children younger than 8 years old complete three tasks from the TEA-Ch2 J [28]. Children aged 8 and above complete the TEA-Ch2 A ver- sion [28] that includes more difficult adaptations of the same three tasks plus one additional measure of set-switching. The Simple Reaction Time subtest mea- sures attention-based reaction time. Children focus on a square centred on a blank screen and press a key as soon as blue blob appears anywhere on screen. The task lasts six minutes on average and average response time in sec- onds is scored. Sustained attention is measured using the Vigil (8 years +) and Barking (< 8 years) subtests that require children to count in their heads the number of auditory items (bleeps or barks) heard at random intervals over ten trials. The number of trials correct is scored. Visual selective attention is assessed using the Hector Cancellation (8 years+) and Balloon Hunt (< 8 years) sub- tests. Both are time-limited cancellation tasks requiring children to cross out as many target items (either balloons or circles) as possible in a visual scene presented on paper. There are six scenes in total for Hector Cancellation and four for Balloon Hunt. Each varies by the number of dis- tractor items. The total number of targets correctly identi- fied across all scenes is recorded. The switching task, Reds, Blues, Bags and Shoes, is administered only to children over the age of 8 years. Children first sort four re- peating visual items (red or blue bags and shoes) accord- ing to colour (red or blue) or use (worn on the hand or foot). In further trials children must switch between the sorting rules after every five items. The raw score is mean reaction time on switch trials. For TEACH-2 tasks raw scores are converted to scaled scores (M=10, SD=3). The Maths Fluency subtest of Woodcock Johnson III Test of Achievement (WJ-III, [48]) was administered to the first 68 children attending the CALM clinic. In this assessment, the child is given several sheets of simple maths calculations and has to respond accurately to as many items as possible in three minutes. It was substituted for the WIAT II Numerical Operations test due to consistently low scores. Recruitment criteria BMC Pediatrics (2019) 19:10 Page 7 of 11 Holmes et al. BMC Pediatrics to scaled scores (M = 10, SD = 3). Note that the DKEFS subtests were not administered to the first 60 children attending the CALM clinic. Children complete four practice items before beginning the test at a set of 12 items corresponding to their chronological age. A basal set is established when a child completes all 12 items in set with one or no errors. If the child makes more than one error, previous sets are administered in reverse order until the basal set is established. Subsequent sets of in- creasing difficulty are administered until the ceiling set is established: eight or more errors in a set of 12 items. Chil- dren can either respond verbally by saying the number of the correct image, or they can point. The test is untimed. The raw score is the number of items correct (the last item in the ceiling set minus total number of errors). Raw scores are converted to standard scores (M = 100, SD = 15). g The Matrix Reasoning subtest of the Wechsler Abbre- viated Scales of Intelligence II (WASI-II, [46]) is used as an index of general reasoning. Children are presented with incomplete matrices of images and asked to select an image to complete each matrix from a choice of four options. For children up to the age of 8 there are a pos- sible 24 matrices to complete. For children aged 9 years and older there are a possible total of 30 matrices to complete. The test is discontinued when the child selects three consecutive incorrect responses. Trials correct are converted to T-scores (M = 10, SD = 10). Spelling, Reading and Maths The Spelling, Word Read- ing and Numerical Operations subtests of the Wechsler Individual Achievement Test II (WIAT II, [45]) are ad- ministered to assess children’s learning. The Spelling test measures spelling using letter sounds initially, progressing to single words that increase in difficulty. The Word Read- ing test is a measure of single word reading that starts with identifying letters, moves on to selecting words with similar sounds and then reading words that increase in complexity. Numerical Operations measures the ability to solve numerical problems on paper. Beginning with num- ber identification and counting, it progresses to simple and more complex mathematical problems. None of the tests are timed. Recruitment criteria To make sure these low scores reflected maths ability and were not caused by the time constraint in the WJ-III, the WIAT II subtest was introduced. A small number of children completed both maths assessments and there were no significant differences in performance across the tests (p > .05). Behaviour Conners The Conners 3- Parent Rating Scale Short Form [10] is used to assess symptoms related to ADHD. Parents / carers rate the frequency over the past month of 45 descrip- tions of problem behaviours. Scores on these items form six subscales consisting of Inattention, Hyperactivity/ Impulsiv- ity, Learning Problems, Executive Function, Aggression, and Peer Relations. The sum of raw scores on each subscale is converted to a T-score (M = 50, SD = 10). Recruitment criteria After each story the child is asked to retell the story in as much detail as possible to provide an index of imme- diate recall. Following a short delay (carrying out a sep- arate task) the child is asked to retell the two stories again (delayed recall), and then asked yes/no factual questions about each story (delayed recognition). Scores of immediate and delayed verbal recall and delayed rec- ognition are converted to scaled scores (M = 10, SD = 3). Executive function The Tower and Trail Making sub- tests of the DKEFS are administered to children aged 8 years and above to measure planning and switching abilities respectively. The Tower Test involves building a tower to match a presented picture using five disks of different sizes arranged on three pegs. The child must build the tower in the fewest number of moves possible and as quickly as possible, moving only one disk at a time and without placing any disk on a smaller disk. There are a total of nine towers to build, with increasing time limits for each trial. The time of the first move, total time taken per trial, total number of rule violations and accuracy are recorded. Total achievement scores are converted to scaled scores (M = 10, SD = 3). The Trails subtest has five conditions. The Visual Scanning and Motor Speed conditions are described under “Speed” above. The Letter Sequencing and Number Sequencing subtests require children to connect letters in alphabet- ical order (A to P) or numbers in ascending order (num- bers 1 to 16). The switching condition, Number-Letter Sequencing involves connecting letters and numbers in an alternating ascending sequence (e.g. A-1, B-2, C-3 etc). For each condition, completion times are converted Children also complete a Following Instructions task [23], in which participants are required to carry out sequences of instructions on an array of props laid out in front of them. The instruction sequences consist of descriptions of actions to be performed on a set of five stationery items (a ruler, an eraser, a pencil, a folder, and a box), in each of three colours (red, yellow, or blue). There are two actions: touch (e.g., touch the red pencil) and pick up (e.g., pick up the yellow ruler). Actions involving touching and picking up are concatenated using the adverb “then” to produce increasingly longer sequences Holmes et al. Structural MRI MRI measures are collected in a one-hour session con- ducted on the same site as the CALM clinic on a 3 T Siemens Prisma with a 32-channel quadrature head coil. Prior to scanning, children are introduced to the MRI environment using a realistic mock scanner. All children practice going into the scanner and staying still. To fa- cilitate this, children play an interactive game that tea- ches them to minimize head movements, which are measured through an accelerometer in a headband. CCC-2 The Children’s Communication Checklist, second edition (CCC-2, [4]) is used to measure communication skills. This 70-item parent / carer rating questionnaire as- sesses language structure and form, and verbal and non- verbal pragmatic communication. Scaled scores (M = 10, SD = 3) are derived for 10 subscales that form three cat- egories measuring different aspects of language use. The first four scales Speech, Syntax, Semantics and Coherence assess language structure, vocabulary use, and discourse, and are areas of communication typically impaired in chil- dren with Specific Language Impairments. The next four scales Inappropriate Initiation, Stereotyped Language, Use of Context and Nonverbal Communication index verbal and nonverbal pragmatic communication skills. The final two scales, Social relations and Interests assess aspects of language behaviour that are usually impaired in Autistic Spectrum Disorders. T1-weighted structural image A high-resolution 3D T1-weighted structural image is acquired using a Magnetization Prepared Rapid Gradient Echo (MPRAGE) sequence with the following parameters: Repetition Time (TR) =2250 milliseconds; Echo Time (TE) =3.02 millisec- onds; Inversion Time (TI) =900 milliseconds; flip angle =9 degrees; number of slices: 192; voxel dimensions =1 mm isotropic; GRAPPA acceleration factor = 2; acquisition time of 4 min and 32 s. T2-weighted structural image A high-resolution 3D T2-weighted structural image is acquired with a Sam- pling Perfection with Application optimized Contrasts using different flip angle Evolution (SPACE) with the fol- lowing parameters: TR = 5060.0 milliseconds, TE =102.9 ms; number of slices =29; voxel dimensions =0.6875 mm × 0.6875 mm × 5.2 mm; GRAPPA acceleration factor = 2; acquisition time of 1 min and 38 s. Learning Vocabulary The Peabody Picture Vocabulary Test (PPVT, [16]) measures receptive vocabulary. It involves selecting one image from four options that represent a stimulus word. Page 8 of 11 Holmes et al. BMC Pediatrics (2019) 19:10 Holmes et al. BMC Pediatrics (2019) 19:10 Holmes et al. BMC Pediatrics disorder. Raw scores are converted to T-scores for each scale and total scores (M = 50, SD = 10). The RCADS questionnaires were not administered to the first 390 families attending CALM. RCADS are scored immedi- ately following the child’s assessment and referrers are informed immediately of scores above clinically signifi- cant cut-offs. Brief The Behavior Rating Inventory of Executive Func- tion (BRIEF, [24]) questionnaire is completed by parents / carers. It contains 80 statements of everyday problem behaviours related a range of executive function difficul- ties that are rated for frequency over the past six months. T-scores are derived for eight subscales: Inhibit, Shift, Emotional control, Initiate, Working memory, Planning, Organisation and Monitor. Three composite scores are also derived: Metacognition, Behaviour Regu- lation and Global Executive Function. All raw scores are converted to T-scores (M = 50, SD 10). Statistical analysis  It will recruit a heterogeneous sample of poor learners, irrespective of diagnoses and comorbidities, which is highly representative of the majority of children struggling at school. Factor analysis, a statistical method that groups variables based on shared variance, will be used to derive under- lying dimensions from the cognitive and behavioural data (e.g. [27]). This technique has been used to identify dimensions of phonological and non-phonological skills in children with diagnosed SLI and dyslexia [39] and separate latent constructs for inattention and hyperactiv- ity in children with ADHD [29].  It will include a comparison group of typical learners to quantify the size of impairment(s) in poor learners.  It will provide a rich source of data for testing theories of cognitive development and disorder.  It will generate a database of developmental data to be made openly accessible to the scientific community 6 months after study completion. Machine-learning approaches will be used to map the multi-dimensional space of the cognitive measures. These methods have rarely been applied to understanding devel- opmental disorders (e.g. [19]) - the only applications in- volve using supervised machine learning in which the learning algorithm attempts to learn about pre-defined categories of children [38]. An unsupervised machine learning approach will be used to learn about the compos- ition of the sample: how children group together across multiple cognitive domains. These approaches will be combined with ways of grouping children according to common cognitive, neural or behavioural profiles. Such methods will include class-based analyses (e.g. latent class or cluster analyses) and clustering algorithms that have been previously used to identify groups of children with distinct learning profiles [2].  The data generated by the project directly address the common and comorbid cognitive developmental difficulties faced within school and in the health services, and the outcomes are of direct relevance to these communities. The CALM project website (http://calm.mrc-cbu.cam.ac.uk/) is designed to promote practitioner-researcher working in these areas and to facilitate knowledge transfer to the inter- national community of interested professional groups. The study has the following limitations. The study has the following limitations.  Recruitment was restricted to non-native English speakers due to restricted availability of standardised measures. Direct group comparisons will be made via MANOVAs to test particular hypotheses as the dataset is formed. Mental health Strengths and difficulties questionnaire The Strengths and Difficulties Questionnaire (SDQ, [25]) asks the par- ent/carer to rate 25 items measuring Emotional Symp- toms, Conduct Problems, Hyperactivity / Inattention, Peer Relationship Problems and Prosocial Behaviour based on their child’s behaviour in the last six months. The first four subscales are summed to provide a total difficulties score. Age norms are available for all scales with cut-offs for assessing clinical levels of internalising and externalising problems. Diffusion-weighted image Diffusion-Weighted Images (DWI) are acquired with a Diffusion Tensor Imaging (DTI) sequence with 64 diffusion gradient directions with a b-value of 1000 s/mm2, plus one image acquired with a b-value of 0. Other parameters are: TR =8500 milliseconds, TE = 90 milliseconds, voxel dimensions = 2 mm isotropic; acquisition time of 10 min and 14 s. RCADs The Revised Children’s Anxiety and Depression Scale (RCADS, [8]) and the RCADS – Parent Version (RCADS-P, [8]) are questionnaires that measure the fre- quency of symptoms of anxiety and low mood as rated by the children themselves (RCADS, 25 items) or their parent / carer (RCADS-P, containing 47 items). Total anxiety and total low mood scores are derived for both scales, as is a combined depression and anxiety score. RCADS-P provides subscale scores for separation anx- iety, social phobia, generalised anxiety, panic disorder, obsessive compulsive disorder, and major depressive Resting state To assess brain connectivity at rest, T2*-weighted fMRI data is acquired while participants rest with their eyes closed using a Gradient-Echo Echo-Planar Imaging (EPI) sequence. A total of 270 volumes are acquired, each containing 32 axial slices; TR =2000 milliseconds, TE =30 milliseconds, flip angle = 78 degrees, voxel dimensions = 3 mm isotropic; acquisition time of 9 min and 6 s. Page 9 of 11 Page 9 of 11 Holmes et al. BMC Pediatrics (2019) 19:10 Holmes et al. BMC Pediatrics Physiological measures authorities and adult social services spend a further £5.3 billion on community services [35]. Using evidence-based approaches to understand and address the causes of learn- ing problems in childhood is the key to delivering social and economic benefits [36]. Our multi-systems approach to identifying the cognitive, neural and genetic dimensions of children’s learning difficulties provides a novel way to enhance our understanding of the common and complex needs of the majority of children who struggle at school, and in doing so illuminates potential targets for interven- tion for individuals. Saliva DNA DNA samples are collected from children in vials using the Oragene® DNA self-collection kits. Chil- dren are asked to produce a saliva sample by first rubbing their cheeks gently for 30 s to create saliva, and then they are asked to spit in a pot. For children who find it hard to create saliva, a small amount (max ¼ tsp) of white table sugar is available to place on the child’s tongue. The saliva samples are stored in Oragene® kits at room temperature (15–30 °C), as per manufacturer instructions until extrac- tion of DNA. DNA is extracted as soon as possible and stored at −80 °C at the Wellcome Trust-MRC Institute of Metabolic Science at Addenbrooke’s Hospital. Our approach has several strengths.  It is a large-scale study designed to identify the di- mensional basis of learning disorders that adopts a systems neuroscience approach spanning cognition, behaviour, the brain and genes. Height and weight Children’s height and weight is mea- sured during the first CALM visit. A wall chart is used to measure height in centimetres and a set of floor scales to measure weight in kilograms.  It identifies dimensions that can be used to inform the development of interventions necessary to meet the needs of the individual child. Statistical analysis Bayesian methods will be employed to evaluate the strength of the evidence for and against the null hypothesis in addition to traditional null hypothesis testing (e.g. [26]).  Some areas of assessment were very limited. In particular, direct tests of language function were limited to a receptive measure of vocabulary only. p y y  The DKEFS tests of executive were restricted to children 8 years and older. Acknowledgements 8. Chorpita BF, Yim L, Moffitt C, Umemoto LA, Francis SE. Assessment of symptoms of DSM-IV anxiety and depression in children: a revised child anxiety and depression scale. Behav Res Ther. 2000;38(8):835–55. The Centre for Attention Learning and Memory (CALM) research clinic is based at and supported by funding from the MRC Cognition and Brain Sciences Unit, University of Cambridge. The Principal Investigators are Joni Holmes (Head of CALM), Susan Gathercole (Chair of CALM Management Committee), Duncan Astle, Tom Manly and Rogier Kievit. Data collection is assisted by a team of researchers and PhD students at the CBSU that includes Annie Bryant, Fánchea Daly, Francesca Woolgar, Sally Butterfield, Joe Bathelt, Erin Hawkins, Sinead O’Brien, Silvana Mareva, Amy Johnson, Cliodhna O’Leary, Joe Rennie, Mengya Zhang, Delia Fuhrmann, Lara Bridge. The authors wish to thank the many professionals working in children’s services in the South-East and East of England for their support, and to the children and their families for giving up their time to visit the clinic. 9. Cohen M. Children’s memory scale. London, UK: Pearson; 1997. 9. Cohen M. Children’s memory scale. London, UK: Pearson; 1997. 10. Conners CK. Conners parent rating scale short form. 3rd ed. London, UK: Pearson; 2008. 10. Conners CK. Conners parent rating scale short form. 3rd ed. London, UK: Pearson; 2008. 11. Cuthbert BN, Insel TR. Toward the future of psychiatric diagnosis: the seven pillars of RDoC. BMC Med. 2013;11(1):126. 12. De Beer J, Engels J, Heerkens Y, van der Klink J. Factors influencing work participation of adults with developmental dyslexia: a systematic review. BMC Public Health. 2014;14(1):77. 13. Delis DC, Kaplan E, Krmaer JH. Delis-Kaplan executive function system. London, UK: Pearson; 2001. 14. Department for Education (2017). Special educational needs in England January 2017). 14. Department for Education (2017). Special educational needs in England January 2017). Discussion  Some assessments were introduced after recruitment had started, generating incomplete data. These include the CNRep and RCADS. Supporting adults with learning difficulties costs the UK’s NHS £560 million per year for inpatient care. Local Page 10 of 11 Holmes et al. BMC Pediatrics Holmes et al. BMC Pediatrics (2019) 19:10 Holmes et al. BMC Pediatrics (2019) 19:10 Received: 12 October 2018 Accepted: 26 December 2018 Received: 12 October 2018 Accepted: 26 December 2018 In summary this study has the potential to make a significant contribution to our understanding of the causes of common learning problems faced by many children in school. Identifying dimensions that distin- guish individuals will provide targets for tailored indi- vidual interventions. Funding Thi This research was funded by the Medical Research Council of Great Britain, the University of Cambridge. The funding body reviewed and approved the study design and analysis. 17. Emerson E, Hatton C. The mental health of children and adolescents with learning disabilities in Britain. Adv Ment Health Learn Disabil. 2007;1(3):62–3 18. Emerson E, Hatton C. CEDR research report 2008 (1): people with learning disabilities in England; 2008. Competing interests 26. Kass RE, Raftery AE. Bayes factors. J Am Stat Assoc. 1995;90(430):773–95. No authors have competing interests with Biomed Central’s guidance. No authors have competing interests with Biomed Central’s guidance. 27. Kotov R, Krueger RF, Watson D, Achenbach TM, Althoff RR, Bagby RM, et al. The hierarchical taxonomy of psychopathology (HiTOP): a dimensional alternative to traditional nosologies. J Abnorm Psychol. 2017;126(4):454. Ethics approval and consent to participate pp p p Ethical approval was granted by the National Health Service (NHS) Health Research Authority NRES Committee East of England, REC approval reference 13/EE/0157, IRAS 127675. Written informed consent was provided by parents/carers with verbal assent given by children. 22. Gathercole SE, Baddeley A. Children’s test of nonword repetition (CN-rep). London, UK: Pearson; 1996. 23. Gathercole SE, Durling E, Evans M, Jeffcock S, Stone S. Working memory abilities and children's performance in laboratory analogues of classroom activities. Appl Cogn Psychol. 2008;22(8):1019–37. 24. Gioia, G. A., Isquith, P K, Guy, S C, Kenworthy, L (2000) Behaviour Rating Inventory of Executive Function - Ages 5–18 (BRIEF) Psychological Assessment Resources: Florida, USA. Availability of data and materialws h d ll b d l b The data will be made openly accessible to the scientific community 6 months after study completion. The data will be made openly accessible to the scientific community 6 months after study completion. 15. Doherty JL, Owen MJ. Genomic insights into the overlap between psychiatric disorders: implications for research and clinical practice. Genome Medicine. 2014;6(4):29. 15. Doherty JL, Owen MJ. Genomic insights into the overlap between psychiatric disorders: implications for research and clinical practice. Genome Medicine. 2014;6(4):29. 16. Dunn, L.M., & Dunn, D. M. (2007). Peabody Picture Vocabulary Test. Pearson Education: Minneapolis, USA. Abbreviations ADHD i ADHD: attention deficit hyperactivity disorder; AWMA: Automated Working Memory Assessment; BRIEF: Behavior Rating Inventory of Executive Function; CALM: Centre for Attention Learning and Memory; CAMHS: Child and Adolescent Mental Health Services; CCC-2: Child Communication Checklist 2; DKEFS: Delis Kaplan Executive Function System; OCD: obsessive compulsive disorder; PhAB: Phonological Assessment Battery; PPVT: Peabody Picture Vocabulary Test; RCADS: Revised Children’s Anxiety and Depression Scale; RDoC: Research Domain Criteria; SaLTs: speech and language therapists; SENCos: Special Educational Needs Coordinators; STM: short-term memory; TD: typically developing; TEACH-2: Test of Everyday Attention for Children 2 3. Bishop DV, Snowling MJ. Developmental dyslexia and specific language impairment: same or different? Psychol Bull. 2004;130(6):858. 3. Bishop DV, Snowling MJ. Developmental dyslexia and specific language impairment: same or different? Psychol Bull. 2004;130(6):858. 4. Bishop DVM. Children's communication checklist (CCC-2). London, UK: Pearson; 2003. 4. Bishop DVM. Children's communication checklist (CCC-2). London, UK: Pearson; 2003. 5. Cain K, Oakhill J, Bryant P. Children's reading comprehension ability: concurrent prediction by working memory, verbal ability, and component skills. J Educ Psychol. 2004;96(1):31. 6. Casey B, Oliveri ME, Insel T. A neurodevelopmental perspective on the research domain criteria (RDoC) framework. Biol Psychiatry. 2014;76(5):350–3 7. Castellanos FX, Sonuga-Barke EJS, Scheres A, Di Martino A, Hyde C, Walters JR. Varieties of attention-deficit/hyperactivity disorder-related intra-individual variability. Biol Psychiatry. 2005;57(11):1416–23. References 1. Alloway TP. Automated working memory assessment. London, UK: Pearson; 2007. 2. Archibald LM, Cardy JO, Joanisse MF, Ansari D. Language, reading, and math learning profiles in an epidemiological sample of school age children PLoS One. 2013;8(10):e77463. 2. Archibald LM, Cardy JO, Joanisse MF, Ansari D. Language, reading, and math learning profiles in an epidemiological sample of school age children. PLoS One. 2013;8(10):e77463. Authors’ contributions 19. Fair DA, Bathula D, Nikolas MA, Nigg JT. Distinct neuropsychological subgroups in typically developing youth inform heterogeneity in children with ADHD. PNAS. 2012;109(17):6769–74. 20. Frederickson N, Reason R, Firth U. Phonological awareness battery (PhAB). GL assessment: London. In: United Kingdom; 1997. 19. Fair DA, Bathula D, Nikolas MA, Nigg JT. Distinct neuropsychological subgroups in typically developing youth inform heterogeneity in children with ADHD. PNAS. 2012;109(17):6769–74. JH and SG led the conception and design of the work and JH took primary responsibility for drafting the manuscript. The CALM team collected the data, and AB was involved in data preparation and analysis. AB commented on drafts. All authors read and approved the final manuscript. Correspondence concerning this article should be sent to JH (joni.holmes@mrc-cbu.cam.ac.uk). 20. Frederickson N, Reason R, Firth U. Phonological awareness battery (P GL assessment: London. In: United Kingdom; 1997. 21. Gathercole SE, Alloway TP, Kirkwood HJ, Elliott JG, Holmes J, Hilton KA. Attentional and executive function behaviours in children with poor working memory. Learn Individ Differ. 2008;18(2):214–23. Consent for publication Not applicable: identifiable data from individual participants is not available. All participants have consented to the publication of anonymised data. 25. Goodman R. The strengths and difficulties questionnaire: a research note. J Child Psychol Psychiatry. 1997;38(5):581–6. 25. Goodman R. The strengths and difficulties quest J Child Psychol Psychiatry. 1997;38(5):581–6. 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Care services for people with learning disabilities and challenging behaviour. https://www.nao.org.uk/report/care- services-for-people-with-learning-disabilities-and-challenging-behaviour/. 36. National Institute for Health and Care Excellence (2015). Costing statement: Challenging behaviour and learning disabilities. https://www.nice.org.uk/ guidance/ng11/resources/costing-statement-pdf-70691581 37. Parsons, S., & Bynner, J. (2005). Does numeracy matter more? National Research and Development Centre for Adult Literacy and Numeracy: IOE London. http://dera.ioe.ac.uk/22317/1/doc_2979.pdf 38. Peng X, Lin P, Zhang T, Wang J. Extreme learning machine-based classification of ADHD using brain structural MRI data. PLoS One. 2013;8(11):e79476. 39. Ramus F, Marshall CR, Rosen S, van der Lely HK. Phonological deficits in specific language impairment and developmental dyslexia: towards a multidimensional model. Brain. 2013;136(2):630–45. 40. Sonuga-Barke EJS. 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Working memory deficits in children with reading difficulties: memory span and dual task coordination. J Exp Child Psychol. 2013;115(1):188–97. 45. Wechsler D. Wechsler individual achievement test – second UK edition (WIAT-II). London, UK: Pearson; 2005. 45. Wechsler D. Wechsler individual achievement test – second UK edition (WIAT-II). London, UK: Pearson; 2005. 46. Wechsler D. Wechsler abbreviated scales of intelligence- second edition (WASI-II). London, UK: Pearson; 2011. 46. Wechsler D. Wechsler abbreviated scales of intelligence- second edition (WASI-II). London, UK: Pearson; 2011. 47. Whitehurst GJ, Lonigan CJ. Child development and emergent literacy. Child Dev. 1998;69(3):848–72. 47. Whitehurst GJ, Lonigan CJ. Child development and emergent literacy. Child Dev. 1998;69(3):848–72. 48. Woodcock, McGrew, & Mather (2007). Woodcock-Johnson III. Rolling Meadows, IL: Riverside. 48. Woodcock, McGrew, & Mather (2007). Woodcock-Johnson III. Rolling Meadows, IL: Riverside. 49. 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Disrupted resting-state attentional networks in T2DM patients
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Disrupted resting-state attentional networks in T2DM patients Wenqing Xia1,2,3,*, Shaohua Wang1,*, Hengyi Rao3, Andrea M Spaeth4, Pin Wang1, Yue Yang1, Rong Huang1, Rongrong Cai1 & Haixia Sun1 Wenqing Xia1,2,3,*, Shaohua Wang1,*, Hengyi Rao3, Andrea M Spaeth4, Pin Wang1, Yue Yang1, Rong Huang1, Rongrong Cai1 & Haixia Sun1 received: 24 October 2014 accepted: 14 May 2015 Published: 08 June 2015 Although Type 2 diabetes mellitus (T2DM) is a well-recognized risk factor for dementia, the neural mechanisms that underlie cognitive impairment in T2DM remain unclear. This study uses resting- state functional magnetic resonance imaging (fMRI) to examine attention network alterations in T2DM and their relationships to impaired cognitive performance. Data-driven independent component analysis was applied to resting-state fMRI data from 38 T2DM patients and 32 healthy controls to identify the dorsal attention network (DAN) and ventral attention network (VAN). Correlations were then determined among the resting-state functional connectivity (rsFC), clinical data, and neuropsychological scores. The T2DM patients exhibited decreased rsFC in the left middle frontal gyrus (MFG) and bilateral inferior parietal lobe (IPL) of the DAN, as well as the left IPL and right MFG/IFG of the VAN. In addition, the rsFC of the left MFG was inversely correlated with the Trail Making Test-B scores; the rsFC of the left IPL was positively correlated with the Digit Span Test scores but negatively correlated with HbA1c; and the rsFC in the right precuneus was positively associated with cognitive performance (without Bonferroni correction). In conclusion, T2DM affects resting-state attentional networks, which may be related to reduced attention and a hyperglycemic state. Worldwide prevalence rates of type 2 diabetes mellitus (T2DM) and dementia are rapidly increasing and have become major global health challenges. An epidemiological study indicates an association between T2DM and cognitive decline1. In addition to memory deficits, some studies have shown that attention is compromised in patients with T2DM2,3. T2DM patients exhibited moderate decrements in attention compared with controls both at baseline and after a 4-year follow up4. We assume that a disruption of the attentional network may underlie the neurophysiological comorbidities of T2DM; however, the precise etiology of the attentional impairment in T2DM remains unclear. gy p Non-invasive neuroimaging techniques have been used to examine brain function changes in T2DM. Using positron emission tomography, one study identified an Alzheimer-like pattern of reduced regional cerebral glucose metabolism in frontal, parietotemporal, and cingulate regions in patients with predia- betes or early T2DM compared to normal controls5. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Material and methodsh Participants. This study was approved by the Research Ethics Committee of the Affiliated Zhongda Hospital of Southeast University. The methods were conduted in accordance with the approved guide- lines. A total of 40 diabetic patients and 35 healthy subjects were recruited from clinics and hospitals after providing written informed consent. All participants were right-handed, were between 45 and 70 years of age, and had at least 6 years of education. All patients who met the diagnosis of T2DM based on the 1999 World Health Organization criteria18 and were on stable therapy with diet, exercise, insulin, or oral medications (The therapeutic agents used by the patients are provided in Supplementary table 1) were included. We considered one as having blood pressure lowering medications or cholesterol lower- ing medications if he/she had used related drugs in the past or currently. Patients with macrovascular diseases (e.g., cerebrovascular, or cardiovascular diseases) or clinically detectable microvascular compli- cations (e.g., retinopathy, nephropathy, or neuropathy) were excluded. No patients complained of chronic pain or suffered symptoms of pain during scanning. Healthy controls matched for age, gender, BMI, and education level were recruited from the community. Individuals with a fasting glucose level >  5.6 mmol/l or a postprandial glucose level >  7.8 mmol/l were excluded. p p g Additional exclusion criteria included having a history of or current stroke, alcoholism, head injury, Parkinson’s disease, epilepsy, major depression or other neurological or psychiatric illnesses, a major medical illness (e.g., cancer, anemia or thyroid dysfunction), and severe visual or hearing loss. Clinical data and neuropsychological test information. Clinical diagnoses were conducted for all subjects after a baseline medical screening, a 50-minute neuropsychological battery, and a laboratory screening. Venous blood samples were obtained at 8 A.M. after an overnight fast of at least 10 hours. Each subject was then instructed to drink a 75 g glucose solution, and a second blood sample was collected 2 hours later. Fasting blood glucose, postprandial blood glucose, HbA1c, triglyceride, total cholesterol, low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) levels were assessed. Carotid artery ultrasound images were also obtained for each participant. Disrupted resting-state attentional networks in T2DM patients Wenqing Xia1,2,3,*, Shaohua Wang1,*, Hengyi Rao3, Andrea M Spaeth4, Pin Wang1, Yue Yang1, Rong Huang1, Rongrong Cai1 & Haixia Sun1 Using resting-state blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI), several studies have showed reduced functional connectivity between the nodes of the default mode network (DMN), such as the posterior cingulated cortex (PCC) and the hippocampus, in T2DM patients compared to normal controls6–8. These rest- ing state functional connectivity (rsFC) studies used seed-based analysis, a hypothesis-driven method, to assess the temporal synchronization of neuronal activity between the seed and other remote areas. Therefore, the findings are limited to the connectivity pattern of the selected seed regions. Furthermore, previous studies have not focused on brain connectivity alteration in attentional networks and their relationships to attention deficits in T2DM. 1Department of Endocrinology, affiliated ZhongDa Hospital of Southeast University, No. 87 Dingjiaqiao Road, Nanjing, China, 210009. 2Medical school of Southeast University, No. 87 Dingjiaqiao Road, Nanjing, China, 210009. 3Center for functional Neuroimaging, University of Pennsylvania, 3710 Hamilton Walk, Philadelphia, PA, USA, 19104. 4Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, 3710 Hamilton Walk, Philadelphia, PA, 19104. *These authors contributed equally to this work. Correspondence and requests for materials should be addressed to S.W. (email: gyjwsh@126.com) Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 1 www.nature.com/scientificreports/ Independent component analysis (ICA) is a data-driven method that automatically identifies mean- ingful brain networks and maps functional connectivity in the brain without the need for a priori defined seed regions9. Instead, ICA decomposes the entire resting-state BOLD data set into spatially distrib- uted components that are maximally independent in a statistical sense10–12. Based on prior ICA-based resting-state fMRI investigations that examined different brain networks13–16, two networks related to attention have been well defined: The dorsal attention network (DAN) is comprised of the bilateral intraparietal sulcus and the frontal eye fields (FEF) and mediates top-down processing of attentional orientation. The ventral attention network (VAN) consists of the right lateralized temporal parietal junc- tion (TPJ) and the ventral frontal cortex (VFC) and is involved in bottom-up processing of attentional re-orientation. Altered connectivity in the DAN and VAN have been demonstrated in different brain dis- orders with cognitive impairment, including Alzheimer’s disease (AD) and hepatic encephalopathy16,17. g p g p p p y In the present study, ICA was used in order to identify the DAN and VAN in a large sample of 70 adults, including 38 T2DM patients and 32 matched healthy controls. Disrupted resting-state attentional networks in T2DM patients Wenqing Xia1,2,3,*, Shaohua Wang1,*, Hengyi Rao3, Andrea M Spaeth4, Pin Wang1, Yue Yang1, Rong Huang1, Rongrong Cai1 & Haixia Sun1 Relationships between attention network connectivity and clinical variables as well as between attention network connectivity and cog- nitive performance were assessed. We hypothesize that T2DM patients would exhibit reduced func- tional connectivity in the DAN and VAN and that functional connectivity within these networks would correlate with cognitive tests of attention. Material and methodsh Quantitative assessments of the white matter hyperintensity (WMH) and lacunar infarcts were made on the fluid-attenuated inversion recovery images based on the age-related white matter changes scale20 with a single-blind method. Participants with a rating score >  1 were excluded. g p g Analyses were conducted using the Data Processing Assistant for rs-fMRI (DPARSF) program21, which is based on statistical parametric mapping (SPM8, http://www.fil.ion.ucl.ac.uk/spm) and rs-fMRI data analysis toolkits (REST, http://www.restfmri.net). Preprocessing was performed as previously described22. Briefly, 240 volumes were scanned, and the first 10 volumes were discarded, followed by a slice-timing adjustment, realignment for head-motion correction, and spatial normalization to the Montreal Neurological Institute (MNI) template (resampling voxel size =  3 ×  3 ×  3 mm3) in addition to smoothing with an isotropic Gaussian kernel (FWHM =  4 mm), detrend and filtering (0.01 −  0.08 Hz).h gi g The data from 5 subjects (2 patients and 3 healthy controls) were excluded from the overall statistical analyses: 2 subjects were excluded for excessive motion (head movement exceeded 2.0 mm of the max- imum translation in any of the x, y, and z directions or 2.0° of the maximum rotation about the three axes), 1 subject was excluded for poor quality images, and 2 subjects were excluded for a WMH rating score >  1. Independent component analysis. ICA was applied to the fMRI data using the groupICA (GICA) of the fMRI toolbox (http://www.nitrc.org/projects/cogicat/, MICA version beta 1.2)23. The fMRI toolbox reduced the data, applied the ICA algorithm and then performed back-reconstruction and converted the data into calibrated rsFC maps. In this study, we performed GICA 100 times and decomposed the dataset into 30 components. In these 30 maps, some maps reflect noise components whereas other maps reflect neuro-anatomical systems. According to previous studies13–16, the DAN is composed of the bilateral intraparietal sulcus and the FEF, whereas the VAN includes the right lateralized TPJ and the VFC. The independent components that best matched the DAN or VAN were identified in each group via visual inspection. Voxelwise-based gray matter volume correction. A voxel-based morphometry (VBM) approach was used to generate gray matter (GM) volume maps of all subjects. VBM was performed using the VBM8 toolbox (http://dbm.neuro.uni-jena.de/vbm) run in the Statistical Parametrical Mapping 8 (http:// www.fil.ion.ucl.ac.uk/spm/) software on MATLAB 7.10.0. Briefly, cerebral tissues were segmented into gray matter, white matter, and cerebrospinal fluid using a unified segmentation algorithm. Material and methodsh T1 magnetic resonance images were normalized to the Montreal Neurological Institute (MNI) template using affine linear registration, followed by Gaussian smoothing (FWHM =  8 mm, because the FWHM should be 2 to 3-fold the voxel size and T1 images have a relatively higher resolution). Finally, the resulting voxelwise GM volume maps were input as covariates during the functional data analysis. Statistical analysis. Demographic and clinical variable analysis. Analysis was performed using SPSS software (version 17.0). Differences in the demographic and cognitive data between the patients and healthy controls were analyzed using a t test for normally distributed variables, a nonparametric Mann-Whitney U test for asymmetrically distributed variables, and a χ 2-test for categorical variables. All tests were conducted using a two-sided α -level of 0.05. fMRI data analysis. The component maps for the participants were entered into a random-effect one-sample t-test to create a sample-specific component map (p <  0.05, after correcting for multiple comparisons using the False Discovery Rate, FDR). One-way ANOVA was used to compare differ- ences in synchronization within the two attentional networks. All statistical analyses were performed with age, gender, education level, and BMI as nuisance covariates to control for potential influences. Monte Carlo simulations were performed using the AFNI AlphaSim program (http://afni.nih.gov/afni/ docpdf/AlphaSim.pdf) (parameters: single voxel p value =  0.05, a minimum cluster size of 85 mm3, FWHM =  4 mm, and within a gray matter mask corresponding to the AAL atlas). Correlation analysis. A ROI-based partial correlation analysis was calculated between the rsFC and the psychometric and clinical results. The mean Z values of each brain area that showed significant rsFC group difference were extracted using REST software (http://restingfmri.sourceforge.net/). Pearson’s correlation coefficients between a change in the rsFC strength and cognitive performance and clinical variables were subsequently analyzed using SPSS software (version 17.0), with a p value <  0.05 considered statistically significant. Age, gender, education level, BMI, hypercholesterolemia, intima-media thickness, and the presence of WMH and lacunar infarcts were entered as covariates. Bonferroni corrections were then used for multiple comparisons. Given the large age range of the study subjects, we also performed multiple regression in SPM8 to investigate the potential altered brain regions that accompanied increased age in each group as well as in the combined group. Material and methodsh y g A battery of cognitive testing, including the Mini Mental State Exam (MMSE), Auditory Verbal Learning Test (AVLT), Rey-Osterrieth Complex Figure Test (CFT), Digit Symbol Substitution Test (DSST), Digit Span Test (DST), Trail Making Test-A and B (TMT-A and TMT-B), and Clock Drawing Test (CDT), was administered in a fixed order to evaluate general mental status, memory, attention, executive function, and visuospatial function. Because depression affects cognitive function and is more common in T2DM patients compared with control subjects19, the Hamilton Depression Scale was also administered by an experienced neuropsychiatrist under single-blind conditions. MRI acquisition and image preprocessing. Imaging data were acquired on a 3.0 T MRI scanner (Siemens MAGENETOM Trio). Cushions and earplugs were used to reduce head motion and scanner noise. Subjects were instructed to lie quietly with their eyes closed but avoid falling asleep, not to think of anything in particular, and to avoid head motion during fMRI. All participants were scanned at 11 A.M. on the same day that the clinical data were collected and the neuropsychological tests were conducted. Fluid-attenuated inversion recovery scans were also acquired: TR =  8,500 ms, TE =  94 ms, slices =  20, thickness =  5 mm, and voxel size 1.3 ×  0.9 ×  5 mm3. Functional images were collected axially using an echo-planar imaging (EPI) sequence with the following parameters: repetition time (TR) =  2000 ms, echo time (TE) =  25 ms, slices =  36, thickness =  4 mm, gap =  0 mm, field of view (FOV) =  240 ×  240 mm2, acquisition matrix =  64 ×  64, and flip angle (FA) =  90°. The resting-state fMRI (rs-fMRI) scan took 8 minutes and 6 seconds. High-resolution 3D T1-weighted axial images spanning the entire brain were acquired using the following parameters: TR =  1900 ms, TE =  2.48 ms, slices =  176, thickness =  1 mm, gap =  0 mm, FA =  90°, acquisition matrix =  256 ×  256, and FOV =  250 ×  250 mm2. The entire imaging protocol took 14 minutes and 23 seconds. Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 2 www.nature.com/scientificreports/ Quantitative assessments of the white matter hyperintensity (WMH) and lacunar infarcts were made on the fluid-attenuated inversion recovery images based on the age-related white matter changes scale20 with a single-blind method. Participants with a rating score >  1 were excluded. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Items T2DM patients (n =  38) Healthy controls (n =  32) p-value Age, years 58.6 ±  8.2 55.6 ±  7.1 0.108 Gender, female (%) 17(45) 15(47) 0.858 Education levels, years 9.7 ±  3.4 10.4 ±  2.0 0.338 Diabetes duration, years 9.9 ±  5.7 – – History of smoking (%) 9(24) 8(25) 0.898 BMI, kg/m2 25.0 ±  2.7 24.3 ±  2.4 0.267 Systolic BP, mmHg 131.6 ±  15.5 129.8 ±  14.3 0.601 Diastolic BP, mmHg 79.3 ±  8.6 80.8 ±  7.3 0.441 HbA1c , % (mmol/mol) 7.7 ±  1.7(61.0 ±  18.6) 5.1 ±  0.5(32.0 ±  5.5) < 0.001* Fasting glucose, mmol/L 8.0 ±  2.3 5.2 ±  0.3 < 0.001* Postprandial glucose, mmol/L 11.8 ±  4.6 6.9 ±  0.8 < 0.001* Triglyceride, mmol/l 1.5 ±  0.7 1.4 ±  0.7 0.858 Total cholesterol, mmol/l 5.5 ±  1.1 5.7 ±  0.8 0. 604 LDL-C, mmol/l 3.4 ±  0.8 3.4 ±  0.5 0.862 HDL-C, mmol/l 1.4 ±  0.3 1.4 ±  0.3 0.699 White matter hyperintensity 0(0–6) 0(0–5) 0.182 Lacunar infarcts (%) 6(15) 4(12.5) 0.695 Intima-media thickness, mm 1.0 ±  0.2 1.0 ±  0.2 0.162 Blood pressure lowering medications (%) 16(42) 11(34) 0.508 Cholesterol lowering medications (%) 10(26) 4(13) 0.150 Table 1. Demographic and clinical characteristics. Values are mean± standard deviation, n(%), or m (range) . *P <  0.05 was considered significant. Abbreviations: LDL-C, low-density lipoprotein cholestero HDL-C, high-density lipoprotein cholesterol. Table 1. Demographic and clinical characteristics. Values are mean± standard deviation, n(%), or median (range) . *P <  0.05 was considered significant. Abbreviations: LDL-C, low-density lipoprotein cholesterol; HDL-C, high-density lipoprotein cholesterol. Table 1. Demographic and clinical characteristics. Values are mean± standard deviation, n(%), or median (range) . *P <  0.05 was considered significant. Abbreviations: LDL-C, low-density lipoprotein cholesterol; HDL-C, high-density lipoprotein cholesterol. www.nature.com/scientificreports/ Items T2DM patients (n =  38) Healthy controls (n =  32) p-value General mental status   MMSE 28.8 ±  1.1 29.1 ±  1.2 0.259 Memory   AVLT- total 32.1 ±  8.3 35.0 ±  5.4 0.092   AVLT-delay 6.2 ±  2.5 6.8 ±  1.7 0.246   CFT-delay 13.3 ±  6.1 19.0 ±  6.3 < 0.001* Attention   TMT-A 72.5 ±  23.4 66.6 ±  17.0 0.231   DSST 43.1 ±  8.5 46.0 ±  8.2 0.154   DST 11.1 ±  2.0 12.3 ±  2.2 0.012* Executive function   TMT-B 189.5 ±  56.6 163.4 ±  50.4 0.048* Visuospatial function   CDT 3.3 ±  0.8 3.6 ±  0.5 0.070   CFT-copy 34.6 ±  2.0 35.6 ±  0.7 0.008* Depression   HAMD 1.1 ±  1.1 1.3 ±  1.0 0.501 Table 2. Cognitive scores and depressive symptoms. Values are mean ±  standard deviation. *P <  0.05 was considered significant. Abbreviations: MMSE, Mini Mental State Exam; AVLT, Auditory Verbal Learning test; CFT, Rey-Osterreith Complex Figure Test; TMT, Trail Making Test; DSST, Digit Symbol Substitution Test; DST, Digit Span Test; CDT, Clock Drawing Test; HAMD, Hamilton Depression Scale. Items T2DM patients (n =  38) Healthy controls (n =  32) p-value General mental status   MMSE 28.8 ±  1.1 29.1 ±  1.2 0.259 Memory   AVLT- total 32.1 ±  8.3 35.0 ±  5.4 0.092   AVLT-delay 6.2 ±  2.5 6.8 ±  1.7 0.246   CFT-delay 13.3 ±  6.1 19.0 ±  6.3 < 0.001* Attention   TMT-A 72.5 ±  23.4 66.6 ±  17.0 0.231   DSST 43.1 ±  8.5 46.0 ±  8.2 0.154   DST 11.1 ±  2.0 12.3 ±  2.2 0.012* Executive function   TMT-B 189.5 ±  56.6 163.4 ±  50.4 0.048* Visuospatial function   CDT 3.3 ±  0.8 3.6 ±  0.5 0.070   CFT-copy 34.6 ±  2.0 35.6 ±  0.7 0.008* Depression   HAMD 1.1 ±  1.1 1.3 ±  1.0 0.501 Table 2. Cognitive scores and depressive symptoms. Values are mean ±  standard deviation. *P <  0.05 was considered significant. Abbreviations: MMSE, Mini Mental State Exam; AVLT, Auditory Verbal Learning test; CFT, Rey-Osterreith Complex Figure Test; TMT, Trail Making Test; DSST, Digit Symbol Substitution Test; DST, Digit Span Test; CDT, Clock Drawing Test; HAMD, Hamilton Depression Scale. Table 2. Cognitive scores and depressive symptoms. Values are mean ±  standard deviation. *P <  0.05 was considered significant. Abbreviations: MMSE, Mini Mental State Exam; AVLT, Auditory Verbal Learning test; CFT, Rey-Osterreith Complex Figure Test; TMT, Trail Making Test; DSST, Digit Symbol Substitution Test; DST, Digit Span Test; CDT, Clock Drawing Test; HAMD, Hamilton Depression Scale. Table 2. Cognitive scores and depressive symptoms. Results Clinical and neuropsychological data. The demographic characteristics and neuropsychological data for each group are presented in Table  1 and Table  2. No significant differences were observed between groups with respect to age, gender, education level, BMI, blood lipids, blood pressure, WMH, Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 3 Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 www.nature.com/scientificreports/ Values are mean ±  standard deviation. *P <  0.05 was considered significant. Abbreviations: MMSE, Mini Mental State Exam; AVLT, Auditory Verbal Learning test; CFT, Rey-Osterreith Complex Figure Test; TMT, Trail Making Test; DSST, Digit Symbol Substitution Test; DST, Digit Span Test; CDT, Clock Drawing Test; HAMD, Hamilton Depression Scale. Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 4 www.nature.com/scientificreports/ Figure 1. The typical anatomical pattern of the dorsal attention network (DAN) and ventral attention network (VAN) in healthy controls (NC) and type 2 diabetes mellitus (T2DM) patients (DM). Networks were identified using independent component analysis (p <  0.05, FDR corrected). Figure 1. The typical anatomical pattern of the dorsal attention network (DAN) and ventral attention network (VAN) in healthy controls (NC) and type 2 diabetes mellitus (T2DM) patients (DM). Networks were identified using independent component analysis (p <  0.05, FDR corrected). lacunar infarcts, intima-media thickness or medication. As expected, T2DM patients had increased HbA1c, fasting and postprandial glucose levels (all p <  0.001) compared with healthy controls. In terms of cognitive performance, T2DM patients had poorer scores for the CFT-copy, CFT-delay, DSST, DST, and TMT-B compared with the controls (p <  0.05). lacunar infarcts, intima-media thickness or medication. As expected, T2DM patients had increased HbA1c, fasting and postprandial glucose levels (all p <  0.001) compared with healthy controls. In terms of cognitive performance, T2DM patients had poorer scores for the CFT-copy, CFT-delay, DSST, DST, and TMT-B compared with the controls (p <  0.05). rsFC differences between patients and controls. The one-sample t-test revealed typical signifi- cant spatial patterns of the DAN and VAN in both the controls and T2DM patients (p <  0.05, corrected; Fig. 1). Fig. 2 displays the rsFC differences in the attentional related network according to two-sample t-tests between groups. Compared with controls, T2DM patients displayed decreased rsFC in the left middle frontal gyrus (MFG) and bilateral inferior parietal lobe (IPL) of the DAN, as well as the left IPL and right MFG/IFG of the VAN (p <  0.05, corrected) (Table 3). Correlations between the rsFC of attentional networks and cognitive performance. In T2DM patients, rsFC in the left MFG was inversely correlated with TMT-B scores (r =  − 0.533, p =  0.001; Fig. 3a), rsFC in the left IPL was positively correlated with DST scores but negatively correlated with the HbA1c (r =  0.403, p =  0.012 and r =  − 0.370, p =  0.022, respectively) (Fig. www.nature.com/scientificreports/ 3b,c). Additionally, a positive association (r =  0.473, p =  0.003) (Fig. 3d) between the CFT scores and the rsFC of the right precuneus was found. However, no significant results remained following a Bonferroni correction because of the many comparisons tested. No significant correlations were observed in the healthy control group. None of these correlations were significant (p <  0.05, corrected) in the VAN or the control group. We also did not detect any significant brain regions (p <  0.05, corrected) affected by an increase in age. Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 5 www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 2. Significant decreases (cold color) and increases (warm color) in the resting-state functional connectivity of the DAN (a) and VAN (b) in T2DM patients. T2DM patients displayed decreased rsFC in the right inferior frontal gyrus (IFG), left middle frontal gyrus (MFG), and bilateral inferior parietal lobe (IPL) of the DAN, as well as the left IPL and right MFG/IFG of the VAN. Thresholds were set at a corrected p <  0.05, determined using a Monte Carlo simulation. Note that the left side corresponds to the right hemisphere. Figure 2. Significant decreases (cold color) and increases (warm color) in the resting-state functional connectivity of the DAN (a) and VAN (b) in T2DM patients. T2DM patients displayed decreased rsFC in the right inferior frontal gyrus (IFG), left middle frontal gyrus (MFG), and bilateral inferior parietal lobe (IPL) of the DAN, as well as the left IPL and right MFG/IFG of the VAN. Thresholds were set at a corrected p <  0.05, determined using a Monte Carlo simulation. Note that the left side corresponds to the right hemisphere. Brain regions MNI Coordinates x, y, z (mm) Peak t score Voxels (mm3) Within DAN   L Middle Frontal Gyrus    − 27, − 9, 57  − 3.0241 114   L Inferior Parietal Lobule       18, − 48, 72 − 3.1839 121   R Superior/ Inferior Parietal Lobule       63, − 27, 21 − 3.5829 97   R Precuneus       15, − 63, 36 4.5389 286 Within VAN   L Inferior Parietal Lobule  − 48, − 51, 36 − 3.3803 90   R Middle/ Inferior Frontal Gyrus 39, 51, − 12 − 2.7926 141 Table 3. Regions showing significant differences in functional connectivity within attention-related brain networks between patients and healthy controls. A corrected threshold of p <  0.05 determined by Monte Carlo simulation was taken as meaning that there was a significant difference between groups. Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 www.nature.com/scientificreports/ Abbreviations: DAN, dorsal attention network; VAN, ventral attention network; MNI: Montreal Neurological Institute; L, left; R, right. Brain regions MNI Coordinates x, y, z (mm) Peak t score Voxels (mm3) Within DAN   L Middle Frontal Gyrus    − 27, − 9, 57  − 3.0241 114   L Inferior Parietal Lobule       18, − 48, 72 − 3.1839 121   R Superior/ Inferior Parietal Lobule       63, − 27, 21 − 3.5829 97   R Precuneus       15, − 63, 36 4.5389 286 Within VAN   L Inferior Parietal Lobule  − 48, − 51, 36 − 3.3803 90   R Middle/ Inferior Frontal Gyrus 39, 51, − 12 − 2.7926 141 Table 3. Regions showing significant differences in functional connectivity within attention-related brain networks between patients and healthy controls. A corrected threshold of p <  0.05 determined by Monte Carlo simulation was taken as meaning that there was a significant difference between groups. Abbreviations: DAN, dorsal attention network; VAN, ventral attention network; MNI: Montreal Neurological Institute; L, left; R, right. Table 3. Regions showing significant differences in functional connectivity within attention-related brain networks between patients and healthy controls. A corrected threshold of p <  0.05 determined by Monte Carlo simulation was taken as meaning that there was a significant difference between groups. Abbreviations: DAN, dorsal attention network; VAN, ventral attention network; MNI: Montreal Neurological Institute; L, left; R, right. Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 6 www.nature.com/scientificreports/ Figure 3. Correlations between the rsFC of specific regions in the DAN and the neuropsychological tests scores and HbA1c of T2DM patients. (a) A correlation between the rsFC of the left MFG and the TMT-B score (r =  − 0.533, p =  0.001). MFG, middle frontal gyrus; TMT -B, Trail Making Test-B. (b) A correlation between the rsFC of the left IPL and the DST score (r =  0.403, p =  0.012). IPL, inferior parietal lobe; DST, Digital Span Test. (c) A correlation between the rsFC of the left IPL and the HbA1c (r =  − 0.370, p =  0.022). (d) A correlation between the rsFC of the left precuneus and the CFT score (r =  0.473, p =  0.003). CFT, Rey- Osterrieth Complex Figure Test. igure 3. Correlations between the rsFC of specific regions in the DAN and the neuropsychological tests g pi g p y g scores and HbA1c of T2DM patients. www.nature.com/scientificreports/ (a) A correlation between the rsFC of the left MFG and the TMT-B score (r =  − 0.533, p =  0.001). MFG, middle frontal gyrus; TMT -B, Trail Making Test-B. (b) A correlation between the rsFC of the left IPL and the DST score (r =  0.403, p =  0.012). IPL, inferior parietal lobe; DST, Digital Span Test. (c) A correlation between the rsFC of the left IPL and the HbA1c (r =  − 0.370, p =  0.022). (d) A correlation between the rsFC of the left precuneus and the CFT score (r =  0.473, p =  0.003). CFT, Rey- Osterrieth Complex Figure Test. Discussion Discussion T2DM patients exhibit disrupted functional integration within attention-related brain networks, including the DAN and VAN, and disruptions in these networks significantly associated not only with neuropsychological scores but also with HbA1c.i T2DM patients exhibit disrupted functional integration within attention-related brain networks, including the DAN and VAN, and disruptions in these networks significantly associated not only with neuropsychological scores but also with HbA1c.i p y g Consistent with previous findings, patients with T2DM exhibited lower scores on all cognitive tests compared to control subjects; significant differences between groups were observed on tests of memory, attention, executive function, and visuospatial function. Notably, T2DM patients exhibit cognitive dec- rements in a variety of cognitive domains, which supports the presence of multidimensional cognitive abnormalities in T2DM patients3,22. Although only one test related to attention, namely DST, exhibited significant diversity between the groups, we believe that this result may be due to the sensitivity of the neuropsychological tests in this limited sample-size cohort. p y g p In the present study the established DAN and VAN regions largely coincide with previously reported findings13–16. T2DM patients differed from healthy control subjects in the rsFC strength in these two attention networks. T2DM patients displayed both increased and decreased rsFC within the DAN, depending on the region, whereas, they also exhibited consistently decreased rsFC within regions of the VAN. T2DM patients displayed decreased rsFC within the IPL/SPL and MFG/IFG, which are core regions of these attention networks. A previous study that examined patients with AD found that these patients also exhibited decreased functional connectivity in the core regions of the DAN, including the IPL and SPL, bilateral IFG, left MFG and superior frontal gyrus (which covers the frontal eye-field)24. In the current study, fewer regions within the VAN displayed different levels of rsFC between patients and control subjects, and fewer significant correlations between the rsFC of regions in the VAN and cognitive performance were observed. Therefore, we suggest the VAN is stable and less susceptible to the impact of both diseases compared with the DAN. However, in contrast to AD in which several studies have suggested that left regions of the DAN are more seriously impaired than right regions24,25, we did not find evidence of lateralization in the impairment of attention networks. Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 Discussion Taken together, although T2DM and AD appear to share a portion of brain pathogenesis26–28 that progress to cognitive impairment, Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 7 www.nature.com/scientificreports/ T2DM-related attentional deficits may be not be comparable to the deficits present in AD patients. Therefore, the differences in cognitive impairment should be noted between the two disease states. hf g In addition to voluntary (top-down) orienting, the DAN also underlies other higher-level cognitive processes, such as visuospatial and executive function29. Consistent with these findings, we observed significant positive associations between TMT-B scores and z-values of the rsFC within the MFG and between DST scores and z-values of the rsFC within the left IPL. The TMT-B is a commonly used neu- ropsychological test that reflects frontal cortical functioning, and the DST is sensitive to attentional and working memory deficits. Our findings are consistent with previous studies showing associations between IPL activity and working memory performance (forward and backward digit span task30 and between DST performance and damage in the left hemisphere IPL31–33. These correlations between decreased rsFCs and poor performances in cognitive tests could potentially support the notion that changes in the DAN reflect neurobehavioral deficits in T2DM patients. Nevertheless, no other studies have found similar changes in this brain network or regions to demonstrate the deficits in attention to date. Several studies that have used cognitive tests with a larger sample size imply that T2DM patients have impaired attentional function. Thus, this issue remains to be confirmed by further studies. hi y In addition to these neuropsychological performance measures, HbA1c was also correlated with rsFC within the left IPL. Although previous research has demonstrated that HbA1c is negatively associated with improved attentional performance34, we did not identify a significant correlation between HbA1c and any of the neuropsychological tests. However, it is possible that changes in rs-fMRI within attention networks precede changes in behavioral tests and that rsFC in the IPL mediates attentional decline in T2DM patients. In-depth longitudinal studies are needed to confirm this speculation.h p p gi p The precuneus plays a central role in visuospatial processing and execution, as well as in higher-order processes, such as voluntary attention shifts35,36. The CFT test is widely used to evaluate deficits in visu- ospatial constructional ability and executive function37, both of which are common consequences of attentional deficits. Discussion We observed a positive correlation between the rsFC within the right precuneus and CFT performance and therefore speculate that increased activity in the precuneus may act as a com- pensatory mechanism to avoid a decrease in the attentional ability of T2DM patients. These correlations were significant prior to multiple comparisons. When a Bonferroni correction was used, no significant correlations survived, which may, in part, because of the relatively strict calculation and limited sample size. Nevertheless, we believe that our research is still meaningful to provide directions for future investi- gations in this field. Another main negative result of this study is the undetectable potential effect of age. Although the effect of age on cognitive function has been proved38,39, it did not significantly influence the brain in the current cohort. Thus, a larger sample size and re-analyzing the data are necessary for future studies.if Previous fMRI studies have also identified differences in the brain between T2DM and healthy con- trols. For example, Musen and colleagues investigated brain abnormalities in T2DM patients using rs-fMRI6. They selected PCC as the ROI to produce meaningful results of altered functional connectivity between PCC and several brain areas, including the middle temporal gyrus, the inferior and medial fron- tal gyri, and the thalamus. Hoogenboom et al. combined diffusion tensor imaging and fMRI to identify the white matter alterations in T2DM patients that correlated with disrupted functional connectivity in the default-mode network40. In addition, to date, three data-driven studies have investigated the potential changes in the brain of T2DM: previous work from our laboratory used the amplitude of low frequency fluctuations (ALFF) method to investigate the neuronal activity of T2DM patients22, Wang et al.41 used the same method to further investigate the effects of diabetic vascular disease on the brain, and Cui et al.42 combined the ALFF with regional homogeneity (ReHo) methods and also observed alterations in the diabetic brain. ALFF and ReHo of the BOLD signal are thought to be indicators of the intensity and temporal synchronization of regional spontaneous neuronal activity in the whole brain43,44, whereas functional connectivity analysis describes spatiotemporal correlations between spatially distinct brain regions, as well as shows the correlations of voxel signals with the signal of a particular component45,46; higher functional connectivity between certain regions represents a higher degree of involvement of a particular network47. These discrepancies also lead to the diversity of results between the current study and previous findings. Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 Discussion pi g Some limitations of our study should be noted. First, considering the current cross-sectional design and limited sample size with potential medication effects in the patients, further studies should try to examine a larger population receiving similar therapies and use a longitudinal approach to verify these findings. Second, we did not measure the intelligence quotient (IQ), which could drive differences in rsFC and cognitive tests. Finally, we only analyzed the rsFC within attentional related networks; however, other brain networks may also be affected by disease status and attentional function during the resting state, such as networks involved in executive function or working memory, which have been confirmed as prominent cognitive impairments in T2DM patients. If positive results are observed, in-depth studies should assess directional connectivity among these various resting-state networks. Conversely, if other networks are not altered, this finding would support the specificity of the current results.i i g pp pi y In conclusion, for the first time, we used a data-driven approach to observe the functional connec- tivity changes within the attentional network in T2DM patients and found a significant disruption of attentional networks in these patients. Several core regions in the DAN, especially the IPL, likely under- lie the attentional deficits in T2DM patients. Our data may potentially support rs-fMRI as a promising Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 8 www.nature.com/scientificreports/ tool to detect attentional changes in T2DM and provide new insights into the neural deficits present in T2DM patients. tool to detect attentional changes in T2DM and provide new insights into the neural deficits present in T2DM patients. References e e e ces 1. Okereke, O. I. et al. 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Spontaneous Brain Activity in Type 2 Diabetics Revealed by Amplitude of Low-Frequency Fluctuations and Its Association with Diabetic Vascular Disease: A Resting-State fMRI Study. PLoS ONE 9 l ( ) 41. Wang, C. X., Fu, K. L., Liu, H. J., Xing, F. & Zhang, S. Y. Spontaneous Brain Activity in Type 2 Diabetics Revealed by Amplitude of Low-Frequency Fluctuations and Its Association with Diabetic Vascular Disease: A Resting-State fMRI Study. PLoS ONE 9, e108883; DOI: 10.1371/journal.pone.0108883 (2014). j 2. Cui, Y. et al. Altered spontaneous brain activity in type 2 diabetes: a resting-state functional MRI study. Diabetes 63, 749–760 (2014). 3. Zang, Y., Jiang, T., Lu, Y., He, Y. & Tian, L. Regional homogeneity approach to fMRI data analysis. Neuroimage 22, 394–400 (2004). 4. Biswal, B., Zerrin Yetkin, F., Haughton, V. M. & Hyde, J. S. Functional connectivity in the motor cortex of resting human brain using echo‐planar mri. Magnet Reson Med 34, 537–541 (1995). g p g 5. Friston, K., Frith, C., Liddle, P. & Frackowiak, R. Functional connectivity: the principal-component analysis of large (PET) data sets. J Cerebr Blood F Met 13, 5–5 (1993). ( ) 6. Power, J. D., Schlaggar, B. L. & Petersen, S. E. Studying Brain Organization via Spontaneous fMRI Signal. Neuron 84, 681–696 (2014). 47. Calhoun, V., Adali, T., Pearlson, G. & Pekar, J. A method for making group inferences from functional MRI data using independent component analysis. Hum Brain Mapp 14, 140–151 (2001). Acknowledgments g We would like to express our heartfelt gratitude to the staff of the Department of Neurology and the Department of Radiology, Affiliated Zhongda Hospital of Southeast University, especially Prof. Chunming Xie, Prof. Feng Bai, and Dr. Yuchen Chen for their selfless help and valuable assistance. We also thank the contribution of Prof. YuFeng Zang, Center for Cognition and Brain Disorders and the Affiliated Hospital, Hangzhou Normal University. W.Q.X acknowledges the financial support from the China Scholarship Council for her joint PhD scholarship (No. 201406090138). This work was partially supported by the National Natural Science Foundation of China (No. 81370921, Wang SH) and the Fundamental Research Funds for the Central Universities and Jiangsu Graduate Innovation Grant (KYZZ_0073, Xia WQ). Author Contributions W.X. wrote the main manuscript, researched data. S.W. designed the experiment, reviewed manuscript. H.R and A.S reviewed manuscript. P.W., R.H., R.C. contributed to discussion. Y.Y., H.S. researched data, contributed discussion. References Transient neural activity in the medial superior frontal gyrus and precuneus time locked with attention shif between object features. Neuroimage 10, 193–199 (1999).f j g 37. Siri, S., Benaglio, I., Frigerio, A., Binetti, G. & Cappa, S. A brief neuropsychological assessment for the differential diagnosis between frontotemporal dementia and Alzheimer’s disease. Eur J Neurol 8, 125–132 (2001). p J , ( ) 38. Hedden, T. et al. Multiple Brain Markers are Linked to Age-Related Variation in Cognition. Cereb Cortex DOI: 10.1093/cercor/ bhu238 (2014). 39. Heise, V. et al. Apolipoprotein E genotype, gender and age modulate connectivity of the hippocampus in healthy adults. NeuroImage 98, 23–30 (2014). Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 9 Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 Additional Information Supplementary information accompanies this paper at http://www.nature.com/srep Competing financial interests: The authors declare no competing financial interests. Competing financial interests: The authors declare no competing financial interests. How to cite this article: Xia, W. et al. Disrupted resting-state attentional networks in T2DM patients. ci. Rep. 5, 11148; doi: 10.1038/srep11148 (2015). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Com- mons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ Scientific Reports | 5:11148 | DOI: 10.1038/srep11148 10
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PhyloPat: phylogenetic pattern analysis of eukaryotic genes
BMC bioinformatics
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6,007
BioMed Central BioMed Central PhyloPat: phylogenetic pattern analysis of eukaryotic genes Tim Hulsen*1, Jacob de Vlieg1,2 and Peter MA Groenen2 Address: 1Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen, Nijmegen, The Netherlands and 2Molecular Design and Informatics, NV Organon, Oss, The Netherlands Email: Tim Hulsen* - T.Hulsen@cmbi.ru.nl; Jacob de Vlieg - J.deVlieg@cmbi.ru.nl; Peter MA Groenen - peter.groenen@organon.com * Corresponding author Received: 08 June 2006 Accepted: 01 September 2006 Received: 08 June 2006 Accepted: 01 September 2006 Received: 08 June 2006 Accepted: 01 September 2006 BMC Bioinformatics 2006, 7:398 doi:10.1186/1471-2105-7-398 This article is available from: http://www.biomedcentral.com/1471-2105/7/398 © 2006 Hulsen et al; licensee BioMed Central Ltd. © 2006 Hulsen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Phylogenetic patterns show the presence or absence of certain genes or proteins in a set of species. They can also be used to determine sets of genes or proteins that occur only in certain evolutionary branches. Phylogenetic patterns analysis has routinely been applied to protein databases such as COG and OrthoMCL, but not upon gene databases. Here we present a tool named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns. Description: PhyloPat is an easy-to-use webserver, which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. We found in total 446,825 genes and 3,164,088 orthologous relationships within the EnsMart v40 database. We used a single linkage clustering algorithm to create 147,922 phylogenetic lineages, using every one of the orthologies provided by Ensembl. PhyloPat provides the possibility of querying with either binary phylogenetic patterns (created by checkboxes) or regular expressions. Specific branches of a phylogenetic tree of the 21 included species can be selected to create a branch-specific phylogenetic pattern. Users can also input a list of Ensembl or EMBL IDs to check which phylogenetic lineage any gene belongs to. The output can be saved in HTML, Excel or plain text format for further analysis. A link to the FatiGO web interface has been incorporated in the HTML output, creating easy access to functional information. Finally, lists of omnipresent, polypresent and oligopresent genes have been included. Conclusion: PhyloPat is the first tool to combine complete genome information with phylogenetic pattern querying. Since we used the orthologies generated by the accurate pipeline of Ensembl, the obtained phylogenetic lineages are reliable. The completeness and reliability of these phylogenetic lineages will further increase with the addition of newly found orthologous relationships within each new Ensembl release. BMC Bioinformatics Open Access http://www.biomedcentral.com/1471-2105/7/398 http://www.biomedcentral.com/1471-2105/7/398 BMC Bioinformatics 2006, 7:398 http://www.biomedcentral.com/1471-2105/7/398 (COG) [1] which included a Phylogenetic Patterns Search (PPS) on its web interface. This phylogenetic pattern tool was further enhanced with the Extended Phylogenetic Pat- terns Search (EPPS) [2] tool, providing the possibility of querying the phylogenetic patterns of the COG protein database using regular expressions. The newest release of the OrthoMCL database, OrthoMCL-DB [3], also offers this possibility. However, suchs tool have only been avail- able for querying proteins, and not for genes. The advan- tage of looking at gene families instead of protein families, is that the view on expansions and deletions is not distorted by any alternative transcripts and splice forms. The PhIGs [4], Hogenom [5] and TreeFam [6] data- bases all offer phylogenetic clustering of genes, but do not have the functionality of phylogenetic patterns. Here we introduce a web tool named PhyloPat that creates the pos- sibility of querying all complete genomes of the highly reliable Ensembl [7] database using any phylogenetic pat- tern. This process was repeated for all genes in all 21 species that were not yet connected to any phylogenetic lineage yet. The complete phylogenetic lineage determination generated 147,922 lineages. Please note that the phyloge- netic order that we have determined here does not affect the construction of the phylogenetic lineages in any way: changing the order only influences the numbering of the phylogenetic lineages but not the contents of the lineages. This is due to our clustering method, in which each orthologous relationship is treated symmetrically. Figure 2 shows the database scheme: the phylogenetic lineages and some extra information have been stored in four tables, optimized for fast querying. Construction & content We generated a set of phylogenetic lineages containing all of the genes in Ensembl [7] that have orthologs in other species according to the EnsMart [8] database. This set covers all of the 21 (eukaryotic) species available in Ens- Mart version 40 (pre-versions and low coverage genomes not taken into account). We collected the complete set of orthologies between these species: 420 species pairs, 446,825 genes and 3,164,088 orthologous relationships. These orthologies consist of 2,000,706 one-to-one, 795,723 one-to-many and 367,659 many-to-many rela- tionships, created by the very extensive orthology predic- tion pipeline [9] from Ensembl. This pipeline starts with the collection of a number of Best Reciprocal Hits (BRH, proven to be accurate [10]) and Best Score Ratio (BSR) val- ues from a WUBlastp/Smith-Waterman whole-genome comparison. These are used to create a graph of gene rela- tions, followed by a clustering step. These clusters are then applied to build a multiple alignment using MUSCLE [11] and a phylogenetic tree using PHYML [12]. Finally, the gene tree is reconciled with the species tree using RAP [5]. From each reconciled gene tree, the above mentioned orthologous relationships are inferred. After the collection of all orthologous pairs, we generated phylogenetic line- ages using a single linkage algorithm. First, we determined the evolutionary order of the studied species using the NCBI Taxonomy [13] database. The phylogenetic tree of these species, together with some phylogenetic branch names, can be seen in Figure 1. Second, we used this phy- logenetic tree as a starting point for building our phyloge- netic lineages. For each gene in the first species (S. cerevisiae), we looked for orthologs in the other 20 species. All orthologs were added to the phylogenetic lineage, and in the next round were checked for orthologs themselves, until no more orthologies were found for any of the genes. Utility & discussion Utility We developed an intuitive web interface (Figure 3) named PhyloPat to query a MySQL database containing these phylogenetic lineages and derived phylogenetic patterns. As input a phylogenetic pattern is used, generated by click- ing a set of radio buttons or by typing a regular expression, or a list of Ensembl or EMBL identifiers. The application of MySQL regular expressions provides enhanced query- ing. The output can be given in HTML, Excel or plain text format. A link to the FatiGO web interface has been incor- porated in the HTML output, creating easy access to func- tional information. Each phylogenetic lineage can be viewed separately by clicking the PhyloPat ID (PPID). This view gives all Ensembl IDs within the phylogenetic lineage plus the HUGO [14] gene names. The web inter- face also provides some example queries, the 100 most occurring patterns, and numerical overviews of lineages that are present in 1) all species 2) almost all species and 3) only one or two species. Finally, a phylogenetic tree of all included species is provided, through which each branch can be selected to view a list of branch-specific genes. This tree can be downloaded in PHYLIP [15] for- mat. Page 2 of 8 (page number not for citation purposes) Background occur only in certain evolutionary branches. The use of phylogenetic patterns has been common practice as increasing amounts of orthology data have become avail- able. One example is Clusters of Orthologous Groups g Phylogenetic patterns show the presence or absence of cer- tain genes or proteins in a set of species. These patterns can be used to determine sets of genes or proteins that Page 1 of 8 (page number not for citation purposes) Page 1 of 8 (page number not for citation purposes) http://www.biomedcentral.com/1471-2105/7/398 Polypresent genes A second measure for evolutionary relatedness is the dis- tribution of 'polypresent' genes: genes that are missing in only one or two species. S. cerevisiae has the highest number of missing polypresent genes: 961 polypresent genes do not occur in S. cerevisiae only, and 854 polypre- sent genes are not present in S. cerevisiae and a second spe- cies. Other high-scoring pairs include both Ciona species (47 absent polypresent genes) and the combination of one of these Ciona species with G. gallus (16 and 14 absent polypresent genes). The relatively high number for the lat- ter pair is striking, because these species are not closely related. One would suspect such a high number only for two species that are relatively closely related, which is the case for the two Ciona species. Phylogenetic tree of all species present in PhyloPat Figure 1 Phylogenetic tree of all species present in PhyloPat. This is the unrooted NCBI Taxonomy tree of all species available in Ensembl and PhyloPat. The numbers are the order in which the species are shown on the PhyloPat results pages. A phylogram version of this tree is available through the website. Phylogenetic tree of all species present in PhyloPat Figure 1 Phylogenetic tree of all species present in PhyloPat. This is the unrooted NCBI Taxonomy tree of all species available in Ensembl and PhyloPat. The numbers are the order in which the species are shown on the PhyloPat results pages. A phylogram version of this tree is available through the website. http://www.biomedcentral.com/1471-2105/7/398 http://www.biomedcentral.com/1471-2105/7/398 http://www.biomedcentral.com/1471-2105/7/398 http://www.biomedcentral.com/1471-2105/7/398 BMC Bioinformatics 2006, 7:398 Phylogenetic tree of all species present in PhyloPat Figure 1 Phylogenetic tree of all species present in PhyloPat. This is the unrooted NCBI Taxonomy tree of all species available in Ensembl and PhyloPat. The numbers are the order in which the species are shown on the PhyloPat results pages. A phylogram version of this tree is available through the website. nigroviridis and T. rubripes (1572 oligopresent genes) and A. gambiae and A. Aegypti (1058 oligopresent genes). These results correspond perfectly with the current opin- ion on evolutionary relationships. It should also be noted that the number of genes present in only one species is this high because of the incomplete orthology informa- tion contained in the EnsMart database. This will improve with each new Ensembl release, as orthology information and functional annotation are expanded in each release. Case study: Hox genes sapiens misses the genes HOXA8, HOXB10, HOXB11, Striking observations can be made with the fish species: all three species have significantly more Hox genes than the mammals. T. nigroviridis, for example, has 57 genes in this lineage, while M. domestica has only 35. These num- bers correspond well with the fact that Teleost fish have at least seven Hox clusters, whereas mammals have only four [21]. Mammals also have less Hox genes per cluster, demonstrating that there has been gene loss within the Hox clusters since the evolution from a vertebrate ances- tor to present-day mammals [22]. Table 2 shows the fur- ther analysis of the Hox genes using the PhyloPat output. H. sapiens misses the genes HOXA8, HOXB10, HOXB11, Case study: Hox genes As a case study we used the highly researched and from an evolutionary point-of-view very interesting Hox genes. First, we searched the Ensembl database for human genes with the term 'hox' in the annotation. We found 44 genes, which were entered into PhyloPat. The output is shown in Table 1. The lists of Ensembl IDs have been replaced by the number of IDs. 32 phylogenetic lineages were found, one of which were already present in C. elegans: PP022041. This lineage contains the Msh homeobox-like proteins. PP024984 and PP027791, containing the HOXC4 and TLX lineages, are only found in the Coelo- mata: A. gambiae and further. No less than 22 lineages originated in the early vertebrates, presented by T. nigro- viridis. HOXD12 and HOXB13 are only present in mam- mals. the 6th level GO biological process annotation (Figure 4a) that omnipresent genes are less often involved in tran- scription compared to a human gene chosen at random, but more often in cellular protein metabolism and estab- lishment of cellular localization. We suggest that the proc- ess of transcription does not need that many genes in the 'lower' species, but in the 'higher' species, like human, many transcription related gene families have expanded ([18], table 1). Analysis of the 6th level GO molecular functions (Figure 4b) shows that many omnipresent genes have ATP binding or pyrophosphatase activity, while the human gene set consists for almost 10% of genes with rhodopsin-like receptor activity. The latter is due to the fact that the GPCR class A family has expanded greatly in mammals ([19], table 2). Finally, the 6th level GO cellular components (Figure 4c) show that a lesser fraction of the omnipresent genes are integral to the plasma membrane. Striking observations can be made with the fish species: all three species have significantly more Hox genes than the mammals. T. nigroviridis, for example, has 57 genes in this lineage, while M. domestica has only 35. These num- bers correspond well with the fact that Teleost fish have at least seven Hox clusters, whereas mammals have only four [21]. Mammals also have less Hox genes per cluster, demonstrating that there has been gene loss within the Hox clusters since the evolution from a vertebrate ances- tor to present-day mammals [22]. Table 2 shows the fur- ther analysis of the Hox genes using the PhyloPat output. H. Omnipresent genes A l i f ll li An analysis of all lineages with the phylogenetic pattern '111111111111111111111' (or MySQL regular expres- sion '^1+$') gives a list of 'omnipresent' genes, i.e. present in all 21 species. We found 1001 omnipresent genes, which are most likely involved in important functions, since they are present in all species. Figure 4 shows the GO annotation [16] for all 2185 human genes within these omnipresent phylogenetic lineages, generated by FatiGO [17]. When human genes are present in the output, FatiGO can be queried by clicking a button below the out- put. To compare the results, we also show the GO annota- tion for the complete set of human genes (31,718 in Ensembl v40). Lines are drawn between similar GO clas- sifications, to facilitate easy comparison between the omnipresent genes and all human genes. It is clear from Page 2 of 8 (page number not for citation purposes) Page 2 of 8 (page number not for citation purposes) Oligopresent genes The distribution of 'oligopresent' genes (genes that exist in only one/two species) can be used to determine which species are evolutionary most related, as the number of shared genes, that are absent in other species, can be used as a measure for the phylogenetic distance [20]. It is apparent that are the closest relatives are C. savignyi and C. intestinalis (1737 oligopresent genes), followed by T. Page 3 of 8 (page number not for citation purposes) Page 3 of 8 (page number not for citation purposes) http://www.biomedcentral.com/1471-2105/7/398 BMC Bioinformatics 2006, 7:398 The PhyloPat database scheme Figure 2 The PhyloPat database scheme. The database scheme shows all four tables used in the application. Table names are in bold, primary keys are in italic. Links between fields are shown with arrows. The left side of each column shows the field names, the right side shows the field types. The Phylo Figure 2 The PhyloPat database scheme Figure 2 The PhyloPat database scheme. The database scheme shows all four tables used in the application. Table names are in bold, primary keys are in italic. Links between fields are shown with arrows. The left side of each column shows the field names, the right side shows the field types. bold, primary keys are in italic. Links between fields are shown names, the right side shows the field types. The PhyloPat web interface (Pattern Search tab) Figure 3 The PhyloPat web interface (Pattern Search tab). The web interface has the menu on the left and the input/ results page on the right. On the pattern search page, the user can generate a phylogenetic pattern by clicking a radio button for each species. 1 = present, * = present/absent, 0 = absent. The buttons directly below put all 21 species on the corresponding mode. MySQL regular expressions offer the possibility of advanced querying. The user can choose to show any number of lineages and choose the output format: HTML, Excel or plain text. HOXC1, HOXC2, HOXC3, HOXC7, HOXD2, HOXD5, HOXD6 and HOXD7. The absence of these 11 genes is in agreement with current knowledge of human Hox genes (figure 3A of [22]). Two exceptions exist: HOXC8 instead of HOXC7, and the absence of HOXA12. The HOXA12 gene cannot be found in the other mammals either. Page 4 of 8 (page number not for citation purposes) Functional annotation PhyloPat can be used for annotation of genes with unknown functions. When a gene with unknown func- tion is clustered in a certain phylogenetic lineage, the function of other genes in that lineage can be assigned to the gene with unknown function. For example, the PP001723 lineage [23] contains a number of genes that have an unknown function, under which the ENSANGG00000008970 gene from A. gambiae and the ENSCING00000000880 gene from C. intestinalis. By using the orthology information provided by Ensembl and the PhyloPat clustering into one lineage, we can see that all of these genes are connected to the human gene KLHDC4. This function can now be assigned to the genes with unknown function. The Phylo Figure 3 The Phylo Figure 3 y ( ) g The PhyloPat web interface (Pattern Search tab). The web interface has the menu on the left and the input/ results page on the right. On the pattern search page, the user can generate a phylogenetic pattern by clicking a radio button for each species. 1 = present, * = present/absent, 0 = absent. The buttons directly below put all 21 species on the corresponding mode. MySQL regular expressions offer the possibility of advanced querying. The user can choose to show any number of lineages and choose the output format: HTML, Excel or plain text. y ( ) g The PhyloPat web interface (Pattern Search tab). The web interface has the menu on the left and the input/ results page on the right. On the pattern search page, the user can generate a phylogenetic pattern by clicking a radio button for each species. 1 = present, * = present/absent, 0 = absent. The buttons directly below put all 21 species on the corresponding mode. MySQL regular expressions offer the possibility of advanced querying. The user can choose to show any number of lineages and choose the output format: HTML, Excel or plain text. Page 4 of 8 (page number not for citation purposes) BMC Bioinformatics 2006, 7:398 http://www.biomedcentral.com/1471-2105/7/398 Gene Ontology annotations of 1) omnipresent and 2) all human genes Figure 4 Gene Ontology annotations of 1) omnipresent and 2) all human genes. The left side shows the Gene Ontology anno- tations for all 2,185 human genes in omnipresent lineages. The right side shows the Gene Ontology annotations for all 31,718 human genes, used as a reference set. Lines are placed between equal annotations for easy comparisons between the left and the right side. a.) 6th level GO Biological Processes. b.) 6th level GO Molecular Functions. c.) 6th level GO Cellular Compo- nents. Gene Onto Figure 4 Gene Ontology annotations of 1) omnipresent and 2) all human genes Figure 4 Gene Ontology annotations of 1) omnipresent and 2) all human genes. The left side shows the Gene Ontology anno- tations for all 2,185 human genes in omnipresent lineages. The right side shows the Gene Ontology annotations for all 31,718 human genes, used as a reference set. Lines are placed between equal annotations for easy comparisons between the left and the right side. a.) 6th level GO Biological Processes. b.) 6th level GO Molecular Functions. The Phylo Figure 3 c.) 6th level GO Cellular Compo- nents. Fam or Hogenom. Furthermore, we aim to provide an easy-to-use web interface in which the Ensembl database can be queried using phylogenetic patterns. In just one second, users can see which gene families are present in a certain species set but missing in another species set. The output of our application can be easily analyzed by the FatiGO tool, like we demonstrated in figure 4. Finally, PhyloPat has the advantage of only relying on the Ensembl database. Treefam and Hogenom use a wide range of gene and protein databases, each with their own standards and methodologies. By using only the Ensembl database (considered by many to be the standard genome database) as input, we create a non-redundant database, through which it is possible to easily study lineage-specific expansions of gene families. Discussion The above examples show that PhyloPat is useful in evo- lutionary studies and gene annotation. It continues on the concept of phylogenetic pattern tools like EPPS [2], and on gene databases like TreeFam [6] and Homogen [5]. The originality of PhyloPat lies in the combination of these two aspects: phylogenetic pattern querying and gene fam- ily databases. In PhyloPat it is possible to determine a spe- cies set that should be included (1), a species set that should be excluded (0) and a species set which presence is indifferent (*). This, and the use of regular expression queries, enables quite complicate phylogenetic patterns searches and clustering. For example, with PhyloPat it is quite easy to find two sets of genes that have completely anti-correlating patterns (like Conclusion '110000011100111111111'). Some of these genes from the different sets might turn out to be analogous, i.e. per- forming the same function but having different ancestor genes. Acknowledgements This work was supported financially by NV Organon. The authors like to thank Erik Franck, Nanning de Jong and Arnold Kuzniar for their sugges- tions. We thank Greer Wilson for critically reading this manuscript. Conclusion Such kind of analysis is very hard to do with Tree- The analyses of the oligopresent, polypresent and omni- present genes, as well as the small case study of the Hox genes, are just a few examples of what can be done with Page 5 of 8 (page number not for citation purposes) Page 5 of 8 (page number not for citation purposes) 7/398 Table 1: Phylogenetic lineages containing human Hox cluster genes MC Bioinformatics 2006, 7:398 http://www.biomedcentral.com/1471-2105/7 ppid sc ce ag aa dm cs ci tn tr ga dr xt gg md bt cf rn mm mm pt hs pattern gene PP022041 0 1 1 1 1 1 1 3 6 5 6 2 2 3 3 2 3 3 2 2 2 011111111111111111111 MSX1, 2 PP024984 0 0 1 0 0 0 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 001000011111001111111 C4 PP027791 0 0 1 1 1 0 0 2 3 3 4 3 2 3 3 3 3 3 3 3 3 001110011111111111111 TLX1, 2, 3 PP049478 0 0 0 0 0 0 2 2 1 1 5 3 1 1 2 3 2 2 2 2 3 000000111111111111111 B8, C8, D8 PP053824 0 0 0 0 0 0 0 1 1 1 2 0 0 1 0 1 0 1 0 1 1 000000011110010101011 D11 PP053827 0 0 0 0 0 0 0 2 2 2 1 1 1 1 1 1 1 1 1 1 1 000000011111111111111 A10 PP053828 0 0 0 0 0 0 0 2 1 1 1 1 2 1 2 1 2 2 2 2 2 000000011111111111111 C13, D13 PP053829 0 0 0 0 0 0 0 6 3 3 4 1 1 2 2 2 2 2 2 2 2 000000011111111111111 A1, B1 PP053830 0 0 0 0 0 0 0 1 1 1 1 0 0 1 0 1 1 1 1 1 1 000000011110010111111 B4 PP053832 0 0 0 0 0 0 0 2 1 1 1 1 0 1 1 1 1 1 1 1 1 000000011111011111111 A5 PP053833 0 0 0 0 0 0 0 2 1 1 1 0 1 1 1 1 1 1 0 1 1 000000011110111111011 B2 PP053834 0 0 0 0 0 0 0 3 1 1 0 1 0 1 1 1 1 1 1 1 1 000000011101011111111 D3 PP053835 0 0 0 0 0 0 0 2 1 1 1 0 1 1 1 1 1 1 1 0 1 000000011110111111101 A9 PP053836 0 0 0 0 0 0 0 2 1 1 1 1 1 1 1 1 1 1 1 1 1 000000011111111111111 A3 PP053838 0 0 0 0 0 0 0 2 1 1 1 0 1 0 1 1 1 1 1 1 1 000000011110101111111 C12 PP053839 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 000000011111111110111 D4 PP053840 0 0 0 0 0 0 0 2 1 1 1 1 2 0 1 0 1 1 1 0 1 000000011111101011101 C11 PP053842 0 0 0 0 0 0 0 4 3 2 2 1 1 1 1 1 1 1 1 1 1 000000011111111111111 A13 PP053844 0 0 0 0 0 0 0 3 2 2 3 1 0 1 1 1 1 1 1 1 1 000000011111011111111 B5 PP053845 0 0 0 0 0 0 0 2 1 1 1 1 1 1 1 1 1 1 0 1 1 000000011111111111011 B3 PP053846 0 0 0 0 0 0 0 2 1 1 2 1 1 1 1 1 1 1 1 1 1 000000011111111111111 D10 PP053847 0 0 0 0 0 0 0 2 2 2 1 1 1 1 1 1 1 1 1 1 1 000000011111111111111 A2 PP053849 0 0 0 0 0 0 0 3 4 1 5 1 1 3 2 3 3 3 3 2 3 000000011111111111111 A6, B6, C6 PP053853 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 1 1 1 0 1 1 000000011101111111011 A4 PP053854 0 0 0 0 0 0 0 3 2 2 5 2 2 2 3 1 3 3 2 1 3 000000011111111111111 B9, C9, D9 PP053858 0 0 0 0 0 0 0 1 1 1 2 0 0 1 1 1 1 1 1 1 1 000000011110011111111 A11 PP070659 0 0 0 0 0 0 0 0 0 1 2 1 2 1 2 2 2 2 2 2 2 000000000111111111111 A7, B7 PP075622 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 1 1 1 1 000000000010001111111 C5 PP084287 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 1 1 1 1 1 000000000001101111111 C10 PP085049 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 1 1 1 1 1 000000000001011011111 D1 PP087941 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 1 000000000000111011111 D12 PP089685 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 000000000000111111111 B13 http://www.biomedcentral.com/1471-2105/7/398 BMC Bioinformatics 2006, 7:398 Table 2: Analysis of phylogenetic lineages containing human Hox cluster genes ppid(s) name cluster A cluster B cluster C cluster D first sp. Abbreviations Abbreviations BRH Best Reciprocal Hit BSR Best Score Ratio COG Clusters of Orthologous Groups EMBL European Molecular Biology Laboratory EPPS Extended Phylogenetic Patterns Search GO Gene Ontology HUGO HUman Genome Organisation MCL Markov Cluster Algorithm MUSCLE MUltiple Sequence Comparison by Log-Expec- tation MySQL My Structured Query Language Conclusion position PP053829, PP085049 HOX1 HOXA1 HOXB1 HOXD1 T. nigrov. anterior PP053847, PP053833 HOX2 HOXA2 HOXB2 T. nigrov. anterior PP053836, PP053845, PP053834 HOX3 HOXA3 HOXB3 HOXD3 T. nigrov. PG3 PP053853, PP053830, PP024984, PP053839 HOX4 HOXA4 HOXB4 HOXC4 HOXD4 A. gamb. central PP053832, PP053844, PP075622 HOX5 HOXA5 HOXB5 HOXC5 T. nigrov. central PP053849 HOX6 HOXA6 HOXB6 HOXC6 T. nigrov. central PP070659 HOX7 HOXA7 HOXB7 G. acul. central PP049478 HOX8 HOXB8 HOXC8 HOXD8 C. intest. central PP053835, PP053854 HOX9 HOXA9 HOXB9 HOXC9 HOXD9 T. nigrov. posterior PP053827, PP084287, PP053846 HOX10 HOXA10 HOXC10 HOXD10 T. nigrov. posterior PP053858, PP053840, PP053824 HOX11 HOXA11 HOXC11 HOXD11 T. nigrov. posterior PP053838, PP087941 HOX12 HOXC12 HOXD12 T. nigrov. posterior PP053842, PP089685, PP053828 HOX13 HOXA13 HOXB13 HOXC13 HOXD13 T. nigrov. posterior PP027791 TLX TLX1 TLX2 TLX3 A. gamb. PP022041 MSX MSX1 MSX2 C. eleg. Table 2: Analysis of phylogenetic lineages containing human Hox cluster genes phylogenetic patterns in general and PhyloPat in particu- lar. Using this tool, it is easy to find genes that e.g. occur for the first time in vertebrates, occur only in a specific number of species, or are unique for a certain species. It will be of help in the annotation of genes with unknown functions. By comparing the genes in lineages with anti- correlating patterns, it will also help finding analogous genes. PhyloPat will be completely recalculated with each major Ensembl release to ensure up-to-date and reliable phylogenetic lineages. Authors contributions TH carried out the construction of the phylogenetic line- ages, designed the database structure, built the website, and drafted the manuscript Availability & requirements PhyloPat is freely available at http://www.cmbi.ru.nl/phy lopat/. JdV participated in the design of the study PG participated in the design and coordination of the study and helped to draft the manuscript Abbreviations BRH Best Reciprocal Hit BSR Best Score Ratio COG Clusters of Orthologous Groups EMBL European Molecular Biology Laboratory EPPS Extended Phylogenetic Patterns Search GO Gene Ontology HUGO HUman Genome Organisation MCL Markov Cluster Algorithm MUSCLE MUltiple Sequence Comparison by Log-Expec- tation MySQL My Structured Query Language References 1. Natale DA, Galperin MY, Tatusov RL, Koonin EV: Using the COG database to improve gene recognition in complete genomes. Genetica 2000, 108(1):9-17. 1. Natale DA, Galperin MY, Tatusov RL, Koonin EV: Using the COG database to improve gene recognition in complete genomes. Genetica 2000, 108(1):9-17. ( ) 2. Reichard K, Kaufmann M: EPPS: mining the COG database by an extended phylogenetic patterns search. Bioinformatics 2003, 19(6):784-785. ( ) 3. 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Li H, Coghlan A, Ruan J, Coin LJ, Heriche JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin Page 7 of 8 (page number not for citation purposes) Page 7 of 8 (page number not for citation purposes) http://www.biomedcentral.com/1471-2105/7/398 http://www.biomedcentral.com/1471-2105/7/398 http://www.biomedcentral.com/1471-2105/7/398 BMC Bioinformatics 2006, 7:398 R: TreeFam: a curated database of phylogenetic trees of ani- mal gene families. Nucleic Acids Res 2006, 34(Database issue):D572-80. ) 7. 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PHYLIP (Phylogeny Inference Package) [http://evolu tion.genetics.washington.edu/phylip.html] 16. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel- Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. ( ) 17. Al-Shahrour F, Diaz-Uriarte R, Dopazo J: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 2004, 20(4):578-580. 18. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hor- nischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31(1):374-378. ( ) 19. 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Sir Paul Nurse, Cancer Research UK Your research papers will be: available free of charge to the entire biomedical community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours — you keep the copyright Submit your manuscript here: http://www.biomedcentral.com/info/publishing_adv.asp BioMedcentral Page 8 of 8 (page number not for citation purposes) Publish with BioMed Central and every scientist can read your work free of charge "BioMed Central will be the most significant development for disseminating the results of biomedical research in our lifetime." Sir Paul Nurse, Cancer Research UK Your research papers will be: available free of charge to the entire biomedical community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours — you keep the copyright Submit your manuscript here: http://www.biomedcentral.com/info/publishing_adv.asp BioMedcentral Publish with BioMed Central and every scientist can read your work free of charge ( ) 22. Minguillon C, Gardenyes J, Serra E, Castro LF, Hill-Force A, Holland PW, Amemiya CT, Garcia-Fernandez J: No more than 14: the end of the amphioxus Hox cluster. Int J Biol Sci 2005, 1(1):19-23. p J ( ) 23. PhyloPat lineage PP001723 [http://www.cmbi.ru.nl/pw/phylopat/ phylopat.php?ppid=PP001723]
https://openalex.org/W1778930322
https://publications.goettingen-research-online.de/bitstream/2/90485/1/art_10.1007_JHEP10%282014%29141.pdf
English
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Measurement of differential production cross-sections for a Z boson in association with b-jets in 7 TeV proton-proton collisions with the ATLAS detector
˜The œJournal of high energy physics/˜The œjournal of high energy physics
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cc-by
30,469
Published for SISSA by Springer Received: July 15, 2014 Accepted: September 13, 2014 Published: October 24, 2014 Received: July 15, 2014 Accepted: September 13, 2014 Published: October 24, 2014 Measurement of differential production cross-sections for a Z boson in association with b-jets in 7 TeV proton-proton collisions with the ATLAS detector JHEP10(2014)141 The ATLAS collaboration The ATLAS collaboration E-mail: atlas.publications@cern.ch E-mail: atlas.publications@cern.ch Abstract: Measurements of differential production cross-sections of a Z boson in associa- tion with b-jets in pp collisions at √s = 7 TeV are reported. The data analysed correspond to an integrated luminosity of 4.6 fb−1 recorded with the ATLAS detector at the Large Hadron Collider. Particle-level cross-sections are determined for events with a Z boson decaying into an electron or muon pair, and containing b-jets. For events with at least one b-jet, the cross-section is presented as a function of the Z boson transverse momentum and rapidity, together with the inclusive b-jet cross-section as a function of b-jet transverse mo- mentum, rapidity and angular separations between the b-jet and the Z boson. For events with at least two b-jets, the cross-section is determined as a function of the invariant mass and angular separation of the two highest transverse momentum b-jets, and as a function of the Z boson transverse momentum and rapidity. Results are compared to leading-order and next-to-leading-order perturbative QCD calculations. Keywords: Electroweak interaction, Hadron-Hadron Scattering, QCD, Heavy quark pro- duction ArXiv ePrint: 1407.3643 ArXiv ePrint: 1407.3643 doi:10.1007/JHEP10(2014)141 doi:10.1007/JHEP10(2014)141 Open Access, Copyright CERN, for the benefit of the ATLAS Collaboration. Article funded by SCOAP3. Contents 1 Introduction 1 2 The ATLAS experiment 4 3 Simulated event samples 4 4 Event selection 5 5 Background estimation and reduction 7 6 Extraction of detector-level signal yields 9 7 Correction to particle-level 11 8 Systematic uncertainties 13 9 Theoretical predictions 18 10 Results 20 11 Conclusions 22 The ATLAS collaboration 33 Contents 1 Introduction 1 2 The ATLAS experiment 4 3 Simulated event samples 4 4 Event selection 5 5 Background estimation and reduction 7 6 Extraction of detector-level signal yields 9 7 Correction to particle-level 11 8 Systematic uncertainties 13 9 Theoretical predictions 18 10 Results 20 11 Conclusions 22 The ATLAS collaboration 33 JHEP10(2014)141 The ATLAS collaboration 1 Introduction The production of a Z boson (using Z as shorthand for Z/γ∗) decaying to electrons or muons provides a clear experimental signature at a hadron collider, which can be used as a probe of the underlying collision processes. Such events provide an opportunity for the study of associated heavy flavour production and dynamics, which can be experimen- tally identified by reconstructing displaced decay vertices associated with the relatively long lifetimes of b-hadrons. Predictions for heavy flavour production typically suffer from larger theoretical uncertainties than those for the more inclusive Z+jets processes, and measurements of Z boson production in association with b-jets can therefore provide im- portant experimental constraints to improve the theoretical description of this process. The Z+b-jets signal is also an important background to ZH associated Higgs boson production with H →b¯b, as well as for potential signatures of physics beyond the Standard Model containing leptons and b-jets in the final state. Two schemes are generally employed in perturbative QCD (pQCD) calculations con- taining heavy flavour quarks. One is the four-flavour number scheme (4FNS), which only – 1 – b b Z g (a) b b Z g (a) q q b b Z (b) q Z b b q (c) Figure 1. Leading order Feynman diagrams contributing to Z+b-jets production. Process 1a is only present in a 5FNS calculation, while 1b and 1c are present in both the 4FNS and 5FNS calculations. q q b b Z (b) q Z b b q (c) (b) (c) (a) Figure 1. Leading order Feynman diagrams contributing to Z+b-jets production. Process 1a is only present in a 5FNS calculation, while 1b and 1c are present in both the 4FNS and 5FNS calculations. JHEP10(2014)141 considers parton densities of gluons and of the first two quark generations in the proton. The other is the five-flavour number scheme (5FNS), which allows a b-quark density in the initial state and raises the prospect that measurements of heavy flavour production could constrain the b-quark parton density function (PDF) of the proton. In a calculation to all orders, the 4FNS and 5FNS methods must give identical results; however, at a given order differences can occur between the two. A recent discussion on the status of theoretical calculations and the advantages and disadvantages of the different flavour number schemes can be found in ref. [1]. 1 Introduction All cross-sections include the Z boson branching fraction, – 2 – Variable Definition Range Integrated cross-section pT(Z) Z boson transverse momentum 0–500 GeV σ(Zb) |y(Z)| Z boson absolute rapidity 0.0–2.5 σ(Zb) pT(b) b-jet pT 20–500 GeV σ(Zb) × Nb-jet |y(b)| b-jet absolute rapidity 0.0–2.4 σ(Zb) × Nb-jet yboost(Z, b) |(y(Z) + y(b))|/2.0 0.0–2.5 σ(Zb) × Nb-jet ∆y(Z, b) |y(Z) −y(b)| 0.0–5.0 σ∗(Zb) × Nb-jet ∆φ(Z, b) |φ(Z) −φ(b)| 0.0–π σ∗(Zb) × Nb-jet ∆R(Z, b) p ∆φ(Z, b)2 + ∆y(Z, b)2 0.0–6.0 σ∗(Zb) × Nb-jet pT(Z) Z boson transverse momentum 0–250 GeV σ(Zbb) |y(Z)| Z boson absolute rapidity 0.0–2.5 σ(Zbb) m(b, b) bb invariant mass 20–350 GeV σ(Zbb) ∆R(b, b) bb angular separation 0.4–5.0 σ(Zbb) Table 1. Definitions of variables for which differential production cross-sections are measured and the ranges over which those measurements are performed. The integral of each differential cross-section yields one of the four integrated cross-sections defined in the text. JHEP10(2014)141 Table 1. Definitions of variables for which differential production cross-sections are measured and the ranges over which those measurements are performed. The integral of each differential cross-section yields one of the four integrated cross-sections defined in the text. Table 1. Definitions of variables for which differential production cross-sections are measured and the ranges over which those measurements are performed. The integral of each differential cross-section yields one of the four integrated cross-sections defined in the text. Br(Z →ℓ+ℓ−), where ℓis a single lepton flavour, and are reported in a restricted fiducial region, defined using particle-level quantities, detailed in section 7, which are chosen to minimise extrapolation from the corresponding measured detector-level quantities. Br(Z →ℓ+ℓ−), where ℓis a single lepton flavour, and are reported in a restricted fiducial region, defined using particle-level quantities, detailed in section 7, which are chosen to minimise extrapolation from the corresponding measured detector-level quantities. 1 Introduction Next-to-leading-order (NLO) matrix element calculations have been available for as- sociated Z+b and Z+b¯b production at parton-level for a number of years [2–4]. The leading order (LO) Feynman diagrams shown in figure 1 illustrate some of the contributing processes. Full particle-level predictions have existed at LO for some time, obtained by matching parton shower generators to LO multi-leg matrix elements in the 4FNS [5, 6], 5FNS [7], or both [8]. More recently, a full particle-level prediction for Z+ ≥2 b-jets at NLO in the 4FNS with matched parton shower has become available [9, 10]. The same framework can also be used to provide a full particle-level prediction for Z+ ≥1 b-jet at NLO in the 5FNS. In this article data are compared with several theoretical predictions following different approaches. Differential measurements of Z+b-jets production have been made in proton-antiproton collisions at √s = 1.96 TeV by the CDF and D0 experiments [11, 12] as well as inclusively in √s = 7 TeV proton-proton collisions at the LHC by the ATLAS and CMS experiments [13, 14]. The results presented in this paper significantly extend the scope of the previous ATLAS measurement, which used around 36 pb−1of data recorded in 2010. The current analysis takes advantage of the full sample of √s = 7 TeV proton-proton collisions recorded in 2011, corresponding to an integrated luminosity of 4.6 fb−1, and uses improved methods for b-jet identification to cover a wider kinematic region. The larger data sample allows differential production cross-section measurements of a Z boson with b-jets at the LHC. These complement the recently reported results of associated production of a Z boson with two b-hadrons at √s = 7 TeV by CMS [15]. A total of 12 differential cross-sections are presented here, covering a variety of Z boson and b-jet kinematics and angular variables sensitive to different aspects of the theoretical predictions, as listed in table 1. 1ATLAS uses a right-handed coordinate system, with the origin at the nominal interaction point, with the beam line defining the z axis, the x-axis pointing towards the centre of the LHC ring, and the y-axis vertically up. The azimuthal angle, φ, is defined in the transverse (x−y) plane, and the pseudo-rapidity is used instead of the polar angle: η = −ln tan(θ/2). Rapidity is defined in the usual way, y = ln[(E + pz)/(E −pz)]/2. 2Two measures of angular separation are used: ∆R = p ∆φ2 + ∆η2, and ∆R = p ∆φ2 + ∆y2. 1 Introduction The results are grouped according to different selections which give four integrated cross-section definitions: The results are grouped according to different selections which give four integrated cross-section definitions: • σ(Zb), the cross-section for events containing a Z boson and one or more b-jets in the fiducial region; • σ(Zb)×Nb-jet , the inclusive cross-section for all b-jets in the fiducial region in events with a Z boson; • σ∗(Zb) × Nb-jet, similar to σ(Zb) × Nb-jet , with the additional requirement that the dilepton system has transverse momentum, pT > 20 GeV, ensuring the φ(Z) coordi- nate1 (which is taken from the direction of the dilepton system) is well defined and not limited by detector resolution. This is necessary for the differential measurements of ∆φ(Z, b) and hence ∆R(Z, b).2 • σ(Zbb), the cross-section for events containing a Z boson and two or more b-jets in the fiducial region. When there are more than two b-jets, quantities are calculated using the two highest pT b-jets in the event. • σ(Zbb), the cross-section for events containing a Z boson and two or more b-jets in the fiducial region. When there are more than two b-jets, quantities are calculated using the two highest pT b-jets in the event. – 3 – This paper will cover the experimental apparatus, simulation and event selection in sections 2, 3 and 4, followed by the description of the methods used to determine back- grounds and extract the signal in sections 5 and 6. Conversion of the measured data to differential cross-sections and the details of the systematic uncertainties are covered in sec- tions 7 and 8. A number of theoretical predictions, detailed in section 9, are compared to the data in section 10, before conclusions are drawn in section 11. 2 The ATLAS experiment The ATLAS experiment [16] is a multi-purpose particle detector with large solid angle coverage around one of the interaction regions of the LHC. It consists of an inner track- ing detector surrounded by a superconducting solenoid providing a 2 T axial magnetic field, followed by electromagnetic and hadronic calorimeters and a muon spectrometer with three superconducting toroid magnets. The inner detector (ID) is made up of a high-granularity silicon pixel detector, a silicon microstrip tracker, and a straw-tube tran- sition radiation tracker. These provide measurements of charged particles in the region |η| < 2.5. The calorimeter system covers |η| < 4.9 and utilises a variety of absorbing and sampling technologies. For |η| < 3.2, the electromagnetic (EM) calorimeters are based on high-granularity lead/liquid-argon (LAr), while the 3.1 < |η| < 4.9 forward region uses copper/LAr. Hadronic calorimetery is based on steel and scintillating tiles for |η| < 1.7, copper/LAr for 1.5 < |η| < 3.2, and tungsten/LAr for 3.1 < |η| < 4.9. The muon spec- trometer (MS) comprises resistive plate and thin gap trigger chambers covering |η| < 2.4, and high-precision drift tubes and cathode strip tracking chambers, covering |η| < 2.7. ATLAS uses a three-level trigger system to select potentially interesting collisions. The Level-1 trigger is hardware based, and uses a subset of detector information to reduce the event rate to at most 75 kHz. Two software-based trigger levels follow, which reduce the event rate to about 300 Hz, for offline analysis. JHEP10(2014)141 3 Simulated event samples The Monte Carlo (MC) simulations of proton-proton collisions and the expected response of the ATLAS detector to simulated particles are used in three ways in this analysis: first, to estimate signal and background contributions to the selected data sample; second, to determine correction factors for detector effects and acceptance when calculating particle- level cross-sections; and finally to estimate systematic uncertainties. Inclusive Z(→ℓℓ) events, produced in associations with both light and heavy flavour jets, are simulated using Alpgen 2.13 [5] interfaced to Herwig 6.520 [17] to model the parton shower and hadronisation, and Jimmy 4.31 [18] to model the underlying event and multi-parton interactions (MPI). Alpgen produces matrix elements with up to five partons using a LO multi-legged approach; these are matched to final state jets using the MLM method [19] to remove overlaps in phase-space between events containing jets produced in the matrix element and jets produced in the parton shower. Samples are generated with the CTEQ6L1 [20] PDF set and the AUET2 tuning of parameters [21] for the description of the – 4 – non-perturbative component of the generated events. In addition, overlaps between samples with heavy-flavour quarks originating from the matrix element and from the parton shower are removed. Events containing b-quarks are reweighted after hadronisation to reproduce b-hadron decay particle multiplicities predicted by the EvtGen package [22], to correct mismodelling found in the decay tables of the Herwig generator version used. Alternative Z(→ℓℓ) samples used for systematic cross-checks are generated with Sherpa 1.4.1 [7]. This generator is based on a multi-leg matrix element calculation using the CT10 [23] PDF set and matched to the parton shower using the CKKW prescription [24]. Backgrounds from t¯t, single top quark production in the s-channel, W + t production, and diboson processes are simulated using mc@nlo 4.01 [25] interfaced to Herwig and Jimmy using the CT10 PDF set. Single top quark production in the t-channel is gener- ated with AcerMC 3.7 [6] interfaced to Pythia 6.425 [26] using the CTEQ6L1 PDF set. Corrections to Herwig b-hadron decay tables using EvtGen are made for both t¯t and ZZ(→b¯bℓℓ) events which are the dominant backgrounds containing real b-jets. Samples of W(→ℓν) events are generated using Alpgen interfaced to Herwig and Jimmy in an identical configuration to that used for Z(→ℓℓ)+jets events described above. 3 Simulated event samples An alterna- tive t¯t sample used for systematic cross-checks is generated with Powheg [27] interfaced to Pythia using the CT10 PDF set. JHEP10(2014)141 The total cross-sections of the W, Z and t¯t simulated samples are normalised to NNLO predictions [28, 29], while other backgrounds are normalised to NLO predictions [30, 31]. All samples are overlaid with minimum bias interactions, generated with Pythia 6.425 using the CTEQ6L1 PDF set and AMBT2b tune [32], to simulate multiple interactions per bunch crossing (pile-up) such that the distribution of the average number of interac- tions observed in 2011 pp collision data, with mean value of 9.1, is accurately reproduced. Furthermore, the samples are weighted such that the z distribution of reconstructed pp interaction vertices matches the distribution observed in data. The ATLAS detector re- sponse is modelled using the Geant4 toolkit [33, 34], and event reconstruction similar to that used for data is performed. 4 Event selection The data analysed were collected by the ATLAS detector in 2011 during stable pp collisions at √s = 7 TeV when all components of the ATLAS detector were fully functioning. Dielectron candidate events were selected with a trigger requiring two electrons with pT > 12 GeV. Dimuon candidate events were selected with a trigger requiring a single muon with pT > 18 GeV. An integrated luminosity of 4.58±0.08 fb−1 [35] was taken with these triggers. The primary interaction vertex (PV) is defined as the vertex with highest P p2 T of ID tracks with pT > 0.4 GeV associated to it. Candidate events are required to have at least three such associated tracks. Electron candidates are reconstructed by associating a cluster of energy deposits in the EM calorimeter to a well reconstructed ID track, and are required to have ET > 20 GeV and |η| < 2.47, excluding the region 1.37 < |η| < 1.52 where the transition between the barrel – 5 – and endcap of the EM calorimeter occurs. Candidates are required to pass a ‘medium’ quality requirement based on analysis of various cluster properties and the associated ID track [36]. Muon candidates are reconstructed by associating well identified ID tracks to MS tracks [37]. Candidates are required to have pT > 20 GeV and |η| < 2.4. Selections on the transverse energy (transverse momentum) of electron (muon) candidates are chosen to ensure the trigger is fully efficient. To ensure that lepton candidates originate from the PV and to suppress those can- didates originating from heavy flavour decays, ID tracks associated to lepton candidates are required to have an absolute longitudinal impact parameter with respect to the PV, |z0|, less than 1 mm and absolute transverse impact parameter, |d0|, no larger than ten (three) times its measured uncertainty for electron (muon) candidates. Muon candidates are additionally required to be isolated from local track activity by rejecting candidates where the summed transverse momenta of additional ID tracks within ∆R = 0.2 from the muon candidate is larger than 10% of the transverse momentum of the candidate it- self. No additional isolation requirement is applied to electron candidates as the quality requirement and impact parameter selections already sufficiently reduce the contribution from jets misidentified as electrons in the calorimeter. 4 Event selection JHEP10(2014)141 Selection efficiencies of lepton candidates as well as their energy resolution and mo- mentum resolution are adjusted in simulation to match those observed in Z →ℓℓevents in data [36, 37]. The lepton energy scales and momentum scales are calibrated based on a comparison of the position of the Z boson mass peak in data and simulation. Events with exactly two lepton candidates of same flavour and opposite measured charge are kept for further analysis, provided the invariant mass of those leptons, mℓℓ, falls in the range 76 < mℓℓ< 106 GeV. Jets are reconstructed from topological energy clusters in the calorimeter [38] using the anti-kt algorithm [39, 40] with radius parameter R = 0.4. The jet energy is calibrated as a function of pT and η using MC simulation after correcting first for the energy offset due to pile-up activity in the calorimeter, and then redefining the origin of the jet to be the event PV. A residual in situ correction determined from Z+jet and γ+jet control samples is applied to jets in data to account for remaining differences in calorimeter response between data and simulation [41]. Jets from pile-up interactions are suppressed by requiring that ID tracks associated to the PV contribute at least 75% of the total scalar sum of transverse momenta from all ID tracks within ∆R = 0.4 from the jet centroid. Calibrated reconstructed jets are required to have pT > 20 GeV, |y| < 2.4 and any jet within ∆R = 0.5 of a selected lepton candidate is removed. Jets containing b-hadrons are identified using a neural network (NN) algorithm, MV1 [42]. The MV1 algorithm takes as inputs the results of lower-level likelihood and NN based b-tagging algorithms, which in turn take both secondary vertex kinematics and impact parameter information with respect to the PV as inputs, obtained from analysing ID tracks within ∆R = 0.4 from the jet centroid. The MV1 variable lies in the range [0,1] with a value closer to unity denoting a higher probability for the jet to be a b-jet. Reconstructed b-jet candidates are selected for the analysis when their MV1 output is greater than the value corresponding to a 75% average b-tagging efficiency in simulated t¯t events. In simulation, – 6 – reconstructed jets are labelled as b-jets if they lie within ∆R = 0.3 from one or more weakly decaying b-hadrons with pT > 5 GeV. 4 Event selection Reconstructed jets not identified as b-jets are considered as c-jets if they lie within ∆R = 0.3 from any c-quark with pT > 5 GeV. All other jets are classified as ‘light-jets’. Tagging efficiencies in simulation are scaled to match those measured in data for all flavours as a function of jet pT (and η for light-jets) using weights derived from control samples enriched in jets of each flavour [42–44]. In each event, the missing transverse momentum, Emiss T , is also used to reject back- grounds which typically contain high energy neutrinos, such as t¯t. The Emiss T is calculated by first forming the vector sum of all calibrated leptons and jets, along with any additional topological energy clusters not already associated to a reconstructed physics object. The magnitude of this sum in the transverse direction is a measure of the energy imbalance in the event, and is taken as the Emiss T [45]. JHEP10(2014)141 Events used for further analysis are separated into two categories: those with at least one tagged jet, referred to as 1-tag events; and those with at least two tagged jets, referred to as 2-tag events, which is a subset of the 1-tag sample. 5 Background estimation and reduction In the Z(→ee)+jets channel the multijet enriched – 7 – [GeV] miss T E 0 50 100 150 200 250 300 Entries / 10 GeV -1 10 1 10 2 10 3 10 1bjet ≥ Z + Alpgen Z+bb t MC@NLO t -1 = 7 TeV, 4.6 fb s ATLAS Simulation (a) [GeV] miss T E 0 50 100 150 200 250 300 Entries / 10 GeV -1 10 1 10 2 10 2bjets ≥ Z + Alpgen Z+bb t MC@NLO t -1 = 7 TeV, 4.6 fb s ATLAS Simulation (b) Figure 2. Comparison of simulated Emiss T distributions for (a) 1-tag events and (b) 2-tag events after all other signal selection criteria are applied, normalised to the expected yields in the data sample. The shaded distributions are signal Alpgen+Herwig+Jimmy events, and the open dis- tributions are selected t¯t events. The vertical line shows the selection applied to the analysis sample to reject t¯t events while keeping signal events. [GeV] miss T E 0 50 100 150 200 250 300 Entries / 10 GeV -1 10 1 10 2 10 2bjets ≥ Z + Alpgen Z+bb t MC@NLO t -1 = 7 TeV, 4.6 fb s ATLAS Simulation (b) [GeV] miss T E 0 50 100 150 200 250 300 Entries / 10 GeV -1 10 1 10 2 10 3 10 1bjet ≥ Z + Alpgen Z+bb t MC@NLO t -1 = 7 TeV, 4.6 fb s ATLAS Simulation (a) JHEP10(2014)141 (b) (a) Figure 2. Comparison of simulated Emiss T distributions for (a) 1-tag events and (b) 2-tag events after all other signal selection criteria are applied, normalised to the expected yields in the data sample. The shaded distributions are signal Alpgen+Herwig+Jimmy events, and the open dis- tributions are selected t¯t events. The vertical line shows the selection applied to the analysis sample to reject t¯t events while keeping signal events. control region is defined by following the full signal event selection with the exception of electron candidate impact parameter requirements, and requiring that one reconstructed electron candidate fails the ‘medium’ quality requirement. As requirements based on the shower shape and associated ID track are applied to both electrons at trigger-level in the default trigger, events for the control region are selected with a trigger which requires only a single electron with ET > 20 GeV. 5 Background estimation and reduction Selected events in data contain the signal of interest as well as various background processes with either real or fake leptons and real or fake b-jets. By far the dominant contributions are Z+jets events where either a light-jet or c-jet has been misidentified as a b-jet. The amount of this background present in data is determined using fits to data as described in section 6. The next most important background arises from t¯t events where both W bosons decay to leptons. This background is estimated using simulated events normalised to the theoretically predicted cross-section. The t¯t background is suppressed by the requirements on mℓℓ, and its overall contribution to the event sample is small. However, it can be significant in some kinematic regions, particularly at higher jet pT. To further reduce the t¯t contamination, events are required to have Emiss T < 70 GeV. Figure 2 shows the Emiss T distributions for signal and t¯t simulations in 1-tag and 2-tag events after combining the electron and muon channels. The 70 GeV selection rejects 44.8% (44.3%) of the t¯t background in 1-tag (2-tag) events while remaining over 99% efficient for signal events. The total contribution to the final data sample from single top quark and diboson processes is estimated using samples of simulated events normalised to their theoretically predicted cross-sections. Other electroweak processes such as W+jets and Z →ττ events are found to have a negligible contribution in the selected phase space. Background contributions from multijet events are estimated using data-driven tech- niques separately in the electron and muon channels for both 1-tag and 2-tag events. Multijet-enriched control regions are used to derive the expected shape of this background in the mℓℓvariable. These control regions drop the b-tagging requirement, and use an extended range 50 < mℓℓ< 200 GeV in order to maximise the available sample size. Studies found that no bias was introduced within the statistical uncertainties between the b-tagged and non-b-tagged samples. 5 Background estimation and reduction This trigger was only available for about one third of the full 2011 data-taking period (1.7 fb−1 in total). In the Z(→µµ)+jets channel the multijet-enriched control region is defined by following the full signal event selection with the exception of muon candidate impact parameter requirements, and inverting the iso- lation selection for both reconstructed muon candidates. In both channels, contributions from non-multijet sources in the control regions are taken from simulation, and subtracted from the data. The remaining distributions are used as shape templates for the dilepton invariant mass distribution of the multijet background. Fits to mℓℓare then made after applying the full signal event selection, fixing the multijet shapes to those measured in the control regions. For 1-tag events the multijet contribution is determined to be 0.1±0.1% in the electron channel and 0.02±0.07% in the muon channel. The control regions are investigated as a function of all variables used to define the differential cross-sections measured here, and no significant variation in the multijet fraction is found; therefore, the measured multijet fractions are assumed to be constant in all differential analysis bins. For 2-tag events the multijet contributions are fitted to be zero, with an uncertainty of approximately 0.5%. This uncertainty is taken as a systematic uncertainty to account for a possible residual multijet contribution, as discussed in section 8. – 8 – CombNNc -4 -2 0 2 4 6 8 10 Entries / 0.67 0 1000 2000 3000 4000 5000 6000 7000 Z+b Z+c Z+light ATLAS Simulation -1 = 7 TeV, 4.6 fb s (a) CombNN -4 -2 0 2 4 6 8 10 Entries / 0.67 0 1000 2000 3000 4000 5000 Z+b Z+c Z+light ATLAS Simulation -1 = 7 TeV, 4.6 fb s (b) Figure 3. Distributions of (a) CombNNc and (b) CombNN for different jet flavours in simulated Z+jets events for all selected tagged jets, in events with at least one tagged jet. The Z →ee and Z →µµ channels are combined and simulated data are normalised such that the predicted number of jets in 4.6 fb−1 are shown. 5 Background estimation and reduction CombNN -4 -2 0 2 4 6 8 10 Entries / 0.67 0 1000 2000 3000 4000 5000 Z+b Z+c Z+light ATLAS Simulation -1 = 7 TeV, 4.6 fb s (b) CombNNc -4 -2 0 2 4 6 8 10 Entries / 0.67 0 1000 2000 3000 4000 5000 6000 7000 Z+b Z+c Z+light ATLAS Simulation -1 = 7 TeV, 4.6 fb s (a) JHEP10(2014)141 (a) (b) Figure 3. Distributions of (a) CombNNc and (b) CombNN for different jet flavours in simulated Z+jets events for all selected tagged jets, in events with at least one tagged jet. The Z →ee and Z →µµ channels are combined and simulated data are normalised such that the predicted number of jets in 4.6 fb−1 are shown. 6 Extraction of detector-level signal yields The extractions of the integrated and differential detector-level signal yields for both the 1-tag and 2-tag selections are performed using maximum-likelihood fits to data based on flavour-sensitive distributions. The distribution used is constructed from the output of a neural network algorithm, JFComb, which is one of the inputs to the MV1 b-tagging algorithm described in section 4. JFComb itself combines the information from two further algorithms, one of which aims to identify weak b →c cascade topologies using secondary vertices and displaced tracks reconstructed within a jet [46], and the other which calculates a likelihood based on the impact parameter significance with respect to the PV of pre- selected tracks within ∆R = 0.4 of the jet centroid [42, 47]. The JFComb algorithm has three outputs in the range [0,1]: pb, pc, and pu, corresponding to the probability that a given jet is a b-jet, c-jet or light-jet, respectively. Combinations of these variables, namely CombNNc = ln(pb/pc) and CombNN = ln(pb/pu) provide good separation between jet flavours as shown in figure 3 for all jets in the Z+jets MC simulation after the 1-tag event selection. In the 1-tag event selection, fits are made to the CombNNc distribution as it is found to give the best statistical separation between b-jets and non-b-jets. Templates are de- rived from MC simulation for all non-multijet contributions. For the multijet background, templates are derived from the respective control regions in each lepton channel after rein- troducing the b-tagging requirement as in the baseline selection. As shown in figure 3a, the c-jet and light-jet CombNNc shapes are very similar. They are therefore combined into a single non-b-jet template before the fit, using the predicted c-to-light jet ratio from simu- lation. Fits to data allow the b- and non-b-jet Z+jets yields to float, while backgrounds from sources other than Z+jets are combined into a single template whose normalisation is determined from the sum of their predicted contributions and fixed in the fit. 6 Extraction of detector-level signal yields Where a per b-jet yield is measured, all tagged jets are used in the fit; where a per-event yield – 9 – CombNNc -4 -2 0 2 4 6 8 10 Entries / 0.67 0 500 1000 1500 2000 2500 ATLAS 1.2<|y(Z)|<1.6 -1 =7TeV, 4.6 fb s Data Z+b Z+non-b non-Z backgrounds (a) CombNNc ∑ -10 -5 0 5 10 15 20 Entries / 1.5 0 20 40 60 80 100 120 ATLAS R(b,b)<5.0 ∆ 3.2< -1 =7TeV, 4.6 fb s Data Z+bb Z+non-bb non-Z backgrounds (b) Figure 4. Example fits to the distribution of (a) CombNNc at jet-level for 1-tag events with 1.2 < |y(Z)| < 1.6, and (b) P(CombNNc) at event-level for 2-tag events with 3.2 < ∆R(b, b) < 5.0. CombNNc ∑ -10 -5 0 5 10 15 20 Entries / 1.5 0 20 40 60 80 100 120 ATLAS R(b,b)<5.0 ∆ 3.2< -1 =7TeV, 4.6 fb s Data Z+bb Z+non-bb non-Z backgrounds (b) CombNNc -4 -2 0 2 4 6 8 10 Entries / 0.67 0 500 1000 1500 2000 2500 ATLAS 1.2<|y(Z)|<1.6 -1 =7TeV, 4.6 fb s Data Z+b Z+non-b non-Z backgrounds (a) JHEP10(2014)141 (b) (a) Figure 4. Example fits to the distribution of (a) CombNNc at jet-level for 1-tag events with 1.2 < |y(Z)| < 1.6, and (b) P(CombNNc) at event-level for 2-tag events with 3.2 < ∆R(b, b) < 5.0. Analysis Data Fitted Components Fixed Components selection yield Z + b(b)-jets [ALPGEN+HJ] Z+(other)jets t¯t other σ(Zb) × Nb-jet 49701 18010±210 [12470] 29780±230 1330 590 σ∗(Zb) × Nb-jet 41243 15640±190 [10460] 23840±210 1230 540 σ(Zb) 47138 16610±200 [11410] 29090±220 930 520 σ(Zbb) 2494 1170±60 [950] 860±50 395 60 Table 2. Detector-level yields for each analysis selection. Statistical uncertainties from the fits to data are shown for the signal and Z+jets backgrounds. The t¯t and other (diboson, single top quark and multijet) background normalisations are also shown. The signal yields predicted by Alpgen+Herwig+Jimmy (ALPGEN+HJ) are shown in square brackets for reference. Table 2. Detector-level yields for each analysis selection. Statistical uncertainties from the fits to data are shown for the signal and Z+jets backgrounds. The t¯t and other (diboson, single top quark and multijet) background normalisations are also shown. The signal yields predicted by Alpgen+Herwig+Jimmy (ALPGEN+HJ) are shown in square brackets for reference. Table 2. Detector-level yields for each analysis selection. 6 Extraction of detector-level signal yields Statistical uncertainties from the fits to data are shown for the signal and Z+jets backgrounds. The t¯t and other (diboson, single top quark and multijet) background normalisations are also shown. The signal yields predicted by Alpgen+Herwig+Jimmy (ALPGEN+HJ) are shown in square brackets for reference. is measured, only the highest pT tagged jet in an event is used in the fit. The electron and muon channel templates in data are combined before the fit to maximise the statistical precision. For measurements of differential cross-sections, these fits are performed indepen- dently in each bin, and figure 4a shows an example fit to the CombNNc distribution in one differential bin, which is typical of the results obtained. Table 2 summarises all signal and background contributions compared to data for the integrated 1-tag selections at detector- level after the jet-flavour fits. Also shown in table 2 are the Alpgen+Herwig+Jimmy 1-tag predictions, where it can be seen that they significantly underestimate the fitted b-jet yields. In the 2-tag event selection fits are made to P(CombNNc), where the sum is over the two highest pT tagged jets in an event. There are six possible flavour combinations of b-jets, c-jets, and light-jets in the Z+jets MC simulation. The highest statistical precision on the signal bb-yield is obtained when the other five flavour combinations are combined into a single non-bb template. However, the shapes of the non-bb templates are not de- generate, as the presence of a single b-jet in the b+light or b + c cases results in a higher value of P(CombNNc) compared to light+light, light+c and c + c cases. Therefore, the – 10 – overall number of these single-b events is important in determining the shape of the non-bb template. As discussed above, and can be seen in table 2, the Alpgen+Herwig+Jimmy simulation is observed to underestimate the b-jet yield in data, and it follows that the number of b+light and b + c events cannot be taken directly from the simulation when forming the non-bb template, but must be measured. To determine the appropriate scaling for the templates containing a single b-jet, a fit is performed to CombNN in an alternative sample containing a reconstructed Z boson with at least two jets, of which exactly one is tagged. 6 Extraction of detector-level signal yields The b-jet, c-jet and light-jet Z+jets yields are allowed to float in the fit, while all non-Z+jets backgrounds are combined into a single template whose normalisation is determined from the sum of their predicted contributions and fixed in the fit; the multijet yields and shapes in this sample are extracted in a fashion analogous to that used for the 1-tag events. Even after scaling up the total Z cross-section to the NNLO prediction as described in section 3, the predicted b-jet yield must be increased by an additional factor of 1.35±0.03 to match the fitted data yield, where the quoted uncertainty is the statistical component of the fit to data. Scale factors for c-jet and light-jet yields are found to be consistent with unity. Based on this result, templates containing one b-jet are weighted by a factor 1.35 compared to the predicted cross-section, while templates with no b-jets are included using the default predicted cross-section. This factor of 1.35 is taken as constant across all distributions as, normalisation aside, the default simulation is found to give a good description of the kinematics of the single b-jet sample. This scale factor is slightly different from the Z+ ≥1 b-jet scale factors in table 2, due to the different jet requirements. A systematic uncertainty on the scale factor is obtained by varying these requirements, as described in section 8. JHEP10(2014)141 Signal fits to data float the Z+jets bb and non-bb yields while combining all other backgrounds into a single template whose normalisation is determined from the sum of their predicted contributions and fixed in the fit. As with 1-tag events, the electron and muon channels are combined before fitting to data to maximise the statistical precision. Figure 4b shows an example fit of P(CombNNc) in one differential bin, and table 2 summarises all signal and background contributions compared to data for the integrated 2-tag selection at detector-level after the jet-flavour fit. All fits are checked with ensemble tests using the simulated samples, including checks for any bias in the fit results compared to the true number of b-jets in the simulation. Negligible biases in the fit responses are observed. 7 Correction to particle-level Signal yields fitted at detector-level are corrected for reconstruction efficiencies and detector resolution effects using simulation. This unfolding procedure determines fiducial particle- level yields in data, which when divided by the measured integrated luminosity determine cross-sections. Particle-level objects are selected with requirements chosen to be close to the corresponding requirements for reconstructed signal candidate detector-level objects, in order to minimise unfolding corrections. Final state electrons and muons are ‘dressed’, such that the four-momentum of collinear photons within ∆R = 0.1 from those leptons are added – 11 – to their four-momentum. These dressed leptons are then required to have pT > 20 GeV and |η| < 2.5. The two leptons with highest pT, same flavour and opposite charge are used to reconstruct the Z boson, with the invariant mass of the pair required to lie in the range 76 < mℓℓ< 106 GeV. Jets of particles, excluding leptons used to reconstruct the Z boson and any photons used in dressing them, but including leptons and neutrinos from heavy flavour decays, are reconstructed with the anti-kt algorithm with radius parameter R = 0.4. As with simulated reconstructed jets, particle-level jets are defined as b-jets if they lie within ∆R = 0.3 from one or more weakly decaying b-hadrons with pT > 5 GeV. Selected jets are required to have pT > 20 GeV and |y| < 2.4. Jets within ∆R = 0.5 of a lepton used to reconstruct the Z boson are discarded. JHEP10(2014)141 The classification of simulated signal events is based on the presence of detector-level and particle-level objects, and matching criteria between the two are defined. The matching criteria require that detector-level and particle-level event selections are passed and that each detector-level b-jet lies within ∆R = 0.4 from a particle-level b-jet. For event-level (jet-level) differential measurements, matched events (b-jets) are used to populate detector response matrices for the distribution in question. These matrices characterise the bin migrations between detector-level and particle-level quantities and are used to unfold the fitted signal yields at detector-level into signal yields at particle-level. Before unfolding, a multiplicative matching correction derived from simulation is ap- plied to the fitted signal yields, to account for cases where the detector-level signal failed the matching criteria. 7 Correction to particle-level This correction is 6–9% for the integrated selections, although it becomes as large as 20% in the lowest bin of b-jet pT in the 1-tag analysis due to migra- tion from particle-level b-jets below the 20 GeV pT threshold. In order to avoid bias in the differential cross-section measurement of b-jet pT, detector-level b-jets are considered as matched if they are associated to particle-level b-jets with pT > 10 GeV. For other variables the migration outside of acceptance is found to introduce negligible bias and hence the particle-level b-jet selection is only relaxed in the unfolding of b-jet pT. For 2-tag events, where simulation sample size for matched events is a limiting factor, the b- tagging efficiency correction is included as part of the matching correction. This allows all detector-level b-jets, tagged or otherwise, to be used in the response matrices. In the 1-tag analysis, corrected fitted yields and response matrices are used as input to an iterative Bayesian technique [48] to extract the particle-level signal yields. Three further iterations on the initial response matrix are required to remove bias from previous iterations as determined from MC simulation ensemble tests of the statistical robustness of the unfolding procedure. The binning of differential distributions is chosen to always be significantly wider than the detector resolution in that quantity, which is only a relevant factor for b-jet pT. Related to this resolution effect, and to again mitigate the biases mentioned above, the response matrix for b-jet pT is also populated with particle jets with pT > 10 GeV, and the portion of the resulting particle-level distribution below 20 GeV is removed. In the 2-tag differential distributions, fewer events are selected and binnings are chosen to optimise statistical precision while maintaining as many bins as possible. This coarse binning results in little bin-to-bin migration, and a negligible difference is observed between the result of the iterative procedure used for 1-tag events and that obtained by – 12 – simply applying fiducial matching and efficiency corrections3 individually for each bin. As a consequence, the latter, more straightforward, technique is used to extract differential yields in 2-tag events. Since the electron and muon Z boson decay channels are combined to increase the precision of the signal fits to data, the corrections and response matrices described above must unfold both channels simultaneously to obtain combined particle-level yields. 3The efficiency correction refers to the multiplicative factor obtained from the ratio of the total number of fiducial particle-level events to the number which is also reconstructed at the detector-level and matched appropriately. 7 Correction to particle-level To val- idate this approach, an identical analysis of each individual lepton channel is performed. Their sum after unfolding is checked for consistency with the default combined unfolded result and excellent agreement is observed in both the 1-tag and 2-tag cases. Furthermore, the results obtained from the individual lepton channels agree reasonably well, being com- patible within 1.7σ or less, considering only the sum in quadrature of the statistical and uncorrelated systematic uncertainties. JHEP10(2014)141 8 Systematic uncertainties Several sources of systematic uncertainty are considered. These can impact either the fit, through modification of template shapes and background normalisations; the unfolding, through modification of correction factors and response matrix; or both the fit and unfold- ing in a correlated manner. Each independent source of uncertainty is varied successively up, and then down by one standard deviation, and in each case the full analysis chain is repeated. The relative change in the result with respect to the default analysis is then assigned as the up or down uncertainty due to that source. The following sources are considered and the resulting uncertainties on the measured 1-tag and 2-tag cross-sections are summarised in table 3. Tagging efficiency and mistag rates. Calibration factors are applied to the jet b- tagging efficiency in simulation to match that measured in data for each flavour. These have associated systematic uncertainties as a function of jet pT (and η for light-jets). For b- jets, the uncertainties derived from calibration analyses are divided into 10 sub-components corresponding to the eigenvectors which diagonalise the associated covariance matrix; each sub-component is then varied independently by ±1σ and the systematic uncertainties from each are added in quadrature. Typically two of the sub-components dominate the un- certainty, with one at around 4.5% at low b-jet pT, and the other rising to around 13% at high b-jet pT. Across other distributions, both remain between 2–3%. For c-jets and light-jets, the mistag correction factors from each respective calibration analysis are varied by ±1σ and propagated through the analysis chain to obtain the corresponding systematic uncertainties. These contribute significantly smaller uncertainties, peaking at around 1% at high b-jet rapidity and low pT. All uncertainties related to b-jets approximately double in size when requiring two tagged jets for the Z+ ≥2 b-jets distributions. – 13 – Source of uncertainty σ(Zb) [%] σ(Zbb) [%] b-jet tagging efficiency 3.4 9.8 c-jet mistag rate 0.2 2.3 light-jet mistag rate 0.4 0.6 JES 2.9 4.7 JER 0.3 0.7 b-jet template shape 4.8 4.8 c-jet template shape 0.2 0.6 light-jet template shape 0.9 0.9 b-jet template scale factor N/A 2.3 MPI 2.5 0.8 gluon splitting 1.2 1.5 background normalisation 1.1 3.6 t¯t modelling 0.0 2.9 MC sample size 1.0 1.4 lepton efficiency, scale and resolution 1.2 1.2 Emiss T 0.1 0.6 luminosity 1.8 1.8 total 7.7 14.0 Table 3. 8 Systematic uncertainties Summary of the systematic uncertainties determined for the cross-section measurements of the Z+ ≥1 b-jet and Z+ ≥2 b-jets final states. JHEP10(2014)141 Table 3. Summary of the systematic uncertainties determined for the cross-section measuremen of the Z+ ≥1 b-jet and Z+ ≥2 b-jets final states. Table 3. Summary of the systematic uncertainties determined for the cross-section measurements of the Z+ ≥1 b-jet and Z+ ≥2 b-jets final states. Jet energy scale. Systematic uncertainties on the difference between the jet energy scale (JES) in data and simulation are derived using a variety of studies based on in situ measurements and simulation [41]. These uncertainties are decomposed into 16 indepen- dent components, including those arising from the influence of close-by low-energy jets, the correction for pile-up activity and differences in detector response to light-quark jets, gluon jets and heavy flavour jets. Each component is propagated through the analysis chain independently by simultaneously varying the signal and background simulation jet response by ±1σ. The impact of the total JES uncertainty on the final cross-sections is typically around 2–5%, rising with pT and rapidity, with uncertainty on the b-jet response uncertainty being an important contribution. Jet energy resolution. Jet energy resolution (JER) is studied in dijet data and com- pared to simulation [49]. Simulated signal and background samples are then modified by applying a Gaussian smearing of the resolution function according to the maximum degra- dation allowed by the JER measurement from data to evaluate the associated systematic variation. This is taken as a symmetrised uncertainty on the measured results, and is typically less than 1%. b-jet template shapes. The uncertainty on the shape of b-jet templates used in fits to data is a dominant contribution to the overall systematic uncertainty for this analysis. The – 14 – Entries / 0.67 0 1000 2000 3000 4000 5000 6000 7000 8000 -1 = 7 TeV, 4.6 fb s Data b-jets non-b-jets ATLAS CombNNc -4 -2 0 2 4 6 8 10 Ratio to simulation 0.8 0.9 1 1.1 1.2 1.3 1.4 -1 = 7 TeV, 4.6 fb s data/simulation systematic template weight Figure 5. The tagged-jet CombNNc distribution in the t¯t enriched control region described in the text, with the simulation split by jet flavour (top), and the ratio of data to default simulation (filled circles, bottom). 8 Systematic uncertainties The dashed line shows the b-jet template reweighting function derived from the difference between data and simulation in this control region. Entries / 0.67 0 1000 2000 3000 4000 5000 6000 7000 8000 -1 = 7 TeV, 4.6 fb s Data b-jets non-b-jets ATLAS CombNNc -4 -2 0 2 4 6 8 10 Ratio to simulation 0.8 0.9 1 1.1 1.2 1.3 1.4 -1 = 7 TeV, 4.6 fb s data/simulation systematic template weight JHEP10(2014)141 Ratio to simulation Figure 5. The tagged-jet CombNNc distribution in the t¯t enriched control region described in the text, with the simulation split by jet flavour (top), and the ratio of data to default simulation (filled circles, bottom). The dashed line shows the b-jet template reweighting function derived from the difference between data and simulation in this control region. shape is cross-checked in a t¯t-enriched control region which requires a single well identified and isolated lepton in association with at least four reconstructed jets passing the same kinematic cuts as signal jets, of which exactly two are tagged with the MV1 algorithm described in section 4. This selects a sample of t¯t events in which over 90% of the tagged jets are expected to be true b-jets. Contributions from W+jets and single top quark events in this control region are estimated from simulation; contributions from other electroweak processes and multijet backgrounds are found to be negligible. A residual underestimate of the total number of events predicted by simulation is found to be less than 10%, and is corrected for by scaling up the t¯t contribution to match the data normalisation. Figure 5 shows the CombNNc distributions for different jet flavours, and the ratio of data to default simulation for all tagged jets in this control region; the corrections of the Herwig b-hadron decays to the EvtGen prediction described in section 3 are applied. It can be seen that the simulation provides a reasonable description of the data; the residual differences of up to 5% are used to derive a b-jet template reweighting function shown by the dashed line in figure 5. Investigation of the control-region data in bins of tagged jet pT and rapidity finds that the deviations between data and simulation have no strong dependence on tagged jet kinematics; this is despite the CombNNc distribution shape itself having a strong depen- dence on tagged jet pT. 8 Systematic uncertainties The reweighting function is used to directly reweight CombNNc – 15 – b-jet distributions in the signal Z+jets simulation and the fits to data are repeated. The relative differences with respect to the default results are typically less than 5%, and this difference is taken as a systematic uncertainty due to b-jet template shape, which is then symmetrised around the nominal value to give an up- and down-uncertainty. It is possi- ble that the b-jet template reweighting function derived reflects some mismodelling of the non-b-jets component in figure 5. To this end the systematic uncertainty is also evaluated by only reweighting b-jet templates for values of CombNNc larger than 2.0. The result is a smaller overall uncertainty; however, as the fraction of b-jets is still larger than the fraction of non-b-jets for CombNNc less than 2.0 in figure 5, the more conservative value obtained from reweighting the full b-jet template is taken as the uncertainty. As a further cross- check, the fits are repeated using b-jet templates obtained from the Sherpa Z+jets sample; deviations observed are all within the uncertainties already derived from the t¯t-enriched control-region method, so no further uncertainty is assigned. JHEP10(2014)141 Non-b-jet template shapes. Mismodelling of template shapes derived from Z+jets simulation for c-jets and light-jets can also cause a systematic shift in the results of fits to data. The corresponding uncertainties are estimated by substituting the default templates with templates derived from the Sherpa Z+jets simulation, which uses a different parton shower and hadronisation model. The difference between the default fit response and the response obtained with the alternative templates is taken as the systematic uncertainty, which is typically less than 1%. Further tests are made by repeating the entire analysis using an MV1 operating point which rejects significantly more c- and light-jet background (but with a lower signal ef- ficiency), reducing the sensitivity to any potential mismodelling of these templates. The results are entirely consistent with those obtained using the default value, so no further uncertainty is assigned. Finally, the template shapes may be influenced by a mismodelling of the light- and c-jet kinematics, and by the light-/c-jet ratio in the simulation when building the non-b template. The data are fitted using CombNN rather than CombNNc (defined in section 6), which provides a better discrimination between light- and c-jets, and all three templates (light-, c- and b-jet) are allowed to float. 8 Systematic uncertainties Across all distributions, the fitted light- and c-jet normalisations are consistent with the prediction of the default simulation within the statistical uncertainties (typically 2–4%), indicating the kinematic modelling of these contributions, and their ratio, is correct. Therefore no further systematic uncertainty is assigned. Template scale factor. The b+c and b+light jet templates in 2-tag events are scaled up by a factor of 1.35, as described in section 6, based on fits to data with two or more jets, of which exactly one is tagged. A fit to integrated 1-tag data yields a factor of 1.48; the default scale factor of 1.35 is varied up and down by 0.13 to cover this difference, resulting in a change in the final cross-sections of around 2%, which is assigned as a symmetric up and down systematic uncertainty. The c- and light-jet fractions in these templates are also independently varied up and down by 0.13, significantly larger than the fit uncertainties and differences in the two control regions used to derive the b-jet scale factor, but chosen – 16 – to based on the b-jet result to provide a conservative bound on mismodelling of the c-jet fraction. This results in a further systematic uncertainty of around 1%. Multiple parton interactions. Associated Z+b-jets production from MPI where the Z and b-jets are produced in separate hard scatters within a single pp interaction (multiple parton interactions) is included in the analysis signal definition. Fits to data and unfolding to particle-level use the MPI fraction predicted by Jimmy in Z+jets simulation to determine its relative contribution to the signal processes. The contribution is largest at lower b-jet pT; any misestimate of this fraction can alter the CombNNc shapes, which are pT-dependent, and can also alter the efficiency correction and the bin-by-bin migration in pT-dependent variables. The default double parton interaction fractions as a function of b-jet pT and rapidity are cross-checked by combining ATLAS measurements of the Z boson production cross-section [50], the differential inclusive b-jet cross-section [51] and pp effective cross- section [52] using the phenomenological model described in reference [52]. The prediction from Jimmy is found to be consistent with this data-based cross-check to within 50%, hence the predicted fraction is varied by this amount to determine an associated systematic uncertainty. The uncertainty is typically around 2% on the measured cross-sections. JHEP10(2014)141 Gluon splitting. 8 Systematic uncertainties The dominant mechanism to produce two b-hadrons in one jet is the g →bb process. An inaccurate estimate of the rate of two b-hadron decay vertices within ∆R = 0.4 from the jet centroid can affect the accuracy of the CombNNc template shapes, by impacting distributions which are inputs to the NN. Furthermore, as gluon splitting becomes more important for high pT jets, a mismodelling of its rate can impact the effi- ciency correction and bin migrations in variables correlated with b-jet pT. No well defined data control region has been identified to constrain this process; therefore the sample of simulated events with reconstructed and particle-level jets matched to two b-hadrons is first enhanced by a factor of 2, then completely removed, with the full analysis being repeated in both cases. This variation is larger than the difference observed between predictions from the default signal Alpgen+Herwig+Jimmy and Sherpa Z+jets simulations and is therefore considered to give a conservative upper limit on the magnitude of this uncertainty, and is found to be less than 2%. Background normalisation. The contributions of t¯t, single top quark and diboson backgrounds are taken from theoretical predictions. To account for theoretical uncertain- ties in these predictions the normalisation of each component is varied independently by ±10%, which covers both cross-section and acceptance uncertainties. For 1-tag events the multijet background is varied within its fitted uncertainty. For 2-tag events, fits for the multijet backgrounds yielded a normalisation close to zero, and the uncertainty from those fits is taken as an upper bound for possible multijet contamination, translating into an uncertainty of 0.5% on the bb yield. Background modelling. A cross-check of t¯t-background modelling is made by substi- tuting the default MC simulation with an alternative sample simulated with Powheg and repeating the data fits. For 1-tag events no significant difference is found, either inclusively – 17 – or differentially. In 2-tag events a systematic deviation in excess of the existing template- shape uncertainty described above is observed. This difference is approximately 3%, which is taken as an additional systematic uncertainty due to t¯t modelling in the 2-tag sample. Signal modelling. The corrections to particle-level cross-sections may include some residual dependence on the modelling of the kinematics in the simulation. To test for this, the particle-level b-jet pT distribution in simulation is reweighted to the measured differential cross-section, and the full analysis repeated. A negligible effect is found. 8 Systematic uncertainties As the main kinematic distributions are generally well modelled by the simulation, no further uncertainties are assigned. JHEP10(2014)141 Simulation sample size. The impact of the finite simulation sample sizes in both the fit template shapes and unfolding procedure are evaluated through ensemble tests, repeating the analysis and randomly fluctuating bin entries of a given distribution in the simulation within their statistical uncertainty. The spread determined from these ensemble tests is around 1%, which is assigned as the systematic uncertainty. Lepton efficiency, energy scale and resolution. The trigger and reconstruction ef- ficiency, energy scale, and resolution of both reconstructed electron and muon candidates have been measured in Z →ℓℓevents and used to correct the simulation as described in section 4. The uncertainties associated with the measurement of these quantities are propagated through the full analysis chain resulting in an uncertainty of around 1% on the final cross-sections. Missing transverse momentum. The calculation of Emiss T in each event is repeated for every systematic variation of reconstructed jet and lepton candidates as described above. An additional uncertainty arises from possible differences in data and simulation between the component of Emiss T from topological clusters not associated to reconstructed physics objects [45]. This additional component is propagated through the analysis as an indepen- dent uncertainty, and is typically well below 1%. Luminosity. The luminosity scale is determined from a single calibration run taken in May 2011. The associated uncertainty is derived from the calibration analysis itself and from the study of its stability across the 2011 data taking period. A total uncertainty of 1.8% is assigned to the luminosity [35]. 9 Theoretical predictions Several theoretical predictions are compared to the measurements. Fixed-order pQCD parton-level predictions at NLO in the 5FNS are obtained from mcfm [53] for both the Z+ ≥1 b-jet and Z+ ≥2 b-jets final states. The calculation of Z+ ≥1 b-jet is made up of several sub-processes [2, 3] at O(α2 S), and the b-quark mass is ignored except in pro- cesses where one b-quark falls outside the acceptance or two b-quarks are merged in a single jet. For Z+ ≥2 b-jets production, the mcfm calculation uses a single process with both b- quarks in acceptance at O(α3 S) and the b-quark mass is ignored throughout. In all cases, the renormalisation and factorisation scales are set to p m(Z)2 + pT (Z)2, and varied up and – 18 – down independently by a factor of two to assess the dependence on this scale choice. The mcfm predictions are performed using the CT10 [23], NNPDF2.3 [54] and MSTW2008 [55] PDF sets. The uncertainties associated with the PDF fits to experimental data are prop- agated appropriately for each PDF set. The dependence on the choice of αS(m(Z)) is assessed by using PDF sets with αS(m(Z)) shifted up and down by the 68% confidence level interval around the default value used in the PDF. For MSTW2008, fits using different b-quark masses are also available. The prediction from mcfm is at the parton-level, so must be corrected for the effects of QED final-state radiation (FSR), hadronisation, underlying event and MPI. The correction for QED FSR is obtained using Photos, interfaced to the Alpgen+Herwig+Jimmy samples used in the data analysis, and evaluated by compar- ing the cross-sections obtained by applying the selection requirements to leptons before, and after FSR. The correction factors for hadronisation, underlying event and MPI are obtained for each differential cross-section from both Pythia and Sherpa, by taking the ratio of the predictions with these effects turned on and turned off. The versions used are Pythia 6.427, with the CTEQ5L PDF set and the Perugia 2011 tune, and Sherpa 1.4.1, with the CT10 PDF set. Differences between the correction factors obtained in Pythia and Sherpa, which are typically at the 1%-level, as well as the 50% uncertainty on MPI described in section 8, are assigned as systematic uncertainties. JHEP10(2014)141 Full particle-level predictions with NLO matrix element calculations are also obtained using amc@nlo [10], in both the 4FNS and 5FNS. 9 Theoretical predictions In the 4FNS, the Z+ ≥2 b-jets process is calculated at O(α3 S), including the effects of the b-quark mass, and interfaced to the MSTW2008NLO nf4 PDF set [55]. No kinematic cuts are applied to the b-jets in this calculation, therefore it is also used to derive a 4FNS prediction for the Z+ ≥1 b-jet final state. For the 5FNS prediction, the more inclusive Z+≥1-jet process is calculated at O(α2 S) neglecting the b-quark mass and using the MSTW2008NLO PDF set. This is then used to derive a 5FNS prediction at O(α2 S) for Z+ ≥1 b-jet and Z+ ≥2 b-jets. The latter process is therefore LO only. In both cases, Herwig++ is used to simulate the hadronisation, underlying event and MPI. Both predictions require a correction for a missing component of MPI, in which the Z boson and b-quarks are produced in separate scatters within the pp collision. This correction is estimated using the Alpgen+Herwig+Jimmy samples where the MPI contribution is included. Since the 4FNS and 5FNS use different matrix elements (Z+bb and Z+jet respectively), a different correction factor is derived in each case. In both the 4FNS and 5FNS predictions from amc@nlo, the renormalisation and factorisation scales are set dynamically to the same definition used for the mcfm prediction. Since variations of the scales are the dominant sources of theory uncertainty, they have been evaluated for all amc@nlo predictions using the same procedure as for mcfm. The overall scale uncertainty is found to have a comparable size in the 4FNS and 5FNS predictions, and to be consistent with the scale uncertainty for mcfm. However, the uncertainty is fully dominated by variations of the renormalisation scale in the 4FNS case, while for the 5FNS renormalisation and factorisation scale variations produce shifts which are similar in magnitude and opposite in direction, giving a total uncertainty dominated by the cases where one is shifted up and the other down (and vice versa). Uncertainties arising from the PDFs and the choice of αS are obtained using mcfm. 9 Theoretical predictions – 19 – σ(Zb)[fb] σ(Zb) × Nb-jet [fb] σ∗(Zb) × Nb-jet[fb] σ(Zbb)[fb] Data 4820 ± 60+360 −380 5390 ± 60 ± 480 4540 ± 55 ± 330 520 ± 20+74 −72 MCFM⊗MSTW2008 5230 ± 30+690 −710 5460 ± 40+740 −740 4331 ± 30+400 −480 410 ± 10+60 −60 MCFM⊗CT10 4850 ± 30+580 −680 5070 ± 30+640 −710 4030 ± 30+350 −450 386 ± 5+55 −50 MCFM⊗NNPDF23 5420 ± 20+670 −710 5660 ± 30+720 −740 4490 ± 30+380 −460 420 ± 10+70 −50 amc@nlo 4FNS⊗MSTW2008 3390 ± 20+580 −480 3910 ± 20+660 −560 3290 ± 20+580 −460 485 ± 7+80 −70 amc@nlo 5FNS⊗MSTW2008 4680 ± 40+550 −580 5010 ± 40+590 −620 4220 ± 40+460 −510 314 ± 9+30 −30 Sherpa⊗CT10 3770 ± 10 4210 ± 10 3640 ± 10 422 ± 2 Alpgen+HJ⊗CTEQ6L1 2580 ± 10 2920 ± 10 2380 ± 10 317 ± 2 Table 4. The measurement and theory predictions for the integrated cross-sections and the in- tegrated inclusive b-jet cross-sections. The mcfm results are corrected for MPI, non-perturbative QCD effects and QED radiation effects. The statistical uncertainty is quoted first in each case. The second uncertainity is either the total systematic uncertainty (data), the sum in quadrature of all theory uncertainties (mcfm), or the scale uncertainty (amc@nlo). JHEP10(2014)141 Table 4. The measurement and theory predictions for the integrated cross-sections and the in- tegrated inclusive b-jet cross-sections. The mcfm results are corrected for MPI, non-perturbative QCD effects and QED radiation effects. The statistical uncertainty is quoted first in each case. The second uncertainity is either the total systematic uncertainty (data), the sum in quadrature of all theory uncertainties (mcfm), or the scale uncertainty (amc@nlo). Predictions are also obtained from Sherpa and Alpgen+Herwig+Jimmy, which combine tree-level matrix elements for multiple jet emissions with a parton shower, hadro- nisation and underlying event package. Alpgen uses the 4FNS and has up to five partons in the matrix element, while Sherpa uses the 5FNS and has up to four partons in the matrix element. 10 Results The cross-sections for Z+ ≥1 b-jet and Z+ ≥2 b-jets are shown in figure 6, and table 4. The mcfm predictions always agree with the data within the combined experimental and theoretical uncertainties. The prediction obtained with CT10 is lower, due primarily to the default choice of αS(m(Z)) in this PDF (0.118) compared to MSTW2008 and NNPDF2.3 (0.120 in each). The predictions do agree within the uncertainty on the choice of αS(m(Z)). For amc@nlo, the 5FNS prediction describes Z+ ≥1 b-jet well, while the 4FNS underes- timates the measured cross-section. This situation is reversed for the Z+ ≥2 b-jets case, where the 4FNS provides a good description, while the 5FNS underestimates the cross- section. However, as explained in section 9, the 5FNS prediction from amc@nlo is only LO for Z+ ≥2 b-jets, which may explain this underestimate. Considering only statistical uncertainties, both the 4FNS prediction from Alpgen+Herwig+Jimmy and the 5FNS prediction from Sherpa underestimate the data, with Alpgen+Herwig+Jimmy being consistently below Sherpa by around 30–40%. Figure 7 shows σ(Zb) × Nb-jet , as a function of the b-jet pT and |y|. The theoretical predictions generally provide a good description of the shape of the data. The 4FNS prediction from amc@nlo underestimates the data most significantly at central rapidities. Figure 8 shows σ(Zb), as a function of the Z boson pT and |y|. In general, all theoretical predictions provide a reasonable description of the shape of the data within uncertainties, – 20 – (Zb) [pb] σ 0 1 2 3 4 5 6 (stat.) -1 = 7 TeV, 4.6 fb s Data syst.) ⊕ (stat. -1 = 7 TeV, 4.6 fb s Data NLO MSTW2008 ⊗ MCFM CT10 ⊗ MCFM NNPDF2.3 ⊗ MCFM MSTW2008 ⊗ aMC@NLO 4FNS MSTW2008 ⊗ aMC@NLO 5FNS LO multileg CT10 ⊗ SHERPA CTEQ6L1 ⊗ ALPGEN+HJ ATLAS 1 b-jet ≥ Z+ (a) (Zbb) [pb] σ 0 0.1 0.2 0.3 0.4 0.5 0.6 (stat.) -1 = 7 TeV, 4.6 fb s Data syst.) ⊕ (stat. -1 = 7 TeV, 4.6 fb s Data NLO MSTW2008 ⊗ MCFM CT10 ⊗ MCFM NNPDF2.3 ⊗ MCFM MSTW2008 ⊗ aMC@NLO 4FNS MSTW2008 ⊗ aMC@NLO 5FNS LO multileg CT10 ⊗ SHERPA CTEQ6L1 ⊗ ALPGEN+HJ ATLAS 2 b-jet ≥ Z+ (b) Figure 6. Cross-sections for (a) Z+ ≥1 b-jet, and (b) Z+ ≥2 b-jets. 10 Results The measurement is shown as a vertical blue line with the inner blue shaded band showing the corresponding statistical uncertainty and the outer green shaded band showing the sum in quadrature of statistical and systematic uncertainties. Comparison is made to NLO predictions from mcfm interfaced to different PDF sets and amc@nlo interfaced to the same PDF set in both the 4FNS and 5FNS. The statistical (inner bar) and total (outer bar) uncertainties are shown for these predictions, which are dominated by the theoretical scale uncertainty calculated as described in the text. Comparisons are also made to LO multi-legged predictions from Alpgen+Herwig+Jimmy and Sherpa; in this case the uncertainty bars are statistical only, and smaller than the marker. (Zb) [pb] σ 0 1 2 3 4 5 6 (stat.) -1 = 7 TeV, 4.6 fb s Data syst.) ⊕ (stat. -1 = 7 TeV, 4.6 fb s Data NLO MSTW2008 ⊗ MCFM CT10 ⊗ MCFM NNPDF2.3 ⊗ MCFM MSTW2008 ⊗ aMC@NLO 4FNS MSTW2008 ⊗ aMC@NLO 5FNS LO multileg CT10 ⊗ SHERPA CTEQ6L1 ⊗ ALPGEN+HJ ATLAS 1 b-jet ≥ Z+ (a) (Zbb) [pb] σ 0 0.1 0.2 0.3 0.4 0.5 0.6 (stat.) -1 = 7 TeV, 4.6 fb s Data syst.) ⊕ (stat. -1 = 7 TeV, 4.6 fb s Data NLO MSTW2008 ⊗ MCFM CT10 ⊗ MCFM NNPDF2.3 ⊗ MCFM MSTW2008 ⊗ aMC@NLO 4FNS MSTW2008 ⊗ aMC@NLO 5FNS LO multileg CT10 ⊗ SHERPA CTEQ6L1 ⊗ ALPGEN+HJ ATLAS 2 b-jet ≥ Z+ (b) JHEP10(2014)141 (b) (a) Figure 6. Cross-sections for (a) Z+ ≥1 b-jet, and (b) Z+ ≥2 b-jets. The measurement is shown as a vertical blue line with the inner blue shaded band showing the corresponding statistical uncertainty and the outer green shaded band showing the sum in quadrature of statistical and systematic uncertainties. Comparison is made to NLO predictions from mcfm interfaced to different PDF sets and amc@nlo interfaced to the same PDF set in both the 4FNS and 5FNS. The statistical (inner bar) and total (outer bar) uncertainties are shown for these predictions, which are dominated by the theoretical scale uncertainty calculated as described in the text. Comparisons are also made to LO multi-legged predictions from Alpgen+Herwig+Jimmy and Sherpa; in this case the uncertainty bars are statistical only, and smaller than the marker. 10 Results though there is evidence for disagreement at very high Z boson pT, and a slope in the ratio of the mcfm prediction to data for the Z boson rapidity. In general, good agreement with the data can be seen for ∆y(Z, b) and yboost(Z, b) in figure 9, though with some evidence for a slope in the ratio of amc@nlo 4FNS relative to the data for yboost(Z, b). In ∆φ(Z, b) (figure 10) the fixed-order pQCD prediction from mcfm has significant discrepancy at ∆φ(Z, b) = π, which also distorts the ∆R(Z, b) prediction. This is due to the fixed-order calculation containing at most one or two outgoing partons in association with the Z boson. In the case of one parton, ∆φ(Z, b) = π by construction, leading to the distorted distribution. The inclusion of higher multiplicity matrix elements in Alpgen and Sherpa, and matching to parton shower models in Alpgen, Sherpa and amc@nlo helps to populate the ∆φ(Z, b) distribution in a way which yields a much better agreement with data. This emphasises the importance of higher order effects when considering such distributions. The region of low ∆φ(Z, b), which is most sensitive to additional QCD radiation as well as soft corrections, is also poorly modelled by mcfm; these effects are not fully captured in the non-perturbative corrections applied to that prediction. For the Z+ ≥2 b-jets differential cross-sections shown in figures 11 and 12, all predic- tions provide reasonable descriptions of the data within the large experimental uncertain- ties. There is some evidence for disagreements between predictions and data at low m(b, b) and low ∆R(b, b). 10 Results Finally, figure 13 compares the mcfm predictions obtained using different PDFs to the data for the Z boson rapidity distribution, which is the distribution found to have the – 21 – 2 [pb/GeV] b-jets /N ) T d(b-jet p (Zb) σ d -4 10 -3 10 -2 10 -1 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.6 0.8 1 1.2 1.4 [GeV] T b-jet p 30 40 50 2 10 2 10 × 2 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 [pb] b-jets /N d(b-jet |y|) (Zb) σ d 0.5 1 1.5 2 2.5 3 3.5 4 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.6 0.8 1 1.2 1.4 b-jet |y| 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) Figure 7. The inclusive b-jet cross-section σ(Zb) × Nb-jet as a function of b-jet pT (a) and |y| (b). The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. 10 Results 2 [pb/GeV] b-jets /N ) T d(b-jet p (Zb) σ d -4 10 -3 10 -2 10 -1 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.6 0.8 1 1.2 1.4 [GeV] T b-jet p 30 40 50 2 10 2 10 × 2 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 [pb] b-jets /N d(b-jet |y|) (Zb) σ d 0.5 1 1.5 2 2.5 3 3.5 4 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.6 0.8 1 1.2 1.4 b-jet |y| 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) JHEP10(2014)141 (b) (a) Figure 7. The inclusive b-jet cross-section σ(Zb) × Nb-jet as a function of b-jet pT (a) and |y| (b). The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. gure 7. The inclusive b-jet cross-section σ(Zb) × Nb-jet as a function of b-jet pT (a) and (b). The top panels show measured differential cross-sections as filled circles with statistical largest dependence on the PDF set used. It can be seen that, while the different PDF sets do yield different results, they all show a similar trend relative to the data, and the differences are small compared to the theoretical scale uncertainty. 11 Conclusions Differential Z+b-jets cross-section measurements from the LHC have been presented using 4.6 fb−1 of √s = 7 TeV pp collision data recorded by the ATLAS detector in 2011. In total, 12 distributions for Z+ ≥1 b-jet and Z+ ≥2 b-jets topologies have been investigated and compared to theoretical pQCD calculations. Next-to-leading-order predictions from mcfm and amc@nlo generally provide the best overall description of the data. The agreement of the amc@nlo cross-section prediction with data differs in the Z+ ≥1 b-jet and Z+ ≥ 2 b-jets cases, with the former better described by the 5FNS prediction and the latter better described by the 4FNS prediction. Even at NLO, scale uncertainties dominate and currently limit any sensitivity to different PDF sets. Descriptions of the shapes of the differential cross-sections are generally good within uncertainties for both LO and NLO predictions. For angular distributions in the Z+ ≥1 b-jet selection, where the fixed-order – 22 – 2 [pb/GeV] (Z)) T d(p (Zb) σ d -4 10 -3 10 -2 10 -1 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.5 1 1.5 2 (Z) [GeV] T p 4 5 6 10 20 30 2 10 2 10 × 2 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 0.5 1 1.5 2 2.5 [pb] d(|y(Z)|) (Zb) σ d 0.5 1 1.5 2 2.5 3 3.5 4 4.5 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.6 0.8 1 1.2 1.4 |y(Z)| 0 0.5 1 1.5 2 2.5 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) Figure 8. The cross-section σ(Zb) as a function of Z boson pT (a) and |y| (b). The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. 11 Conclusions 2 [pb/GeV] (Z)) T d(p (Zb) σ d -4 10 -3 10 -2 10 -1 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.5 1 1.5 2 (Z) [GeV] T p 4 5 6 10 20 30 2 10 2 10 × 2 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 0.5 1 1.5 2 2.5 [pb] d(|y(Z)|) (Zb) σ d 0.5 1 1.5 2 2.5 3 3.5 4 4.5 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.6 0.8 1 1.2 1.4 |y(Z)| 0 0.5 1 1.5 2 2.5 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) JHEP10(2014)141 (b) (a) Figure 8. The cross-section σ(Zb) as a function of Z boson pT (a) and |y| (b). The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. NLO prediction is observed to break down, the differential shapes in data are well modelled by LO multi-legged predictions. NLO prediction is observed to break down, the differential shapes in data are well modelled by LO multi-legged predictions. Acknowledgments We thank CERN for the very successful operation of the LHC, as well as the support staff from our institutions without whom ATLAS could not be operated efficiently. We acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Aus- tralia; BMWF and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Re- public; DNRF, DNSRC and Lundbeck Foundation, Denmark; EPLANET, ERC and NSRF, European Union; IN2P3-CNRS, CEA-DSM/IRFU, France; GNSF, Georgia; BMBF, DFG, HGF, MPG and AvH Foundation, Germany; GSRT and NSRF, Greece; ISF, MIN- ERVA, GIF, I-CORE and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; FOM and NWO, Netherlands; BRF and RCN, Norway; MNiSW and NCN, Poland; GRICES and FCT, Portugal; MNE/IFA, Romania; MES of Russia and – 23 – -1 [pb] b-jets /N y(Z,b) ∆ d *(Zb) σ d 0.5 1 1.5 2 2.5 3 3.5 4 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ (Z)>20 GeV T p Data NLO 0.6 0.8 1 1.2 1.4 y(Z,b) ∆ -1 10 1 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 0.5 1 1.5 2 2.5 [pb] b-jets /N (Z,b)) boost d(y (Zb) σ d 1 2 3 4 5 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.6 0.8 1 1.2 1.4 (Z,b) boost y 0 0.5 1 1.5 2 2.5 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) Figure 9. The inclusive b-jet cross-sections σ∗(Zb) × Nb-jet as a function of ∆y(Z, b) (a) and σ(Zb) × Nb-jet as a function of yboost(Z, b) (b). The former inclusive cross-section requires that the Z boson pT be at least 20 GeV. The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. Acknowledgments The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. -1 [pb] b-jets /N y(Z,b) ∆ d *(Zb) σ d 0.5 1 1.5 2 2.5 3 3.5 4 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ (Z)>20 GeV T p Data NLO 0.6 0.8 1 1.2 1.4 y(Z,b) ∆ -1 10 1 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 0.5 1 1.5 2 2.5 [pb] b-jets /N (Z,b)) boost d(y (Zb) σ d 1 2 3 4 5 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ Data NLO 0.6 0.8 1 1.2 1.4 (Z,b) boost y 0 0.5 1 1.5 2 2.5 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) JHEP10(2014)141 (b) (a) Figure 9. The inclusive b-jet cross-sections σ∗(Zb) × Nb-jet as a function of ∆y(Z, b) (a) and σ(Zb) × Nb-jet as a function of yboost(Z, b) (b). The former inclusive cross-section requires that the Z boson pT be at least 20 GeV. The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. ROSATOM, Russian Federation; JINR; MSTD, Serbia; MSSR, Slovakia; ARRS and MIZˇS, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SER, SNSF and Cantons of Bern and Geneva, Switzerland; NSC, Taiwan; TAEK, Turkey; STFC, the Royal Society and Leverhulme Trust, United Kingdom; DOE and NSF, United States of America. The crucial computing support from all WLCG partners is acknowledged gratefully, in particular from CERN and the ATLAS Tier-1 facilities at TRIUMF (Canada), NDGF (Denmark, Norway, Sweden), CC-IN2P3 (France), KIT/GridKA (Germany), INFN-CNAF (Italy), NL-T1 (Netherlands), PIC (Spain), ASGC (Taiwan), RAL (U.K.) and BNL (U.S.A.) and in the Tier-2 facilities worldwide. Acknowledgments – 24 – 0 0.5 1 1.5 2 2.5 3 [pb/rad.] b-jets /N (Z,b) φ ∆ d *(Zb) σ d -1 10 1 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ (Z)>20 GeV T p Data NLO 1 2 (Z,b) φ ∆ 0 0.5 1 1.5 2 2.5 3 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 1 2 3 4 5 6 [pb] b-jets /N R(Z,b) ∆ d *(Zb) σ d -2 10 -1 10 1 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ (Z)>20 GeV T p Data NLO 0.5 1 1.5 R(Z,b) ∆ 0 1 2 3 4 5 6 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) Figure 10. The inclusive b-jet cross-section σ∗(Zb) × Nb-jet as a function of ∆φ(Z, b) (a) and ∆R(Z, b) (b). The inclusive cross-section requires that the Z boson pT be at least 20 GeV. The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total the- oretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dom- inant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alp- gen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. Acknowledgments 0 0.5 1 1.5 2 2.5 3 [pb/rad.] b-jets /N (Z,b) φ ∆ d *(Zb) σ d -1 10 1 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ (Z)>20 GeV T p Data NLO 1 2 (Z,b) φ ∆ 0 0.5 1 1.5 2 2.5 3 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 1 2 3 4 5 6 [pb] b-jets /N R(Z,b) ∆ d *(Zb) σ d -2 10 -1 10 1 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 1 b-jet ≥ Z+ (Z)>20 GeV T p Data NLO 0.5 1 1.5 R(Z,b) ∆ 0 1 2 3 4 5 6 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) JHEP10(2014)141 (a) (b) Figure 10. The inclusive b-jet cross-section σ∗(Zb) × Nb-jet as a function of ∆φ(Z, b) (a) and ∆R(Z, b) (b). The inclusive cross-section requires that the Z boson pT be at least 20 GeV. The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total the- oretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dom- inant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alp- gen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. – 25 – JHEP10(2014)141 0 50 100 150 200 250 [pb/GeV] (Z)) T d(p (Zbb) σ d -3 10 -2 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 2 b-jets ≥ Z+ Data NLO 0.5 1 (Z) [GeV] T p 0 50 100 150 200 250 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0 0.5 1 1.5 2 2.5 [pb] d(|y(Z)|) (Zbb) σ d 0.1 0.2 0.3 0.4 0.5 0.6 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 2 b-jets ≥ Z+ Data NLO 0.5 1 |y(Z)| 0 0.5 1 1.5 2 2.5 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) Figure 11. Acknowledgments The cross-section σ(Zbb) as a function of Z boson pT (a), and |y| (b). The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. 0 0.5 1 1.5 2 2.5 [pb] d(|y(Z)|) (Zbb) σ d 0.1 0.2 0.3 0.4 0.5 0.6 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 2 b-jets ≥ Z+ Data NLO 0.5 1 |y(Z)| 0 0.5 1 1.5 2 2.5 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) 0 50 100 150 200 250 [pb/GeV] (Z)) T d(p (Zbb) σ d -3 10 -2 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 2 b-jets ≥ Z+ Data NLO 0.5 1 (Z) [GeV] T p 0 50 100 150 200 250 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) (b) (a) Figure 11. The cross-section σ(Zbb) as a function of Z boson pT (a), and |y| (b). The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. Acknowledgments – 26 – JHEP10(2014)141 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 [pb] R(b,b) ∆ d (Zbb) σ d 0.05 0.1 0.15 0.2 0.25 0.3 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 2 b-jets ≥ Z+ Data NLO 0.5 1 R(b,b) ∆ 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) 50 100 150 200 250 300 350 [pb/GeV] d m(b,b) (Zbb) σ d -4 10 -3 10 -2 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 2 b-jets ≥ Z+ Data NLO 0.5 1 m(b,b) [GeV] 50 100 150 200 250 300 350 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 [pb] R(b,b) ∆ d (Zbb) σ d 0.05 0.1 0.15 0.2 0.25 0.3 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 2 b-jets ≥ Z+ Data NLO 0.5 1 R(b,b) ∆ 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 Data LO multileg 0.4 0.6 0.8 1 1.2 (b) Figure 12. The cross-section σ(Zbb) as a function of m(b, b) (a) and ∆R(b, b) (b). The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. 50 100 150 200 250 300 350 [pb/GeV] d m(b,b) (Zbb) σ d -4 10 -3 10 -2 10 aData -1 = 7 TeV, 4.6 fb s MCFM aMC@NLO 5FNS aMC@NLO 4FNS ALPGEN+HJ SHERPA ATLAS 2 b-jets ≥ Z+ Data NLO 0.5 1 m(b,b) [GeV] 50 100 150 200 250 300 350 Data LO multileg 0.4 0.6 0.8 1 1.2 (a) (b) (a) Figure 12. The cross-section σ(Zbb) as a function of m(b, b) (a) and ∆R(b, b) (b). Acknowledgments The top panels show measured differential cross-sections as filled circles with statistical (inner) and total (outer bar) uncertainties. Overlayed for comparison are the NLO predictions from mcfm and amc@nlo both using the MSTW2008 PDF set. The shaded bands represents the total theoretical uncertainty for mcfm and the uncertainty bands on amc@nlo points represent the dominant theoretical scale uncertainty only. Also overlaid are LO multi-legged predictions for Alpgen+Herwig+Jimmy and Sherpa. The middle panels show the ratio of NLO predictions to data, and the lower panels show the ratio of LO predictions to data. – 27 – JHEP10(2014)141 0 0.5 1 1.5 2 2.5 [pb] d(|y(Z)|) (Zb) σ d 0.5 1 1.5 2 2.5 3 3.5 4 4.5 -1 = 7 TeV, 4.6 fb s Data MSTW2008 ⊗ MCFM NNPDF2.3 ⊗ MCFM CT10 ⊗ MCFM ATLAS 1 b-jet ≥ Z+ |y(Z)| 0 0.5 1 1.5 2 2.5 Data NLO 0.8 1 1.2 1.4 (a) 0 0.5 1 1.5 2 2.5 [pb] d(|y(Z)|) (Zbb) σ d 0.1 0.2 0.3 0.4 0.5 0.6 -1 = 7 TeV, 4.6 fb s Data MSTW2008 ⊗ MCFM NNPDF2.3 ⊗ MCFM CT10 ⊗ MCFM ATLAS 2 b-jets ≥ Z+ |y(Z)| 0 0.5 1 1.5 2 2.5 Data NLO 0.5 1 (b) Figure 13. The mcfm prediction using different PDF sets for the cross-sections σ(Zb) (a) and σ(Zbb) (b) as a function of the Z boson |y|. The top panels show measured differential cross- sections as filled circles with statistical (inner) and total (outer bar) uncertainties. The shaded band represents the total theoretical uncertainty for mcfm interfaced to the MSTW2008 PDF set. Uncertainties on mcfm predictions with alternative PDF sets are statistical only. The lower panel shows the ratio of each prediction to data. 0 0.5 1 1.5 2 2.5 [pb] d(|y(Z)|) (Zbb) σ d 0.1 0.2 0.3 0.4 0.5 0.6 -1 = 7 TeV, 4.6 fb s Data MSTW2008 ⊗ MCFM NNPDF2.3 ⊗ MCFM CT10 ⊗ MCFM ATLAS 2 b-jets ≥ Z+ |y(Z)| 0 0.5 1 1.5 2 2.5 Data NLO 0.5 1 (b) 0 0.5 1 1.5 2 2.5 [pb] d(|y(Z)|) (Zb) σ d 0.5 1 1.5 2 2.5 3 3.5 4 4.5 -1 = 7 TeV, 4.6 fb s Data MSTW2008 ⊗ MCFM NNPDF2.3 ⊗ MCFM CT10 ⊗ MCFM ATLAS 1 b-jet ≥ Z+ |y(Z)| 0 0.5 1 1.5 2 2.5 Data NLO 0.8 1 1.2 1.4 (a) (b) (a) Figure 13. Acknowledgments The mcfm prediction using different PDF sets for the cross-sections σ(Zb) (a) and σ(Zbb) (b) as a function of the Z boson |y|. The top panels show measured differential cross- sections as filled circles with statistical (inner) and total (outer bar) uncertainties. The shaded band represents the total theoretical uncertainty for mcfm interfaced to the MSTW2008 PDF set. 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Fakhrutdinov129, S. Falciano133a, R.J. Falla77, J. Faltova128, Y. Fang33a, M. Fanti90a,90b, A. The ATLAS collaboration Cortes-Gonzalez12, G. Cortiana100, G. Costa90a, M.J. Costa168, D. Costanzo140, D. Cˆot´e8, G. Cottin28, G. Cowan76, B.E. Cox83, K. Cranmer109, G C 29 S C ´ ´ R di 55 F C i li79 W A C ibb 147a 147b M C i i O t 119 , , , , p , A.M. Cooper-Sarkar119, N.J. Cooper-Smith76, K. Copic15, T. Cornelissen176, M. Corradi20a, F Corriveau86,i A Corso Radu164 A Cortes Gonzalez12 G Cortiana100 G Costa90a A.M. Cooper-Sarkar119, N.J. Cooper-Smith76, K. Copic15, T. Cornelissen176, M. Corradi20a, F. Corriveau86,i, A. Corso-Radu164, A. Cortes-Gonzalez12, G. Cortiana100, G. Costa90a, M.J. Costa168, D. Costanzo140, D. Cˆot´e8, G. Cottin28, G. Cowan76, B.E. Cox83, K. Cranmer109, G. Cree29, S. Cr´ep´e-Renaudin55, F. Crescioli79, W.A. Cribbs147a,147b, M. Crispin Ortuzar119, M.J. Costa168, D. Costanzo140, D. Cˆot´e8, G. Cottin28, G. Cowan76, B.E. Cox83, K. Cranmer109 G. Cree29, S. Cr´ep´e-Renaudin55, F. Crescioli79, W.A. Cribbs147a,147b, M. Crispin Ortuzar119, – 34 – M. Cristinziani21, V. Croft105, G. Crosetti37a,37b, C.-M. Cuciuc26a, T. Cuhadar Donszelmann140 J. Cummings177, M. Curatolo47, C. Cuthbert151, H. Czirr142, P. Czodrowski3, Z. Czyczula177, g , , , , , y S. D’Auria53, M. D’Onofrio73, M.J. Da Cunha Sargedas De Sousa125a,125b, C. Da Via83, W. Dabrowski38a, A. Dafinca119, T. Dai88, O. Dale14, F. Dallaire94, C. Dallapiccola85, M. Dam3 A.C. Daniells18, M. Dano Hoffmann137, V. Dao48, G. Darbo50a, S. Darmora8, J.A. Dassoulas42, A. Dattagupta60, W. Davey21, C. David170, T. Davidek128, E. Davies119,c, M. Davies154, A. Dattagupta60, W. Davey21, C. David170, T. Davidek128, E. Davies119,c, M. Davies154, O. Davignon79, A.R. Davison77, P. Davison77, Y. Davygora58a, E. Dawe143, I. Dawson140, R.K. Daya-Ishmukhametova85, K. De8, R. de Asmundis103a, S. De Castro20a,20b, S. De Cecco79, R.K. Daya-Ishmukhametova85, K. De8, R. de Asmundis103a, S. De Castro20a,20b, S. De Cecco79 A. De Salvo133a, U. De Sanctis165a,165b, A. De Santo150, J.B. De Vivie De Regie116, a,165b, A. De Santo150, J.B. De Vivie De Regie1 A. De Salvo133a, U. De Sanctis165a,165b, A. De Santo150, J.B. De Vivie De Regie116, W.J. Dearnaley71, R. Debbe25, C. Debenedetti138, B. Dechenaux55, D.V. Dedovich64 JHEP10(2014)141 JHEP10(2014)141 I. Deigaard106, J. Del Peso81, T. Del Prete123a,123b, F. Deliot137, C.M. Delitzsch49, I. Deigaard106, J. Del Peso81, T. Del Prete123a,123b, F. Deliot137, C.M. Delitzsch49, M. Deliyergiyev74, A. Dell’Acqua30, L. Dell’Asta22, M. Dell’Orso123a,123b, M. Della Pi Deliyergiyev74, A. Dell’Acqua30, L. Dell’Asta22, M. Dell’Orso123a,123b, M. Della Pietra103a,h, D. della Volpe49, M. Delmastro5, P.A. Delsart55, C. Deluca106, S. Demers177, M. Demichev64 della Volpe49, M. Delmastro5, P.A. Delsart55, C. Deluca106, S. Demers177, M. Demichev64, A. The ATLAS collaboration Farbin8, A. Farilla135a, T. Farooque12 rrell15, S.M. Farrington171, P. Farthouat30, F. Fassi136e, P. Fassnacht30, D. Fassouliotis9, S. Farrell15, S.M. Farrington171, P. Farthouat30, F. Fassi136e, P. Fassnacht30, D. Fassouliotis9 A. Favareto50a,50b, L. Fayard116, P. Federic145a, O.L. Fedin122,j, W. Fedorko169, Favareto50a,50b, L. Fayard116, P. Federic145a, O.L. Fedin122,j, W. Fedorko169, M. Fehling-Kaschek48, S. Feigl30, L. Feligioni84, C. Feng33d, E.J. Feng6, H. Feng88, A.B. Fenyuk129, S. Fernandez Perez30, S. Ferrag53, J. Ferrando53, A. Ferrari167, P. Ferrari106 R. Ferrari120a, D.E. Ferreira de Lima53, A. Ferrer168, D. Ferrere49, C. Ferretti88, , , , p , p , M. Fincke-Keeler170, K.D. Finelli151, M.C.N. Fiolhais125a,125c, L. Fiorini168, A. Firan A. Fischer2, J. Fischer176, W.C. Fisher89, E.A. Fitzgerald23, M. Flechl48, I. Fleck142, P. Fleischmann88, S. Fleischmann176, G.T. Fletcher140, G. Fletcher75, T. Flick176, A. Floderus80, L.R. Flores Castillo174,k, A.C. Florez Bustos160b, M.J. Flowerdew100, A. Formica137, A. Forti83, D. Fortin160a, D. Fournier116, H. Fox71, S. Fracchia12, P. Francavilla79, M. Franchini20a,20b, S. Franchino30, D. Francis30, L. Franconi118, M. Franklin57, S. Franz61, M. Fraternali120a,120b, S.T. French28, C. Friedrich42, F. Friedrich44, D. Froidevaux30, J.A. Frost28, C. Fukunaga157, E. Fullana Torregrosa82, B.G. Fulsom144, J. Fuster168, C. Gabaldon55, O. Gabizon173, – 35 – A. Gabrielli20a,20b, A. Gabrielli133a,133b, S. Gadatsch106, S. Gadomski49, G. Gagliardi50a,50b, P. Gagnon60, C. Galea105, B. Galhardo125a,125c, E.J. Gallas119, V. Gallo17, B.J. Gallop130, P. Gallus127, G. Galster36, K.K. Gan110, R.P. Gandrajula62, J. Gao33b,g, Y.S. Gao144,e, F.M. Garay Walls46, F. Garberson177, C. Garc´ıa168, J.E. Garc´ıa Navarro168, M. Garcia-Sciveres R.W. Gardner31, N. Garelli144, V. Garonne30, C. Gatti47, G. Gaudio120a, B. Gaur142, L. Gauthier94, P. Gauzzi133a,133b, I.L. Gavrilenko95, C. Gay169, G. Gaycken21, E.N. Gazis10 P. Ge33d, Z. Gecse169, C.N.P. Gee130, D.A.A. Geerts106, Ch. Geich-Gimbel21, K. Gellerstedt147a,147b, C. Gemme50a, A. Gemmell53, M.H. Genest55, S. Gentile133a,1 K. Gellerstedt147a,147b, C. Gemme50a, A. Gemmell53, M.H. Genest55, S. Gentile133a,133b, g g B. Giacobbe20a, S. Giagu133a,133b, V. Giangiobbe12, P. Giannetti123a,123b, F. Gianotti30, B. Gibbard25, S.M. Gibson76, M. Gilchriese15, T.P.S. Gillam28, D. Gillberg30, G. Gilles34, JHEP10(2014)141 B. Gibbard25, S.M. Gibson76, M. Gilchriese15, T.P.S. Gillam28, D. Gillberg30, G. Gilles34, D.M. Gingrich3,d, N. Giokaris9, M.P. Giordani165a,165c, R. Giordano103a,103b, F.M. Giorgi20a, D.M. Gingrich3,d, N. Giokaris9, M.P. Giordani165a,165c, R. Giordano103a,103b, F.M. Giorgi20a, F.M. Giorgi16, P.F. Giraud137, D. Giugni90a, C. Giuliani48, M. Giulini58b, B.K. Gjelsten118, S. Gkaitatzis155, I. Gkialas155,l, L.K. Gladilin98, C. Glasman81, J. Glatzer30, P.C.F. Glaysher46, A. Glazov42, G.L. Glonti64, M. Goblirsch-Kolb100, J.R. Goddard75, J. Godfrey143, J. Godlewski3 C. Goeringer82, S. Goldfarb88, T. Golling177, D. Golubkov129, A. Gomes125a,125b,125d, L.S. Gomez Fajardo42, R. Gon¸calo125a, J. The ATLAS collaboration Goncalves Pinto Firmino Da Costa137, L. Gonella21, S. Gonz´alez de la Hoz168, G. Gonzalez Parra12, S. Gonzalez-Sevilla49, L. Goossens30, P.A. Gorbounov96, H.A. Gordon25, I. Gorelov104, B. Gorini30, E. Gorini72a,72b, A. Goriˇsek74, E. Gornicki39, A.T. Goshaw6, C. G¨ossling43, M.I. Gostkin64, M. Gouighri136a, D. Goujdami136c, M.P. Goulette49, A.G. Goussiou139, C. Goy5, S. Gozpinar23, H.M.X. Grabas137, L. Graber54, I. Grabowska-Bold38a, P. Grafstr¨om20a,20b, K-J. Grahn42, J. Gramling49, E. Gramstad118, S. Grancagnolo16, V. Grassi149, V. Gratchev122, H.M. Gray30, E. Graziani135a, O.G. Grebenyuk122, Z.D. Greenwood78,m, K. Gregersen77, I.M. Gregor42, P. Grenier144, J. Griffiths8, A.A. Grillo138, K. Grimm71, S. Grinstein12,n, Ph. Gris34, Y.V. Grishkevich98, P. Grohs44, A. Grohsjean42, E. Gross173, J. Gros G.C. Grossi134a,134b, J. Groth-Jensen173, Z.J. Grout150, L. Guan33b, F. Guescini49, D. Gue O. Gueta154, C. Guicheney34, E. Guido50a,50b, T. Guillemin116, S. Guindon2, U. Gul53, C. Gumpert44, J. Gunther127, J. Guo35, S. Gupta119, P. Gutierrez112, N.G. Gutierrez Ortiz53, C. Gutschow77, N. Guttman154, C. Guyot137, C. Gwenlan119, C.B. Gwilliam73, A. Haas109, C. Haber15, H.K. Hadavand8, N. Haddad136e, P. Haefner21, S. Hageb¨ock21, Z. Hajduk39, H. Hakobyan178, M. Haleem42, D. Hall119, G. Halladjian89, K. Hamacher176, P. Hamal114, K. Hamano170, M. Hamer54, A. Hamilton146a, S. Hamilton162, G.N. Hamity146c, P.G. Hamne L. Han33b, K. Hanagaki117, K. Hanawa156, M. Hance15, P. Hanke58a, R. Hanna137, J.B. Hanse Han33b, K. Hanagaki117, K. Hanawa156, M. Hanc J.D. Hansen36, P.H. Hansen36, K. Hara161, A.S. Hard174, T. Harenberg176, F. Hariri116, S. Harkusha91, D. Harper88, R.D. Harrington46, O.M. Harris139, P.F. Harrison171, F. Hartjes106 M. Hasegawa66, S. Hasegawa102, Y. Hasegawa141, A. Hasib112, S. Hassani137, S. Haug17, Hasegawa66, S. Hasegawa102, Y. Hasegawa141, A. Hasib112, S. Hassani137, S. Haug17, M. Hauschild30, R. Hauser89, M. Havranek126, C.M. Hawkes18, R.J. Hawkings30, A.D. Hawkins8 Hauschild30, R. Hauser89, M. Havranek126, C.M. Hawkes18, R.J. Hawkings30, A.D. Hawkins80, T. Hayashi161, D. Hayden89, C.P. Hays119, H.S. Hayward73, S.J. Haywood130, S.J. Head18 T. Heck82, V. Hedberg80, L. Heelan8, S. Heim121, T. Heim176, B. Heinemann15, L. Heinrich109, C. Helsens30, J. Henderson119, R.C.W. Henderson71, Y. Heng174, C. Hengler42, A. Henrichs177, , , , g , g A.M. Henriques Correia30, S. Henrot-Versille116, C. Hensel54, G.H. Herbert16, Y. Hern´andez Jim´enez168, R. Herrberg-Schubert16, G. Herten48, R. Hertenberger99, L. Hervas30, G G H k h77 N P H 106 R Hi kli 75 E Hi ´ R d i 168 E Hill170 J C Hill28 , g , , g , G.G. Hesketh77, N.P. Hessey106, R. Hickling75, E. Hig´on-Rodriguez168, E. Hill170, J.C. Hill28, K.H. Hiller42, S. Hillert21, S.J. Hillier18, I. Hinchliffe15, E. Hines121, M. The ATLAS collaboration Kastanas14, Y. Kataoka156, A. Katre49, J. Katzy42, V. Kaushik7, K. Kawagoe69, T. Kawamoto156, G. Kawamura54, S. Kazama156, V.F. Kaz M.Y. Kazarinov64, R. Keeler170, R. Kehoe40, M. Keil54, J.S. Keller42, J.J. Kempster76, M.Y. Kazarinov64, R. Keeler170, R. Kehoe40, M. Keil54, J.S. Keller42, J.J. Kempster76, F. Khalil-zada11, H. Khandanyan147a,147b, A. Khanov113, A. Khodinov97, A. Khomich58a, F. Khalil-zada11, H. Khandanyan147a,147b, A. Khanov113, A. Khodinov97, A. Khomich58a, T.J. Khoo28, G. Khoriauli21, A. Khoroshilov176, V. Khovanskiy96, E. Khramov64, J. Khubu H.Y. Kim8, H. Kim147a,147b, S.H. Kim161, N. Kimura172, O. Kind16, B.T. King73, M. King168, R.S.B. King119, S.B. King169, J. Kirk130, A.E. Kiryunin100, T. Kishimoto66, D. Kisielewska3 F. Kiss48, T. Kittelmann124, K. Kiuchi161, E. Kladiva145b, M. Klein73, U. Klein73, K. Kleinknecht82, P. Klimek147a,147b, A. Klimentov25, R. Klingenberg43, J.A. Klinger83 einknecht82, P. Klimek147a,147b, A. Klimentov25, R. Klingenberg43, J.A. Klinger83, T. Klioutchnikova30, P.F. Klok105, E.-E. Kluge58a, P. Kluit106, S. Kluth100, E. Kneringer61, Klioutchnikova30, P.F. Klok105, E.-E. Kluge58a, P. Kluit106, S. Kluth100, E. Kneringer61, E.B.F.G. Knoops84, A. Knue53, D. Kobayashi158, T. Kobayashi156, M. Kobel44, M. Kocian14 B.F.G. Knoops84, A. Knue53, D. Kobayashi158, T. Kobayashi156, M. Kobel44, M. Kocian144, P. Kodys128, P. Koevesarki21, T. Koffas29, E. Koffeman106, L.A. Kogan119, S. Kohlmann176, Kodys128, P. Koevesarki21, T. Koffas29, E. Koffeman106, L.A. Kogan119, S. Kohlmann176, Kohout127, T. Kohriki65, T. Koi144, H. Kolanoski16, I. Koletsou5, J. Koll89, A.A. Komar95,∗, Z. Kohout127, T. Kohriki65, T. Koi144, H. Kolanoski16, I. Koletsou5, J. Koll89, A.A. Komar95,∗ Y. Komori156, T. Kondo65, N. Kondrashova42, K. K¨oneke48, A.C. K¨onig105, S. K¨onig82, Y. Komori156, T. Kondo65, N. Kondrashova42, K. K¨oneke48, A.C. K¨onig105, S. K¨onig82, Kono65,r, R. Konoplich109,s, N. Konstantinidis77, R. Kopeliansky153, S. Koperny38a, T. Kono65,r, R. Konoplich109,s, N. Konstantinidis77, R. Kopeliansky153, S. Koperny38a, L. K¨opke82, A.K. Kopp48, K. Korcyl39, K. Kordas155, A. Korn77, A.A. Korol108,t, I. Korolk K¨opke82, A.K. Kopp48, K. Korcyl39, K. Kordas155, A. Korn77, A.A. Korol108,t, I. Korolkov12, E.V. Korolkova140, V.A. Korotkov129, O. Kortner100, S. Kortner100, V.V. Kostyukhin21, E.V. Korolkova140, V.A. Korotkov129, O. Kortner100, S. Kortner100, V.V. Kostyukhin21, R. Kowalewski170, T.Z. Kowalski38a, W. Kozanecki137, A.S. Kozhin129, V. Kral127, R. Kowalewski170, T.Z. Kowalski38a, W. Kozanecki137, A.S. Kozhin129, V. Kral127, V.A. Kramarenko98, G. Kramberger74, D. Krasnopevtsev97, M.W. Krasny79, A. Kr J.K. Kraus21, A. Kravchenko25, S. Kreiss109, M. Kretz58c, J. Kretzschmar73, K. Kreutzfeldt52 J.K. Kraus21, A. Kravchenko25, S. Kreiss109, M. Kretz58c, J. Kretzschmar73, K. Kreu P. Krieger159, K. Kroeninger54, H. Kroha100, J. Kroll121, J. Kroseberg21, J. Krstic13a, U. Kruchonak64, H. Kr¨uger21, T. Kruker17, N. Krumnack63, Z.V. Krumshteyn64, A. Kr M.C. Kruse45, M. The ATLAS collaboration Hirose158, D. Hirschbuehl176, J. Hobbs149, N. Hod106, M.C. Hodgkinson140, P. Hodgson140, A. Hoecker30, M.R. Hoeferkamp104, F. Hoenig99, J. Hoffman40, D. Hoffmann84, J.I. Hofmann58a, M. Hohlfeld8 T.R. Holmes15, T.M. Hong121, L. Hooft van Huysduynen109, J-Y. Hostachy55, S. Hou152, – 36 – A. Hoummada136a, J. Howard119, J. Howarth42, M. Hrabovsky114, I. Hristova16, J. Hrivnac116, , , , y , , T. Hryn’ova5, C. Hsu146c, P.J. Hsu82, S.-C. Hsu139, D. Hu35, X. Hu25, Y. Huang42, Z. Hubac y , , , , , , g , F. Hubaut84, F. Huegging21, T.B. Huffman119, E.W. Hughes35, G. Hughes71, M. Huhtinen30, T.A. H¨ulsing82, M. Hurwitz15, N. Huseynov64,b, J. Huston89, J. Huth57, G. Iacobucci49, G. Iakovidis10, I. Ibragimov142, L. Iconomidou-Fayard116, E. Ideal177, P. Iengo103a, O. Igonkina10 T. Iizawa172, Y. Ikegami65, K. Ikematsu142, M. Ikeno65, Y. Ilchenko31,o, D. Iliadis155, N. I Y. Inamaru66, T. Ince100, P. Ioannou9, M. Iodice135a, K. Iordanidou9, V. Ippolito57, A. Irles Quiles168, C. Isaksson167, M. Ishino67, M. Ishitsuka158, R. Ishmukhametov110, A. Irles Quiles168, C. Isaksson167, M. Ishino67, M. Ishitsuka158, R. Ishmukhametov110, H. Iwasaki65, J.M. Izen41, V. Izzo103a, B. Jackson121, M. Jackson73, P. Jackson1, M.R. Jaekel30, H. Iwasaki65, J.M. Izen41, V. Izzo103a, B. Jackson121, M. Jackson73, P. Jackson1, M.R. Jaekel30, JHEP10(2014)141 E. Jansen77, H. Jansen30, J. Janssen21, M. Janus171, G. Jarlskog80, N. Javadov64,b, T. Jav˚urek48, S. J´ez´equel5, H. Ji174, J. Jia149, Y. Jiang33b, M. Jimenez Belenguer42, S. Jin33a, A. Jinaru26a, K. Jon-And147a,147b, G. Jones171, R.W.L. Jones71, T.J. Jones73, J. Jongmanns58a, Jon-And147a,147b, G. Jones171, R.W.L. Jones71, T.J. Jones73, J. Jongmanns58a, K. Jon-And147a,147b, G. Jones171, R.W.L. Jones71, T.J. Jones73, J. Jongmanns58a, 125 125b 83 148 174 43 30 M. Jorge125a,125b, K.D. Joshi83, J. Jovicevic148, X. Ju174, C.A. Jung43, R.M. Jungst30, P.M. Jorge125a,125b, K.D. Joshi83, J. Jovicevic148, X. Ju174, C.A. Jung43, R.M. Jungst30, P. Jussel61, A. Juste Rozas12,n, M. Kaci168, A. Kaczmarska39, M. Kado116, H. Kagan110, Jussel61, A. Juste Rozas12,n, M. Kaci168, A. Kaczmarska39, M. Kado116, H. Kagan110, M. Kagan144, E. Kajomovitz45, C.W. Kalderon119, S. Kama40, A. Kamenshchikov129, Kagan144, E. Kajomovitz45, C.W. Kalderon119, S. Kama40, A. Kamenshchikov129, Kanaya156, M. Kaneda30, S. Kaneti28, V.A. Kantserov97, J. Kanzaki65, B. Kaplan109, N. Kanaya156, M. Kaneda30, S. Kaneti28, V.A. Kantserov97, J. Kanzaki65, B. Kaplan109, A. Kapliy31, D. Kar53, K. Karakostas10, N. Karastathis10, M. Karnevskiy82, S.N. Karpov64, Kapliy31, D. Kar53, K. Karakostas10, N. Karastathis10, M. Karnevskiy82, S.N. Karpov64, Z.M. Karpova64, K. Karthik109, V. Kartvelishvili71, A.N. Karyukhin129, L. Kashif174, Karpova64, K. Karthik109, V. Kartvelishvili71, A.N. Karyukhin129, L. Kashif174, G. Kasieczka58b, R.D. Kass110, A. The ATLAS collaboration Kruskal22, T. Kubota87, S. Kuday4a, S. Kuehn48, A. Kugel58c, A. Kuhl138, T. Kuhl42, V. Kukhtin64, Y. Kulchitsky91, S. 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Lenzen176, B. Lenzi30, , , , y , , , R. Leone7, S. Leone123a,123b, K. Leonhardt44, C. Leonidopoulos46, S. Leontsinis10, C. Leroy94, JHEP10(2014)141 JHEP10(2014)141 C.G. Lester28, C.M. Lester121, M. Levchenko122, J. Levˆeque5, D. Levin88, L.J. Levinson173, M. Levy18, A. Lewis119, G.H. Lewis109, A.M. Leyko21, M. Leyton41, B. Li33b,u, B. Li84, H. Li149 y , , , y , y , , , , H.L. Li31, L. Li45, L. Li33e, S. Li45, Y. Li33c,v, Z. Liang138, H. Liao34, B. Liberti134a, P. Lichard30, K. Lie166, J. Liebal21, W. Liebig14, C. Limbach21, A. Limosani87, S.C. Lin152,w, T.H. Lin82, F. Linde106, B.E. Lindquist149, J.T. Linnemann89, E. Lipeles121, A. Lipniacka14, M. Lisovyi42, T M Liss166 D Lissauer25 A Lister169 A M Litke138 B Liu152 D Liu152 J B Liu33b F. Linde106, B.E. Lindquist149, J.T. Linnemann89, E. Lipeles121, A. Lipniacka14, M. Lisovyi42, T.M. Liss166, D. Lissauer25, A. Lister169, A.M. Litke138, B. Liu152, D. Liu152, J.B. Liu33b, K. Liu33b,x, L. Liu88, M. Liu45, M. Liu33b, Y. Liu33b, M. Livan120a,120b, S.S.A. Livermore119, A. Lleres55, J. Llorente Merino81, S.L. Lloyd75, F. Lo Sterzo152, E. Lobodzinska42, P. Loch7, W.S. Lockman138, T. Loddenkoetter21, F.K. Loebinger83, A.E. Loevschall-Jensen36, A. Loginov177, T. Lohse16, K. Lohwasser42, M. Lokajicek126, V.P. Lombardo5, B.A. Long22, J.D. Long88, R.E. Long71, L. Lopes125a, D. Lopez Mateos57, B. Lopez Paredes140, I. Lopez Paz J. Lorenz99, N. Lorenzo Martinez60, M. Losada163, P. Loscutoff15, X. Lou41, A. The ATLAS collaboration Lounis116, J. Love6, P.A. Love71, A.J. Lowe144,e, F. Lu33a, N. Lu88, H.J. Lubatti139, C. Luci133a,133b, A. Lucotte55, F. Luehring60, W. Lukas61, L. Luminari133a, O. Lundberg14 B. Lund-Jensen 8, M. Lungwitz8 , D. Lynn 5, R. Lysak 6, E. Lytken80, H. Ma 5, L.L. Ma33d, G. Maccarrone47, A. Macchiolo100, J. Machado Miguens125a,125b, D. Macina30, D. Madaffari84, G. Maccarrone47, A. Macchiolo100, J. Machado Miguens125a,125b, D. Macina30, D. Madaffari84, R. Madar48, H.J. Maddocks71, W.F. Mader44, A. Madsen167, M. Maeno8, T. Maeno25, E. Magradze54, K. Mahboubi48, J. Mahlstedt106, S. Mahmoud73, C. Maiani137, C. Maidantchik24a, A.A. Maier100, A. Maio125a,125b,125d, S. Majewski115, Y. Makida65, N. Makovec116, P. Mal137,y, B. Malaescu79, Pa. Malecki39, V.P. Maleev122, F. Malek55, U. Mallik62, D. Malon6, C. Malone144, S. Maltezos10, V.M. Malyshev108, S. Malyukov30, J. Mamuzic13b, B. Mandelli30, L. Mandelli90a, I. Mandi´c74, R. Mandrysch62, J. Maneira125a, J. Mamuzic , B. Mandelli , L. Mandelli , I. Mandic , R. Mandrysch , J. Maneira , A Manfredini100 L Manhaes de Andrade Filho24b J A Manjarres Ramos160b A Mann99 A. Manfredini100, L. Manhaes de Andrade Filho24b, J.A. Manjarres Ramos160b, A. Mann99, P.M. Manning138, A. Manousakis-Katsikakis9, B. Mansoulie137, R. Mantifel86, L. Mapelli30, L. March168, J.F. Marchand29, G. Marchiori79, M. Marcisovsky126, C.P. Marino170, L. March168, J.F. Marchand29, G. Marchiori79, M. Marcisovsky126, C.P. Marino170, M. Marjanovic13a, C.N. Marques125a, F. Marroquim24a, S.P. Marsden83, Z. Marshall15, L.F. Marti17, S. Marti-Garcia168, B. Martin30, B. Martin89, T.A. Martin171, V.J. Martin46, B. Martin dit Latour14, H. Martinez137, M. Martinez12,n, S. Martin-Haugh130, A.C. Martyniuk77, M. Marx139, F. Marzano133a, A. Marzin30, L. Masetti82, T. Mashimo156, R. Mashinistov95, J. Masik83, A.L. Maslennikov108, I. Massa20a,20b, L. Massa20a,20b, N. Massol5, P. Mastrandrea149, A. Mastroberardino37a,37b, T. Masubuchi156, P. M¨attig176, J. Mattmann82, J. Maurer26a, S.J. Maxfield73, D.A. Maximov108,t, R. Mazini152, L. Mazzaferro134a,134b, G. Mc Goldrick159, S.P. Mc Kee88, A. McCarn88, R.L. McCarthy149, T.G. McCarthy29, N.A. McCubbin130, K.W. McFarlane56,∗, J.A. Mcfayden77, G. Mchedlidze54, S.J. McMahon130, R.A. McPherson170,i, A. Meade85, J. Mechnich106, M. Medinnis42, S. Meehan31, S. Mehlhase99, A. Mehta73, K. Meier58a, C. Meineck99, B. Meirose80, C. Melachrinos31, B.R. Mellado Garcia146c, F. Meloni17, A. Mengarelli20a,20b, S. Menke100, E. Meoni162, K.M. Mercurio57, S. Mergelmeyer21, N. Meric137, P. Mermod49, L. Merola103a,103b, C. Meroni90a, F.S. Merritt31, H. Merritt110, A. Messina30,z, J. Metcalfe25, A.S. Mete164, C. Meyer82, C. Meyer121, J-P. Meyer137, J. Meyer30, L. March , J.F. Marchand , G. Marchiori , M. Marcisovsky , C.P. Marino , M. Marjanovic13a, C.N. Marques125a, F. Marroquim24a, S.P. Marsden83, Z. Marshall15, L.F. Marti17, S. Marti-Garcia168, B. Martin30, B. The ATLAS collaboration Martin89, T.A. Martin171, V.J. Martin46, B. Martin dit Latour14, H. Martinez137, M. Martinez12,n, S. Martin-Haugh130, A.C. Martyniuk77, M. Marx139, F. Marzano133a, A. Marzin30, L. Masetti82, T. Mashimo156, R. Mashinistov95, J. Masik83, A.L. Maslennikov108, I. Massa20a,20b, L. Massa20a,20b, N. Massol5, P. Mastrandrea149, A. Mastroberardino37a,37b, T. Masubuchi156, P. M¨attig176, J. Mattmann82, J. Maurer26a, S.J. Maxfield73, D.A. Maximov108,t, R. Mazini152, L. Mazzaferro134a,134b, G. Mc Goldrick159, S.P. Mc Kee88, A. McCarn88, R.L. McCarthy149, T.G. McCarthy29, N.A. McCubbin130, K.W. McFarlane56,∗, J.A. Mcfayden77, G. Mchedlidze54, S.J. McMahon130, R.A. McPherson170,i, A. Meade85, J. Mechnich106, M. Medinnis42, S. Meehan31, S. Mehlhase99, A. Mehta73, K. Meier58a, C. Meineck99, B. Meirose80, C. Melachrinos31, B.R. Mellado Garcia146c, F. Meloni17, A. Mengarelli20a,20b, S. Menke100, E. Meoni162, K.M. Mercurio57, S. Mergelmeyer21, N. Meric137, P. Mermod49, L. Merola103a,103b, C. Meroni90a, F.S. Merritt31, H. Merritt110, A. Messina30,z, J. Metcalfe25, A.S. Mete164, C. Meyer82, C. Meyer121, J-P. Meyer137, J. Meyer30, M. Marjanovic13a, C.N. Marques125a, F. Marroquim24a, S.P. Marsden83, Z. Marshall15, L.F. Marti17, S. Marti-Garcia168, B. Martin30, B. Martin89, T.A. Martin171, V.J. Martin46, – 38 – R.P. Middleton130, S. Migas73, L. Mijovi´c21, G. Mikenberg173, M. Mikestikova126, M. Mikuˇz74, A. Milic30, D.W. Miller31, C. Mills46, A. Milov173, D.A. Milstead147a,147b, D. Milstein173, R.P. Middleton130, S. Migas73, L. Mijovi´c21, G. Mikenberg173, M. Mikestikova126, M. Mikuˇz74, 30 31 46 173 147 147b 173 A. Milic30, D.W. Miller31, C. Mills46, A. Milov173, D.A. Milstead147a,147b, D. Milstein173, , , , , , , A.A. Minaenko129, I.A. Minashvili64, A.I. Mincer109, B. Mindur38a, M. Mineev64, Y. Ming174, L.M. Mir12, G. Mirabelli133a, T. Mitani172, J. Mitrevski99, V.A. Mitsou168, S. Mitsui65, A. Miucci49, P.S. Miyagawa140, J.U. Mj¨ornmark80, T. Moa147a,147b, K. Mochizuki84, S. Mohapatra35, W. Mohr48, S. Molander147a,147b, R. Moles-Valls168, K. M¨onig42, C. Monini55, J. Monk36, E. Monnier84, J. Montejo Berlingen12, F. Monticelli70, S. Monzani133a,133b, R.W. Moore3, A. Moraes53, N. Morange62, D. Moreno82, M. Moreno Ll´acer54, P. Morettini50a L. Morvaj102, H.G. Moser100, M. Mosidze51b, J. Moss110, K. Motohashi158, R. Mount144, L. Morvaj102, H.G. Moser100, M. Mosidze51b, J. Moss110, K. Motohashi158, R. Mount144, E. Mountricha25, S.V. Mouraviev95,∗, E.J.W. Moyse85, S. Muanza84, R.D. Mudd18, F. Mueller5 JHEP10(2014)141 JHEP10(2014)141 J. Mueller124, K. Mueller21, T. Mueller28, T. Mueller82, D. Muenstermann49, Y. Munwes154, J. Mueller124, K. Mueller21, T. Mueller28, T. Mueller82, D. Muenstermann49, Y. Munwes154, A. Murillo Quijada18, W.J. Murray171,130, H. Musheghyan54, E. Musto153, A.G. Myagkov129,aa, J.A. Murillo Quijada18, W.J. Murray171,130, H. Musheghyan54, E. Musto153, A.G. Myagko M. Myska127, O. Nackenhorst54, J. Nadal54, K. Nagai61, R. Nagai158, Y. Nagai84, K. Nagano65, M. The ATLAS collaboration Myska127, O. Nackenhorst54, J. Nadal54, K. Nagai61, R. Nagai158, Y. Nagai84, K. Nagano65, A. Nagarkar110, Y. Nagasaka59, M. Nagel100, A.M. Nairz30, Y. Nakahama30, K. Nakamur Nagarkar110, Y. Nagasaka59, M. Nagel100, A.M. Nairz30, Y. Nakahama30, K. Nakamura65, T. Nakamura156, I. Nakano111, H. Namasivayam41, G. Nanava21, R. Narayan58b, T. Nakamura156, I. Nakano111, H. Namasivayam41, G. Nanava21, R. Narayan58b, T. Nattermann21, T. Naumann42, G. Navarro163, R. Nayyar7, H.A. Neal88, P.Yu. Nechaeva95, T. Nattermann21, T. Naumann42, G. Navarro163, R. Nayyar7, H.A. Neal88, P.Yu. Nechae T.J. Neep83, P.D. Nef144, A. Negri120a,120b, G. Negri30, M. Negrini20a, S. Nektarijevic49, T.J. Neep83, P.D. Nef144, A. Negri120a,120b, G. Negri30, M. Negrini20a, S. Nektarijevic49, A. Nelson164, T.K. Nelson144, S. Nemecek126, P. Nemethy109, A.A. Nepomuceno24a, M. N Nelson164, T.K. Nelson144, S. Nemecek126, P. Nemethy109, A.A. Nepomuceno24a, M. Nessi30,ab, M.S. Neubauer166, M. Neumann176, R.M. Neves109, P. Nevski25, P.R. Newman18, D.H. N S. Neubauer166, M. Neumann176, R.M. Neves109, P. Nevski25, P.R. Newman18, D.H. Nguyen6, R.B. Nickerson119, R. Nicolaidou137, B. Nicquevert30, J. Nielsen138, N. Nikiforou35, B. Nickerson119, R. Nicolaidou137, B. Nicquevert30, J. Nielsen138, N. Nikiforou35, A. Nikiforov16, V. Nikolaenko129,aa, I. Nikolic-Audit79, K. Nikolics49, K. Nikolopoulos18, Nikiforov16, V. Nikolaenko129,aa, I. Nikolic-Audit79, K. Nikolics49, K. Nikolopoulos18, P. Nilsson8, Y. Ninomiya156, A. Nisati133a, R. Nisius100, T. Nobe158, L. Nodulman6, P. Nilsson8, Y. Ninomiya156, A. Nisati133a, R. Nisius100, T. Nobe158, L. Nodulman6, Nomachi117, I. Nomidis29, S. Norberg112, M. Nordberg30, O. Novgorodova44, S. Nowak100, M. Nomachi117, I. Nomidis29, S. Norberg112, M. Nordberg30, O. Novgorodova44, S. Nowak100 o ac , o d s , S o be g , o dbe g , O ovgo odova , S owa , M. Nozaki65, L. Nozka114, K. Ntekas10, G. Nunes Hanninger87, T. Nunnemann99, E. Nurse77, F N i87 B J O’B i 46 F O’ d 7 D C O’N il143 V O’Sh 53 F G O kh 29 d M. Nozaki65, L. Nozka114, K. Ntekas10, G. Nunes Hanninger87, T. Nunnemann99, E. Nurse77, M. Nozaki65, L. Nozka114, K. Ntekas10, G. Nunes Hanninger87, T. Nunnemann99, E. Nurse77, H. Oberlack100, T. Obermann21, J. Ocariz79, A. Ochi66, M.I. Ochoa77, S. Oda69, S. Odaka65, H. Oberlack100, T. Obermann21, J. Ocariz79, A. Ochi66, M.I. Ochoa77, S. Oda69, S. Odaka65, H. Ogren60, A. Oh83, S.H. Oh45, C.C. Ohm15, H. Ohman167, W. Okamura117, H. 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Protopapadaki137, S. Protopopescu25, J. Proudfoot6, M. Przybycien38a, H. Przysiezniak5, E. Ptacek115, D. Puddu135a,135b, E. Pueschel85, D. Pu JHEP10(2014)141 JHEP10(2014)141 M. Purohit25,ad, P. Puzo116, J. Qian88, G. Qin53, Y. Qin83, A. Quadt54, D.R. Quarrie15, M. Purohit25,ad, P. Puzo116, J. Qian88, G. Qin53, Y. Qin83, A. Quadt54, D.R. Quarrie15, W.B. Quayle165a,165b, M. Queitsch-Maitland83, D. Quilty53, A. Qureshi160b, V. Radeka25, Q y , Q , Q y , Q , , V. Radescu42, S.K. Radhakrishnan149, P. Radloff115, P. Rados87, F. Ragusa90a,90b, G. Rahal179, V. Radescu42, S.K. Radhakrishnan149, P. Radloff115, P. Rados87, F. Ragusa90a,90b, G. Rahal1 S. Rajagopalan25, M. Rammensee30, A.S. Randle-Conde40, C. Rangel-Smith167, K. Rao164, F. Rauscher99, T.C. Rave48, T. Ravenscroft53, M. Raymond30, A.L. Read118, N.P. Readioff73, D.M. Rebuzzi120a,120b, A. Redelbach175, G. Redlinger25, R. Reece138, K. Reeves41, L. Rehnisch1 H. Reisin27, M. Relich164, C. Rembser30, H. Ren33a, Z.L. Ren152, A. Renaud116, M. Rescigno133 S. Resconi90a, O.L. Rezanova108,t, P. Reznicek128, R. Rezvani94, R. Richter100, M. Ridel79, sconi90a, O.L. Rezanova108,t, P. Reznicek128, R. Rezvani94, R. Richter100, M. Ridel79, eck16, J. Rieger54, M. Rijssenbeek149, A. Rimoldi120a,120b, L. Rinaldi20a, E. Ritsch61, I. Riu12, P. Rieck16, J. Rieger54, M. Rijssenbeek149, A. Rimoldi120a,120b, L. Rinaldi20a, E. Ritsch61, I. Riu F. Rizatdinova113, E. Rizvi75, S.H. Robertson86,i, A. Robichaud-Veronneau86, D. Robinson28 F. Rizatdinova113, E. Rizvi75, S.H. Robertson86,i, A. Robichaud-Veronneau86, D. Robinson28, J.E.M. Robinson83, A. Robson53, C. Roda123a,123b, L. Rodrigues30, S. Roe30, O. Røhne118, S. Rolli162, A. Romaniouk97, M. Romano20a,20b, E. Romero Adam168, N. Rompotis139, S. Rolli162, A. Romaniouk97, M. Romano20a,20b, E. Romero Adam168, N. Rompotis139, M. Ronzani48, L. Roos79, E. Ros168, S. Rosati133a, K. Rosbach49, M. Rose76, P. Rose138, P.L. Rosendahl14, O. Rosenthal142, V. Rossetti147a,147b, E. Rossi103a,103b, L.P. Rossi50a, P.L. Rosendahl14, O. Rosenthal142, V. Rossetti147a,147b, E. Rossi103a,103b, L.P. Rossi50a, P.L. Rosendahl14, O. Rosenthal142, V. Rossetti147a,147b, E. Rossi103a,103b, L.P. Rossi50a, R. Rosten139, M. Rotaru26a, I. Roth173, J. Rothberg139, D. Rousseau116, C.R. Royon137, A. Rozanov84, Y. Rozen153, X. Ruan146c, F. The ATLAS collaboration Olivares Pino46, Oliveira Damazio25, E. Oliver Garcia168, A. Olszewski39, J. Olszowska39, A. Onofre125a,125e, D. Oliveira Damazio25, E. Oliver Garcia168, A. Olszewski39, J. Olszowska39, A. Onofre125a,12 P.U.E. Onyisi31,o, C.J. Oram160a, M.J. Oreglia31, Y. Oren154, D. Orestano135a,135b, N. Orlando72a,72b, C. Oropeza Barrera53, R.S. Orr159, B. Osculati50a,50b, R. Ospanov121, Orlando72a,72b, C. Oropeza Barrera53, R.S. Orr159, B. Osculati50a,50b, R. Ospanov121, Otero y Garzon27, H. Otono69, M. Ouchrif136d, E.A. Ouellette170, F. Ould-Saada118, G. Otero y Garzon27, H. Otono69, M. Ouchrif136d, E.A. Ouellette170, F. Ould-Saada118, G. Otero y Garzon , H. Otono , M. Ouchrif , E.A. Ouellette , F. Ould Saada , A. Ouraou137, K.P. Oussoren106, Q. Ouyang33a, A. Ovcharova15, M. Owen83, V.E. Ozcan19a A. Ouraou137, K.P. Oussoren106, Q. Ouyang33a, A. Ovcharova15, M. Owen83, V.E. Ozcan Ouraou137, K.P. Oussoren106, Q. Ouyang33a, A. Ovcharova15, M. Owen83, V.E. Ozcan19a, N. Ozturk8, K. Pachal119, A. Pacheco Pages12, C. Padilla Aranda12, M. Pag´aˇcov´a48, Ozturk8, K. Pachal119, A. Pacheco Pages12, C. Padilla Aranda12, M. Pag´aˇcov´a48, S. Pagan Griso15, E. Paganis140, C. Pahl100, F. Paige25, P. Pais85, K. Pajchel118, G. Palacin Pagan Griso15, E. Paganis140, C. Pahl100, F. Paige25, P. Pais85, K. Pajchel118, G. Palacino160b, Palestini30, M. Palka38b, D. Pallin34, A. Palma125a,125b, J.D. Palmer18, Y.B. Pan174, S. Palestini30, M. Palka38b, D. Pallin34, A. Palma125a,125b, J.D. Palmer18, Y.B. Pan174, E. Panagiotopoulou10, J.G. Panduro Vazquez76, P. Pani106, N. Panikashvili88, S. Panitkin25, E. Panagiotopoulou10, J.G. Panduro Vazquez76, P. Pani106, N. Panikashvili88, S. Panitkin25, D. Pantea26a, L. Paolozzi134a,134b, Th.D. Papadopoulou10, K. Papageorgiou155,l, A. Paramo D. Paredes Hernandez34, M.A. Parker28, F. Parodi50a,50b, J.A. Parsons35, U. Parzefall48, q , gg , , , , G. P´asztor29, S. Pataraia176, N.D. Patel151, J.R. Pater83, S. Patricelli103a,103b, T. Pauly30, J. Pearce170, M. Pedersen118, S. Pedraza Lopez168, R. Pedro125a,125b, S.V. Peleganchuk108, D. Pelikan167, H. Peng33b, B. Penning31, J. Penwell60, D.V. Perepelitsa25, E. Perez Codina160a M.T. P´erez Garc´ıa-Esta˜n168, V. Perez Reale35, L. Perini90a,90b, H. Pernegger30, R. Perrino72 R. Peschke42, V.D. Peshekhonov64, K. Peters30, R.F.Y. Peters83, B.A. Petersen30, T.C. Petersen36, E. Petit42, A. Petridis147a,147b, C. Petridou155, E. Petrolo133a, F. Petrucci135a,135b, N.E. Pettersson158, R. Pezoa32b, P.W. Phillips130, G. Piacquadio144, E. Pianori171, A. Picazio49, E. Piccaro75, M. Piccinini20a,20b, R. Piegaia27, D.T. Pignotti110, – 39 – J.E. Pilcher31, A.D. Pilkington77, J. Pina125a,125b,125d, M. Pinamonti165a,165c,ac, A. Pinder119 J.L. Pinfold3, A. Pingel36, B. Pinto125a, S. Pires79, M. Pitt173, C. Pizio90a,90b, L. Plazak145a, , g , , , , , , M.-A. Pleier25, V. Pleskot128, E. Plotnikova64, P. Plucinski147a,147b, S. Poddar58a, F. Podlyski34 R. Poettgen82, L. Poggioli116, D. The ATLAS collaboration Rubbo12, I. Rubinskiy42, V.I. Rud98, C. Rud M.S. Rudolph159, F. R¨uhr48, A. Ruiz-Martinez30, Z. Rurikova48, N.A. Rusakovich64, A. Ruschke99, J.P. Rutherfoord7, N. Ruthmann48, Y.F. Ryabov122, M. Rybar128, G. Ryb N.C. Ryder119, A.F. Saavedra151, S. Sacerdoti27, A. Saddique3, I. Sadeh154, H.F-W. Sadrozinski138, R. Sadykov64, F. Safai Tehrani133a, H. Sakamoto156, Y. Sakurai172, G Salamanna135a,135b A Salamon134a M Saleem112 D Salek106 P H Sales De Bruin139 H.F-W. Sadrozinski138, R. Sadykov64, F. Safai Tehrani133a, H. Sakamoto156, Y. Sakurai172, G. Salamanna135a,135b, A. Salamon134a, M. Saleem112, D. Salek106, P.H. Sales De Bruin139, D. Salihagic100, A. Salnikov144, J. Salt168, D. Salvatore37a,37b, F. Salvatore150, A. Salvucci105 lihagic100, A. Salnikov144, J. Salt168, D. Salvatore37a,37b, F. Salvatore150, A. Salvucci105, D. Salihagic , A. Salnikov , J. Salt , D. Salvatore , F. Salvatore , A. Salvucci , A. Salzburger30, D. Sampsonidis155, A. Sanchez103a,103b, J. S´anchez168, V. Sanchez Martinez168 A. Salzburger30, D. Sampsonidis155, A. Sanchez103a,103b, J. S´anchez168, V. Sanchez Martinez lzburger30, D. Sampsonidis155, A. Sanchez103a,103b, J. S´anchez168, V. Sanchez Martinez168, H. Sandaker14, R.L. Sandbach75, H.G. Sander82, M.P. Sanders99, M. Sandhoff176, T. Sandov Sandaker14, R.L. Sandbach75, H.G. Sander82, M.P. Sanders99, M. Sandhoff176, T. Sandoval28, C. Sandoval163, R. Sandstroem100, D.P.C. Sankey130, A. Sansoni47, C. Santoni34, Sandoval163, R. Sandstroem100, D.P.C. Sankey130, A. Sansoni47, C. Santoni34, R. Santonico134a,134b, H. Santos125a, I. Santoyo Castillo150, K. Sapp124, A. Sapronov64, Santonico134a,134b, H. Santos125a, I. Santoyo Castillo150, K. Sapp124, A. Sapronov64, J.G. Saraiva125a,125d, B. Sarrazin21, G. Sartisohn176, O. Sasaki65, Y. Sasaki156, G. Sauvage5,∗, G. Saraiva125a,125d, B. Sarrazin21, G. Sartisohn176, O. Sasaki65, Y. Sasaki156, G. Sauvage5,∗, E. Sauvan5, P. Savard159,d, D.O. Savu30, C. Sawyer119, L. Sawyer78,m, D.H. Saxon53, J. Saxo , , , y , y , , , C. Sbarra20a, A. Sbrizzi3, T. Scanlon77, D.A. Scannicchio164, M. Scarcella151, V. Scarfone37a,37b, C. Sbarra20a, A. Sbrizzi3, T. Scanlon77, D.A. Scannicchio164, M. Scarcella151, V. Scarfone37a,37b, U. Sch¨afer82, A.C. Schaffer116, D. Schaile99, R.D. Schamberger149, V. Scharf58a, U. Sch¨afer82, A.C. Schaffer116, D. Schaile99, R.D. Schamberger149, V. Scharf58a, V.A. Schegelsky122, D. Scheirich128, M. Schernau164, M.I. Scherzer35, C. Schiavi50a,50 J. Schieck99, C. Schillo48, M. Schioppa37a,37b, S. Schlenker30, E. Schmidt48, K. Schmieden30, C. Schmitt82, C. Schmitt99, S. Schmitt58b, B. Schneider17, Y.J. Schnellbach73, U. Schnoor44 L. Schoeffel137, A. Schoening58b, B.D. Schoenrock89, A.L.S. Schorlemmer54, M. Schott82, D S h 160a J S h 25 S S h 159 M S h 175 C S h d 82 N S h h82 L. Schoeffel137, A. Schoening58b, B.D. Schoenrock89, A.L.S. Schorlemmer54, M. Schott82, L. Schoeffel , A. Schoening , B.D. The ATLAS collaboration Schoenrock , A.L.S. Schorlemmer , M. Schott , D. Schouten160a, J. Schovancova25, S. Schramm159, M. Schreyer175, C. Schroeder82, N. Schuh82, y M.J. Schultens21, H.-C. Schultz-Coulon58a, H. Schulz16, M. Schumacher48, B.A. Schumm138, Ph. Schune137, C. Schwanenberger83, A. Schwartzman144, Ph. Schwegler100, Ph. Schwemling137, – 40 – R. Schwienhorst89, J. Schwindling137, T. Schwindt21, M. Schwoerer5, F.G. Sciacca17, E. Scifo116 , g , , , , G. Sciolla23, W.G. Scott130, F. Scuri123a,123b, F. Scutti21, J. Searcy88, G. Sedov42, E. Sedykh , , , , y , , y S.C. Seidel104, A. Seiden138, F. Seifert127, J.M. Seixas24a, G. Sekhniaidze103a, S.J. Sekula40, , , , , , , K.E. Selbach46, D.M. Seliverstov122,∗, G. Sellers73, N. Semprini-Cesari20a,20b, C. Serfon30, L. Serin116, L. Serkin54, T. Serre84, R. Seuster160a, H. Severini112, T. Sfiligoj74, F. Sforza100 Serin116, L. Serkin54, T. Serre84, R. Seuster160a, H. Severini112, T. Sfiligoj74, F. Sforza100, A. Sfyrla30, E. Shabalina54, M. Shamim115, L.Y. Shan33a, R. Shang166, J.T. Shank22, yrla30, E. Shabalina54, M. Shamim115, L.Y. Shan33a, R. Shang166, J.T. Shank22, M. Shapiro15, P.B. Shatalov96, K. Shaw165a,165b, C.Y. Shehu150, P. Sherwood77, L. Shi152 S. Shimizu66, C.O. Shimmin164, M. Shimojima101, M. Shiyakova64, A. Shmeleva95 S. Shimizu66, C.O. Shimmin164, M. Shimojima101, M. Shiyakova64, A. Shmeleva95, P. Sicho126, O. Sidiropoulou155, D. Sidorov113, A. Sidoti133a, F. Siegert44, Dj. Sijacki13a, P. Sicho126, O. Sidiropoulou155, D. Sidorov113, A. Sidoti133a, F. Siegert44, Dj. Sijacki13a, , p , , , g , j j , J. Silva125a,125d, Y. Silver154, D. Silverstein144, S.B. Silverstein147a, V. Simak127, O. Simard JHEP10(2014)141 JHEP10(2014)141 Lj. Simic13a, S. Simion116, E. Simioni82, B. Simmons77, R. Simoniello90a,90b, M. Simonyan Lj. Simic13a, S. Simion116, E. Simioni82, B. Simmons77, R. Simoniello90a,90b, M. Simonyan3 Sinervo159, N.B. Sinev115, V. Sipica142, G. Siragusa175, A. Sircar78, A.N. Sisakyan64,∗, P. Sinervo159, N.B. Sinev115, V. Sipica142, G. Siragusa175, A. Sircar78, A.N. Sisakyan64,∗, S.Yu. Sivoklokov98, J. Sj¨olin147a,147b, T.B. Sjursen14, H.P. Skottowe57, K.Yu. Skovpen108 Yu. Sivoklokov98, J. Sj¨olin147a,147b, T.B. Sjursen14, H.P. Skottowe57, K.Yu. Skovpen108, P. Skubic112, M. Slater18, T. Slavicek127, K. Sliwa162, V. Smakhtin173, B.H. Smart46, ubic112, M. Slater18, T. Slavicek127, K. Sliwa162, V. Smakhtin173, B.H. Smart46, L. Smestad14, S.Yu. Smirnov97, Y. Smirnov97, L.N. Smirnova98,af, O. Smirnova80, K.M. mestad14, S.Yu. Smirnov97, Y. Smirnov97, L.N. Smirnova98,af, O. Smirnova80, K.M. Smith53, M. Smizanska71, K. Smolek127, A.A. Snesarev95, G. Snidero75, S. Snyder25, R. Sobie170,i, Smizanska71, K. Smolek127, A.A. Snesarev95, G. Snidero75, S. Snyder25, R. Sobie170,i, F. Socher44, A. Soffer154, D.A. Soh152,ae, C.A. Solans30, M. Solar127, J. Solc127, E.Yu. So Socher44, A. Soffer154, D.A. Soh152,ae, C.A. Solans30, M. The ATLAS collaboration Solar127, J. Solc127, E.Yu. Soldatov97, U. Soldevila168, A.A. Solodkov129, A. Soloshenko64, O.V. Solovyanov129, V. Solovyev122, Soldevila168, A.A. Solodkov129, A. Soloshenko64, O.V. Solovyanov129, V. Solovyev122, P. Sommer48, H.Y. Song33b, N. Soni1, A. Sood15, A. Sopczak127, B. Sopko127, V. Sopko12 Sommer48, H.Y. Song33b, N. Soni1, A. Sood15, A. Sopczak127, B. Sopko127, V. Sopko127, V. Sorin12, M. Sosebee8, R. Soualah165a,165c, P. Soueid94, A.M. Soukharev108, D. South42 Sorin12, M. Sosebee8, R. Soualah165a,165c, P. Soueid94, A.M. Soukharev108, D. South42, Spagnolo72a,72b, F. Span`o76, W.R. Spearman57, F. Spettel100, R. Spighi20a, G. Spigo30, S. Spagnolo72a,72b, F. Span`o76, W.R. Spearman57, F. Spettel100, R. Spighi20a, G. Spigo30 M. Spousta128, T. Spreitzer159, B. Spurlock8, R.D. St. Denis53,∗, S. Staerz44, J. Stahlman121 M. Spousta128, T. Spreitzer159, B. Spurlock8, R.D. St. Denis53,∗, S. Staerz44, J. Stahlm Stamen58a, E. Stanecka39, R.W. Stanek6, C. Stanescu135a, M. Stanescu-Bellu42, R. Stamen58a, E. Stanecka39, R.W. Stanek6, C. Stanescu135a, M. Stanescu-Bellu42, M.M. Stanitzki42, S. Stapnes118, E.A. Starchenko129, J. Stark55, P. Staroba126, P. Starovoito M.M. Stanitzki42, S. Stapnes118, E.A. Starchenko129, J. Stark55, P. Staroba126, P. Starovoitov42, ewski39, P. Stavina145a,∗, P. Steinberg25, B. Stelz O. Stelzer-Chilton160a, H. Stenzel52, S. Stern100, G.A. Stewart53, J.A. Stillings21, M. O. Stelzer-Chilton160a, H. Stenzel52, S. Stern100, G.A. Stewart53, J.A. Stillings21, M.C. Stockton M. Stoebe86, G. Stoicea26a, P. Stolte54, S. Stonjek100, A.R. Stradling8, A. Straessner44, M.E. Stramaglia17, J. Strandberg148, S. Strandberg147a,147b, A. Strandlie118, E. Strauss144, M.E. Stramaglia17, J. Strandberg148, S. Strandberg147a,147b, A. Strandlie118, E. Strauss144 rauss112, P. Strizenec145b, R. Str¨ohmer175, D.M. Strom115, R. Stroynowski40, S.A. Stucci17, M. Strauss112, P. Strizenec145b, R. Str¨ohmer175, D.M. Strom115, R. Stroynowski40, S.A. Stu B. Stugu14, N.A. Styles42, D. Su144, J. Su124, R. Subramaniam78, A. Succurro12, Y. Sugaya Stugu14, N.A. Styles42, D. Su144, J. Su124, R. Subramaniam78, A. Succurro12, Y. Sugaya117, C. Suhr107, M. Suk127, V.V. Sulin95, S. Sultansoy4c, T. Sumida67, S. Sun57, X. Sun33a, hr107, M. Suk127, V.V. Sulin95, S. Sultansoy4c, T. Sumida67, S. Sun57, X. Sun33a, Sundermann48, K. Suruliz140, G. Susinno37a,37b, M.R. Sutton150, Y. Suzuki65, M. Svatos126, J.E. Sundermann48, K. Suruliz140, G. Susinno37a,37b, M.R. Sutton150, Y. Suzuki65, M. Svatos12 edish169, M. Swiatlowski144, I. Sykora145a, T. Sykora128, D. Ta89, C. Taccini135a,135b, S. Swedish169, M. Swiatlowski144, I. Sykora145a, T. Sykora128, D. Ta89, C. Taccini135a,135b, ckmann42, J. Taenzer159, A. Taffard164, R. Tafirout160a, N. Taiblum154, H. Takai25, K. Tackmann42, J. Taenzer159, A. Taffard164, R. Tafirout160a, N. Taiblum154, H. Takai25, R. Takashima68, H. Takeda66, T. Takeshita141, Y. Takubo65, M. Talby84, A.A. Talyshev108,t R. Takashima68, H. Takeda66, T. Takeshita141, Y. Takubo65, M. Talby84, A.A. Talyshev108,t Y.C. The ATLAS collaboration Tam175, K.G. Tan87, J. Tanaka156, R. Tanaka116, S. Tanaka132, S. Tanaka65, J.Y.C. Tam175, K.G. Tan87, J. Tanaka156, R. Tanaka116, S. Tanaka132, S. Tanaka65, A.J. Tanasijczuk143, B.B. Tannenwald110, N. Tannoury21, S. Tapprogge82, S. Tarem153, F. Tarrade29, G.F. Tartarelli90a, P. Tas128, M. Tasevsky126, T. Tashiro67, E. Tassi37a,37b, A. Tavares Delgado125a,125b, Y. Tayalati136d, F.E. Taylor93, G.N. Taylor87, W. Taylor160b, A. Tavares Delgado125a,125b, Y. Tayalati136d, F.E. Taylor93, G.N. Taylor87, W. Taylor160b g , , , g , H. Ten Kate30, P.K. Teng152, J.J. Teoh117, S. Terada65, K. Terashi156, J. Terron81, S. Terzo1 H. Ten Kate30, P.K. Teng152, J.J. Teoh117, S. Terada65, K. Terashi156, J. Terron81, S. Terzo g M. Testa47, R.J. Teuscher159,i, J. Therhaag21, T. Theveneaux-Pelzer34, J.P. Thomas18, 47, R.J. Teuscher159,i, J. Therhaag21, T. Theveneaux-Pelzer34, J.P. Thomas18, J. Thomas-Wilsker76, E.N. Thompson35, P.D. Thompson18, P.D. Thompson159, A.S. Thompson5 S. Tok´ar145a, K. Tokushuku65, K. Tollefson89, L. Tomlinson83, M. Tomoto102, L. Tompkins31, K. Toms104, N.D. Topilin64, E. Torrence115, H. Torres143, E. Torr´o Pastor168, J. Toth84,ah, – 41 – F. Touchard84, D.R. Tovey140, H.L. Tran116, T. Trefzger175, L. Tremblet30, A. Tricoli30, ger160a, S. Trincaz-Duvoid79, M.F. Tripiana12, W. Trischuk159, B. Trocm´e55, I.M. Trigger160a, S. Trincaz-Duvoid79, M.F. Tripiana12, W. Trischuk159, B. Trocm´e55, gg C. Troncon90a, M. Trottier-McDonald143, M. Trovatelli135a,135b, P. True89, M. Trzebinski39, A. Trzupek39, C. Tsarouchas30, J.C-L. Tseng119, P.V. Tsiareshka91, D. Tsionou137, G. Tsipolitis10, N. Tsirintanis9, S. Tsiskaridze12, V. Tsiskaridze48, E.G. Tskhadadze51a, I.I. Tsukerman96, V. Tsulaia15, S. Tsuno65, D. Tsybychev149, A. Tudorache26a, V. Tudora A.N. Tuna121, S.A. Tupputi20a,20b, S. Turchikhin98,af, D. Turecek127, I. Turk Cakir4d, R. Turra90a,90b, P.M. Tuts35, A. Tykhonov49, M. Tylmad147a,147b, M. Tyndel130, K. Uchida21, R. Turra90a,90b, P.M. Tuts35, A. Tykhonov49, M. Tylmad147a,147b, M. Tyndel130, K. Uchida21, A. Undrus25, G. Unel164, F.C. Ungaro48, Y. Unno65, D. Urbaniec35, P. Urquijo87, G. Usai8, A. Undrus25, G. Unel164, F.C. Ungaro48, Y. Unno65, D. Urbaniec35, P. Urquijo87, G. Usai8, A. Usanova61, L. Vacavant84, V. Vacek127, B. Vachon86, N. Valencic106, S. Valentinetti20a,20b JHEP10(2014)141 JHEP10(2014)141 A. Valero168, L. Valery34, S. Valkar128, E. Valladolid Gallego168, S. Vallecorsa49, J.A. Valls Ferrer168, W. Van Den Wollenberg106, P.C. Van Der Deijl106, R. van der H. van der Graaf106, R. Van Der Leeuw106, D. van der Ster30, N. van Eldik30, P. van Gemmeren6 J. Van Nieuwkoop143, I. van Vulpen106, M.C. van Woerden30, M. Vanadia133a,133b, W. Vandelli R. Vanguri121, A. Vaniachine6, P. Vankov42, F. Vannucci79, G. Vardanyan178, R. Vari133a, E.W. Varnes7, T. Varol85, D. Varouchas79, A. Vartapetian8, K.E. Varvell151, F. Vazeille34, T. Vazquez Schroeder54, J. Veatch7, F. Veloso125a,125c, S. The ATLAS collaboration Veneziano133a, A. Ventura72a,72b, D. Ventura85, M. Venturi170, N. Venturi159, A. Venturini23, V. Vercesi120a, M. Verducci133a,133b W. Verkerke106, J.C. Vermeulen106, A. Vest44, M.C. Vetterli143,d, O. Viazlo80, I. Vichou166 T. Vickey146c,ai, O.E. Vickey Boeriu146c, G.H.A. Viehhauser119, S. Viel169, R. Vigne30, M. Villa20a,20b, M. Villaplana Perez90a,90b, E. Vilucchi47, M.G. Vincter29, V.B. Vinogradov64, J. Virzi15, I. Vivarelli150, F. Vives Vaque3, S. Vlachos10, D. Vladoiu99, M. Vlasak127, A. Vogel21, M. Vogel32a, P. Vokac127, G. Volpi123a,123b, M. 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Wasicki42, P.M. Watkins18, A.T. Watson18, I.J M.F. Watson18, G. Watts139, S. Watts83, B.M. Waugh77, S. Webb83, M.S. Weber17, Watson18, G. Watts139, S. Watts83, B.M. Waugh77, S. Webb83, M.S. Weber17, S.W. Weber175, J.S. Webster31, A.R. Weidberg119, P. Weigell100, B. Weinert60, J. Weingarten54 C. Weiser48, H. Weits106, P.S. Wells30, T. Wenaus25, D. Wendland16, Z. Weng152,ae, T. Wengler3 eiser48, H. Weits106, P.S. Wells30, T. Wenaus25, D. Wendland16, Z. Weng152,ae, T. Wengler30, S. Wenig30, N. Wermes21, M. Werner48, P. Werner30, M. Wessels58a, J. Wetter162, K. Whalen29 Wenig30, N. Wermes21, M. Werner48, P. Werner30, M. Wessels58a, J. Wetter162, K. Whalen29, A. White8, M.J. White1, R. White32b, S. White123a,123b, D. Whiteson164, D. Wicke176, White8, M.J. White1, R. White32b, S. White123a,123b, D. Whiteson164, D. Wicke176, F.J. Wickens130, W. Wiedenmann174, M. Wielers130, P. Wienemann21, C. Wiglesworth36, J. Wickens130, W. Wiedenmann174, M. Wielers130, P. Wienemann21, C. Wiglesworth36, L.A.M. Wiik-Fuchs21, P.A. Wijeratne77, A. Wildauer100, M.A. Wildt42,ak, H.G. Wilkens30, J.Z. Will99, H.H. Williams121, S. Williams28, C. Willis89, S. Willocq85, A. Wilson88, J.Z. Will99, H.H. Williams121, S. Williams28, C. Willis89, S. Willocq85, A. Wilson88, J. Wittkowski99, S.J. Wollstadt82, M.W. Wolter39, H. Wolters125a,125c, B.K. Wosiek39, S. Yanush92, L. The ATLAS collaboration Yao33a, W-M. Yao15, Y. Yasu65, E. Yatsenko42, K.H. Yau Wong21, J. Ye40, S. Ye25, A.L. Yen57, E. Yildirim42, M. Yilmaz4b, R. Yoosoofmiya124, K. Yorita172, R. Yoshida6, – 42 – K. Yoshihara156, C. Young144, C.J.S. Young30, S. Youssef22, D.R. Yu15, J. Yu8, J.M. Yu88, J. Yu113, L. Yuan66, A. Yurkewicz107, I. Yusuff28,an, B. Zabinski39, R. Zaidan62, A.M. Zaitsev129,aa, A. Zaman149, S. Zambito23, L. Zanello133a,133b, D. Zanzi100, C. Zeitnitz176 M. Zeman127, A. Zemla38a, K. Zengel23, O. Zenin129, T. ˇZeniˇs145a, D. Zerwas116, Zevi della Porta57, D. Zhang88, F. Zhang174, H. Zhang89, J. Zhang6, L. Zhang152, X. Zhang33d, Zhang116, Z. Zhao33b, A. Zhemchugov64, J. Zhong119, B. Zhou88, L. Zhou35, N. Zhou164, 33d 33 88 33b 33 95 175 C.G. Zhu33d, H. Zhu33a, J. Zhu88, Y. Zhu33b, X. Zhuang33a, K. Zhukov95, A. Zibell175, D. Zieminska60, N.I. Zimine64, C. Zimmermann82, R. Zimmermann21, S. Zimmermann21, G. Zurzolo103a,103b, V. Zutshi107, L. Zwalinski30. M. zur Nedden16, G. Zurzolo103a,103b, V. Zutshi107, L. Zwalinski30. JHEP10(2014)141 1 Department of Physics, University of Adelaide, Adelaide, Australia 1 Department of Physics, University of Adelaide, Adelaide, Australia 2 Physics Department, SUNY Albany, Albany NY, United States of America 2 Physics Department, SUNY Albany, Albany NY, United States of America 3 Department of Physics, University of Alberta, Edmonton AB, Canada 3 Department of Physics, University of Alberta, Edmonton AB, Canada 4 (a) Department of Physics, Ankara University, Ankara; (b) Department of Physics, Gazi University, Ankara; (c) Division of Physics TOBB University of Economics and Technology Ankara; 4 (a) Department of Physics, Ankara University, Ankara; (b) Department of Physics, Gazi University, Ankara; (c) Division of Physics, TOBB University of Economics and Technology, Ankara; Ankara; (c) Division of Physics, TOBB University of Economics and Technology, Ankara; (d) Turkish Atomic Energy Authority, Ankara, Turkey (d) Turkish Atomic Energy Authority, Ankara, Turke P3 and Universit´e de Savoie, Annecy-le-Vieux, Franc 6 High Energy Physics Division, Argonne National Laboratory, Argonne IL, United States of America 7 Department of Physics, University of Arizona, Tucson AZ, United States of America 8 Department of Physics, The University of Texas at Arlington, Arlington TX, United States of America 9 Physics Department, University of Athens, Athens, Greece 9 Physics Department, University of Athens, Athens, Greece 10 Physics Department, National Technical University of Athens, Zografou, Greece 10 Physics Department, National Technical University of Athens, Zografou, Greece 11 Institute of Physics, Azerbaijan Academy of Sciences, Baku, Azerbaijan 12 cs, Azerbaijan Academy of Sciences, Baku, Azerbaija 12 Institut de F´ısica d’Altes Energies and Departament de F´ısica de la Universitat Aut`onoma de Barcelona, Barcelona, Spain 12 Institut de F´ısica d’Altes Energies and Departament de F´ısica de la Universitat Aut`onoma de Barcelona, Barcelona, Spain 13 (a) Institute of Physics, University of Belgrade, Belgrade; (b) Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia 13 (a) Institute of Physics, University of Belgrade, Belgrade; (b) Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia University of Belgrade, Belgrade, Serbia 14 Department for Physics and Technology, University of Bergen, Bergen, Norway 15 14 Department for Physics and Technology, University of Bergen, Bergen, Norway 15 Physics Division, Lawrence Berkeley National Laboratory and University of California, Berkeley CA, United States of America 15 Physics Division, Lawrence Berkeley National Laboratory and University of California, Berkeley CA, United States of America 16 Department of Physics, Humboldt University, Berlin, Germany 17 Albert Einstein Center for Fundamental Physics and Laboratory for High Energy Physics, University of Bern, Bern, Switzerland 18 School of Physics and Astronomy, University of Birmingham, Birmingham, United Kingdom 19 (a) Department of Physics, Bogazici University, Istanbul; (b) Department of Physics, Dogus University, Istanbul; (c) Department of Physics Engineering, Gaziantep University, Gaziantep, Turkey 20 (a) INFN Sezione di Bologna; (b) Dipartimento di Fisica e Astronomia, Universit`a di Bologna, Bologna, Italy 21 Physikalisches Institut, University of Bonn, Bonn, Germany 22 Department of Physics, Boston University, Boston MA, United States of America 23 Department of Physics, Brandeis University, Waltham MA, United States of America 24 (a) Universidade Federal do Rio De Janeiro COPPE/EE/IF, Rio de Janeiro; (b) Federal University of Juiz de Fora (UFJF), Juiz de Fora; (c) Federal University of Sao Joao del Rei (UFSJ), Sao Joao del Rei; (d) Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo, Brazil 25 Physics Department, Brookhaven National Laboratory, Upton NY, United State 26 (a) National Institute of Physics and Nuclear Engineering, Bucharest; (b) National Institute for Research and Development of Isotopic and Molecular Technologies, Physics Department, Cluj Napoca; (c) University Politehnica Bucharest, Bucharest; (d) West University in Timisoara, Timisoara, Romania – 43 – 27 Departamento de F´ısica, Universidad de Buenos Aires, Buenos Aires, Argentina 28 Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom 29 Department of Physics, Carleton University, Ottawa ON, Canada 30 CERN, Geneva, Switzerland , , 31 Enrico Fermi Institute, University of Chicago, Chicago IL, United States of America 31 Enrico Fermi Institute, University of Chicago, Ch , y f g , g , f 32 (a) Departamento de F´ısica, Pontificia Universidad Cat´olica de Chile, Santiago; (b) Departamento de F´ısica, Universidad T´ecnica Federico Santa Mar´ıa, Valpara´ıso, Chile , y f g , g , f 32 (a) Departamento de F´ısica, Pontificia Universidad Cat´olica de Chile, Santiago; (b) Departamento 32 (a) Departamento de F´ısica, Pontificia Universidad Cat´olica de Chile, Sa de F´ısica, Universidad T´ecnica Federico Santa Mar´ıa, Valpara´ıso, Chile 32 (a) Departamento de F´ısica, Pontificia Universidad Cat´olica de Chile, Santiago; (b) Dep de F´ısica, Universidad T´ecnica Federico Santa Mar´ıa, Valpara´ıso, Chile 33 (a) Institute of High Energy Physics, Chinese Academy of Sciences, Beijing; (b) Department of Modern Physics, University of Science and Technology of China, Anhui; (c) Department of Physics, Nanjing University, Jiangsu; (d) School of Physics, Shandong University, Shandong; (e) Physics Department, Shanghai Jiao Tong University, Shanghai, China 33 (a) Institute of High Energy Physics, Chinese Academy of Sciences, Beijing; (b) Department of Modern Physics, University of Science and Technology of China, Anhui; (c) Department of Physics, Nanjing University, Jiangsu; (d) School of Physics, Shandong University, Shandong; (e) Physics Department, Shanghai Jiao Tong University, Shanghai, China 34 Laboratoire de Physique Corpusculaire, Clermont Universit´e and Universit´e Blaise Pascal and CNRS/IN2P3, Clermont-Ferrand, France JHEP10(2014)141 JHEP10(2014)141 CNRS/IN2P3, Clermont-Ferrand, France 35 Nevis Laboratory, Columbia University, Irvington NY, United States of America 35 Nevis Laboratory, Columbia University, Irv 36 Niels Bohr Institute, University of Copenhagen, Kobenhavn, Denmark 37 (a) INFN Gruppo Collegato di Cosenza, Laboratori Nazionali di Frascati; (b) D Fisica, Universit`a della Calabria, Rende, Italy 37 (a) INFN Gruppo Collegato di Cosenza, Laboratori Nazionali di Frascati; (b) Dipartimento di (a) INFN Gruppo Collegato di Cosenza, Laboratori 37 (a) INFN Gruppo Collegato di Cosenza, Laborat Fisica, Universit`a della Calabria, Rende, Italy Fisica, Universit`a della Calabria, Rende, Italy 38 (a) AGH University of Science and Technology, Faculty of Physics and Applied Computer Science Krakow; (b) Marian Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland 38 (a) AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Krakow; (b) Marian Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland 39 The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, Krakow, AGH University of Science and Technology, Faculty of Physics and Applied Computer Scienc Krakow; (b) Marian Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland 39 AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Krakow; (b) Marian Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland 39 The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, Krakow, Poland 39 The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, Krakow, Poland 40 Physics Department, Southern Methodist University, Dallas TX, United States of America 41 Physics Department, University of Texas at Dallas, Richardson TX, United States of America 42 S G 40 Physics Department, Southern Methodist University, Dallas TX, United States of America s Department, University of Texas at Dallas, Richard 41 Physics Department, University of Texas at Dalla 41 Physics Department, University of Texas at Dallas, Richardson TX, United States of America 42 42 DESY, Hamburg and Zeuthen, Germany 43 Institut f¨ur Experimentelle Physik IV, Technische Universit¨at Dortmund, Dortmund, Germany 45 Department of Physics, Duke University, Durham NC, United States of America 46 SUPA - School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom SUPA - School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom INFN Laboratori Nazionali di Frascati, Frascati, Italy 47 INFN Laboratori Nazionali di Frascati, Frascati, Italy 47 INFN Laboratori Nazionali di Frascati, Frascati, Italy 48 Fakult¨at f¨ur Mathematik und Physik, Albert-Ludwigs-Universit¨at, Freiburg, Germany Fakult¨at f¨ur Mathematik und Physik, Albert-Ludwigs- 49 Section de Physique, Universit´e de Gen`eve, Geneva, Switzerland 50 (a) INFN Sezione di Genova; (b) Dipartimento di Fisica, Universit`a di Genova, Genova, Italy 51 (a) E. 1 Department of Physics, University of Adelaide, Adelaide, Australia Andronikashvili Institute of Physics, Iv. 1 Department of Physics, University of Adelaide, Adelaide, Australia Javakhishvili Tbilisi State Universit (b) High Energy Physics Institute, Tbilisi State University, Tbilisi, Georgia f y , (b) High Energy Physics Institute, Tbilisi State University, Tbilisi, Georgia 52 II Physikalisches Institut, Justus-Liebig-Universit¨at Giessen, Giessen, Germany 53 SUPA - School of Physics and Astronomy, University of Glasgow, Glasgow, United Kingdom 54 II Physikalisches Institut, Georg-August-Universit¨at, G¨ottingen, Germany 55 Laboratoire de Physique Subatomique et de Cosmologie, Universit´e Grenoble-Alpes, CNRS/IN2P3, Grenoble, France 56 Department of Physics, Hampton University, Hampton VA, United States of America 57 57 Laboratory for Particle Physics and Cosmology, Harvard University, Cambridge MA, United States of America 58 (a) Kirchhoff-Institut f¨ur Physik, Ruprecht-Karls-Universit¨at Heidelberg, Heidelberg; (b) Ph ik li h I tit t R ht K l U i it¨t H id lb H id lb (c) ZITI 58 (a) Kirchhoff-Institut f¨ur Physik, Ruprecht-Karls-Universit¨at Heidelberg, Heidelberg; (b) Physikalisches Institut, Ruprecht-Karls-Universit¨at Heidelberg, Heidelberg; (c) ZITI technische Informatik, Ruprecht-Karls-Universit¨at Heidelberg, Mannheim, Germany (b) Physikalisches Institut, Ruprecht-Karls-Universit¨at Heidelberg, Heidelberg; (c) ZITI Institut f¨ur technische Informatik, Ruprecht-Karls-Universit¨at Heidelberg, Mannheim, Germany 59 Faculty of Applied Information Science, Hiroshima Institute of Technology, Hiroshima, Jap 60 Department of Physics, Indiana University, Bloomington IN, United States of America 61 p f y , y, g , f 61 Institut f¨ur Astro- und Teilchenphysik, Leopold-Franzens-Universit¨at, Innsbruck, Austria itut f¨ur Astro- und Teilchenphysik, Leopold-Franzens 62 University of Iowa, Iowa City IA, United States of America 63 Department of Physics and Astronomy, Iowa State University, Ames IA, United States of Ameri 63 Department of Physics and Astronomy, Iowa State University, oint Institute for Nuclear Research, JINR Dubna, Du 64 Joint Institute for Nuclear Research, JINR Dubna, Dubna, Russia 65 KEK, High Energy Accelerator Research Organization, Tsukuba, Japan 66 Graduate School of Science, Kobe University, Kobe, Japan – 44 – 67 Faculty of Science, Kyoto University, Kyoto, Japan 68 Kyoto University of Education, Kyoto, Japan 69 Department of Physics, Kyushu University, Fukuoka, Japan 70 Instituto de F´ısica La Plata, Universidad Nacional de La Plata and CONICET, La Plata, Argentina 70 Instituto de F´ısica La Plata, Universidad Nacional de La Plata and CONICET, La Plata, Argentina 71 Ph i D t t L t U i it L t U it d Ki d 70 Instituto de F´ısica La Plata, Universidad Nacional de La Plata and CON sics Department, Lancaster University, Lancaster, U 72 (a) INFN Sezione di Lecce; (b) Dipartimento di Matematica e Fisica, Universit`a del Salento, Lecc Italy 73 Oliver Lodge Laboratory, University of Liverpool, Liverpool, United Kingdom partment of Physics, Joˇzef Stefan Institute and Unive 74 Department of Physics, Joˇzef Stefan Institute and University of Ljubljana, Ljubljana, Slovenia 75 School of Physics and Astronomy, Queen Mary University of London, London, United Kingdom School of Physics and Astronomy, Queen Mary University of London, London, United Kingdom 76 Department of Physics, Royal Holloway University of London, Surrey, United Kingdom 76 Department of Physics, Royal Holloway University of London, Surrey, United Kingdom JHEP10(2014)141 Department of Physics and Astronomy, University College London, London, United Kingdom 78 Louisiana Tech University, Ruston LA, United States of America 78 Louisiana Tech University, Ruston LA, United States of America 78 Louisiana Tech University, Ruston LA, United States of America 79 Laboratoire de Physique Nucl´eaire et de Hautes Energies, UPMC and Universit´e Paris-Diderot and CNRS/IN2P3, Paris, France 80 Fysiska institutionen, Lunds universitet, Lund, Sweden 81 Departamento de Fisica Teorica C-15, Universidad Autonoma de Madrid, Madrid, Spain 82 Institut f¨ur Physik, Universit¨at Mainz, Mainz, Germany 82 Institut f¨ur Physik, Universit¨at Mainz, Mainz, Germany School of Physics and Astronomy, University of Man 84 CPPM, Aix-Marseille Universit´e and CNRS/IN2P3, Marseille, France / 85 Department of Physics, University of Massachusetts, Amherst MA, United States of America 86 Department of Physics, McGill University, Montreal QC, Canada 87 School of Physics, University of Melbourne, Victoria, Australia 88 Department of Physics, The University of Michigan, Ann Arbor MI, United States of America 89 Department of Physics and Astronomy, Michigan State University, East Lansing MI, United States of America 90 (a) INFN Sezione di Milano; (b) Dipartimento di Fisica, Universit`a di Milano, Milano, Italy (a) INFN Sezione di Milano; (b) Dipartimento di Fisi 91 B.I. 1 Department of Physics, University of Adelaide, Adelaide, Australia Dodge Department of Physics and Astronomy, University of Oklahoma, Norman OK, United States of America f 113 Department of Physics, Oklahoma State University, Stillwater OK, United States of America Department of Physics, Oklahoma State University, 114 Palack´y University, RCPTM, Olomouc, Czech Republic 114 Palack´y University, RCPTM, Olomouc, Czech Republic 115 Center for High Energy Physics, University of Oregon, Eugene OR, United States of America 115 Center for High Energy Physics, University of Oregon, Eugene OR, 116 LAL, Universit´e Paris-Sud and CNRS/IN2P3, Orsay, France 117 Graduate School of Science, Osaka University, Osaka, Japan 118 Department of Physics, University of Oslo, Oslo, Norway 119 Department of Physics, Oxford University, Oxford, United Kingdom JHEP10(2014)141 121 Department of Physics, University of Pennsylvania, Philadelphia PA, United States of Americ 121 Department of Physics, University of Pennsylvania, Philadelphia PA, 122 Petersburg Nuclear Physics Institute, Gatchina, Russia 123 (a) INFN Sezione di Pisa; (b) Dipartimento di Fisica E. Fermi, Universit`a di Pisa, Pisa, Italy 124 Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh PA, United States of America 123 (a) INFN Sezione di Pisa; (b) Dipartimento di Fisica E. Fermi, Universit`a di Pisa, Pisa, Italy 123 (a) INFN Sezione di Pisa; (b) Dipartimento di Fisica E. 1 Department of Physics, University of Adelaide, Adelaide, Australia Stepanov Institute of Physics, National Academy of Sciences of Belarus, Minsk, Republic of Belarus 92 National Scientific and Educational Centre for Particle and High Energy Physics, Minsk, Republic of Belarus 93 Department of Physics, Massachusetts Institute of Technology, Cambridge MA, United States of America 94 Group of Particle Physics, University of Montreal, Montreal QC, Canada 95 P.N. Lebedev Institute of Physics, Academy of Sciences, Moscow, Russia 96 Institute for Theoretical and Experimental Physics (ITEP), Moscow, Russia 97 Moscow Engineering and Physics Institute (MEPhI), Moscow, Russia 98 D.V.Skobeltsyn Institute of Nuclear Physics, M.V.Lomonosov Moscow State University, Moscow, Russia 100 Max-Planck-Institut f¨ur Physik (Werner-Heisenberg-Institut), M¨unchen, Germ ax-Planck-Institut f¨ur Physik (Werner-Heisenberg-In 101 Nagasaki Institute of Applied Science, Nagasaki, Japan 102 Graduate School of Science and Kobayashi-Maskawa Institute, Nagoya University, Nagoya, Japan 103 (a) INFN Sezione di Napoli; (b) Dipartimento di Fisica, Universit`a di Napoli, Napoli, Italy 104 104 Department of Physics and Astronomy, University of New Mexico, Albuquerque NM, United Stat of America 105 Institute for Mathematics, Astrophysics and Particle Physics, Radboud University Nijmegen/Nikhef, Nijmegen, Netherlands 105 Institute for Mathematics, Astrophysics and Particle Physics, Radboud University Nijmegen/Nikhef Nijmegen Netherlands Institute for Mathematics, Astrophysics and Particle Physics, Radboud University Nijmegen/Nikhef, Nijmegen, Netherlands 106 Nikhef National Institute for Subatomic Physics and University of Amsterdam, Amsterdam, Netherlands 107 Department of Physics, Northern Illinois University, DeKalb IL, United States of America 108 Budker Institute of Nuclear Physics, SB RAS, Novosibirsk, Russia 109 Department of Physics, New York University, New York NY, United States of America – 45 – 110 Ohio State University, Columbus OH, United States of America 111 Faculty of Science, Okayama University, Okayama, Japan 112 Homer L. 1 Department of Physics, University of Adelaide, Adelaide, Australia Petersburg State Polytechnical University, St. Petersburg, Russia k Also at Chinese University of Hong Kong China j Also at Department of Physics, St. Petersburg State Polytechnical University, St. Petersburg, Russ k j Also at Department of Physics, St. Petersburg State Polytechnical Univers Also at Department of Physics, St. 1 Department of Physics, University of Adelaide, Adelaide, Australia Fermi, Universit`a di Pisa, Pisa, Italy 124 Department of Physics and Astronomy University of Pittsburgh Pittsburgh PA United States of 124 Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh PA, United States of America 125 (a) Laboratorio de Instrumentacao e Fisica Experimental de Particulas - LIP, Lisboa; (b) Faculdade de Ciˆencias, Universidade de Lisboa, Lisboa; (c) Department of Physics, University of Coimbra, Coimbra; (d) Centro de F´ısica Nuclear da Universidade de Lisboa, Lisboa; (e) Departamento de Fisica, Universidade do Minho, Braga; (f) Departamento de Fisica Teorica y del Cosmos and CAFPE, Universidad de Granada, Granada (Spain); (g) Dep Fisica and CEFITEC of Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal 126 Institute of Physics, Academy of Sciences of the Czech Republic, Praha, Czech Republic 127 Czech Technical University in Prague, Praha, Czech Republic 129 State Research Center Institute for High Energy Physics, Protvino, Russia nstitute for High Energy Physics, Protvino, Russia 130 Particle Physics Department, Rutherford Appleton Laboratory, Didcot, United Kingdom 131 Physics Department, University of Regina, Regina SK, Canada 132 Ritsumeikan University, Kusatsu, Shiga, Japan 133 (a) INFN Sezione di Roma; (b) Dipartimento di Fisica, Sapienza Universit`a di Roma, Roma, Italy 134 ( ) (b) 134 (a) INFN Sezione di Roma Tor Vergata; (b) Dipartimento di Fisica, Universit`a di Roma Tor Vergata, Roma, Italy g , , y 135 (a) INFN Sezione di Roma Tre; (b) Dipartimento di Matematica e Fisica, Universit`a Roma Tre, Roma, Italy 136 (a) Facult´e des Sciences Ain Chock, R´eseau Universitaire de Physique des Hautes Energies - Universit´e Hassan II, Casablanca; (b) Centre National de l’Energie des Sciences Techniques Nucleaires, Rabat; (c) Facult´e des Sciences Semlalia, Universit´e Cadi Ayyad, LPHEA-Marrakech; (d) F lt´ d S i U i it´ M h d P i d LPTPM O jd (e) F lt´ d 135 (a) INFN Sezione di Roma Tre; (b) Dipartimento di Matematica e Fisica, Universit`a Roma Tre, Roma, Italy Roma, Italy 136 (a) Facult´e des Sciences Ain Chock, R´eseau Universitaire de Physique des Hautes Energies - Universit´e Hassan II, Casablanca; (b) Centre National de l’Energie des Sciences Techniques Nucleaires, Rabat; (c) Facult´e des Sciences Semlalia, Universit´e Cadi Ayyad, LPHEA-Marrakech; (d) Facult´e des Sciences, Universit´e Mohamed Premier and LPTPM, Oujda; (e) Facult´e des sciences, Universit´e Mohammed V-Agdal, Rabat, Morocco 136 (a) Facult´e des Sciences Ain Chock, R´eseau Universitaire de Physique des Hautes Energies - Faculte des Sciences Ain Chock, Reseau Universitaire de Physique des Hautes Energies Universit´e Hassan II, Casablanca; (b) Centre National de l’Energie des Sciences Techniques Universit´e Hassan II, Casablanca; (b) Centre National de l’Energie des Sciences Techniques Universite Hassan II, Casablanca; (b) Centre National de l’Energie des Sciences Techniques Nucleaires, Rabat; (c) Facult´e des Sciences Semlalia, Universit´e Cadi Ayyad, LPHEA-Marrakech; (d) Facult´e des Sciences, Universit´e Mohamed Premier and LPTPM, Oujda; (e) Facult´e des sciences, Universit´e Mohammed V-Agdal, Rabat, Morocco Nucleaires, Rabat; (c) Facult´e des Sciences Semlalia, Universit´e Cadi Ayyad, LPHEA-Marrakech; (d) Facult´e des Sciences, Universit´e Mohamed Premier and LPTPM, Oujda; (e) Facult´e des i U i it´ M h d V A d l R b t M nces, Universit´e Mohammed V-Agdal, Rabat, Morocc 137 DSM/IRFU (Institut de Recherches sur les Lois Fondamentales de l’Univers), CEA Saclay (Commissariat `a l’Energie Atomique et aux Energies Alternatives), Gif-sur-Yvette, France 138 Santa Cruz Institute for Particle Physics, University of California Santa Cruz, Santa Cruz CA, United States of America 139 Department of Physics, University of Washington, Seattle WA, United States of America 4 140 Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom 141 D t t f Ph i Shi h U i it N J 140 Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom 141 Department of Physics, Shinshu University, Nagano, Japan 142 Fachbereich Physik, Universit¨at Siegen, Siegen, Germany achbereich Physik, Universit¨at Siegen, Siegen, Germa 143 Department of Physics, Simon Fraser University, Burnaby BC, Canada 144 SLAC National Accelerator Laboratory, Stanford CA, United States of America 145 (a) Faculty of Mathematics, Physics & Informatics, Comenius University, Bratislava; (b) Department of Subnuclear Physics, Institute of Experimental Physics of the Slovak Academy of Sciences, Kosice, Slovak Republic (b) Department of Subnuclear Physics, Institute of Experimental Physics of the Slovak Academy of Sciences, Kosice, Slovak Republic – 46 – 146 (a) Department of Physics, University of Cape Town, Cape Town; (b) Department of Physics, University of Johannesburg, Johannesburg; (c) School of Physics, University of the Witwatersrand Johannesburg, South Africa 147 (a) Department of Physics, Stockholm University; (b) The Oskar Klein Centre, Stockholm, Swede 148 Physics Department, Royal Institute of Technology, Stockholm, Sweden 149 D t t f Ph i & A t d Ch i t St B k U i it St B k NY artment, Royal Institute of Technology, Stockholm, S 149 Departments of Physics & Astronomy and Chemistry, Stony Brook University, Stony Brook NY, United States of America 150 Department of Physics and Astronomy, University of Sussex, Brighton, United Kingdom 151 151 School of Physics, University of Sydney, Sydney, Australia 152 Institute of Physics, Academia Sinica, Taipei, Taiwan 153 Department of Physics, Technion: Israel Institute of Technology, Haifa, Israel 4 154 Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel JHEP10(2014)141 JHEP10(2014)141 155 Department of Physics, Aristotle University of Thessaloniki, Thessaloniki, Greece 156 International Center for Elementary Particle Physics and Department of Physics, The University of Tokyo, Tokyo, Japan 157 Graduate School of Science and Technology, Tokyo Metropolitan University, Tokyo, Japan 158 Department of Physics, Tokyo Institute of Technology, Tokyo, Japan 159 Department of Physics, University of Toronto, Toronto ON, Canada 160 ( ) (b) of Physics, University of Toronto, Toronto ON, Can 160 (a) TRIUMF, Vancouver BC; (b) Department of Physics and Astronomy, York University, Toronto ON, Canada 161 Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan 162 Department of Physics and Astronomy, Tufts University, Medford MA, United States of America 163 Centro de Investigaciones, Universidad Antonio Narino, Bogota, Colombia 164 Department of Physics and Astronomy, University of California Irvine, Irvine CA, United States of America 165 (a) INFN Gruppo Collegato di Udine, Sezione di Trieste, Udine; (b) ICTP, Trieste; (c) Dipartimento di Chimica, Fisica e Ambiente, Universit`a di Udine, Udine, Italy ( ) INFN Gruppo Collegato di Udine, Sezione di Trieste, Udine; ( ) ICTP, Trieste; (c) Dipartimento di Chimica, Fisica e Ambiente, Universit`a di Udine, Udine, Italy (c) Dipartimento di Chimica, Fisica e Ambiente, Universit`a di Udine, Udine, Italy 166 Department of Physics, University of Illinois, Urbana IL, United States of America 167 Department of Physics and Astronomy, University of Uppsala, Uppsala, Sweden 168 Instituto de F´ısica Corpuscular (IFIC) and Departamento de F´ısica At´omica, Molecular y Nuclear and Departamento de Ingenier´ıa Electr´onica and Instituto de Microelectr´onica de Barcelona 168 Instituto de F´ısica Corpuscular (IFIC) and Departamento de F´ısica At´omica, Molecular y Nuclear and Departamento de Ingenier´ıa Electr´onica and Instituto de Microelectr´onica de Barcelona (IMB-CNM), University of Valencia and CSIC, Valencia, Spain Instituto de Fısica Corpuscular (IFIC) and Departamento de Fısica Atomica, Molecular y Nuclear and Departamento de Ingenier´ıa Electr´onica and Instituto de Microelectr´onica de Barcelona (IMB CNM) U i it f V l i d CSIC V l i S i 169 Department of Physics, University of British Columbia, Vancouver BC, Canad ent of Physics, University of British Columbia, Vanc 170 Department of Physics and Astronomy, University of Victoria, Victoria BC, Canada 171 Department of Physics, University of Warwick, Coventry, United Kingdom 172 Waseda University, Tokyo, Japan 172 Waseda University, Tokyo, Japan 173 Department of Particle Physics, The Weizmann Institute of Science, Rehovot, Israel 174 Department of Physics, University of Wisconsin, Madison WI, United States of America 176 Fachbereich C Physik, Bergische Universit¨at Wuppertal, Wuppertal, German 177 Department of Physics, Yale University, New Haven CT, United States of America 177 Department of Physics, Yale University, New Haven CT, United States of America 178 Yerevan Physics Institute, Yerevan, Armenia 179 Centre de Calcul de l’Institut National de Physique Nucl´eaire et de Physique des Particules (IN2P3), Villeurbanne, France 179 Centre de Calcul de l’Institut National de Physique Nucl´eaire et de Physique des Particules (IN2P3), Villeurbanne, France a Also at Department of Physics, King’s College London, London, United Kingdom b Also at Institute of Physics, Azerbaijan Academy of Sciences, Baku, Azerbaijan c Also at Particle Physics Department, Rutherford Appleton Laboratory, Didcot, United Kingdom c Also at Particle Physics Department, Rutherford Appleton Laboratory, Didcot, United Kingdom d Also at TRIUMF, Vancouver BC, Canada c Also at Particle Physics Department, Rutherf d Also at TRIUMF, Vancouver BC, Canada , , e Also at Department of Physics, California State University, Fresno CA, United States of America f Al t T k St t U i it T k R i e Also at Department of Physics, California State University, Fresno CA, United States of America f Also at Tomsk State University, Tomsk, Russia e Also at Department of Physics, California State University, Fresno CA, United States of America e Also at Department of Physics, California Sta f Also at Tomsk State University, Tomsk, Russia g Also at CPPM, Aix-Marseille Universit´e and CNRS/IN2P3, Marseille, France h Also at Universit`a di Napoli Parthenope, Napoli, Italy – 47 – i Also at Institute of Particle Physics (IPP), Canada f y ( ), j Also at Department of Physics, St. 1 Department of Physics, University of Adelaide, Adelaide, Australia Petersburg State k Also at Chinese University of Hong Kong, China l Also at Department of Financial and Management Engineering, University of the Aegean, Chios, Greece m Also at Louisiana Tech University, Ruston LA, United States of America n Also at Institucio Catalana de Recerca i Estudis Avancats, ICREA, Barcelona, Spain o Also at Department of Physics, The University of Texas at Austin, Austin TX, United States of America p Also at Institute of Theoretical Physics, Ilia State University, Tbilisi, Georgia q Also at CERN, Geneva, Switzerland lso at Ochadai Academic Production, Ochanomizu U JHEP10(2014)141 JHEP10(2014)141 s Also at Manhattan College, New York NY, United States of America t Also at Novosibirsk State University, Novosibirsk, Russia u Also at Institute of Physics, Academia Sinica, Taipei, Taiwan v Also at LAL, Universit´e Paris-Sud and CNRS/IN2P3, Orsay, France lso at LAL, Universit´e Paris-Sud and CNRS/IN2P3, w Also at Academia Sinica Grid Computing, Institute of Physics, Academia Sinica, Taipei, Taiwan x Also at Laboratoire de Physique Nucl´eaire et de Hautes Energies, UPMC and Universit´e Paris-Diderot and CNRS/IN2P3, Paris, France x Also at Laboratoire de Physique Nucl´eaire et de Hautes Energies, UPMC and Universit´e Paris-Diderot and CNRS/IN2P3, Paris, France y Also at School of Physical Sciences, National Institute of Science Education and Research, Bhubaneswar, India z Also at Dipartimento di Fisica, Sapienza Universit`a di Roma, Roma, Italy z Also at Dipartimento di Fisica, Sapienza Universit`a di Roma, Roma, Italy Also at Moscow Institute of Physics and Technology State University, Dolgoprudny, Russia aa Also at Moscow Institute of Physics and Technology State University, Dolg ab Also at section de Physique, Universit´e de Gen`eve, Geneva, Switzerland ab Also at section de Physique, Universit´e de Gen`eve, Geneva, Switzerland ac Also at International School for Advanced Studies (SISSA), Trieste, Italy ac Also at International School for Advanced Studies (SISSA), Trieste, Italy ad Also at Department of Physics and Astronomy, University of South Carolina, Columbia SC, United States of America ae Also at School of Physics and Engineering, Sun Yat-sen University, Guangzhou, China af Also at Faculty of Physics, M.V.Lomonosov Moscow State University, Moscow, Russia ag Also at Moscow Engineering and Physics Institute (MEPhI), Moscow, Russia ag Also at Moscow Engineering and Physics Institute (MEPhI), Moscow, Russia h ah Also at Institute for Particle and Nuclear Physics, Wigner Research Centre for Physics, Budapes Hungary partment of Physics, Oxford University, Oxford, Uni aj Also at Department of Physics, Nanjing University, Jiangsu, China ak Also at Institut f¨ur Experimentalphysik, Universit¨at Hamburg, Hamburg, Germany al Also at Department of Physics, The University of Michigan, Ann Arbor MI, United States of America am Also at Discipline of Physics, University of KwaZulu-Natal, Durban, South Africa an Also at University of Malaya, Department of Physics, Kuala Lumpur, Malaysia ∗Deceased an Also at University of Malaya, Department of Physics, Kuala Lumpur, Malaysia ∗D d – 48 –
https://openalex.org/W4247215274
https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2003-4-4-108
English
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Judgement call
Genome biology
2,003
cc-by
2,370
Comment Judgement call Gregory A Petsko comment Address: Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA. E-mail: petsko@brandeis.edu Published: 28 March 2003 Genome Biology 2003, 4:108 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2003/4/4/108 © 2003 BioMed Central Ltd © 2003 BioMed Central Ltd © 2003 BioMed Central Ltd It was Hiawatha Bray, a columnist for The Boston Globe who writes about information technology, who broke the story, at least in my town. In a column on 3 February this year, he recounted what happened to the Litchfield brothers, a pair of British computer security experts whose company, Next Gen- eration Software, specializes in developing programs to help businesses and governments defend against computer viruses and hackers. Mark and David Litchfield are experts at finding weaknesses in widely used software, and last year they found a bug in Microsoft’s SQL Server database software. To establish that the bug could be used to cripple computer networks, David Litchfield wrote an exploit program, a kind of dummy virus. The existence of the bug, a buffer overflow problem, was then communicated to Microsoft, which published a fix in July. Other security experts had already been asking for copies of the exploit program so they could test their own systems and become familiar with this new potential method of attack- ing networks, and David Litchfield eventually released his code, but only after the patch to fix the program had been pub- lished. He thought, quite reasonably, that once the fix was available, SQL Server users would no longer be vulnerable. widely available. But these colleagues don’t have to live with the feelings of responsibility that the Litchfields now have. So from now on, every bug they discover - and they’ve already found others, in Microsoft’s Windows XP and 2000 operating systems - will call for their judgement. A similar judgement call was made a few weeks ago by the editors of a number of life-science journals, who released a statement of a new policy regarding the publication of reports of scientific research in areas such as microbiology and genomics that could potentially be of use to bioterror- ists. Comment Judgement call Gregory A Petsko The policy, which has received widespread attention, permits the journals to request that experimental details be omitted from papers if, in the view of the editors or a panel of experts (depending on the journal), the information could be misused. In some cases, publication of the work could be embargoed altogether. The policy has been sharply criticized. The arguments against it would be familiar to the Litchfields: that any form of censorship runs contrary to the spirit of science; that it creates a slippery slope leading to government control; that free exchange of ideas and data represents the best way to anticipate possible misuses of science and technology and to generate the methods to counter them. He was wrong. On the last weekend in January, the Slammer worm struck. Millions of computers were attacked, and the entire worldwide web was crippled for some time. Busi- nesses are estimated to have lost tens of billions of dollars. It seems that many corporations and individuals hadn’t yet bothered to install the patch. And David Litchfield discov- ered, to his horror, that his code was used as the template for the worm. To be sure, any good programmer could have worked out the code without help, but because of the Litch- fields’ well-meaning publication of their exploit program, that hadn’t been necessary. Now Mark and David Litchfield must decide whether they will ever again publish or distrib- ute their exploit programs. They have received hundreds of e-mails from colleagues begging them to continue releasing such code, because many in the computer business believe that the best way to deal with such weaknesses in widely dis- seminated programs is to publicize them and make examples The demand for freedom of inquiry and the open exchange of information always wars with the demand for security. While recognizing that absolute security is impossible, governments have a legitimate right - and a duty - to take reasonable steps to protect the lives of their citizens. In a repressive society, such steps are merely part of the general curtailing of liberty. But in a free society the trick is to strike a balance between protection and oppression. There is always a danger, as the witch-hunting excesses of the Cold War remind us, that one can destroy a free society in the name of saving it. Comment Judgement call Gregory A Petsko But I wonder if many scientists - who after all tend to have a mostly positive view of human nature as a result of largely associating with other scientists, a class of humanity not known for crimes or acts of violence - have a realistic perspective on the existence of evil. I once taught a course in the social history of the detective story to a class of extremely bright, well-read college fresh- men. As part of the discussion one afternoon, I asked them if they thought that evil existed. Almost to a person, they argued that real evil was a literary abstraction. Historical examples I offered were dismissed as illustrating madness, not evil. The notion that someone could be technically sane yet delight in human suffering and death was something they were neither prepared nor willing to accept. I suspect that many scientists may feel the same way. Professional writers, whose careers depend on understanding the human condition, tend to be less starry-eyed. Two noted science-fiction authors have explored this subject in stories that are eerily similar. The older story, ‘The Supreme Moment’, was unpublished during the lifetime of its author, Robert E. Howard, best known for his fantasy tales of Conan the Barbarian. It was eventually published in 1984 in Crypt of Cthulhu magazine #25 and reprinted in The New Howard Reader #1, edited by Joseph W. Marek. The story concerns five wealthy, powerful men who are trying to convince a crip- pled scientist to save the human race from a fungus that is spreading across the earth, destroying all vegetation. The sci- entist, Zan Uller, knows how to make a fungicide but refuses to reveal the formula. As a justification, he explains that he had a tormented childhood and a career bedeviled by sabo- tage from rival scientists, persecution by religious fanatics, and ridicule for his discoveries. His five visitors threaten to force him to reveal the formula by torture, believing it justi- fied to save the planet. Before they can act, to forestall them and to take his vengeance on a world that has given him nothing but misery, Uller commits suicide. Both Howard and de Camp recognize that there can be people who are capable of great acts of malice and vindic- tiveness. Comment Judgement call Gregory A Petsko Although he doubts that the US government would do that he is con- vinced that if he turns over his information to them it will eventually become more widely known: as the theft of the atom-bomb secrets proved, nothing can be kept hidden forever. In thoughts that chillingly echo our concerns about rogue states and terrorist organizations with weapons of mass destruction, Ormont decides that sooner or later some ‘crackpot’ head of state will use this capability to wreak havoc on a planet-wide scale. He then reflects on his own life history. Like Uller in The Supreme Moment, he had a child- hood filled with physical and verbal abuse. His marriage failed and most of his other human contacts have been brief and hostile. An attempt at therapy quickly ended when he resented the psychiatrist’s description of his personality as schizoid. Now in his mid-50s, enfeebled by a heart condition and with little will to live, he has become thoroughly misan- thropic. He guesses that even if he publishes his formula in an obscure place, it would be discovered and used by a madman within a decade or two, and it is unlikely that he would live to see the end of the world. Finally, he reaches a decision: “There is one way I can be happy during my remaining years, and that is by the knowledge that all these bastards will get theirs someday ... I hate everybody ... I shall write my report.” disturbing tendencies to ignore the fundamental freedoms of its citizens for the sake of what many of us believe is a false sense of security. Other governments are unlikely to resist the temptation at least to control the public’s access to infor- mation, a goal that many in power have secretly harbored for years. But I am not in favor of doing nothing. At the heart of many of the objections to the policy of the journal editors, I believe, is a basic sense that the corruption of biology for evil purposes is unlikely. I recognize, and share, the concerns of my colleagues that even self-censorship, as a concept, sets a dangerous precedent. Comment Judgement call Gregory A Petsko I am completely in agreement with those who worry that this danger is near. The US government has recently shown Genome Biology 2003, 4:108 108.2 Genome Biology 2003, Volume 4, Issue 4, Article 108 Petsko http://genomebiology.com/2003/4/4/108 Petsko L. Sprague de Camp. A physicist, Wade Ormont, has developed a formula for a nuclear reaction using iron, a cheap, widely available material. If he publishes the details of his discovery, he realizes that the probability is high that someone will eventually use it to destroy the world. Although he doubts that the US government would do that he is con- vinced that if he turns over his information to them it will eventually become more widely known: as the theft of the atom-bomb secrets proved, nothing can be kept hidden forever. In thoughts that chillingly echo our concerns about rogue states and terrorist organizations with weapons of mass destruction, Ormont decides that sooner or later some ‘crackpot’ head of state will use this capability to wreak havoc on a planet-wide scale. He then reflects on his own life history. Like Uller in The Supreme Moment, he had a child- hood filled with physical and verbal abuse. His marriage failed and most of his other human contacts have been brief and hostile. An attempt at therapy quickly ended when he resented the psychiatrist’s description of his personality as schizoid. Now in his mid-50s, enfeebled by a heart condition and with little will to live, he has become thoroughly misan- thropic. He guesses that even if he publishes his formula in an obscure place, it would be discovered and used by a madman within a decade or two, and it is unlikely that he would live to see the end of the world. Finally, he reaches a decision: “There is one way I can be happy during my remaining years, and that is by the knowledge that all these bastards will get theirs someday ... I hate everybody ... I shall write my report.” L. Sprague de Camp. A physicist, Wade Ormont, has developed a formula for a nuclear reaction using iron, a cheap, widely available material. If he publishes the details of his discovery, he realizes that the probability is high that someone will eventually use it to destroy the world. Comment Judgement call Gregory A Petsko It used to be argued that no one would be likely to use a chemical, biological or nuclear weapon since to do so would lead to far too great a risk of the user’s own destruc- tion, either through retaliation or the failure to control the damage from one’s own use. The advent of suicide bombers and eschatological cults like Aum Shinrikyo should dispel that notion. There are people who would not blanch at the end of the world, or at least the destruction of large parts of it, and who hold their own lives (or, more commonly, the lives of their followers) very cheaply. Some of them are neither so insane as to be incapable of cunning nor so tech- nically inept as to be unable to adapt ‘peaceful’ discoveries to their own ends. It is true that most of their activities up to now have been of the low-tech kind, and they probably will continue to be for the near future, but it is indisputable that at least some of them have tried to obtain or develop biologi- cal weapons, and it seems certain that such attempts will continue. ‘Judgement Day’, by L. Sprague de Camp (who, interest- ingly, was chosen to complete Howard’s unfinished Conan stories after the latter’s early death), was published in the August 1955 issue of Astounding Science Fiction magazine and later reprinted by Ballantine Books in The Best of “We often forget that our actions…can have very real conse- quences in real life,” David Litchfield wrote shortly after the Slammer incident. I think the biological community has to face the fact that software experts - and physicists and chemists - are no longer alone in their nightmares over the Genome Biology 2003, 4:108 Genome Biology 2003, Volume 4, Issue 4, Article 108 Petsko 108.3 Genome Biology 2003, http://genomebiology.com/2003/4/4/108 possible misuse of their discoveries. Until human evolution, ethically speaking, catches up with technological evolution, we will all have to live with this possibility. The policy adopted by the journal editors seems to me a wise attempt to seize the initiative from those in government who would use the public’s increasing fear of biology as a license for repressive control of scientific research and publication. As a community, I think we should adhere to this policy for the time being while continuing to debate its merits and considering alterna- tives. Genome Biology 2003, Volume 4, Issue 4, Article 108 Petsko 108.3 Genome Biology 2003, 4:108 Comment Judgement call Gregory A Petsko During these discussions, we will no doubt also be asking ourselves how we would feel, and what the consequences to our profession would be, if one of our publications were to form the blueprint for a terrorist act. If we have trouble imagining the answers, Mark and David Litchfield do not. comment Genome Biology 2003, 4:108
https://openalex.org/W2104627972
https://europepmc.org/articles/pmc3708926?pdf=render
English
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An Enzyme That Inactivates the Inflammatory Mediator Leukotriene B4 Restricts Mycobacterial Infection
PloS one
2,013
cc-by
5,283
Received March 22, 2013; Accepted May 22, 2013; Published July 11, 2013 Copyright:  2013 Tobin et al. This is an open-access article distributed under the terms of the Creative Commons Attributi unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Funded by grants from the NIH (L.R.), a Mallinckrodt Scholar Award (D.M.T.), a postdoctoral fellowship from the education the NWRCE for Biodefense and Emerging Infectious Diseases (L.R. and D.C.K.). D.M.T. is a recipient of the NIH Director’s New Innovator A of the NIH Director’s Pioneer Award. The funders had no role in study design, data collection and analysis, decision to publish, or pre Funding: Funded by grants from the NIH (L.R.), a Mallinckrodt Scholar Award (D.M.T.), a postdoctoral fellowship from the educational ministry of Spain (F.J.R.), the NWRCE for Biodefense and Emerging Infectious Diseases (L.R. and D.C.K.). D.M.T. is a recipient of the NIH Director’s New Innovator Award and L.R. is a recipient of the NIH Director’s Pioneer Award. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Competing Interests: The authors have declared that no competing interests exist. * E-mail: david.tobin@duke.edu (DT); lalitar@uw.edu (LR) David M. Tobin1,2,3*, Francisco J. Roca4, John P. Ray4, Dennis C. Ko1,2,3, Lalita Ra 1 Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America, 2 Center for Microbial Pathogenesis, Duke University Medical Center, Durham, North Carolina, United States of America, 3 Center for AIDS Research, Duke University Medical Center, Durham, North Carolina, United States of America, 4 Department of Microbiology, University of Washington, Seattle, Washington, United States of America, 5 Department of Medicine, University of Washington, Seattle, Washington, United States of America, 6 Department of Immunology, University of Washington, Seattle, Washington, United States of America Introduction bacterial growth culminating in macrophage lysis, macrophage necrosis occurs in LTA4H/TNF excess despite an initial reduction in intracellular bacterial growth [2]. An effective host immune response balances effective microbial killing mechanisms and damage to the host itself. Recent work has shown dysregulation of these responses in tuberculosis, either by immunodeficiency or by overexuberant immune activation, worsens outcome by increasing bacterial burdens [1,2]. The balance of pro- and anti-inflammatory eicosanoids is particularly critical in the regulation of the host response to infecting mycobacteria [2,3]. The enzyme LTA4H, which catalyzes the synthesis of LTB4 from its unstable precursor LTA4 [4] sits at a key crossroads regulating the balance between the anti-inflamma- tory lipoxins and pro-inflammatory LTB4 [2,5]. In zebrafish larvae infected with Mycobacterium marinum, LTA4H deficiency and excess both produce hypersusceptibility with increased bacterial burdens [2]. LTB4 is induced in human tuberculosis [7], and the zebrafish findings are corroborated in humans [2]. A human promoter variant that increases LTA4H expression is associated with a similar increase in tuberculosis severity as a low-LTA4H expressing promoter variant. As in zebrafish, the two variants correlate clinically with a high and low inflammatory state, respectively. Importantly, high-activity LTA4H genotypes show strong association with a genotype-dependent response to adjunc- tive anti-inflammatory therapy in TB meningitis. The implication of LTB4 as a pharmacologically correctible host susceptibility determinant, led us to investigate whether additional modulators of LTB4 might influence tuberculosis susceptibility and provide therapeutic targets for adjunctive therapies. The susceptibility of LTA4H deficiency is mediated by the lipoxin excess that results from blocking the enzymatic pathway to LTB4 synthesis rather than compromised LTB4 production per se [2]. In contrast, excess LTB4 activity resulting from LTA4H excess plays a critical role in a hyperinflammatory route to increased disease severity [2]. A mechanistic dissection revealed that LTA4H overexpression produces TNF excess during infection and can be rescued by genetic knockdown or pharmacological modulation of TNF [2]. Albeit by a distinct mechanism, LTA4H/TNF excess converges on the same pathway to hypersusceptibility as LTA4H/ TNF deficiency: necrosis of infected macrophages that releases the bacteria into the growth-promoting extracellular environment [6]. While LTA4H/TNF deficiency permits uncontrolled intracellular Abstract While tuberculosis susceptibility has historically been ascribed to failed inflammation, it is now known that an excess of leukotriene A4 hydrolase (LTA4H), which catalyzes the final step in leukotriene B4 (LTB4) synthesis, produces a hyperinflammatory state and tuberculosis susceptibility. Here we show that the LTB4-inactivating enzyme leukotriene B4 dehydrogenase/prostaglandin reductase 1 (LTB4DH/PTGR1) restricts inflammation and independently confers resistance to tuberculous infection. LTB4DH overexpression counters the susceptibility resulting from LTA4H excess while ltb4dh- deficient animals can be rescued pharmacologically by LTB4 receptor antagonists. These data place LTB4DH as a key modulator of TB susceptibility and suggest new tuberculosis therapeutic strategies. Citation: Tobin DM, Roca FJ, Ray JP, Ko DC, Ramakrishnan L (2013) An Enzyme That Inactivates the Inflammatory Mediator Leukotriene B4 Restricts Mycobacterial Infection. PLoS ONE 8(7): e67828. doi:10.1371/journal.pone.0067828 Editor: Keertan Dheda, University of Cape Town, South Africa Received March 22, 2013; Accepted May 22, 2013; Published July 11, 2013 Received March 22, 2013; Accepted May 22, 2013; Published July 11, 2013 Results and Discussion We targeted LTB4DH/PTGR1 (henceforth referred to as LTB4DH), an LTB4-inactivating enzyme [8,9] not previously implicated in mycobacterial susceptibility (Fig. 1a). In isolated polymorphonuclear leukocytes, LTB4 is inactivated by omega oxidation via P450 while in other tissues via dehydrogenation through LTB4DH; notably the omega oxidation pathway is not predominant in monocytes, suggesting that dehydrogenation may represent the main inactivation pathway in these immune cells most closely associated with tuberculosis [9–11]. Consistent with this, LTB4DH/PTGR1 activity is prevalent in human monocytes PLOS ONE | www.plosone.org July 2013 | Volume 8 | Issue 7 | e67828 1 LTB4DH Restricts Mycobacterial Infection y Figure 1. (a) Schematic of LTB4 pathway, with proposed roles for the enzymes LTA4H and LTB4DH in synthesis and inactivation of LTB4, respectively highlighted in red. (b) Mean ratio (6SEM) of mutant to wildtype mRNA levels in uninfected 3 dpf lta4hzm5961 animals compared to wildtype animals in four biological replicates. P = 0.007; one sample, two-tailed t test. (c) Number of cells recruited to hindbrain ventricle 6 hpi of sibling wildtype or ltb4dh morphant embryos after infection at 24 hpf with 90–100 CFU M. marinum. P = 0.005; Students’s unpaired t-test. (d) Mean(6SEM) number of bacteria per infected macrophage in 14 wildtype and 14 ltb4dh morphant siblings at 72 hpi after infection with 100–150 erp mutant bacteria. P = 0.003; Student’s unpaired t-test. Representative of two independent experiments. (e) Quantitation of bacterial burden by FPC at 5 dpi after infection of sibling controls or ltb4dh morphants with 79621 CFU wildtype M. marinum. P = 0.002; Student’s unpaired t-test. PLOS ONE | www.plosone.org 2 July 2013 | Volume 8 | Issue 7 | e67828 Figure 1. (a) Schematic of LTB4 pathway, with proposed roles for the enzymes LTA4H and LTB4DH in synthesis and inactivation of LTB4, respectively highlighted in red. (b) Mean ratio (6SEM) of mutant to wildtype mRNA levels in uninfected 3 dpf lta4hzm5961 animals compared to wildtype animals in four biological replicates. P = 0.007; one sample, two-tailed t test. (c) Number of cells recruited to hindbrain ventricle 6 hpi of sibling wildtype or ltb4dh morphant embryos after infection at 24 hpf with 90–100 CFU M. marinum. P = 0.005; Students’s unpaired t-test. (d) Mean(6SEM) number of bacteria per infected macrophage in 14 wildtype and 14 ltb4dh morphant siblings at 72 hpi after infection with 100–150 erp mutant bacteria. P = 0.003; Student’s unpaired t-test. Representative of two independent experiments. LTB4DH Restricts Mycobacterial Infection Representative of four independent experiments. (f) Representative images of wildtype granuloma and bacterial extracellular cording in ltb4dh morphant. Scale bars, 20 mM. (g) Quantitation of bacterial burden by FPC at 3 dpi of sibling controls, ltb4dh morphants and ltb4dh/TNF double morphants with 90610 CFU wildtype M. marinum. Statistical comparisons by one-way ANOVA with Tukey’s post hoc test. (h) Quantitation of bacterial burden by FPC at 4 dpi after infection of sibling controls or ltb4dh morphants in vehicle (0.5% DMSO) alone or treated with 10 mM U75302. (i) Relative TNF levels in wildtype siblings or ltb4dh morphant larvae 24 hpi with 150–200 CFU M. marinum with or without the addition of 10 mM U75302. doi:10.1371/journal.pone.0067828.g001 (as assessed by a second role for the enzyme in lipoxin modification), but this activity is largely absent in human PMNs [12]. The zebrafish orthologue of human LTB4DH shares 61% amino acid identity (Fig. 2). All key residues shown to interact with NADP+ in the guinea pig LTB4DH crystal structure are conserved between zebrafish, humans and guinea pigs (Fig. 2) [13]. We found baseline ltb4dh RNA levels to be lower in lta4h mutant zebrafish than in wildtype siblings (Fig. 1b), suggesting that the ltb4dh promoter or transcript stability responds to feedback signals within this pathway. RNA levels of the myeloid transcrip- tion factor pu.1 were not affected by the lta4h mutation, providing an internal control (Fig. 1b). Thus, production of ltb4dh, the downstream inactivating enzyme, may be limited when its LTB4 substrate is not produced due to lack of the upstream enzyme responsible for its generation. This interplay suggests that the two enzymes can function together to regulate LTB4. (as assessed by a second role for the enzyme in lipoxin modification), but this activity is largely absent in human PMNs [12]. The zebrafish orthologue of human LTB4DH shares 61% amino acid identity (Fig. 2). All key residues shown to interact with NADP+ in the guinea pig LTB4DH crystal structure are conserved between zebrafish, humans and guinea pigs (Fig. 2) [13]. We found baseline ltb4dh RNA levels to be lower in lta4h mutant zebrafish than in wildtype siblings (Fig. 1b), suggesting that the ltb4dh promoter or transcript stability responds to feedback signals within this pathway. RNA levels of the myeloid transcrip- tion factor pu.1 were not affected by the lta4h mutation, providing an internal control (Fig. 1b). Results and Discussion (e) Quantitation of bacterial burden by FPC at 5 dpi after infection of sibling controls or ltb4dh morphants with 79621 CFU wildtype M. marinum. P = 0.002; Student’s unpaired t-test. July 2013 | Volume 8 | Issue 7 | e67828 PLOS ONE | www.plosone.org 2 LTB4DH Restricts Mycobacterial Infection LTB4DH Restricts Mycobacterial Infection LTB4DH Restricts Mycobacterial Infection hypersusceptibility phenotype as LTA4H overexpression. ltb4dh morphants exhibited the same sequence of phenotypes as LTA4H excess created by mRNA expression: initial decreased intracellular bacterial burden after mycobacterial infection degenerated within a few days into increased bacterial burdens associated with cording morphology characteristic of macrophage lysis and extracellular residence (Fig. 1d–f and Fig. 3a). Morpholino inhibition of TNF in the background of ltb4dh morphants restored wildtype infection burden and removed the cording phenotype, showing that TNF is a key mediator of susceptibility as it is with LTA4H excess [2] (Fig. 1g and Fig. 3b). Figure 3. a) Percentage of animals with cording at 4 dpi from 34 ltb4dh morphants and 45 wildtype siblings infected with 100–150 wildtype M. marinum. P = 0.003; Fisher’s exact test of contingency table. b) Percentage of animals in Fig. 1g with cording at 4 dpi among sibling wildtype, ltb4dh morphant and ltb4dh/tnf double morphant animals. **P = 0.004, *P = 0.043; Fisher’s exact test of contingency table comparing wildtype and ltb4dh/tnf double morphant each to ltb4dh morphant. c) Percentage of animals in Fig. 1h with cording at 4 dpi among sibling widtype, ltb4dh morphants treated with 10 mM U75302 and ltb4dh morphants in vehicle (0.5% DMSO). ***P,0.0001, **P = 0.01; Fisher’s exact test of contingency table comparing wildtype and U75302-treated ltb4dh morphant each to vehicle-treated ltb4dh morphant. doi:10.1371/journal.pone.0067828.g003 If the hypersusceptibility of ltbd4h morphants is due to excess LTB4, then it should be possible to rescue this phenotype pharmacologically by blocking LTB4 activity. Accordingly, a LTB4 receptor antagonist reversed the cording-associated hyper- susceptibility of ltb4dh morphants while restoring excess tnf to wildtype levels (Fig. 1g,h and Fig. 3c). Conversely, interventions that compromise production of anti-inflammatory lipoxins should have a detrimental effect in ltbd4h morphants, as they do in states of LTA4H excess [2]. A known 15-lipoxygenase inhibitor produced the expected worsened bacterial burden accompanied by a further increase in tnf (Fig. 4). Together these results provide functional evidence that both excess LTA4H and reduced LTB4DH result in increased LTB4 activity, which in turn produces mycobacterial hypersusceptibility through TNF-mediat- ed hyperinflammation. These findings suggest that, despite a degree of co-regulation of LTB4 production and inactivation, LTB4DH levels can independently modulate control of infection. Importantly, the detrimental effects of LTB4DH deficiency can be countered by pharmacological antagonism of LTB4 activity or by directly targeting the resulting excess TNF. LTB4DH Restricts Mycobacterial Infection y g g g To probe further if LTB4DH can function as an independent resistance factor in humans, we used a dataset from an existing microarray analysis of human HapMap lymphoblastoid cell lines (LCLs) [14] to examine whether the correlation between lta4h and ltb4dh expression observed in the zebrafish was conserved in humans. We interrogated the collection of Asian cell lines, in which we had previously observed an effect on transcriptional activity of a common LTA4H promoter polymorphism [2]. As in the zebrafish, we found a direct correlation between LTA4H and LTB4DH RNA levels; individual cell lines with higher LTA4H transcript levels had higher LTB4DH expression (Fig. 5a). The level of correlation (r2 of 0.2, P = 0.0003) suggests that there is ample space for additional genetic and non-genetic factors to influence LTB4DH expression in humans. Thus, the detrimental effects of LTA4H excess may be dampened only to a limited extent by compensatory induction of the inactivating enzyme, This idea is supported by our zebrafish findings that LTB4DH reduction is an independent and pharmacologically correctible source of hypersusceptibility. Figure 3. a) Percentage of animals with cording at 4 dpi from 34 ltb4dh morphants and 45 wildtype siblings infected with 100–150 wildtype M. marinum. P = 0.003; Fisher’s exact test of contingency table. b) Percentage of animals in Fig. 1g with cording at 4 dpi among sibling wildtype, ltb4dh morphant and ltb4dh/tnf double morphant animals. **P = 0.004, *P = 0.043; Fisher’s exact test of contingency table comparing wildtype and ltb4dh/tnf double morphant each to ltb4dh morphant. c) Percentage of animals in Fig. 1h with cording at 4 dpi among sibling widtype, ltb4dh morphants treated with 10 mM U75302 and ltb4dh morphants in vehicle (0.5% DMSO). ***P,0.0001, **P = 0.01; Fisher’s exact test of contingency table comparing wildtype and U75302-treated ltb4dh morphant each to vehicle-treated ltb4dh morphant. Figure 3. a) Percentage of animals with cording at 4 dpi from 34 ltb4dh morphants and 45 wildtype siblings infected with 100–150 wildtype M. marinum. P = 0.003; Fisher’s exact test of contingency table. b) Percentage of animals in Fig. 1g with cording at 4 dpi among sibling wildtype, ltb4dh morphant and ltb4dh/tnf double morphant animals. **P = 0.004, *P = 0.043; Fisher’s exact test of contingency table comparing wildtype and ltb4dh/tnf double morphant each to ltb4dh morphant. c) Percentage of animals in Fig. LTB4DH Restricts Mycobacterial Infection Thus, production of ltb4dh, the downstream inactivating enzyme, may be limited when its LTB4 substrate is not produced due to lack of the upstream enzyme To determine if LTB4DH functions to limit the inflammatory effects of LTB4, we knocked down ltb4dh expression using antisense morpholinos. Even at baseline, ltb4dh morphants exhibited 2.9+/ 20.4 fold increased tnf RNA expression over wildtype siblings (P = 0.04; three biological replicates). In addition to increased tnf expression, LTA4H-overexpressing zebrafish exhibit increased macrophage recruitment to bacteria introduced into the hindbrain ventricle, a compartment normally lacking macrophages [2]. So too did the LTB4DH morphants (Fig. 1c). Thus both the overexpression of the enzyme that produces LTB4 and inhibition of its inactivating enzyme result in the signature hyperinflamma- tory phenotypes attributable to excess levels of LTB4. Our in vivo Figure 2. Amino acid alignment of human LTB4DH/PTGR1 with its closest zebrafish orthologue. Identical residues are starred. Residues predicted by crystal structure to interact with NADP+ are shaded with light blue boxes13. doi:10.1371/journal.pone.0067828.g002 Figure 2. Amino acid alignment of human LTB4DH/PTGR1 with its closest zebrafish orthologue. Identical residues are starred. Residues predicted by crystal structure to interact with NADP+ are shaded with light blue boxes13. doi:10.1371/journal.pone.0067828.g002 July 2013 | Volume 8 | Issue 7 | e67828 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org 3 LTB4DH Restricts Mycobacterial Infection LTB4DH Restricts Mycobacterial Infection 1h with cording at 4 dpi among sibling widtype, ltb4dh morphants treated with 10 mM U75302 and ltb4dh morphants in vehicle (0.5% DMSO). ***P,0.0001, **P = 0.01; Fisher’s exact test of contingency table comparing wildtype and U75302-treated ltb4dh morphant each to vehicle-treated ltb4dh morphant. yp p y We asked if increasing LTB4DH expression levels in vivo might ameliorate the LTA4H-high susceptibility phenotype, thus pro- viding additional potential targets for intervention. Overexpression of LTB4DH mRNA was sufficient to rescue the LTA4H-high phenotype (Fig. 5b). In contrast, LTB4DH overexpression did not worsen infection of wildtype animals (Fig. 5b), consistent with previous data where pharmacological inhibition of LTB4 receptor did not increase susceptibility [2]. The lack of a protective role for LTB4 in tuberculosis is in contrast to the case of other infections where a protective role has been noted for this inflammatory mediator [15–17]. In tuberculosis, LTB4 may mediate only pathogenesis, as it does in a variety of inflammatory diseases - asthma, atherosclerosis, rheumatoid arthritis, gout, obesity and cancer [18–24]. Accordingly, we find that excess LTB4 resulting p doi:10.1371/journal.pone.0067828.g003 findings are consistent with the proposed role of LTB4DH as a negative regulator of LTB4 activity [8]. findings are consistent with the proposed role of LTB4DH as a negative regulator of LTB4 activity [8]. Thus establishing a functional role for LTB4DH in LTB4 inactivation, we asked if LTB4DH deficiency produced the same PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org July 2013 | Volume 8 | Issue 7 | e67828 4 LTB4DH Restricts Mycobacterial Infection Figure 4. a) Quantitation of bacterial burden by FPC at 3 dpi of sibling controls or ltb4dh morphants with 90610 CFU wildtype M. marinum in vehicle (0.5% DMSO) alone or treated with 100 nM PD146176. Statistical comparisons by one-way ANOVA with Tukey’s post hoc test. b) Relative TNF levels in 1 dpi larvae after injection with LTB4DH morpholino and infection with 150–200 CFU M. marinum with or without the addition of 500 nM PD146176. doi:10.1371/journal.pone.0067828.g004 Figure 4. a) Quantitation of bacterial burden by FPC at 3 dpi of sibling controls or ltb4dh morphants with 90610 CFU wildtype M. marinum in vehicle (0.5% DMSO) alone or treated with 100 nM PD146176. Statistical comparisons by one-way ANOVA with Tukey’s post hoc test. b) Relative TNF levels in 1 dpi larvae after injection with LTB4DH morpholino and infection with 150–200 CFU M. LTB4DH Restricts Mycobacterial Infection marinum with or without the addition of 500 nM PD146176. doi:10.1371/journal.pone.0067828.g004 Bacterial Strains In conclusion, these findings implicate a downstream inactivat- ing enzyme of a pro-inflammatory eicosanoid as an important controller of mycobacterial resistance. Despite finding some degree of co-regulation of LTB4DH and LTA4H in both zebrafish and humans, ltb4dh serves as an independent susceptibility locus in the zebrafish. Similarly, human variation in LTB4DH may influence TB susceptibility. Our work suggests that pharmacolog- ical interventions can compensate for the consequences of LTB4DH reduction, providing new approaches to titering eicosanoid balance. LTB4-mediated inflammation may have relevance to oncogenic transformation, as LTB4 and components of its synthetic pathway are induced in different cancers [23–25]. Particularly intriguing from a therapeutic perspective is the ability of gallic acid and a purified compound from Radix astragali to induce LTB4DH expression and limit oncogenic transformation [26]. Specific pharmacological inducers of LTB4DH expression, besides serving as novel anti-inflammatory therapies, may provide a new route to addressing the known hypersusceptibility to tuberculosis of individuals with high LTA4H expression [2]. WT strain M (ATCC #BAA-535) was transformed with plasmids containing transcriptional fusions of the gene encoding Wasabi to a constitutively-expressed Mycobacterium marinum promoter as described [27]. The erp mutant expressing msp-12::gfp [28] was used for quantitation of intracellular bacterial burdens in Fig. 1d. Bacteria were grown in 7H9 media supplemented with oleic acid-albumin-dextrose-complex and 0.05% Tween-80 unless otherwise stated. Materials and Methods from two independent deviations in its metabolic pathway produces hypersusceptibility to mycobacterial infection. References 10. Shak S, Goldstein IM (1984) Omega-oxidation is the major pathway for the catabolism of leukotriene B4 in human polymorphonuclear leukocytes. The Journal of biological chemistry 259: 10181–10187. 1. Agarwal N, Lamichhane G, Gupta R, Nolan S, Bishai WR (2009) Cyclic AMP intoxication of macrophages by a Mycobacterium tuberculosis adenylate cyclase. Nature 460: 98–102. 2. Tobin DM, Roca FJ, Oh SF, McFarland R, Vickery TW, et al. (2012) Host Genotype-Specific Therapies Can Optimize the Inflammatory Response to Mycobacterial Infections. Cell 148: 434–446. 11. Soberman RJ, Harper TW, Murphy RC, Austen KF (1985) Identification and functional characterization of leukotriene B4 20-hydroxylase of human polymorphonuclear leukocytes. Proceedings of the National Academy of Sciences of the United States of America 82: 2292–2295. y 3. Bafica A, Scanga CA, Serhan C, Machado F, White S, et al. (2005) Host control of Mycobacterium tuberculosis is regulated by 5-lipoxygenase-dependent lipoxin production. The Journal of clinical investigation 115: 1601–1606. 12. Maddox JF, Serhan CN (1996) Lipoxin A4 and B4 are potent stimuli for human monocyte migration and adhesion: selective inactivation by dehydrogenation and reduction. The Journal of experimental medicine 183: 137–146. 4. Haeggstrom JZ, Funk CD (2011) Lipoxygenase and leukotriene pathways: biochemistry, biology, and roles in disease. Chemical reviews 111: 5866–5898. 13. Hori T, Yokomizo T, Ago H, Sugahara M, Ueno G, et al. (2004) Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reduc- tase catalytic mechanism and a possible Src homology 3 domain binding loop. The Journal of biological chemistry 279: 22615–22623. 5. Serhan CN (2007) Resolution phase of inflammation: novel endogenous anti- inflammatory and proresolving lipid mediators and pathways. Annual review of immunology 25: 101–137. 14. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nature genetics 39: 1217–1224. 6. Roca FJ, Ramakrishnan L (2013) TNF Dually Mediates Resistance And Susceptibility To Mycobacteria Via Mitochondrial Reactive Oxygen Species. Cell In press. 15. Serezani CH, Perrela JH, Russo M, Peters-Golden M, Jancar S (2006) Leukotrienes are essential for the control of Leishmania amazonensis infection and contribute to strain variation in susceptibility. Journal of immunology 177: 3201–3208. 7. el-Ahmady O, Mansour M, Zoeir H, Mansour O (1997) Elevated concentrations of interleukins and leukotriene in response to Mycobacterium tuberculosis infection. Annals of clinical biochemistry 34 (Pt 2): 160–164. 8. Yokomizo T, Izumi T, Takahashi T, Kasama T, Kobayashi Y, et al. RT-PCR Quantitative RT-PCR was performed as previously described [2,32]. Total RNA obtained by Trizol extraction from infected or mock-injected embryos were used as templates for generating cDNA (Superscript II reverse transcriptase; random hexamer primers; Invitrogen) for quantitative real-time RT-PCR analysis. qRT-PCR assays were performed such that each 20 mL reaction contained either 250 nM of gene-specific primers or b-actin specific control primers. SYBR green PCR Master Mix (Applied Biosystems) was used at 1X. All qRT-PCR assays were performed in triplicate with an ABI Prism 7300 Real Time PCR System (Applied Biosystems). Data were normalized to b-actin (DDCT analysis). Primer sets used for ltb4dh were F 59 TCTTGGAT- GACTGGCCTCAT 39 and R 59 TCCTGGTTTGATGGCA- CATA 39. Statistical Analysis Statistical analysis was performed with Prism (Graphpad Software) for all comparisons. Statistical analysis was performed with Prism (Graphpad Software) for all comparisons. Acknowledgments We thank C. N. Serhan for advice, discussion and critical review of the manuscript; J. Cameron for fish facility management. Funded by grants from the NIH (L.R.), a Mallinckrodt Scholar Award (D.M.T.), a postdoctoral fellowship from the educational ministry of Spain (F.J.R.), the NWRCE for Biodefense and Emerging Infectious Diseases (L.R. and D.C.K.). D.M.T. is a recipient of the NIH Director’s New Innovator Award and L.R. is a recipient of the NIH Director’s Pioneer Award. lta4h and ltb4dh RNA was synthesized using the mMessage mMachine kit (Ambion) and the polyA Tailing kit (Ambion). 2– 4 nL of RNA was injected at one-four cell stage at a concentration of 200 ng/mL to create LTA4H-high animals and to overexpress ltb4dh. Pharmacological Interventions in Zebrafish After infection, small molecules were applied via soaking. Solutions were changed daily. All conditions and controls were Microscopy Morpholinos were obtained from Genetools (Eugene, OR). Control and tnf morpholinos were as previously described [31,32]. ltb4dh morpholino targeted with an injection volume of 2–4 nL of 1 mM morpholino targeting the start codon (sequence 59 CTTGAGCCATGACTCTTTTTTTGCA 39, with complement of ATG bolded). All morpholino infections were performed on paired needles; an equal number of morpholino and control animals were injected on each needle in an alternating sequence to reduce variations in dosage between groups. Microscopy was performed on a Nikon E600 equipped with DIC optics, a Nikon D-FL-E fluorescence unit with 100 W Mercury lamp and MFC-1000 z-step controller (Applied Scientific Instrumentation) or, for whole animal images, a motorized Nikon inverted Ti-E microscope. Objectives used included 26 Apo Objective 0.1 NA, 106 Plan Fluor 0.3 NA, 406 Plan Fluor 0.75 NA and 606 Oil Plan Apo, 1.4 NA. Widefield fluorescence and DIC images were captured on a CoolSnap HQ or CoolSnap CF CCD camera (Photometrics) using MetaMorph 7.1 (Molecular Devices). Author Contributions Conceived and designed the experiments: DMT FJR JPR LR. Performed the experiments: DMT FJR JPR. Analyzed the data: DMT FJR JPR LR. Contributed reagents/materials/analysis tools: DCK. Wrote the paper: DMT LR. Analyzed and interpreted the expression data from the HapMap samples: DCK. Prepared the figures: JPR. Edited the manuscript: DMT FJR JPR DCK LR. Conceived and designed the experiments: DMT FJR JPR LR. Performed the experiments: DMT FJR JPR. Analyzed the data: DMT FJR JPR LR. Contributed reagents/materials/analysis tools: DCK. Wrote the paper: DMT LR. Analyzed and interpreted the expression data from the HapMap samples: DCK. Prepared the figures: JPR. Edited the manuscript: DMT FJR JPR DCK LR. Zebrafish Strains and Infections All experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of the University of Washington. Zebrafish embryos of the AB line were injected with Mm or PBS (mock-injected) using phenol red as a visual marker at 30 hours post fertilization or 48 hours post fertilization (hpf) via caudal vein as described [29]. Hindbrain ventricle injections were performed as described at 24 hpf [30]. Innocula at injection were determined injecting the same volume onto selective bacteriologic plates and enumerating bacteria when colonies formed in 5–7 days. Bacterial burdens of larvae were determined by fluorescence pixel counts (FPC) as described in [27]. After images have been taken with Figure 5. (a) LTA4H and LTB4DH mRNA expression from 14 in lymphoblastoid cell lines (LCLs) from Asian cohorts represented in the HapMap project (CHB+JPT). R2 = 0.2, P,0.0001; linear regression and F test. (b) Quantitation of bacterial burden by FPC at 3 dpi of sibling controls and LTA4H-high overexpressing simultaneously or not ltb4dh with 90610 CFU wildtype M. marinum. Statistical comparisons by one-way ANOVA with Tukey’s post hoc test. doi:10.1371/journal.pone.0067828.g005 Figure 5. (a) LTA4H and LTB4DH mRNA expression from 14 in lymphoblastoid cell lines (LCLs) from Asian cohorts represented in the HapMap project (CHB+JPT). R2 = 0.2, P,0.0001; linear regression and F test. (b) Quantitation of bacterial burden by FPC at 3 dpi of sibling controls and LTA4H-high overexpressing simultaneously or not ltb4dh with 90610 CFU wildtype M. marinum. Statistical comparisons by one-way ANOVA with Tukey’s post hoc test. doi:10.1371/journal.pone.0067828.g005 July 2013 | Volume 8 | Issue 7 | e67828 PLOS ONE | www.plosone.org 5 LTB4DH Restricts Mycobacterial Infection standardized to a final concentration of 0.5% DMSO. PD 146176 (BIOMOL) was applied at a final concentration of 500 nM 16 hpi. U75302 (BIOMOL) was applied at a concentration of 10 mM directly after infection. standardized exposure times, FPC counts the number of pixels in each image with values above a background threshold, as determined by matched images of uninfected animals. 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(2002) Real-time visualization of mycobacterium-macrophage interactions leading to initiation of granuloma formation in zebrafish embryos. Immunity 17: 693–702. 24. Yokomizo T, Kato K, Terawaki K, Izumi T, Shimizu T (2000) A second leukotriene B(4) receptor, BLT2. A new therapeutic target in inflammation and immunological disorders. The Journal of experimental medicine 192: 421–432. 31. Roca FJ, Mulero I, Lopez-Munoz A, Sepulcre MP, Renshaw SA, et al. (2008) Evolution of the inflammatory response in vertebrates: fish TNF-alpha is a powerful activator of endothelial cells but hardly activates phagocytes. Journal of immunology 181: 5071–5081. g J p 25. References (1993) Enzymatic inactivation of leukotriene B4 by a novel enzyme found in the porcine kidney. Purification and properties of leukotriene B4 12-hydroxydehy- drogenase. The Journal of biological chemistry 268: 18128–18135. 16. 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PLOS ONE | www.plosone.org July 2013 | Volume 8 | Issue 7 | e67828 July 2013 | Volume 8 | Issue 7 | e67828 6 LTB4DH Restricts Mycobacterial Infection Zhao Y, Weng CC, Tong M, Wei J, Tai HH (2010) Restoration of leukotriene B(4)-12-hydroxydehydrogenase/15- oxo-prostaglandin 13-reductase (LTBDH/ PGR) expression inhibits lung cancer growth in vitro and in vivo. Lung cancer 68: 161–169. 32. Tobin DM, Vary JC Jr, Ray JP, Walsh GS, Dunstan SJ, et al. (2010) The lta4h locus modulates susceptibility to mycobacterial infection in zebrafish and humans. Cell 140: 717–730. 26. Wei L, Liu J, Le XC, Han Y, Tong Y, et al. (2011) Pharmacological induction of leukotriene B4–12-hydroxydehydrogenase suppresses the oncogenic transfor- 7 PLOS ONE | www.plosone.org July 2013 | Volume 8 | Issue 7 | e67828 PLOS ONE | www.plosone.org 7
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English
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Treewidth of the Kneser Graph and the Erdős-Ko-Rado Theorem
˜The œElectronic journal of combinatorics/˜The œjournal of combinatorics
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6,812
Abstract Treewidth is an important and well-known graph parameter that measures the complexity of a graph. The Kneser graph Kneser(n, k) is the graph with vertex set [n] k  , such that two vertices are adjacent if they are disjoint. We determine, for large values of n with respect to k, the exact treewidth of the Kneser graph. In the process of doing so, we also prove a strengthening of the Erd˝os-Ko-Rado Theorem (for large n with respect to k) when a number of disjoint pairs of k-sets are allowed. Keywords: graph theory; Kneser graph; treewidth; separators; Erd˝os-Ko-Rado Treewidth of the Kneser Graph and the Erd˝os-Ko-Rado Theorem David R. Wood † School of Mathematical Sciences Monash University Melbourne, Australia d id d@ h d Daniel J. Harvey ∗ Department of Mathematics and Statistics The University of Melbourne Melbourne, Australia Daniel J. Harvey ∗ Department of Mathematics and Statistics The University of Melbourne Melbourne, Australia d.harvey@pgrad.unimelb.edu.au Submitted: Dec 17, 2013; Accepted: Feb 20, 2014; Published: Feb 28, 2014 Mathematics Subject Classifications: 05C75, 05D05 †Supported by the Australian Research Council. ∗Supported by an Australian Postgraduate Award. † 1 Introduction A tree decomposition of a graph G is a pair (T, (Bx ⊂V (G) : x ∈V (T))) where T is a tree and (Bx ⊆V (G) : x ∈V (T)) is a collection of sets, called bags, indexed by the nodes of T. The following properties must also hold: • for each v ∈V (G), the nodes of T that index the bags containing v induce a non- empty connected subtree of T, • for each v ∈V (G), the nodes of T that index the bags containing v induce a non- empty connected subtree of T, • for each vw ∈E(G), there exists some bag containing both v and w. 1 1 the electronic journal of combinatorics 21(1) (2014), #P1.48 The width of a tree decomposition is the size of the largest bag, minus 1. The treewidth of a graph G, denoted tw(G), is the minimum width of a tree decomposition of G. Treewidth is an important concept in modern graph theory. Treewidth was initially defined by Halin [6] (with different nomenclature to the modern standard) and then later by Robertson and Seymour [16], who used it in their famous series of papers proving the Graph Minor Theorem [15]. The treewidth of a graph essentially describes how “tree-like” it is, where lower treewidth implies a more “tree-like” structure. (A forest has treewidth at most 1, for example.) Treewidth is also of key interest in the field of algorithm design—for example, treewidth is a key parameter in fixed-parameter tractability [1]. Let [n] = {1, . . . , n}. For any set S ⊆[n], a subset of S of size k is called a k-set, or occasionally a k-set in S. Let S k  denote the set of all k-sets in S. We say two sets intersect when they have non-empty intersection. [ ] The Kneser graph Kneser(n, k) is the graph with vertex set [n] k  , such that two vertices are adjacent if they are disjoint. Kneser graphs were first investigated by Kneser [9]. The chromatic number of the graph Kneser(n, k) was shown to be n −2k + 2 by Lov´asz [11], as Kneser originally conjectured. This was an important proof due to the development of the topological methods involved. Many other proofs of this result have been found, for example consider [19], which gives a more combinatorial version. 1 Introduction The Kneser graph is also of interest with regards to fractional chromatic number [17]. The famous Erd˝os-Ko-Rado Theorem [2] has a well-known relationship to the Kneser graph, as does the generalisation to cross- intersecting families by Pyber [14]. We discuss these in more detail in Section 2, and shall use both of these results to prove the following two theorems about the treewidth of the Kneser graph. Theorem 1. Let G be a Kneser graph with n ⩾4k2 −4k + 3 and k ⩾3. Then tw(G) = n −1 k  −1. This theorem is our main result, giving an exact answer for the treewidth of the Kneser graph when n is sufficiently large. In order to prove this, we show that n−1 k  −1 is both an upper bound and lower bound on the treewidth. We construct a tree decomposition directly in Section 3 to prove an upper bound. In Section 4 we prove the lower bound by using the relationship between treewidth and separators. In Section 6, we further conjecture that Theorem 1 extends to lower values of n. j We also prove the following more precise result when k = 2 Theorem 2. Let G be a Kneser graph with k = 2. Then Theorem 2. Let G be a Kneser graph with k = 2. Then Theorem 2. Let G be a Kneser graph with k = 2. Then a Kneser graph with k = 2. Then tw(G) =          0 if n ⩽3 1 if n = 4 4 if n = 5 n−1 2  −1 if n ⩾6. tw(G) =          0 if n ⩽3 1 if n = 4 4 if n = 5 n−1 2  −1 if n ⩾6. tw(G) =          0 if n ⩽3 1 if n = 4 4 if n = 5 n−1 2  −1 if n ⩾6. the electronic journal of combinatorics 21(1) (2014), #P1.48 2 the electronic journal of combinatorics 21(1) (2014), #P1.48 2 the electronic journal of combinatorics 21(1) (2014), #P1.48 the electronic journal of combinatorics 21(1) (2014), #P1.48 2 The upper bounds for Theorem 2 are proved in Section 3, and the lower bounds in Section 5. Finally, in the process of proving Theorem 1, we prove the following generalisation of the Erd˝os-Ko-Rado Theorem (Theorem 6 in Section 2), which says that if n ⩾2k and H is a complete subgraph in the complement of Kneser(n, k) then |H| ⩽ n−1 k−1  . We prove the same bound for balanced complete multipartite graphs. Theorem 3. Say p ∈[ 2 3, 1) and n ⩾max(4k2−4k+3, 1 1−p(k2−1)+2). If H is a complete multipartite subgraph of the complement of Kneser(n, k) such that no colour class contains more than p|H| vertices, then |H| ⩽ n−1 k−1  . Theorem 3. Say p ∈[ 2 3, 1) and n ⩾max(4k2−4k+3, 1 1−p(k2−1)+2). If H is a complete multipartite subgraph of the complement of Kneser(n, k) such that no colour class contains more than p|H| vertices, then |H| ⩽ n−1 k−1  . Note that similar, but incomparable, generalisations of the Erd˝os-Ko-Rado Theorem have recently been explored in [5, 4, 18]. Theorem 3 is proven in Section 4, since it follows almost directly from our proof of the lower bound on the treewidth of a Kneser graph. 2 Basic Definitions and Preliminaries If n ⩾2k + 1 and A is an independent set such that |A| = n−1 k−1  , then A = {v|i ∈v} for a fixed element i ∈[n]. Theorem 6 (Erd˝os-Ko-Rado [2, 7]). Let G be Kneser(n, k) for some n ⩾2k. Then α(G) = n−1 k−1  . If n ⩾2k + 1 and A is an independent set such that |A| = n−1 k−1  , then A = {v|i ∈v} for a fixed element i ∈[n]. The original Erd˝os-Ko-Rado Theorem defines A as a set of k-sets in [n], such that the k-sets of A pairwise intersect. Our formulation in terms of vertices in the Kneser graph is clearly equivalent. We will use Theorem 6 when determining an upper bound for tw(G). The second major result is by Pyber [14]. Let A and B be sets of vertices of the Kneser graph G, such that for all v ∈A and w ∈B the pair vw is not an edge. Then we say the pair (A, B) are cross-intersecting families. Theorem 7 (Erd˝os-Ko-Rado for Cross-Intersecting Families [14, 13]). Let n ⩾2k and let (A, B) be cross-intersecting families in the Kneser graph G. Then |A||B| ⩽ n−1 k−1 2. If n ⩾2k + 1 and (A, B) are cross-intersecting families such that |A||B| = n−1 k−1 2, then A = B = {v|i ∈v} for a fixed element i ∈[n]. Theorem 7 (Erd˝os-Ko-Rado for Cross-Intersecting Families [14, 13]). Let n ⩾2k and let (A, B) be cross-intersecting families in the Kneser graph G. Then |A||B| ⩽ n−1 k−1 2. If n ⩾2k + 1 and (A, B) are cross-intersecting families such that |A||B| = n−1 k−1 2, then A = B = {v|i ∈v} for a fixed element i ∈[n]. As with Theorem 6, the original formulation by Pyber of Theorem 7 is more general. We have given the result in an equivalent form that is sufficient for our requirements. Let X be a 2 3-separator and A,B the parts of the vertex partition of G −X as in Lemma 5. Now for all v ∈A and w ∈B, v and w are in different components and as such are non-adjacent. So (A, B) are cross-intersecting families. We know |A| = c|G−X| where 1 3 ⩽c ⩽1 2. By Theorem 7, it follows that c(1 −c)|G −X|2 ⩽ n−1 k−1 2. 2 Basic Definitions and Preliminaries From now on, we refer to the graph Kneser(n, k) as G, with n and k implicit. Let ∆(H) be the maximum degree of a graph H and δ(H) be the minimum degree of a graph H. Also let α(H) be the size of the largest independent set of H, where an independent set is a set of pairwise non-adjacent vertices. If k = 1, then G is the complete graph. If n < 2k then G contains no edges. If n = 2k then G is an induced matching. From now on, we shall assume that n ⩾2k + 1 and k ⩾2, since the treewidth is trivial in the other cases. In order to prove a lower bound on the treewidth of the Kneser graph, we use a known result about the relationship between treewidth and separators. Definition Given a constant p ∈[ 2 3, 1), a p-separator (of order k) is a set X ⊂V (G) such that |X| ⩽k and no component of G −X contains more than p|G −X| vertices. Theorem 4. [16] For each p ∈[ 2 3, 1), every graph G has a p-separator of order tw(G)+1. It can easily be shown that we can partition the components of G −X into two parts, such that the components in a part contain, in total, at most p|G −X| vertices. This gives the following lemma. Lemma 5. Let X be a p-separator. Then V (G −X) can be partitioned into two parts A and B, with no edge between A and B, such that • (1 −p)|G −X| ⩽|A| ⩽1 2|G −X|, • 1 2|G −X| ⩽|B| ⩽p|G −X|. • (1 −p)|G −X| ⩽|A| ⩽1 2|G −X|, • 1 2|G −X| ⩽|B| ⩽p|G −X|. • (1 −p)|G −X| ⩽|A| ⩽1 2|G −X|, • 1 2|G −X| ⩽|B| ⩽p|G −X|. We use a few important well known combinatorial results. We use a few important well known combinatorial results. We use a few important well known combinatorial results. We use a few important well known combinatorial results. 3 the electronic journal of combinatorics 21(1) (2014), #P1.48 3 Theorem 6 (Erd˝os-Ko-Rado [2, 7]). Let G be Kneser(n, k) for some n ⩾2k. Then α(G) = n−1 k−1  . 2 Basic Definitions and Preliminaries 4 the electronic journal of combinatorics 21(1) (2014), #P1.48 Lemma 8 (A first set minimises the shadow [10, 8] (see [3] for a short proof)). Let X be a set of a-sets on [b], c ⩽a and S be the c-shadow of X. Suppose |X| is fixed but X is not. Then |S| is minimised when X is first. This idea is also used by Pyber [14] and Matsumoto and Tokushige [13]. Intuitively, the shadow S should be minimised whenever the a-sets of X “overlap” as much as possible, so that each c-set in S is a subset of as many a-sets as possible. 3 Upper Bound for Treewidth This section proves the upper bounds on tw(G) in Theorems 1 and 2. In both Theorem 1 and 2, the upper bound is almost always n−1 k  −1. The only exceptions are the trivial cases (when n ⩽2k), and the case when k = 2 and n = 5, which is the Petersen graph. The Petersen graph is well-known to have treewidth 4 ([12], for example). What follows is a general upper bound on the treewidth of any graph, which is sufficient to prove the remaining cases. Lemma 9. If H is any graph, then tw(H) ⩽max{∆(H), |V (H)| −α(H) −1}. mma 9. If H is any graph, then tw(H) ⩽max{∆(H), |V (H)| −α(H) −1}. Proof. Let α := α(H). We shall construct a tree decomposition with underlying tree T, where T is a star with α(H) leaves. Let R be the bag indexed by the central node of T, and label the other bags B1, . . . , Bα. Let X := {x1, . . . xα} be a maximum independent set in H. Let R := V (H) −X and Bi := N(xi) ∪{xi} for all i ∈{1, . . . , α}. We now show this is a tree decomposition: Any vertex not in X is contained in R. Given the structure of the star, any induced subgraph containing the central node is connected. Alternatively, if a vertex is in X, then it appears only in bags indexed by leaves. However, since X is an independent set, xi ∈X appears only in Bi, not in any other bag Bj. A single node is obviously connected. If vw is an edge of H, then at most one of v and w is in X. Say v = xi ∈X. Then v, w both appear in the bag Bi Otherwise neither vertex is in X and both vertices appear in R appear in the bag Bi. Otherwise neither vertex is in X, and both vertices appear in R. So this is a tree decomposition. The size of R is |V (H)| −α(H). The size of Bi is the degree of xi, plus one, which is at most ∆(H) + 1. From here our lemma is proven. So this is a tree decomposition. The size of R is |V (H)| −α(H). 2 Basic Definitions and Preliminaries It follows that |G −X| ⩽ 3 √ 2 n−1 k−1  . (We leave the precise calculation to the reader.) This gives a lower bound on |X|, and as such a lower bound on the treewidth (by Theorem 4). Hence tw(G) ⩾ n k  − 3 √ 2 n−1 k−1  −1. √ However, note that the parts A and B of V (G −X) are vertex disjoint, but that the definition of a pair of cross-intersecting families does not require this. In fact, Theorem 7 shows that in the case where |A||B| is maximised, A = B. We show we can do better than the above na¨ıve lower bound on tw(G) when A and B are disjoint. Before considering our final preliminary, we provide the following definitions. Consider all of the a-sets in [b]. Define the colexicographic or colex ordering on the a-sets as follows: if x and y are distinct a-sets, then x < y when max(x −y) < max(y −x). This is a strict total order. A set X of a-sets in [b] is first if X consists of the first |X| a-sets in the colex ordering of all the a-sets in [b]. Now consider the colex ordering of a-sets in [b]. All of the a-sets in [i] (where i < b) come before any a-set containing an element greater than or equal to i + 1. To see this, note if x is an a-set in [i] and y is an a-set with j ∈y such that j ⩾i + 1, then max(x −y) ⩽max(x) ⩽i, and max(y −x) ⩾j ⩾i + 1 since j ∈y −x. We will use this when determining the make-up of first sets in Section 4. Let X be a set of a-sets in [b]. For c ⩽a, the c-shadow of X is the set {x : |x| = c, and ∃y ∈X such that x ⊆y}. That is, the c-shadow contains all c-sets that are contained within a-sets of X. If x is an a-set in [b], let the complement of x be the (b −a)-set y = [b] −x. If X is a set of a-sets on [b], then the complement of X is X := {y : y is the complement of some x ∈X}. Note |X| = |X|. 4 Separators in the Kneser Graph To complete the proof of Theorem 1, it is sufficient to prove a lower bound on the treewidth. The following lemma, together with Theorem 4, provides this. It is the heart of the proof of Theorem 3. Lemma 11. Let X be a p-separator of the Kneser graph G. If n ⩾max(4k2 −4k + 3, 1 1−p(k2 −1) + 2), then |X| ⩾ n−1 k  . Proof. Assume, for the sake of a contradiction, that |X| < n−1 k  . Then |G −X| > n−1 k−1  . By Lemma 5, G −X has two parts A and B such that (1 −p)|G −X| ⩽|A| ⩽1 2|G −X| and 1 2|G −X| ⩽|B| ⩽p|G −X| and no edge has an endpoint in both A and B. Proof. Assume, for the sake of a contradiction, that |X| < n−1 k  . Then |G −X| > n−1 k−1  . By Lemma 5, G −X has two parts A and B such that (1 −p)|G −X| ⩽|A| ⩽1 2|G −X| and 1 2|G −X| ⩽|B| ⩽p|G −X| and no edge has an endpoint in both A and B. 2| | | | | | For a given element i ∈[n], let Ai := {v ∈A : i ∈v}. Also define A−i := {v ∈A : i /∈ v}. So Ai and A−i partition the set A, for any choice of i. Define analogous sets for B. Claim 1. There exists some i such that |Bi| ⩾1 k|B|. Proof. Since |A| ⩾(1−p)|G−X| > 0, there is a vertex v ∈A. Without loss of generality, v = {1, . . . , k}. Each w ∈B is not adjacent to v, and so w and v intersect. Thus each w must contain at least one of 1, . . . , k. Hence at least one of these elements appears in at least 1 k|B| of the vertices of B, as required. Without loss of generality, |Bn| ⩾1 k|B|. Claim 2. |Bn| > n−3 k−2  + n−2 k−2  . Without loss of generality, |Bn| ⩾1 k|B|. Claim 2. |Bn| > n−3 k−2  + n−2 k−2  . Claim 2. |Bn| > n−3 k−2  + n−2 k−2  . Proof. |B| ⩾ 1 2|G −X| ⩾ 1 2 n−1 k−1  . 3 Upper Bound for Treewidth The size of Bi is the degree of xi, plus one, which is at most ∆(H) + 1. From here our lemma is proven. We now consider this result for the Kneser graph itself. Lemma 10. If G is a Kneser graph with k ⩾2 and n ⩾2k + 1, then tw(G) ⩽ n k−1  −1. Proof. By Lemma 9 and Theorem 6, and since n ⩾2k + 1, tw(G) ⩽max {∆(G), |V (G)| −α(G) −1} = max n −k k  , n k  − n −1 k −1  −1  . Since k ⩾2, tw(G) ⩽ n−1 k  −1, as required. tw(G) ⩽max {∆(G), |V (G)| −α(G) −1} = max n −k k  , n k  − n −1 k −1  −1  . Since k ⩾2, tw(G) ⩽ n−1 k  −1, as required. Since k ⩾2, tw(G) ⩽ n−1 k  −1, as required. Since k ⩾2, tw(G) ⩽ n−1 k  −1, as required. the electronic journal of combinatorics 21(1) (2014), #P1.48 5 the electronic journal of combinatorics 21(1) (2014), #P1.48 4 Separators in the Kneser Graph Then by Claim 1 and our subsequent assumption, |Bn| ⩾ 1 k|B| ⩾ 1 2k|G −X| ⩾ 1 2k n−1 k−1  . Assume for the sake of a contradiction that |Bn| ⩽ n−3 k−2  + n−2 k−2  . So 1 2k n −1 k −1  ⩽ n −3 k −2  + n −2 k −2  . Thus Thus (n −1)! ⩽2k(k −1)((n −k)(n −3)! + (n −2)!). Hence Hence n2 −3n + 2 = (n −1)(n −2) ⩽2k(k −1)(2n −k −2) = 4k2n −4kn −2k3 −2k2 + 4k. So n2 + (4k −4k2 −3)n + 2k3 + 2k2 −4k + 2 ⩽0. Since n ⩾4k2 −4k + 3, it follows 2k3 + 2k2 −4k + 2 ⩽0. Given that k ⩾1, this provides our desired contradiction. n2 −3n + 2 = (n −1)(n −2) ⩽2k(k −1)(2n −k −2) = 4k2n −4kn −2k3 −2k2 + 4k. So n2 + (4k −4k2 −3)n + 2k3 + 2k2 −4k + 2 ⩽0. Since n ⩾4k2 −4k + 3, it follows 2k3 + 2k2 −4k + 2 ⩽0. Given that k ⩾1, this provides our desired contradiction. Consider the set A−n, that is, the complements of the vertices in A that do not contain n. So every set in A−n contains n. Let A−n ∗:= {v −n : v ∈A−n}. That is, remove n from each set in A−n. There is clearly a one-to-one correspondence between (n −k)-sets in A−n and (n −k −1)-sets in A−n ∗. ( ) Similarly, define B∗ n := {v −n : v ∈Bn}. That is, remove from each vertex of Bn the element n, which they all contain. The resultant sets are (k −1)-sets in [n −1]. 6 6 the electronic journal of combinatorics 21(1) (2014), #P1.48 Claim 3. If v∗∈B∗ n and w∗∈A−n ∗, then v∗̸⊆w∗. Claim 3. If v∗∈B∗ n and w∗∈A−n ∗, then v∗̸⊆w∗. Proof. Assume, for the sake of a contradiction, that v∗⊆w∗. Then it follows that v ⊂w, by re-adding n to both sets. Thus v and w are adjacent. However, v ∈Bn ⊂B and w ∈An ⊂A, which is a contradiction. Proof. Assume, for the sake of a contradiction, that v∗⊆w∗. Then it follows that v ⊂w, by re-adding n to both sets. Thus v and w are adjacent. However, v ∈Bn ⊂B and w ∈An ⊂A, which is a contradiction. 4 Separators in the Kneser Graph Let S be the (k −1)-shadow of A−n ∗. Hence if v ∈B∗ n, then v /∈S, by Claim 3. So, it follows that [ 1] B∗ n ⊆ [n −1] k −1  −S. Hence we have an upper bound for |B∗ n| when we take |S| to be minimised. By Lemma 8, |S| is minimised when A−n ∗is first. | | n 3 Hence we have an upper bound for |B∗ n| when we take |S| to be minimised. By Lemma 8, |S| is minimised when A−n ∗is first. Claim 4. |A−n| ⩽ n−3 k−2  . Lemma 8, |S| is minimised when A−n is first. Claim 4. |A−n| ⩽ n−3 k−2  . Claim 4. |A−n| ⩽ n−3 k−2  . Proof. |A−n| = |A−n| = |A−n ∗|, so it is sufficient to show that |A−n ∗| ⩽ n−3 k−2  . Assume for the sake of contradiction that |A−n ∗| ⩾ n−3 k−2  = n−3 n−k−1  . Firstly, we show that |S| ⩾ n−3 k−1  . It is sufficient to prove this lower bound when |S| is minimised. Hence we can assume that A−n ∗is first, and contains the first n−3 n−k−1  (n −k −1)-sets in the colexicographic ordering. That is, it contains all (n −k −1)-sets on [n −3]. This is because there are n−3 n−k−1  such sets, and they come before all other sets in the ordering. In that case, S contains all (k −1)-sets in [n −3]. Since all of the (k −1)-sets in [n −3] are in S, it follows that |S| ⩾ n−3 k−1  , as required. k 1  Then it follows that |B∗ n| ⩽ n−1 k−1  − n−3 k−1  = n−3 k−2  + n−2 k−2  . However, |B∗ n| = |Bn| > n−3 k−2  + n−2 k−2  by Claim 2. This provides our desired contradiction. Claim 5. |An| ⩾ k k+1|A|. Proof. First we show that |An| ⩾k|A−n|. Suppose otherwise, for the sake of a con- tradiction. By Claim 4, |A| = |An| + |A−n| < (k + 1)|A−n| ⩽(k + 1) n−3 k−2  . But |A| ⩾(1 −p)|G −X|. Hence (1 −p) n−1 k−1  < (k + 1) n−3 k−2  . Thus (n −1)(n −2) < 1 1−p(k + 1)(k −1)(n −k) ⩽ 1 1−p(k + 1)(k −1)(n −2). 4 Separators in the Kneser Graph An = A. Claim 7. An = A. Proof. This follows by essentially the same argument as Claim 6. Assume our claim does not hold and there exists v ∈A such that n /∈v. By Claim 6, |Bn| = |B| ⩾1 2 n−1 k−1  . There is an upper bound on |Bn| equal to the upper bound on |An| in the previous proof. Then 1 2 n −1 k −1  ⩽|B| = |Bn| ⩽k n −2 k −2  , and so n ⩽2k(k −1) + 1. This contradicts our lower bound on n. and so n ⩽2k(k −1) + 1. This contradicts our lower bound on n. Claims 6 and 7 show that every vertex in G −X = A ∪B contains n. Thus |G −X| ⩽ n−1 k−1  and |X| ⩾ n−1 k  , our desired contradiction. By Lemma 11, if X is a 2 3-separator of the Kneser graph G and n ⩾4k2 −4k +3, then |X| ⩾ n−1 k  . Hence by Theorem 4, tw(G) ⩾ n−1 k  −1. This proves Theorem 1. Al L 11 ll t Th 3 Proof of Theorem 3. Let C1, . . . , Cr be the colour classes of H. Recall G = Kneser(n, k). Let X := V (G) −V (H), so that X, C1, . . . , Cr is a partition of the vertex set of G (and also G). In G there are no edges between any pair Ci, Cj, and |Ci| ⩽p|H| = p|G −X| for each i. So X is a p-separator of G, and |X| ⩾ n−1 k  by Lemma 11. Hence |H| ⩽ n−1 k−1  . Proof of Theorem 3. Let C1, . . . , Cr be the colour classes of H. Recall G = Kneser(n, k). Let X := V (G) −V (H), so that X, C1, . . . , Cr is a partition of the vertex set of G (and also G). In G there are no edges between any pair Ci, Cj, and |Ci| ⩽p|H| = p|G −X| for each i. So X is a p-separator of G, and |X| ⩾ n−1 k  by Lemma 11. Hence |H| ⩽ n−1 k−1  . 4 Separators in the Kneser Graph Thus n < 1 1−p(k2 −1) + 1, which contradicts our lower bound on n. Proof. First we show that |An| ⩾k|A−n|. Suppose otherwise, for the sake of a con- tradiction. By Claim 4, |A| = |An| + |A−n| < (k + 1)|A−n| ⩽(k + 1) n−3 k−2  . But |A| ⩾(1 −p)|G −X|. Hence (1 −p) n−1 k−1  < (k + 1) n−3 k−2  . Thus (n −1)(n −2) < 1 1−p(k + 1)(k −1)(n −k) ⩽ 1 1−p(k + 1)(k −1)(n −2). Thus n < 1 1−p(k2 −1) + 1, which contradicts our lower bound on n. Then |An| ⩾k|A−n| = k(|A| −|An|). So (k + 1)|An| ⩾k|A| as required. Then |An| ⩾k|A−n| = k(|A| −|An|). So (k + 1)|An| ⩾k|A| as required. Claim 6. Bn = B. Claim 6. Bn = B. Proof. Suppose, for the sake of a contradiction, that there exists some vertex v ∈B such that n /∈v. So each w ∈An contains n (by definition) and some element of v (which is not n), since vw is not an edge. Any vertex of An can be constructed as follows—take element n, choose one of the k elements of v, and choose the remaining k −2 elements from the remaining n −2 elements of [n]. Thus |An| ⩽1 · k n −2 k −2  . 7 7 the electronic journal of combinatorics 21(1) (2014), #P1.48 Note this is actually a weak upper bound, since we have counted some of the vertices of An more than once. Recall |A| ⩾(1 −p)|G −X| ⩾(1 −p) n−1 k−1  . So by Claim 5, Note this is actually a weak upper bound, since we have counted some of the vertices of An more than once. Recall |A| ⩾(1 −p)|G −X| ⩾(1 −p) n−1 k−1  . So by Claim 5, (1 −p)k (k + 1) n −1 k −1  ⩽ k k + 1|A| ⩽k n −2 k −2  . Thus n−1 k−1 ⩽ 1 1−p(k + 1) and n ⩽ 1 1−p(k2 −1) + 1, which contradicts our lower bound on n Thus n−1 k−1 ⩽ 1 1−p(k + 1) and n ⩽ 1 1−p(k2 −1) + 1, which contradicts our lower bound on n. Thus n−1 k−1 ⩽ 1 1−p(k + 1) and n ⩽ 1 1−p(k2 −1) + 1, which contradicts our lower bound on n. Claim 7. the electronic journal of combinatorics 21(1) (2014), #P1.48 5 Lower Bound for Treewidth in Theorem 2 By Theorem 6, V (G −X) is too large to be an independent set, and so it contains an edge, with both endpoints in A or both endpoints in B. has the benefit of being the same on both parts.) Since n ⩾6, it follows that |A|, |B| ⩾2. By Theorem 6, V (G −X) is too large to be an independent set, and so it contains an edge, with both endpoints in A or both endpoints in B. g Without loss of generality this edge is {1, 2}{3, 4} ∈A. Then B ⊆{{1, 3}, {1, 4}, {2, 3}, {2, 4}}. If B contains an edge, then V (G −X) ⊆{{1, 2}, {1, 3}, {1, 4}, {2, 3}, {2, 4}, {3, 4}} and has maximum order 6. Otherwise, without loss of generality, B = {{1, 3}, {1, 4}} and A = {{3, 4}, {1, i}|i /∈{1, 3, 4}}, so |G −X| = n. (Note A must be exactly that set, or |G −X| is too small.) Without loss of generality this edge is {1, 2}{3, 4} ∈A. Then B ⊆{{1, 3}, {1, 4}, {2, 3}, {2, 4}}. If B contains an edge, then V (G −X) ⊆{{1, 2}, {1, 3}, {1, 4}, {2, 3}, {2, 4}, {3, 4}} and has maximum order 6. Otherwise, without loss of generality, B = {{1, 3}, {1, 4}} and A = {{3, 4}, {1, i}|i /∈{1, 3, 4}}, so |G −X| = n. (Note A must be exactly that set, or |G −X| is too small.) If n ⩾7, then |G −X| ⩾7 and the first case cannot occur. However in the second case, |B| = 2 < 1 3 · 7 ⩽1 3n. So neither case can occur, and we have forced a contradiction on either |G −X| or |B|. This completes the proof when n ⩾7. Hence, let n = 6, and note |G −X| = 6 in either case. | | Now we use the fact that X is a subset of some bag Bx. Now for all x ∈V (T), |Bx| ⩽ 5 2  −1 = 9. Since |G −X| = 6, it follows |X| = 9. Hence X is exactly a bag of maximum order. For either choice of G −X, note that A is a connected component. So there is some subtree of T −x that contains all vertices of A. 5 Lower Bound for Treewidth in Theorem 2 Let y be the node of this subtree adjacent to x. Also note, for either choice of G −X, that each vertex of X has a neighbour in A. So every vertex of Bx is also in bag By, which contradicts our normalisation. Thus, if n ⩾6, then tw(G) ⩾ n−1 2  −1. This completes the proof of Theorem 2. 5 Lower Bound for Treewidth in Theorem 2 To complete our proof of Theorem 2, we need to obtain a lower bound on the treewidth when k = 2. If n ⩽4, then Theorem 2 is trivial. When n = 5, then G is the Petersen graph, which contains a K5-minor forcing tw(G) ⩾4. Hence we may assume that n ⩾6. Assume, for the sake of a contradiction that tw(G) < n−1 2  −1. Let (T, (Bx : x ∈ V (T))) be a minimum width tree decomposition for G, and normalise the tree decompo- sition such that if xy ∈E(T), then Bx ̸⊆By and By ̸⊆Bx. By Theorem 4, there exists a 2 3-separator X such that |X| < n−1 2  . In fact, by the original proof in [16], we can go further and assert that X is a subset of a bag of (Bx : x ∈V (T)). To complete our proof of Theorem 2, we need to obtain a lower bound on the treewidth when k = 2. If n ⩽4, then Theorem 2 is trivial. When n = 5, then G is the Petersen graph, which contains a K5-minor forcing tw(G) ⩾4. Hence we may assume that n ⩾6. Assume, for the sake of a contradiction that tw(G) < n−1 2  −1. Let (T, (Bx : x ∈ V (T))) be a minimum width tree decomposition for G, and normalise the tree decompo- sition such that if xy ∈E(T), then Bx ̸⊆By and By ̸⊆Bx. By Theorem 4, there exists a 2 3-separator X such that |X| < n−1 2  . In fact, by the original proof in [16], we can go further and assert that X is a subset of a bag of (Bx : x ∈V (T)). ( ( )) Now |G −X| = n 2  −|X| > n−1 1  = n −1. By Lemma 5, V (G −X) has two parts A and B such that 1 3|G−X| ⩽|A|, |B| ⩽2 3|G−X| and there is no edge with an endpoint in A and B. (Note that this bound on |A| and |B| is slightly weaker than in Lemma 5, but 8 the electronic journal of combinatorics 21(1) (2014), #P1.48 has the benefit of being the same on both parts.) Since n ⩾6, it follows that |A|, |B| ⩾2. 6 Open Questions We conjecture that Theorem 1 should also hold for smaller values of n. Conjecture 12. Let G be a Kneser graph with n ⩾3k and k ⩾2. Then tw(G) = n−1 k  −1. This conjecture follows directly from Theorem 2 when k = 2. The Petersen graph also shows that n ⩾3k is a tight bound when k = 2. In general, we can determine a slightly better tree decomposition when n < 3k −1. Let X = {v ∈V (G) : 1 ∈v}, and let W be an independent set in V (G) −X such that no two vertices of W have a common neighbour in X. We define a tree decomposition for G with underlying tree T as follows. Let r denote the root node of T, and let r have one child node for each vertex in W and each vertex in X adjacent to no vertex in W. Label each of these child nodes by their associated vertex of G. Let each node labeled by a vertex w ∈W have one child node for each vertex of N(w) ∩X. Label each of those child nodes by their associated vertex of G, and note that since every vertex of X has at most one neighbour in W, no vertex of G labels more than one node of T. Define the bag indexed by r to be V (G) −W −X. Note this bag contains less than n−1 k  vertices when W ̸= ∅. If a node is labeled by a vertex v ∈X, let the corresponding bag be N(v)∪{v}. These bags contain n−k k  +1 vertices. If a node is labeled by a vertex w ∈W, let the corresponding bag be {w} ∪{u : uw ∈E(G), 1 /∈u} ∪{u : ux ∈E(G) 9 the electronic journal of combinatorics 21(1) (2014), #P1.48 where xw ∈E(G) and 1 ∈x}. These bags contain less than n−1 k  vertices whenever |W| ⩾2, since they contain no vertex in X, and each contains only one vertex from W. This is a valid tree decomposition, but we omit the proof. When |W| ⩾2, the width of this tree decomposition is less than the width given by Lemma 9. However, when |W| ⩽1, this tree decomposition has the same width as given by Lemma 9. We can construct W such that |W| ⩾2 iffn < 3k −1. 6 Open Questions For example, let W = {{2, . . . , (k + 1)}, {(k + 1), . . . , 2k}}. If n ⩽3k −2, then any vertex of X must be non-adjacent to at least one vertex of W. Alternatively, if n ⩾3k −1 and |W| ⩾2, then there exists two vertices x, y ∈W such that |x ∪y| ⩽2k −1. Then X contains a vertex adjacent to both x and y. Hence, for general n, we cannot improve the lower bound on n in Theorem 1 to 3k −2 or below. This does leave a question about what may occur for n = 3k −1. It is possible that Theorem 1 holds for n ⩾3k −1, with the Petersen graph as a single exception. Acknowledgements Thanks to Alex Scott for helpful conversations, and for pointing out references [4, 5, 18]. References [1] Hans L. Bodlaender. A tourist guide through treewidth. Acta Cybernet., 11(1-2):1– 21, 1993. [1] Hans L. Bodlaender. A tourist guide through treewidth. Acta Cybernet., 11(1-2):1– 21, 1993. [2] Paul Erd˝os, Chao Ko, and Richard Rado. Intersection theorems for systems of finite sets. Quart. J. Math. Oxford Ser. (2), 12:313–320, 1961. [3] P´eter Frankl. A new short proof for the Kruskal-Katona theorem. Discrete Math., 48(2-3):327–329, 1984. [4] D´aniel Gerbner, Nathan Lemons, Cory Palmer, D¨om¨ot¨or P´alv¨olgyi, Bal´azs Patk´os, and Vajk Sz´ecsi. Almost cross-intersecting and almost cross-sperner pairs of families of sets. Graphs and Combinatorics, 29:489–498, 2013. [5] D´aniel Gerbner, Nathan Lemons, Cory Palmer, Bal´azs Patk´os, and Vajk Sz´ecsi. Almost intersecting families of sets. SIAM. Discrete Mathematics, 26(4):1657–1669, 2012. [6] Rudolf Halin. S-functions for graphs. J. Geometry, 8(1-2):171–186, 1976. [7] Gyula O. H. Katona. A simple proof of the Erd˝os-Chao Ko-Rado theorem. J. Combin. Theory Ser. B, 13:183–184, 1972. [8] Gyula O.H. Katona. A theorem of finite sets. In Theory of graphs (Proc. Colloq., Tihany, 1966), pages 187–207. Academic Press, New York, 1968. [9] Martin Kneser. Aufgabe 360. Jahresber. Deutsch. Math.-Verein., 58:27, 1955. [10] Joseph B. Kruskal. The number of simplices in a complex. In Mathematical opti- mization techniques, pages 251–278. Univ. of California Press, Berkeley, Calif., 1963. the electronic journal of combinatorics 21(1) (2014), #P1.48 10 [11] L´aszl´o Lov´asz. Kneser’s conjecture, chromatic number, and homotopy. J. Combin. Theory Ser. A, 25(3):319–324, 1978. [12] Lambertus Marchal. Treewidth. PhD thesis, Maastricht University, 2012. [13] Makoto Matsumoto and Norihide Tokushige. The exact bound in the Erd˝os-Ko-Rado theorem for cross-intersecting families. J. Combin. Theory Ser. A, 52(1):90–97, 1989. [14] L´aszl´o Pyber. A new generalization of the Erd˝os-Ko-Rado theorem. J. Combin. Theory Ser. A, 43(1):85–90, 1986. [15] Neil Robertson and Paul D. Seymour. Graph minors I–XXIII. J. Combin. Theory Ser. B, 1983–2012. [16] Neil Robertson and Paul D. Seymour. Graph minors. II. Algorithmic aspects of tree-width. J. Algorithms, 7(3):309–322, 1986. 17] Edward R. Scheinerman and Daniel H. Ullman. Fractional graph theory. W [17] Edward R. Scheinerman and Daniel H. Ullman. Fractional graph theory. Wiley, 1997. [18] Alex Scott and Elizabeth Wilmer. Hypergraphs of bounded disjointness. 2013. arXiv:1306.4236. [18] Alex Scott and Elizabeth Wilmer. Hypergraphs of bounded disjointness. 2013. arXiv:1306.4236. [19] G¨unter M. Ziegler. Generalized Kneser coloring theorems with combinatorial proofs. Inventiones Math, 147:671–691, 2001. 11 11 the electronic journal of combinatorics 21(1) (2014), #P1.48 the electronic journal of combinatorics 21(1) (2014), #P1.48
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Strategi Peningkatan Kualitas Hubungan Keluarga dalam Situasi Suami Bekerja di Luar Negeri
Syakhshiyyah
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Volume 3 Nomor 2 Juli – Desember 2023 Syakhshiyyah Jurnal Hukum Keluarga Islam E-ISSN 2986-5409 Volume 3 Nomor 2 Juli – Desember 2023 Syakhshiyyah Jurnal Hukum Keluarga Islam E-ISSN 2986-5409 E-ISSN 2986-5409 Strategi Peningkatan Kualitas Hubungan Keluarga dalam Situasi Suami Bekerja di Luar Negeri Nyimas Lidya Putri Institut Agama Islam Negeri Metro, Indonesia nyimaslidyaputripertiwi@metrouniv.ac.id Aziza Aziz Rahmaningsih Institut Agama Islam Negeri Metro, Indonesia azizaaziz98@gmail.com Hanisah Nurhalimah Isanti Putri Institut Agama Islam Negeri Metro, Indonesia hanisa@gmail.com Sudirman Institut Agama Islam Negeri Metro, Indonesia sudirmanhk2@gmail.com Article History: DOI: https://doi.org/10.32332/syakhshiyyah.v3i2.8143 Copyright ©2023 Author Received: 23-11-2023 Revised: 28-12-2023 Accepted: 28-12-2023 Published: 30-12-2023 Abstract: The problem that arises is how to produce concrete sweats to produce a samawa family in a situation where the hubby works abroad. Families left at home must face colorful changes in their family dynamics, and it's important to identify strategies and sweats that can help them maintain balance and harmony in the family. The exploration system is written descriptively qualitatively, empirical normative exploration system, using field data (field exploration). The normative exploration was carried out grounded on scientific journal material related to perfecting the quality of family connections. In qualitative exploration, this study aims to explain strategies for perfecting the quality of families whose misters work abroad. The way to apply it in forming a sakinah family is by fulfilling each other's Hanisah Nurhalimah Isanti Putri Institut Agama Islam Negeri Metro, Indonesia hanisa@gmail.com Sudirman Institut Agama Islam Negeri Metro, Indonesia sudirmanhk2@gmail.com Article History: DOI: https://doi.org/10.32332/syakhshiyyah.v3i2.8143 Copyright ©2023 Author Received: 23-11-2023 Revised: 28-12-2023 Accepted: 28-12-2023 Published: 30-12-2023 Abstract: The problem that arises is how to produce concrete sweats to produce a samawa family in a situation where the hubby works abroad. Families left at home must face colorful changes in their family dynamics, and it's important to identify strategies and sweats that can help them maintain balance and harmony in the family. The exploration system is written descriptively qualitatively, empirical normative exploration system, using field data (field exploration). The normative exploration was carried out grounded on scientific journal material related to perfecting the quality of family connections. In qualitative exploration, this study aims to explain strategies for perfecting the quality of families whose misters work abroad. The way to apply it in forming a sakinah family is by fulfilling each other's rights and scores as hubby and woman. By means of family time, and dividing each other's tasks or places in taking care of the ménage. ps://doi.org/10.29300/jpkth.v7i2.1601. 2 Jumanatul Ali, Al-Qur’an dan Terjemah (Bandung: Departemen Agama RI, 2015). AFKAR : Jurnal Pemikiran Keislaman dan Tafsir Hadis, no. 2 (2018): https://doi.org/10.29300/jpkth.v7i2.1601. Volume 3 Nomor 2 Juli – Desember 2023 Syakhshiyyah Jurnal Hukum Keluarga Islam E-ISSN 2986-5409 occasionally they feel lonely when they're far down from their children, still, communication between parents and children still goes well. It's carried out well and forming a sakinah, mawadah, warahmah family can also be formed on the base of strong religion, an open station towards each other, an station of honesty, and forbearance tutored to children and other family members and always be thankful for the blessings and food that Allah SWT has given us. Article History: DOI: https://doi.org/10.32332/syakhshiyyah.v3i2.8143 Copyright ©2023 Author Received: 23-11-2023 Revised: 28-12-2023 Accepted: 28-12-2023 Published: 30-12-2023 Keywords: Samawa; Family; Harmony. Keywords: Samawa; Family; Harmony. Keywords: Samawa; Family; Harmony. Volume 3 Nomor 2 Tahun 2023 Nyimas Lidya Putri dkk. Abstrak: Kekerasan dalam rumah tangga (KDRT) dan pemerkosaan dalam perkawinan merupakan masalah serius yang terus menerus menjadi perhatian di Indonesia. KDRT didefinisikan sebagai kekerasan yang dilakukan oleh individu yang tinggal bersama korban, sedangkan pemerkosaan dalam perkawinan adalah tindakan pemaksaan hubungan seksual oleh suami terhadap istri tanpa persetujuan. Penelitian ini bertujuan untuk mengeksplorasi dampak KDRT dan pemerkosaan dalam perkawinan terhadap integritas keluarga di Indonesia. Analisis dilakukan melalui studi literatur mendalam dan analisis kasus yang terjadi antara tahun 2020 hingga 2023. Hasil penelitian menunjukkan bahwa faktor-faktor seperti budaya patriarki, ketidaksetaraan kekuasaan dalam rumah tangga, kurangnya pemahaman agama yang benar dan tekanan sosial-ekonomi merupakan penyebab utama kekerasan. Dampak yang ditimbulkan meliputi kerugian fisik dan psikologis bagi korban, keretakan hubungan keluarga, dan penurunan kualitas hidup dalam komunitas. Penelitian ini menekankan pentingnya edukasi publik, reformasi hukum, dukungan bagi korban, dan peran aktif komunitas serta lembaga keagamaan dalam pencegahan dan penanganan KDRT dan pemerkosaan dalam perkawinan. Dengan pendekatan holistik, diharapkan kekerasan dalam rumah tangga dapat diminimalisasi sehingga tercipta keluarga yang sakinah, mawaddah, warahmah. Kata Kunci: Kekerasan dalam Rumah Tangga; Pemerkosaan; Sakinah Mawaddah Warahmah. Kata Kunci: Kekerasan dalam Rumah Tangga; Pemerkosaan; Sakinah Mawaddah Warahmah. 1 Henderi Kusmidi, “Konsep Sakinah, Mawaddah dan Rahmah Dalam Pernikahan,” E Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 225 1 Henderi Kusmidi, “Konsep Sakinah, Mawaddah dan Rahmah Dalam Pernikahan,” E AFKAR : Jurnal Pemikiran Keislaman dan Tafsir Hadis, no. 2 (2018): 6 1 Henderi Kusmidi, “Konsep Sakinah, Mawaddah dan Rahmah Dalam Pernikahan,” EL- AFKAR : Jurnal Pemikiran Keislaman dan Tafsir Hadis, no. 2 (2018): 63, https://doi.org/10.29300/jpkth.v7i2.1601. 2 Jumanatul Ali, Al-Qur’an dan Terjemah (Bandung: Departemen Agama RI, 2015). Kata Kunci: Kekerasan dalam Rumah Tangga; Pemerkosaan; Sakinah Mawaddah Warahmah. J f , ( ) , https://doi.org/10.29300/jpkth.v7i2.1601. 2 Jumanatul Ali, Al-Qur’an dan Terjemah (Bandung: Departemen Agama RI, 2015). Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 226 A. PENDAHULUAN Perkawinan merupakan suatu media untuk membentuk suatu keluarga yang tenteram dan penuh kasih sayang. Dalam pandangan Al-Qur'an salah satu tujuan pernikahan adalah untuk menciptakan sakinah, mawaddah dan rahmah antara suami, isteri dan anak-anaknya.1 Allah SWT berfirman dalam Surat ar-Rum (30) 21: َوَ مِنْ اٰيٰتِه اَنْ خَلَقَ لَكُمْ مِِّنْ اَنْفُسِكُمْ اَزْ وَ اجًا لِِّتَسْكُنُوْْٓ ا اِلَيْهَا وَ جَعَلَ بَيْنَكُمْ مَّوَ دَّةً وَّ ر َحْمَةً ۗاِنَّ فِيْ ذٰلِكَ َلَ ٰيٰتٍ لِِّقَوْ مٍ يَّتَفَكَّرُوْ ن Artinya: “dan di antara tanda-tanda kebesarannya-Nya ialah Dia menciptakan pasangan-pasangan untukmu dari jenismu sendiri, agar kamu cenderung dan merasa tenteram kepadanya, dan dijadikan-Nya diantaramu rasa kasih dan sayang. Sesungguhnya pada yang demikian itu benar-benar terdapat tanda-tanda Kebesaran Allah bagi kaum yang berfikir.” (QS. Ar-Rum: 21).2 Perkawinan merupakan suatu media untuk membentuk suatu keluarga yang tenteram dan penuh kasih sayang. Dalam pandangan Al-Qur'an salah satu tujuan pernikahan adalah untuk menciptakan sakinah, mawaddah dan rahmah antara suami, isteri dan anak-anaknya.1 Allah SWT berfirman dalam Surat ar-Rum (30) 21: َوَ منْ اٰيٰته اَنْ خَلَقَ لَكُمْ مِّنْ اَنْفُسكُمْ اَزْ وَ اجًا لِّتَسْكُنُوْْٓ ا الَيْهَا وَ جَعَلَ بَيْنَكُمْ مَّوَ دَّةً وَّ رَحْمَةً ۗانَّ فيْ ذٰلكَ َلَ ٰيٰت لِّقَوْ م يَّتَفَكَّرُوْ ن Artinya: “dan di antara tanda-tanda kebesarannya-Nya ialah Dia menciptakan pasangan-pasangan untukmu dari jenismu sendiri, agar kamu cenderung dan merasa tenteram kepadanya, dan dijadikan-Nya diantaramu rasa kasih dan sayang. Sesungguhnya pada yang demikian itu benar-benar terdapat tanda-tanda Kebesaran Allah bagi kaum yang berfikir.” (QS. Ar-Rum: 21).2 Nyimas Lidya Putri dkk. Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 Upaya mewujudkan keluarga yang sakinah mawaddah wa rahmah (samawa) tersebut terdapat keterbatasan misalnya dengan krisis ekonomi yang terbatas atau dalam keluarga tersebut, dengan adanya krisis ekonomi dalam suatu keluarga menjadi satu permasalahan di keluarga, sehingga kepala keluarga memutuskan untuk meninggalkan atau berpisah dari keluarga untuk mencari rezeki sampai keluar negeri. migrasi tenaga kerja ke luar negeri, khususnya oleh suami yang meninggalkan keluarganya di tanah air untuk bekerja di luar negeri, telah menjadi salah satu aspek penting dalam dinamika sosial keluarga di berbagai negara. Sehingga menimbulkan tantangan besar berkait terhadap keluarga yang harmonis. Ketika suami bekerja di luar negeri, keluarga sering kali dihadapkan pada berbagai tantangan, seperti komunikasi jarak jauh, perasaan kesepian, dan perubahan peran dalam keluarga. Permasalahan yang muncul adalah bagaimana menciptakan upaya konkret untuk mewujudkan keluarga samawa dalam situasi di mana suami bekerja di luar negeri. Keluarga yang ditinggalkan di rumah harus menghadapi berbagai perubahan dalam dinamika keluarga mereka, dan penting untuk mengidentifikasi strategi dan upaya yang dapat membantu mereka menjaga keseimbangan dan keharmonisan dalam keluarga. Pada era globalisasi yang semakin maju dan peluang kerja di luar negeri menciptakan fenomena sosial baru yaitu para suami meninggalkan keluarga untuk bekerja di luar negeri demi meningkatkan kesejahteraan keluarga kecil. Keputusan para suami ini dikarenakan alasan ekonomi, sehingga dampak kualitas hubungan keluarga menjadi perhatian utama, sehingga adanya dinamika keluarga dalam kualitas hubungan antara keluarga. Keputusan untuk berpisah demi mencari peluang kerja yang lebih baik sering kali merupakan pilihan yang sulit, dan dapat berdampak terhadap kualitas hubungan keluarga tidak bisa diabaikan. Dalam situasi suami sebagai pimpinan keluarga bekerja di luar negeri, keluarga tersebut menghadapi tantangan yang mempengaruhi dinamika hubungan suami-istri, menjalankan peran sebagai orang tua dan anak, dan kesejahteraan keluarga secara keseluruhan. Situasi tersebut menciptakan sebuah konteks yang memerlukan perhatian khusus, strategi yang bijaksana, dan pemahaman yang dalam tentang cara menjaga kualitas hubungan keluarga dalam jarak yang terpisah. Ini bukan hanya sebuah Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 226 Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 kisah tentang keberanian suami yang mencari penghidupan yang lebih baik atau kisah kesetiaan pasangan di negara asal, tetapi juga merupakan cerita tentang ketahanan keluarga dalam menghadapi tantangan yang kompleks. Penting untuk diingat bahwa kondisi seperti ini dapat mempengaruhi kesejahteraan emosional dan psikologis dari semua anggota keluarga yang terlibat. Pada gilirannya, hal ini berdampak pada hubungan yang ada di dalam keluarga tersebut. Nyimas Lidya Putri dkk. Oleh karena itu, dalam upaya untuk menjaga kualitas hubungan keluarga dalam situasi di mana suami bekerja di luar negeri, diperlukan strategi yang efektif yang melibatkan komunikasi yang kuat, dukungan emosional, penyelesaian konflik, dan pemahaman mendalam tentang perbedaan budaya. Perlunya mengeksplorasi berbagai strategi yang dapat diterapkan untuk mengatasi tantangan dalam keluarga seperti ini dan memastikan bahwa keluarga tetap kuat dan harmonis, meskipun terpisah oleh jarak fisik dan perbedaan budaya. Penelitian ini bertujuan untuk menjelaskan berbagai faktor yang memengaruhi upaya mewujudkan keluarga samawa pada keluarga yang suaminya bekerja di luar negeri. Dengan memahami faktor-faktor ini, diharapkan dapat dikembangkan rekomendasi dan strategi konkret yang dapat membantu keluarga dalam situasi serupa untuk mencapai keseimbangan dan harmoni dalam kehidupan keluarga mereka. Bandung: Pustaka Setia, 2013). 6 Mohammad Idris Ramulyo, Hukum Perkawinan Islam (Jakarta: Bumi Aksara, 2014). g 5 Boedi Abdullah dan Beni Ahmad Saebani, Perkawinan & Perceraian Keluarga Musli (Bandung: Pustaka Setia, 2013). 3 Lindha Pradhipti Oktarina, Mahendra Wijaya, dan Argyo Demartoto, “Pemaknaan Perkawinan (Studi Kasus Pada Perempuan Lajang Yang Bekerjadi Kecamatan Bulukerto Kabupaten Wonogiri),” Jurnal Analisa Sosiologi 4, no. 1 (2018), https://doi.org/10.20961/jas.v4i1.17412. ( p j g g j Wonogiri),” Jurnal Analisa Sosiologi 4, no. 1 (2018), https://doi.org/10.2096 4 Rakhmat “UU No 1 Tahun 1974 Tentang Perkawinan ” 1974 Rakhmat, UU No. 1 Tahun 1974 Tentang Perkawinan, 1974. 5 Boedi Abdullah dan Beni Ahmad Saebani, Perkawinan & Perceraian B. METODE Metode penelitian ditulis secara deskriptif kualitatif, Metode Penelitian normative empiris, dengan menggunakan data lapangan (field research). Pada penelitian normative dilakukan berdasarkan dari bahan jurnal ilmiah terkait peningkatan kualitas hubungan Keluarga. Dalam penelitian kualitatif dalam penelitian ini bertujuan untuk menjelaskan mengenai strategi peningkatan kualitas keluarga, yang suaminya bekerja di luar negeri. Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 227 Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 4 Rakhmat, “UU No. 1 Tahun 1974 Tentang Perkawinan,” 1974. 5 B di Abd ll h d B i Ah d S b i P k i & P i K l M l g ), J g , ( ), p // g/ / 4 Rakhmat, “UU No. 1 Tahun 1974 Tentang Perkawinan,” 1974. Boedi Abdullah dan Beni Ahmad Saebani, Perkawinan & Perceraian Keluarga Muslim (Bandung: Pustaka Setia, 2013). 6 Mohammad Idris Ramulyo, Hukum Perkawinan Islam (Jakarta: Bumi Aksara, 2014). 4 Rakhmat, “UU No. 1 Tahun 1974 Tentang Perkawinan,” 1974. 5 Boedi Abdullah dan Beni Ahmad Saebani, Perkawinan & Perceraian Keluarga Muslim 5 Boedi Abdullah dan Beni Ahmad Saebani, Perkawinan & Perceraian Keluarga Muslim (Bandung: Pustaka Setia, 2013). 6 Mohammad Idris Ramulyo Hukum Perkawinan Islam (Jakarta: Bumi Aksara 2014) oed bdu a da ung: Pustaka Setia, 2013). 4 Rakhmat, “UU No. 1 Tahun 1974 Tentang Perkawinan,” 1974. 5 Boedi Abdullah dan Beni Ahmad Saebani, Perkawinan & Perceraian Keluarga Muslim d P k S i 2013) C. HASIL DAN PEMBAHASAN 1. Nilai-nilai Keluarga Sakinah Mawadah Warahmah dalam Menciptakan Keluarga Harmonis P k i d l h lih lif l d i i k hid j k g Perkawinan adalah suatu peralihan atau life cycle dari tingkat hidup remaja ke tingkat hidup berkeluarga dari semua manusia di dunia.3 Adapun yang dimaksud dengan nikah dari segi istilah sebagaimana dijelaskan dalam Undang-Undang Perkawinan No. 1 Tahun 1974 pasal 1, adalah “ikatan lahir batin antara seorang pria dengan seorang wanita sebagai suami istri dengan tujuan membentuk keluarga (rumah tangga) yang bahagia dan kekal berdasarkan Ketuhanan Yang Maha Esa”.4 Ulama Hanabilah mengatakan bahwa perkawinan adalah akad dengan menggunakan lafaz inkah atau tazwij untuk mendapatkan kepuasan, artinya seorang laki-laki dapat memperoleh kepuasan dari seorang perempuan dan sebaliknya. Dalam pengertian diatas, terdapat kata-kata milik yang mengandung pengertian hak untuk memiliki melalui akad nikah. Oleh karena itu, suami istri dapat saling mengambil manfaat untuk mencapai kehidupan dalam ruamh tangganya yang bertujuan membentuk keluarga sakinah, mawaddah, warahmah di dunia.5 Tujuan perkawinan ialah menurut perintah Allah untuk memeroleh keturunan yang sah dalam masyarakat, dengan mendirikan rumah tangga yang damai dan teratur. Tujuan perkawinan dalam Islam adalah untuk memenuhi tuntutan hajat tabiat kemanusiaan, berhubungan antara laki-laki dan perempuan dalam rangka mewujudkan suatu keluarga yang bahagia atas dasar cinta dan kasih sayang, untuk memperoleh keturunan yang sah dalam masyarakat dalam mengikuti ketentuan- ketentuan yang diatur oleh syariah.6 Tujuan perkawinan dalam Islam tidak hanya sekedar pada batas pemenuhan nafsu biologis atau pelampiasan nafsu seksual, tetapi memiliki tujuan-tujuan penting yang berkaitan dengan sosial, psikologi dan agama, tujuan tersebut yakni: 1. Memelihara gen manusia, Pernikahan sebagai sarana untuk memelihara keberlangsungan gen manusia, alat reproduksi dan regenerasi dari masa ke 1. Memelihara gen manusia, Pernikahan sebagai sarana untuk memelihara keberlangsungan gen manusia, alat reproduksi dan regenerasi dari masa ke Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 228 Volume 3 Nomor 2 Tahun 2023 Nyimas Lidya Putri dkk. masa sehingga manusia dapat memakmurkan hidup dan melaksanakan tugas sebagai khalifah Allah. masa sehingga manusia dapat memakmurkan hidup dan melaksanakan tugas sebagai khalifah Allah. masa sehingga manusia dapat memakmurkan hidup dan melaksanakan tugas sebagai khalifah Allah. 2. Pernikahan adalah tiang keluarga yang teguh dan kokoh di dalamnya terdapat hak-hak dan kewajiban yang sakral dan religius. 2. Pernikahan adalah tiang keluarga yang teguh dan kokoh di dalamnya terdapat hak-hak dan kewajiban yang sakral dan religius. 3. Nikah sebagai perisai diri manusia, Nikah dapat menjaga diri dan menjauhkan diri dari pelanggaran yang diharamkan oleh agama. 3. Nikah sebagai perisai diri manusia, Nikah dapat menjaga diri dan menjauhkan diri dari pelanggaran yang diharamkan oleh agama. 4. 7 Abdul Aziz Muhammad Azzam dan Abdul Wahhab Sayyed Hawwas, Fiqh Munakahat: Khitbah, Nikah, dan Talak (Jakarta: Amzah, 2009), 40–42. 7 Abdul Aziz Muhammad Azzam dan Abdul Wahhab Sayyed Hawwas, Fiqh Munakahat: Khitbah, Nikah, dan Talak (Jakarta: Amzah, 2009), 40–42. 8 Riana Friska Siahaan, “Membangun Keluarga yang Sukses dan Harmonis,” Jurnal Keluarga Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 229 Riana Friska Siahaan, Membang Sehat Sejahtera 14, no. 28 (2016): 59–75. , , (J , ), 8 Riana Friska Siahaan, “Membangun Keluarga yang Sukses dan Harmonis,” Jurnal Keluarg 8 Riana Friska Siahaan, Membangun Keluarga yang Sukses dan Harmonis, Jurnal Keluarg Sehat Sejahtera 14, no. 28 (2016): 59–75. , , (J , ), 8 Riana Friska Siahaan, “Membangun Keluarga yang Sukses dan Harmonis,” Jurnal Keluarga Sehat Sejahtera 14, no. 28 (2016): 59–75. 7 Abdul Aziz Muhammad Azzam dan Abdul Wahhab Sayyed Hawwas, Fiqh Munakahat: Khitbah, Nikah, dan Talak (Jakarta: Amzah, 2009), 40–42. 8 Riana Friska Siahaan, “Membangun Keluarga yang Sukses dan Harmonis,” Jurnal Keluarga Sehat Sejahtera 14, no. 28 (2016): 59–75. C. HASIL DAN PEMBAHASAN 1. Nilai-nilai Keluarga Sakinah Mawadah Warahmah dalam Menciptakan Keluarga Harmonis P k i d l h lih lif l d i i k hid j k Melawan hawa nafsu. Nikah dapat menyalurkan hawa nafsu manusia menjadi terpelihara. melakukan maslahat orang lain dan melaksanakan hak-hak istri dan anak-anak serta mendidik mereka.7 4. Melawan hawa nafsu. Nikah dapat menyalurkan hawa nafsu manusia menjadi terpelihara. melakukan maslahat orang lain dan melaksanakan hak-hak istri dan anak-anak serta mendidik mereka.7 Dengan demikian pernikahan menandai dimulainya kehidupan baru sepasang manusia. Pernikahan yang merupakan fondasi awal dalam suatu keluarga sehingga perlu diupayakan kuat dalam menjadi benteng diri untuk menjauhkan diri dari larangan Allah, sehingga peran pernikahan dapat menjadi bentuk perlawanan terhadap hawa nafsu serta mampu menjaga dan memperbaiki keturunan yang lebih baik lagi dan menjadikan keluarga yang lebih berkualitas. Menurut Hasan Basri yang dikutip oleh Riana Friska Siahaan, Keluarga yang harmonis dan berkualitas yaitu keluarga yang rukun berbahagia, tertib, disiplin, saling menghargai, penuh pemaaf, tolong menolong dalam kebajikan, memiliki etos kerja yang baik, bertetangga dengan saling menghormati, taat mengerjakan ibadah, berbakti pada yang lebih tua, mencintai ilmu pengetahuan dan memanfaatkan waktu luang dengan hal yang positif dan mampu memenuhi dasar keluarga. 8 Dengan begitu keluarga dapat dikatakan harmonis merupakan keluarga dengan ketenteraman, kasih sayang dan keturunan generasi masyarakat yang baik sehingga dapat saling membantu dan saling melengkapi ketidaksempurnaan seseorang. AlQur’an menganjurkan pernikahan perlu menciptakan sakinah, mawaddah, dan rahmah antara suami, isteri, dan anak-anaknya. Hal ini ditegaskan dalam QS. Ar- Rum/30: 21 َْوَمِنْ آَيَتِهِ أَنْ خَلَقَ لَكُمْ مِنْ أَن ْفُسِكُمْ أَزْوَاجًا لِتَسْكُنُوا إِلَي ْهَا وَجَعَلَ ب َي ْنَكُمْ مَوَدَّةً وَرَح َةً إِنَّ ِفِ ذََٰلِكَ َلَ َيَتٍ لِقَوْمٍ ي َت َفَكَّرُون Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 Artinya: dan di antara tanda-tanda kekuasaan-Nya ialah Dia menciptakan untukmu isteri-isteri dari jenismu sendiri, supaya kamu cenderung dan merasa tenteram kepadanya, dan dijadikan-Nya diantaramu rasa kasih dan sayang. Sesungguhnya pada yang demikian itu benar-benar terdapat tanda- tanda bagi kaum yang berfikir.9 Keluarga sakinah mawaddah warahmah merupakan keluarga yang selalu diberikan kedamaian, ketenteraman, penuh cinta, dan kasih sayang Kunci utama untuk mendapatkan keluarga yang sakinah mawaddah wa rahmah adalah meluruskan niat berkeluarga karena ingin mendapat ridha dari Allah Swt. 10 Keluarga sakinah atau harmonis adalah keluarga yang hidup tenteram dan bahagia, selalu saling berkasih sayang, menghargai, memberi, membantu, mengerti dan memahami, berupaya menyempurnakan tugas dan tanggung jawabnya terhadap Allah, keluarga maupun masyarakat. Ada tiga bekal utama untuk mencapai kebahagiaan dalam rumah tangga sebagai berikut: pertama, Membangun jiwa sakinah. Kata sakinah dari kata sakana yang berarti tenang. Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 230 9 Departemen Agama RI, Al-Qur’an dan Terjemahnya (Bandung: Jumanatul Ali, 2015), 176. 9 Departemen Agama RI, Al-Qur’an dan Terjemahnya (Bandung: Jumanatul Ali, 2015), 176. 10 Taufiq Andrianto, Romantika Perkawinan (Yogyakarta: Pustaka Mahendra, 2013), 72–73. 9 Departemen Agama RI, Al-Qur’an dan Terjemahnya (Bandung: Jumanatul Ali, 2015), 176. 10 Taufiq Andrianto, Romantika Perkawinan (Yogyakarta: Pustaka Mahendra, 2013), 72–73. p g Q j y ( g J ) 10 Taufiq Andrianto, Romantika Perkawinan (Yogyakarta: Pustaka Mahendra, 2013), 72–73. 11 Arisman, Menuju Gerbang Pernikahan (Guepedia, 2021). j g ( p ) 12 Samsul Arifin, Pendidikan Agama Islam (Banjarbaru: Grafika Wangi Kalimantan, 2017). 2017). 14 Yupi Supartini, Konsep Dasar Keperawatan Anak (Jakarta: EGC, 2004). C. HASIL DAN PEMBAHASAN 1. Nilai-nilai Keluarga Sakinah Mawadah Warahmah dalam Menciptakan Keluarga Harmonis P k i d l h lih lif l d i i k hid j k Ketenangan dalam rumah tangga dapat dicapai dengan banyak berdzikir kepada Allah Swt. Kedua, Menghidupkan semangat mawaddah. Mawaddah berarti cinta. Mawaddah sangat bersifat pribadi tanpa mawaddah, kehidupan keluarga akan terasa hampa dan menjenuhkan. Mawaddah terlepas dari persoalan fisik. Maka dari itu, Allah SWT memberi penyeimbangnya yakni rahmah, agar saat cinta mulai kehilangan cahaya, masih ada semangat rahmah yang akan menjaganya. Ketiga, Mempertahankan spirit rahmah. Rahmah artinya kasih sayang. Kata rahmah lebih mencerminkan sikap saling memahami kekurangan masing-masing, kemudian berusaha untuk saling melengkapi. Sikap ini menekankan adanya tolong-menolong dalam bersinergi, sehingga kekurangan menjadi kesempurnaan. Sikap rahmah lebih sering berperan ketika semangat cinta mulai menurun. Mawaddah dan rahmah bagaikan sepasang sayap. Bila sayap tersebut berfungsi dengan baik maka tujuan kehidupan keluarga yang penuh berkah dan diridhai Allah Swt. akan tercapai. Nyimas Lidya Putri dkk. g g f g ( 017). 14 Yupi Supartini, Konsep Dasar Keperawatan Anak (Jakarta: EGC, 2004). 13 Sri Lestari, Psikologi Keluarga: Penanaman Nilai Dan Konflik Keluarga (Jakarta: Kencan 2017) 11 A i M j G b P ik h (G di 2021) 13 Sri Lestari, Psikologi Keluarga: Penanaman Nilai Dan Konflik Keluarga (Jakarta: Kencana, 017). 14 Yupi Supartini, Konsep Dasar Keperawatan Anak (Jakarta: EGC, 2004). Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 231 Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 Keluarga sakinah, bahwa dalam rumah tangga keserasian dan keselarasan perlu dijaga untuk mendapatkan suatu rumah tangga yang harmonis. Dalam hidup berkeluarga hendaknya antara anggota-anggotanya saling mencintai, saling membantu, saling menyayangi dan menghormati. Dalam membina keluarga Sakinah Mawaddah Warahmah sangat memerlukan indikator-indikator sebagai berikut: 1. Terciptanya kehidupan beragama dalam keluarga, sebuah keluarga yang harmonis ditandai dengan terciptanya kehidupan beragama dalam rumah tangga.11 Hal ini penting karena di dalam agama terdapat nilai-nilai moral dan etika kehidupan. Kehidupan beragama dalam keluarga ditandai dengan tumbuhnya rasa aman dan kasih sayang antar anggota keluarga yang saling mencintai dan menyayangi. Terciptanya kehidupan beragama dalam keluarga adalah tersedianya waktu untuk bersama keluarga interaksi segitiga antara ayah, ibu dan anak saling menghargai dalam interaksi ayah, ibu dan anak keluarga menjadi prioritas utama dalam sebuah keluarga.12 1. Terciptanya kehidupan beragama dalam keluarga, sebuah keluarga yang harmonis ditandai dengan terciptanya kehidupan beragama dalam rumah tangga.11 Hal ini penting karena di dalam agama terdapat nilai-nilai moral dan etika kehidupan. Kehidupan beragama dalam keluarga ditandai dengan tumbuhnya rasa aman dan kasih sayang antar anggota keluarga yang saling mencintai dan menyayangi. Terciptanya kehidupan beragama dalam keluarga adalah tersedianya waktu untuk bersama keluarga interaksi segitiga antara ayah, ibu dan anak saling menghargai dalam interaksi ayah, ibu dan anak keluarga menjadi prioritas utama dalam sebuah keluarga.12 2. Adanya waktu luang bersama keluarga. Keluarga yang harmonis akan selalu menyediakan waktu bersama dengan keluarga, agar kebersamaan dalam keluarga selalu terjalin sehingga ketahanan keluarga dapat tercipta.13 Walaupun itu hanya sekedar berkumpul, makan bersama, menemani anak bermain dan mendengarkan masalah dan keluhan-keluhan anak, dalam kebersamaan ini anak akan merasa dirinya diperhatikan oleh orang tuanya, sehingga anak akan lebih betah di rumah. 3. Adanya komunikasi yang baik antar anggota keluarga. Dapat membuat keluarga harmonis, karena di dalam komunikasi yang baik akan membuat keluarga tidak canggung dalam menceritakan masalah yang sedang dihadapi. Karena adanya komunikasi tersebut dapat membantu anggota keluarga dalam menghadapi masalah yang ada.14 3. Adanya komunikasi yang baik antar anggota keluarga. Dapat membuat keluarga harmonis, karena di dalam komunikasi yang baik akan membuat keluarga tidak canggung dalam menceritakan masalah yang sedang dihadapi. Karena adanya komunikasi tersebut dapat membantu anggota keluarga dalam menghadapi masalah yang ada.14 4. Saling menghargai antar anggota keluarga, keluarga yang harmonis adalah keluarga yang memberikan tempat bagi setiap anggota keluarga, menghargai 4. 11 Arisman Menuju Gerbang Pernikahan (Guepedia 2021) Nyimas Lidya Putri dkk. Saling menghargai antar anggota keluarga, keluarga yang harmonis adalah keluarga yang memberikan tempat bagi setiap anggota keluarga, menghargai Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 231 Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 perubahan yang terjadi dan mengajarkan anak tentang keterampilan berkomunikasi dengan lingkungan. Sikap menghargai orang tua bisa ditunjukkan oleh anak dengan cara memberikan prestasi yang diperoleh anak.15 Membina keluarga sakinah diperlukannya indikator tersebut untuk dapat menciptakan keharmonisan dalam rumah tangga, diperlukan kan pemahaman terhadap nilai-nilai moral dan etika kehidupan serta saling menghargai antar keluarga dengan cara komunikasi yang baik dan meluangkan waktu bersama keluarga dapat menciptakan suasana yang harmonis dalam kehidupan keluarga. ( g j y ) 16 Eka Rahmah Eliyani, “Keterbukaan Komunikasi Interpersonal Pasangan Suami Ister Ilmu Komunikasi 2, no. 2 (2013): 87. 15 Jalaluddin Rakhmat dan Muhtar Gandaatmaja, Keluarga Muslim dalam Masyarakat Modern (Bandung: Remaja Rosdakarya, 1993). Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 232 15 Jalaluddin Rakhmat dan Muhtar Gandaatmaja, Keluarga Muslim dalam Masyarakat Modern (Bandung: Remaja Rosdakarya, 1993). 16 Eka Rahmah Eliyani, “Keterbukaan Komunikasi Interpersonal Pasangan Suami Isteri,” 2. Strategi Peningkatan kualitas Hubungan Keluarga pada Suami yang Bekerja di Luar Negeri Suami istri yang tinggal berjauhan (long distance married) dimaksudkan yaitu pasangan yang menikah secara resmi namun karena situasi atau kondisi tertentu mengharuskan suami atau istri tidak bisa hidup bersama dalam satu rumah. Tinggal berjauhan dalam hal ini maksudnya berada dengan jarak yang cukup jauh, misalnya antar pulau atau antar negara sehingga tidak memungkinkan pasangan suami istri untuk bertemu dalam waktu yang diharapkan. Jarak yang jauh dan biaya yang besar merupakan indikator pasangan suami istri yang tinggal berjauhan. Sehingga waktu untuk bertemu dan berkumpul dengan keluarga sangat terbatas.16 Faktor Penyebab Hubungan Long Distance Relationship Kaufmann menyatakan bahwa faktor-faktor yang menyebabkan individu menjalani hubungan jarak jauh diantaranya yaitu: Faktor Pendidikan adalah salah satu faktor penyebab hubungan jarak jauh adalah ketika individu berusaha untuk mencapai pendidikan yang lebih tinggi sehingga hubungan pasangan keluarga harus berpisah untuk sementara waktu. Faktor Karier Hubungan jarak jauh juga berhubungan dengan kecenderungan sosial pada saat ini. Faktor ekonomi. Pemahaman masyarakat terhadap keluarga sakinah adalah menanamkan sikap saling percaya, jujur bersikap baik dan peduli dalam mendidik anak-anak. Pemahaman masyarakat yang dimaksud adalah sebagian masyarakat yang pernah 15 Jalaluddin Rakhmat dan Muhtar Gandaatmaja, Keluarga Muslim dalam Masyarakat Modern (Bandung: Remaja Rosdakarya, 1993). 16 Ek R h h Eli i “K b k K ik i I l P S i I i ” Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 mengalami long distance married (LDM) karena bekerja di luar negeri. Dengan pemahaman tersebut berarti masyarakat telah menerapkan indikator yang telah di jelaskan. Adapun dalam lapangan pengimplementasikan keluarga sakinah dalam keluarga bagi suami yang bekerja di Luar Negeri terbentuk dengan etika dan nilai- nilai agama yang kuat dan sikap saling terbuka dengan demikian sudah terciptanya fondasi bahkan perisai kuat dalam suatu keluarga. Nick Stinnet dan John Defrain dalam studi yang berjudul “The National Study on Family Strength” mengemukakan langkah-langkah membangun keluarga harmonis yaitu: menciptakan kehidupan beragama dalam keluarga, meluangkan waktu yang cukup serta berinteraksi yang baik dengan keluarga dengan tujuan memperkuat intensitas keluarga yang berkualitas dan memecahkan atau mencari solusi dalam permasalahan yang datang pada keluarga.17 Menciptakan kehidupan beragama dalam keluarga diperlukan karena di dalam agama diajarkan norma-norma dan etika moral kehidupan. Penelitian oleh kedua profesor di atas menyimpulkan bahwa keluarga yang di dalamnya tidak ditopang dengan nilai-nilai religius, atau komitmen agamanya lemah, atau bahkan tidak mempunyai agama sama sekali, lebih berisiko empat kali lipat untuk berakhir menjadi keluarga yang tidak bahagia. 17 Imam Mustofa, “Keluarga Sakinah dan Tantangan Globalisasi,” Al-Mawarid: Jurnal Hukum Islam 18 (2008): 227–28, https://doi.org/10.20885/almawarid.vol18.art5. Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 233 17 Imam Mustofa, “Keluarga Sakinah dan Tantangan Globalisasi,” Al-Mawarid: Jurnal Hukum lam 18 (2008): 227–28, https://doi.org/10.20885/almawarid.vol18.art5. 2. Strategi Peningkatan kualitas Hubungan Keluarga pada Suami yang Bekerja di Luar Negeri Seperti broken home, perceraian, perselingkuhan, pecandu alkohol dan lain sebagainya. Kemudian perlunya meluangkan waktu yang cukup untuk bersama keluarga. Suasana kebersamaan diciptakan untuk pemeliharaan keluarga. Serta pentingnya Interaksi sesama anggota keluarga sehingga dapat menciptakan hubungan yang baik antar anggota keluarga. Dengan begitu dapat menciptakan hubungan yang baik sesama anggota keluarga dengan saling menghargai dan memperkuat persatuan dalam keluarga, Jika ada masalah sekecil apa pun harus sesegera mungkin diselesaikan jangan sampai membuat bangunan tersebut longgar dan rapuh. Jika terjadi krisis atau benturan dalam keluarga, maka yang harus jadi prioritas adalah kebutuhan keluarga . Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 234 Nyimas Lidya Putri dkk. Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 Dalam mewujudkan konsep untuk menuju keluarga yang sakinah, suatu keluarga harus bisa memenuhi hak dan kewajibannya masing-masing terutama seorang suami yang bertanggungjawab penuh atas keluarganya dengan memenuhi semua kebutuhan rumah tangganya. Begitu pun dengan seorang istri juga harus bisa memenuhi kewajibannya secara batin kepada suaminya. Ketika suami dan istri sudah memenuhi hak dan kewajibannya, maka keluarga yang sakinah akan bisa terwujud secara perlahan. Adapun faktor kendala yang di alami sebagian masyarakat terhadap keharmonisan keluarga yaitu : Ekonomi, faktor ini merupakan hal penting yang dapat mempengaruhi keharmonisan suatu keluarga karena dalam suatu keluarga keuangan keluarga untuk hidup sehingga sosok suami yang dijadikan sebagai kepala rumah tangga diberi kepercayaan untuk mampu menghidupi keluarganya. Dan rasa khawatir yang berlebihan dalam suatu rumah tangga yang memang menjadi salah satu faktor yang membuat kedua belah pihak saling curiga dan tidak percaya. Kendala yang di alami masyarakat dapat diatasi dengan konsep Samawa dalam suatu keluarga seperti, Bertanggung jawab atas hak dan kewajiban. Di dalam setiap keluarga pasti ada hak dan kewajiban setiap anggota keluarga. Terutama ayah yang sebagai kepala rumah tangga mempunyai hak atas anak dan istrinya, juga memiliki kewajiban untuk memenuhi kebutuhan rumah tangganya, Dan Saling Percaya, di dalam hidup berkeluarga memang rasa percaya adalah satu kunci untuk keluarga tetap harmonis, karena jika dalam suatu keluarga tercipta rasa saling percaya, maka kelangsungan hidup berkeluarga akan menjadi bahagia, terutama juga untuk anak-anaknya. Seperti yang dijelaskan dalam Q.S. An-Najm ayat 28: ِٱْلْ َْ ًا إ َّ ٱلظََّّ َّلَ ُْ َّ ُ َ إَّلَّ ٱلظََّّ إ ْ لْ ا َلَُ وَمَا َلَُم بِهِۦ مِنْ عِلْمٍ ۖ إِن ي َتَّبِعُونَ إَِّلَّ ٱلظَّنَّ ۖ وَإِنَّ ٱلظَّنَّ َّلَ ي ُغِْنِ مِنَ ٱْلَْق ِ شَيْ ًا Artinya: Dan mereka tidak mempunyai ilmu tentang itu. Mereka tidak lain hanyalah mengikuti dugaan, dan sesungguhnya dugaan itu tidak berfaedah sedikit pun terhadap kebenaran. Dengan demikian konsep samawa itu perlu di bangun oleh kedua pasangan atau satu tim keluarga, tidak hanya dari sebelah pihak saja, agar terbangun ikatan yang harmonis dalam keluarga yang baik sehingga dalam bertindak ataupun mengatur keluarga terutama dalam mengambil keputusan memang harus tepat dan Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 234 Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 234 | 234 Nyimas Lidya Putri dkk. D. KESIMPULAN Keluarga sakinah mawaddah warahmah dalam membina keluarga yang harmonis bagi suami yang pernah bekerja di luar negeri menurut perspektif hukum Islam bahwa dalam membina suatu rumah tangga memang harus didasari dengan keimanan, ketakwaan kepada Allah SWT, agar apa pun yang kita jalani dalam melakukan sesuatu hal dapat terlaksanakan dengan baik dan membentuk keluarga sakinah, mawadah, warahmah juga dapat terbentuk atas dasar agama yang kuat, sikap saling terbuka, sikap jujur, dan tenggang rasa yang diajarkan kepada anak- anak dan anggota keluarga lainnya serta selalu bersyukur atas nikmat dan rezeki yang di belikan oleh Allah SWT. Ada beberapa cara implementasi dalam membentuk keluarga sakinah adalah dengan cara saling memenuhi hak dan kewajiban sebagai suami istri, dengan cara family time, dan saling membagi tugas atau peran dalam mengurus rumah tangga. Terkadang mereka merasa kesepian ketika berjauhan dengan anak-anaknya, walaupun demikian komunikasi antara anak-anak orang tua tetap berjalan dengan baik. Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 harus bisa saling meluangkan waktu untuk bisa berkumpul dan bercengkerama satu sama lain agar konsep untuk membangun keluarga yang sakinah, mawadah, warahmah dapat berjalan dengan baik. Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 235 E. REFERENSI Abdullah, Boedi, dan Beni Ahmad Saebani. Perkawinan & Perceraian Keluarga Muslim. Bandung: Pustaka Setia, 2013. Ali, Jumanatul. Al-Qur’an dan Terjemah. Bandung: Departemen Agama RI, 2015. Arifin, Samsul. Pendidikan Agama Islam. Banjarbaru: Grafika Wangi Kalimantan, 2017. Arisman. Menuju Gerbang Pernikahan. Guepedia, 2021. Arisman. Menuju Gerbang Pernikahan. Guepedia, 2021. Azzam, Abdul Aziz Muhammad, dan Abdul Wahhab Sayyed Hawwas. Fiqh Munakahat: Khitbah, Nikah, dan Talak. Jakarta: Amzah, 2009. Eliyani, Eka Rahmah. “Keterbukaan Komunikasi Interpersonal Pasangan Suami Isteri.” Ilmu Komunikasi 2, no. 2 (2013): 87. Kusmidi, Henderi. “Konsep Sakinah, Mawaddah dan Rahmah Dalam Pernikahan.” EL-AFKAR : Jurnal Pemikiran Keislaman dan Tafsir Hadis, no. 2 (2018): 63. https://doi.org/10.29300/jpkth.v7i2.1601. Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 235 Nyimas Lidya Putri dkk. Volume 3 Nomor 2 Tahun 2023 Lestari, Sri. Psikologi Keluarga: Penanaman Nilai Dan Konflik Keluarga. Jakarta: Kencana, 2017. Mustofa, Imam. “Keluarga Sakinah dan Tantangan Globalisasi.” Al-Mawarid: Jurnal Hukum Islam 18 (2008): 227–28. https://doi.org/10.20885/almawarid.vol18.art5. Oktarina, Lindha Pradhipti, Mahendra Wijaya, dan Argyo Demartoto. “Pemaknaan Perkawinan (Studi Kasus Pada Perempuan Lajang Yang Bekerjadi Kecamatan Bulukerto Kabupaten Wonogiri).” Jurnal Analisa Sosiologi 4, no. 1 (2018). https://doi.org/10.20961/jas.v4i1.17412. Rakhmat. “UU No. 1 Tahun 1974 Tentang Perkawinan,” 1–15, 1974. Rakhmat, Jalaluddin, dan Muhtar Gandaatmaja. Keluarga Muslim dalam Masyarakat Modern. Bandung: Remaja Rosdakarya, 1993. Ramulyo, Mohammad Idris. Hukum Perkawinan Islam. Jakarta: Bumi Aksara, 2014 RI, Departemen Agama. Al-Qur’an dan Terjemahnya. Bandung: Jumanatul Ali, 2015 Siahaan, Riana Friska. “Membangun Keluarga yang Sukses dan Harmonis.” Jurnal Keluarga Sehat Sejahtera 14, no. 28 (2016): 59–75. Supartini, Yupi. Konsep Dasar Keperawatan Anak. Jakarta: EGC, 2004. Taufiq Andrianto. Romantika Perkawinan. Yogyakarta: Pustaka Mahendra, 2013. Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 236 Strategi Peningkatan Kualitas Hubungan Keluarga dalam … | 236
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Cooperation on dynamic networks within an uncertain reputation environment
Scientific reports
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This document is published at: Lozano, P., Antonioni, A., Tomassini, M. y Sánchez, A. (2018). Cooperation on dynamic networks within an uncertain reputation environment. Scientific Reports, 8, 9093. DOI: https://doi.org/10.1038/s41598-018-27544-5 © 2018 The Author(s). This article is licensed under a under a Creative Commons Attribution 4.0 International License. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. This document is published at: Pablo Lozano1,2, Alberto Antonioni1,3,4, Marco Tomassini5 & Angel Sánchez1,2,3,6 Reputation plays a key role among the mechanisms supporting cooperation in our society. This is a well- known observation and, in fact, several studies have shown that reputation may substantially increase cooperation among subjects playing Prisoner’s Dilemma games in the laboratory. Unfortunately, recent experiments indicate that when reputation can be faked cooperation can still be maintained at the expense of honest subjects who are deceived by the dishonest ones. As experimental work is limited due to financial and other reasons, we present here an agent-based simulation model inspired by, and calibrated against, the results obtained in the experiment. We thus simulate much larger population sizes over longer times, and test other model parameters to see whether the observed behavior generalizes in those yet untried conditions. The results show that the collective behavior is qualitatively similar in larger systems and stable over longer times horizons. We conclude that the findings of the experimental work are meaningful, taking into account that the model is strictly tailored to our particular experimental setting and therefore it is a possible explanation of our observations whose applicability to other contexts requires further research. We argue that simulations like the ones presented here may also be useful to cheaply and quickly suggest settings and options to enhance and facilitate further experiments, which, in turn, may provide new tests of the models themselves. Reputation is one of the most important mechanisms that allow cooperation to evolve and stabilize in social interactions. Building and maintaining a good reputation is key in this respect because it encourages trust and socially responsible behavior. For reputation to be useful, it has to take the form of some “marker” or some public information that characterizes a particular individual and must be easily recognized and interpreted by others. In contrast to direct reciprocity, which requires repeated interactions between the same people to support coopera- tion, reputation is an indirect mechanism that relies on an individual’s previous behavior with other individuals. This behavior is somehow made public knowledge in different forms and thus requires communication and infor- mation capabilities. Thus, when encountering another previously unseen person, individuals can act on the basis of the reputation of the former. Cooperation is costly but helps build a good reputation which, in turn, may lead to more cooperative acts towards oneself and to a better functioning society as a whole. This document is published at: Lozano, P., Antonioni, A., Tomassini, M. y Sánchez, A. (2018). Cooperation on dynamic networks within an uncertain reputation environment. Scientific Reports, 8, 9093. DOI: https://doi.org/10.1038/s41598-018-27544-5 © 2018 The Author(s). This article is licensed under a under a Creative Commons Attribution 4.0 International License. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. © 2018 The Author(s). This article is licensed under a under a Creative Commons Attribution 4.0 International License. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. www.nature.com/scientificreports www.nature.com/scientificreports Cooperation on dynamic networks within an uncertain reputation environment Received: 20 February 2018 Accepted: 1 May 2018 Published: xx xx xxxx Pablo Lozano1,2, Alberto Antonioni1,3,4, Marco Tomassini5 & Angel Sánchez1,2,3,6 Summary of the Experimental Setup In our experimental sessions seven groups of twenty subjects connected in a social network played a Prisoner’s Dilemma game with their neighbors13. In this two-person game, players must decide whether to cooperate (C) or to defect (D). Similarly to several recent experimental settings (e.g.11,21–23), the chosen action is the same with all neighbors. Note that if actions could be chosen independently for each neighbor the network structure becomes almost irrelevant and the system turns to a collection of independent pairwise games. If both agents cooperate, each receives a payoff R. If one defects and the other cooperates, the defector receives T and the cooperator receives the payoff S. If both defect, each receives P. Since T > R > P ≥ S, defection is a dominant strategy and a rational payoff-maximizing player will choose to defect, although mutual cooperation yields a higher collec- tive payoff, whence the dilemma. Subjects played a weak PD game (P = S) with their immediate neighbors with T = 10, R = 7, P = 0, and S = 0. Payoff values are the same as those used in11, where it was shown that the pos- sibility to rewire links allows for cooperation to emerge when information about past actions of others, which amounts to their reputation, is available. The initial set of connections between the participants was chosen to be a regular lattice of degree 4. Participants played 30 rounds of the sequence described below. See13 for more details on the experimental protocol. Th f l d h h d h h h b f h The reputation of a player was expressed through a cooperation index α which is the number of times the player has cooperated in the last five moves, thus α ∈ [0, 5]. We considered two treatments: a baseline one, called Real Reputation (RR) in which the cooperation index cannot be manipulated, and a modified one in which par- ticipants were informed that all of them were allowed to vary their cooperation index by paying a cost, called Fake Reputation (FR). At the beginning, all players receive an initial α of 3 based on the actions sequence CDCDC. Note that this form of reputation is related to but different from the one used in11 where explicit past choices of each player were available to all others. www.nature.com/scientificreports/ experiments with human subjects11–13,21–24. Of particular relevance for us here are the experiments reported in references11–13 which examine the interplay of the dynamical network factor and of the reputation knowledge on the amount of cooperation. These studies conclude that it is reputation that plays the most important role in the evolution of cooperation in the population. p p p The previous discussion and the cited research both assume that reputation is perfectly reliable and truly reflects the behavior of an individual, e.g., under the form of a list of individual’s actions extending in the past for a given length. However, in the real world this information can be manipulated in various ways, leading to uncertainty about the true reputation an individual is worth. Manipulating one’s reputation is difficult as long as individuals interact face-to-face in small groups where unfair behavior is simpler to spot and very detrimental to an individual if discovered. It has been recently shown that indirect reciprocity in groups fails to work if only an image scoring is available and there is uncertainty about individual reputation25. In the modern society many social and commercial interactions take place through communication networks26 and a variety of social media. In most instances, such interactions involve people who know each other only through an online identity27, with- out any connection whatsoever in the physical world. This makes manipulating a piece of information such as an individual’s reputation easier and much more likely, while, on the other hand, it affects many more people as the interactions in the digital world take place with larger numbers of subjects.i g p g j In a recent experiment we framed this question in a simplified environment as a dyadic Prisoner’s Dilemma (PD)28,29 in which participants were allowed to modify their reputation by paying a cost13 and, critically, they had no way to know whether another player’s reputation was true or fake. y p y p Our experiment highlighted interesting behaviors and collective emergent phenomena although the results from the laboratory are still limited in several ways. Due to their high cost and the time and organization they take it is very difficult to go beyond the study of only a few experimental conditions at best, which means that the influence of the variation of several parameters cannot be studied in practice. www.nature.com/scientificreports/ It is also the case that the number of participants is usually severely limited to a few tens owing to the classroom sizes of the typical laboratory. There have been recent advances on this last point and it is now possible to run experiments with hundreds, or even thousands, of participants by using suitable web-based interfaces (see, e.g.30) but this is not yet widespread prac- tice. Besides, experiments with large populations have problems of their own and the exploration of the parameter space remains out of the question. p q In view of this situation we argue here that experiments can be usefully complemented and calibrated by numerical simulation models. However, by this we do not mean the standard theoretical models based on rep- licator dynamics ideas and on microscopic strategy revision rules like payoff-based or imitation-based31, which turn out to be mostly inapplicable to complex situations like the one studied in our experiment. Rather, we think of suitable numerical versions of the actual behavioral strategies that people use when playing in the laboratory. So, in our view, experiments and computer simulations go hand in hand, with experiments suggesting suitable behavioral models and simulations extending the domain of exploration of the parameter space that cannot be reached by experiments alone. In turn, numerical simulation results can also suggest new experiments or exper- imental settings that would have been difficult to design without that knowledge.i gfi g g To make the article self-contained and for the sake of the reader, we first summarize the experimental setting in the next section. In the rest of the paper we present the numerical model that has been designed starting from the experimental results and its application to a more complete study of the model parameters. We conclude with the discussion of the obtained results and some suggestions for further work. Pablo Lozano1,2, Alberto Antonioni1,3,4, Marco Tomassini5 & Angel Sánchez1,2,3,6 While direct reciprocity is at work in small groups and organizations in which people meet frequently and repeatedly, reputation is a more general indirect mechanism that may work in larger and/or anonymous groups. g y g y g p Cooperation based on reputational knowledge, or indirect reciprocity, has long been studied through theoret- ical models1–6, as well as experimentally7–13. In the present study we are particularly concerned with interacting populations that take the form of a social network in which each individual has a certain number of primary neighbors. In this context, it is crucially important that individuals in the network have control over which part- ners they interact with. In other words, they must be able to form new links and severe unwanted ones based on the availability of information about the actions of current and possible partners. If this is the case, cooperation may evolve and maintain itself to a remarkable degree thanks to positive assortment among cooperators. This has been convincingly shown in theoretical models and numerical simulations14–20 and, most importantly, by recent 1Grupo Interdisciplinar de Sistemas Complejos (GISC), Departamento de Matemáticas, Universidad Carlos III de Madrid, E-28911, Leganés, Madrid, Spain. 2Unidad Mixta de Comportamiento y Complejidad Social UC3M-UV-UZ (UMICCS), Madrid, Spain. 3Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, E-50018, Zaragoza, Spain. 4Department of Economics, University College London, London, UK. 5Information Systems Department, Faculty of Business and Economics, University of Lausanne, CH-1015, Lausanne, Switzerland. 6UC3M-BS Institute for Financial Big Data (IFiBiD), Universidad Carlos III de Madrid, 28903, Getafe, Madrid, Spain. Correspondence and requests for materials should be addressed to A.A. (email: alberto.antonioni@gmail.com) SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 1 www.nature.com/scientificreports/ SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 Model Descriptionh Then, the agent chooses to cooperate with probability pcoop = Fαˆ i, where F is a tunable parameter on the agent’s decision-making process. Neighborhood modification. Agents may suppress, unilaterally, a link with the neighbor that has the worst coop- eration index, and they can propose a link to a random agent, which was not already linked to them. The suppres- sion of the link occurs with probability pcut, which is based on the complementary probability paccept = 1 − pcut of accepting a link. The probability of link acceptance, paccept, is based on the average cooperation index of the agent’s neighborhood, αˆ i, and on the cooperation index of the agent that has proposed the link, αj. Link acceptance. Agents evaluate all the link proposals by seeing the corresponding agent’s cooperation index, αj, of all their potential neighbors. We assume that when αj > αˆ i we have paccept = 1 and paccept = 0 for αj = 0. In all the other cases, when 0 < αj < αˆ i we have paccept = αj/αˆ i. Feedback on payoffs. All agents receive their payments by accumulating payoffs from all the PD games in which they are involved.h The FR treatment is identical to the RR treatment but the agents never know if the observed cooperation index is the real one. Consequently, as in13, there is an additional stage between the first and second stage of the RR treatment. In that additional stage, agents can pay a cost in order to increase their observable cooperation index. This modification costs 4 points per increased point, as in13, and the purchased points are only valid for the round they are currently playing.ih In the simulated FR treatment, we introduce a new kind of agent type, called cheater, to be defined below. The fraction of cheaters in the agent population is regulated by the parameter fch ∈ [0, 1], where fch = 1 stands for a population entirely composed by cheater agents. All the other agents are called reliable. A cheater agent defects with probability ρ ∈[0, 1] D ch and it behaves as a reliable agent with probability ρ − 1 D ch, i.e. cooperates with prob- ability pcoop = Fαˆ i. Model Descriptionh p Initial setup. The initial configuration for the set of N agents is a random regular random graph of degree 4, which represents a dynamical network where edges can be created and removed during the model dynamics. The initial degree is chosen to be the same as in the experimental treatments in13. Every agent i has a cooper- ation index αi, that indicates how many times the agent cooperated in the last five rounds, that is, αi ∈ [0, 5]. Cooperation indices are part of the information provided during the experiment at each round to each agent about their neighbors. The agents play a Prisoner’s Dilemma (PD) game with their neighbors using the same strategy against all of them, as described in the experimental setting. To compare with the results of the previous experiment, the payoff values have been chosen to be the same as in13, i.e., T = 10, R = 7 and P = S = 0. Agent dynamics. Following the experimental setting (see previous section and13), two model treatments have been considered: one in which the cooperation index cannot be manipulated (RR), and a modified one in which agents can change their cooperation index by paying a cost (FR). At the beginning, agents receive a random sequence of past actions of length five, so their initial cooperation index has an average value of 2.5 but it may be different for each of them. This is slightly different from the corresponding experimental setup but it is done to avoid the possibility of entering a loop of stereotyped behavior, given the greater regularity of the model evolution rules described below. Mirroring the experiment, in the RR treatment, each round has four stages named: action choice, neighbor- hood modification, link acceptance, payoff feedback. These proceed as follows: Action choice. Agents receive information on the cooperation index of their current neighbors, and select coop- eration or defection as the action for all the PD games with their neighbors. Each agent computes the normalized average cooperation index of its neighbors as α α = ∑ ∈ η ∈ ˆ /5 [0, 1] i k j j 1 i i , where ki is the number of neighbors of agent i and ηi is the set of agent i’s neighbors numbers. Summary of the Experimental Setup In contrast, in our experiment there is some uncertainty about the current behavior of a player even in the RR treatment. This uncertainty comes about because only the number of coop- erative actions of the current first neighbors and potential partners is known, but not their order. In addition, neighbors are just unlabeled anonymous individuals who cannot be recognized from one round to the next. As a result, only an average success rate of interactions with other unspecified participants is provided. SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 2 www.nature.com/scientificreports/ In the Real Reputation (RR) treatment each round consisted of the following four stages: (i) action choice; (ii) neighborhood modification; (iii) link acceptance decision; (iv) feedback on payoffs. In the first stage, players receive information on the cooperation index of their current neighbors and have to select one of two actions. In the second stage, participants may decide to unilaterally suppress a link with a neighbor and they are also given the option to offer a link to a new, randomly chosen partner; in both cases, they only know the α value of the corresponding subject. In the following stage, participants see all link proposals from other players (and their α), which they can either accept or reject. After these decision stages a new network is formed, and subjects accumu- late their payoff by playing the PD game in pairs with their current neighbors. They are neither informed about their neighbors’ payoffs nor about their neighbors’ individual current actions. Participants never know the full network topology.hf p gy The Fake Reputation (FR) treatment is identical to the RR treatment with the following fundamental differ- ence: participants never know whether the observed cooperation index α of their partners is the real one or has been modified. Consequently, in this setup there is an additional stage between the first and the second stage of the RR treatment during which participants may choose to pay a cost in order to modify their α value. The chosen cost was 4 points per modified reputational point, per round. There is no cost if one just wants to show her true cooperation index. SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 Results We present the results of numerically simulated systems for the RR and FR treatments using the same number of agents (20) as in the laboratory experiments13, and adopting the agent update rules described in the previous section. The maximum number of rounds we simulated in this study was 100, instead of the 30 used in the exper- imental setting, to check the stability of our results with a longer time horizon. We have studied a wide range of values for all the model parameters: fch, ρD ch and ρR rel. We have also considered the effect of a damping term on the action decision making process varying the parameter F. For the FR treatment, the initial fraction of cheater agents in the population was chosen to be fch = 0.5, that is, half of the population plays as a cheater agent while the other half as a reliable one. The value fch = 0.5 is similar to what we empirically measured in13. Also, according to experimental results, we use ρ = .0 25 R rel , that is, the probability that a reliable agent purchases reputational points. We then investigate system dynamics for ρ < .0 5 D ch and F = 0.95 and 1. Figure 1 shows how the cooperation index evolves as a function of the round number during the simulations for different values of ρD ch and for F = 0.95. The RR model, i.e. ρ = = = . f F 0, 0, 0 95 ch R rel , is also shown for comparison. Results for F = 1 are similar and have been omitted. The observable cooperation index (Fig. 1, right image) reaches higher values, as it intuitively should, and similarly to what was observed in the experiment13.ht y p The model parameter selection has been made after comparing the simulation results with the ones in13 and selecting those values that give the aggregate behavior that appears to be closer to the experimental results. We found that the most suitable choices were: ρ = .0 3 D ch , ρ = .0 25 R rel , fch = 0.5, and F = 0.95. Cooperation index. Simulated results are compared with empirical ones in Fig. 2 adopting F = 0.95. The results are quite close to the experimental ones. www.nature.com/scientificreports/ Standard deviations are shown as error bars. Table 1. Variables and parameters of the model and their meanings. Figure 1. Simulated cooperation indices for cheaters’ behavior. Cooperation index as a function of the rounds of play in the simulated RR and FR model. (a) real cooperation index evolution; (b) observable cooperation index evolution. Results are averages of 25 runs. Standard deviations are shown as error bars. Figure 1. Simulated cooperation indices for cheaters’ behavior. Cooperation index as a function of the rounds of play in the simulated RR and FR model. (a) real cooperation index evolution; (b) observable cooperation index evolution. Results are averages of 25 runs. Standard deviations are shown as error bars. For the sake of clarity, the main variables and parameters of the model are summarized, with their meanings, in Table 1. For the sake of clarity, the main variables and parameters of the model are summarized, with their meanings, in Table 1. SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 Model Descriptionh Whenever a cheater agent i has a cooperation index smaller than its neighbourhood average cooperation index, that is, αi < αˆ i, it purchases reputational points for that round until αi ≥ αˆ i. On the other hand, reliable agents purchase reputational points until αi ≥ αˆ i with probability ρ ∈[0, 1] R rel and with probability ρ − 1 R rel they keep their cooperation index unchanged. SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 3 www.nature.com/scientificreports/ www.nature.com/scientificreports/ tificreports/ αi cooperation index of agent i αˆi average cooperation index of agent i’s neighbors F factor on agents’ decision (model parameter, [MP]) pcoop = Fαˆi probability of cooperation for reliable agents paccept probability of accepting a new link pcut = 1 − paccept probability of cutting a link to a neighbor fch fraction of cheater agents in the population (MP) ρD ch probability of direct defection for cheater agents (MP) ρR rel probability of purchasing reputation for reliable agents (MP) Table 1. Variables and parameters of the model and their meanings. Figure 1. Simulated cooperation indices for cheaters’ behavior. Cooperation index as a function of the rounds of play in the simulated RR and FR model. (a) real cooperation index evolution; (b) observable cooperation index evolution. Results are averages of 25 runs. Standard deviations are shown as error bars. αi cooperation index of agent i αˆi average cooperation index of agent i’s neighbors F factor on agents’ decision (model parameter, [MP]) pcoop = Fαˆi probability of cooperation for reliable agents paccept probability of accepting a new link pcut = 1 − paccept probability of cutting a link to a neighbor fch fraction of cheater agents in the population (MP) ρD ch probability of direct defection for cheater agents (MP) ρR rel probability of purchasing reputation for reliable agents (MP) Table 1. Variables and parameters of the model and their meanings. αi cooperation index of agent i αˆi average cooperation index of agent i’s neighbors F factor on agents’ decision (model parameter, [MP]) pcoop = Fαˆi probability of cooperation for reliable agents paccept probability of accepting a new link pcut = 1 − paccept probability of cutting a link to a neighbor fch fraction of cheater agents in the population (MP) ρD ch probability of direct defection for cheater agents (MP) ρR rel probability of purchasing reputation for reliable agents (MP) Table 1. Variables and parameters of the model and their meanings. Table 1. Variables and parameters of the model and their meanings. Table 1. Variables and parameters of the model and their meanings. Table 1. Variables and parameters of the model and their meanings. Figure 1. Simulated cooperation indices for cheaters’ behavior. Cooperation index as a function of the rounds of play in the simulated RR and FR model. (a) real cooperation index evolution; (b) observable cooperation index evolution. Results are averages of 25 runs. Results The RR parameter values are: fch = 0, ρ = 0 R rel ; while FR ones are: fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel . Figure 3. Comparison of individual players’ average behavior (cheating/cooperation). Each individual is represented by a dot whose abscissa gives the average number of points purchased per round and whose ordinate represents the individual’s cooperation frequency averaged over all rounds in the simulation run. The inset panel reports the same data from the experiment in13. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Figure 3. Comparison of individual players’ average behavior (cheating/cooperation). Each individual is represented by a dot whose abscissa gives the average number of points purchased per round and whose ordinate represents the individual’s cooperation frequency averaged over all rounds in the simulation run. The inset panel reports the same data from the experiment in13. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Purchased points. As said above, the FR treatment is characterized by the fact that players, unknown to the others, are allowed to purchase reputation points at each round. A useful view of the individual’s behavior is given by a plot in which each individual is represented by a dot. The x-coordinate of a given individual is the average number of points she has purchased per round during the run; the y-coordinate of the individual gives her coop- eration frequency during the run. This is what is depicted in Fig. 3. The inset panel in this figure represents the same data for the experimental results. The vertical line is an arbitrary (but, as can be seen from the plot, reasona- ble, in so far as there are seemingly two different groups of subjects) threshold that separates players that buy less than half a point per round in average, from those that buy more than half a point. For the sake of clarity, we recall here that we dubbed the first group of players “reliable”, while the others were called “cheaters”. Results It can be observed that, for the chosen parameter set, a difference of about half a point exists between real and visible cooperation in the FR treatment. Of course, the similarity between experimental and simulated results is not surprising: it was expected since we chose parameter values in the model that were suggested by the experimental results. Indeed, our goal is not to have generic agents that collectively behave as the real ones, which would be almost hopeless, but rather “statistical” agents that individu- ally resemble the human ones that took part in the experiment in their decison-making behavior. In other words, the intention here is not to “explain” the observed behavior. On the contrary, we assume this behavior in order to enhance by simulation the limited range of the experimental settings. SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 4 www.nature.com/scientificreports/ Figure 2. Comparison between empirical and simulated results. Cooperation index as a function of round. Left image: average experimental results13. Right image: numerical simulation results. Results are averages over 25 repetitions. The RR parameter values are: fch = 0, ρ = 0 R rel ; while FR ones are: fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel . Figure 3. Comparison of individual players’ average behavior (cheating/cooperation). Each individual is represented by a dot whose abscissa gives the average number of points purchased per round and whose ordinate represents the individual’s cooperation frequency averaged over all rounds in the simulation run. The inset panel reports the same data from the experiment in13. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Figure 2. Comparison between empirical and simulated results. Cooperation index as a function of round. Left image: average experimental results13. Right image: numerical simulation results. Results are averages over 25 repetitions. The RR parameter values are: fch = 0, ρ = 0 R rel ; while FR ones are: fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel . Figure 2. Comparison between empirical and simulated results. Cooperation index as a function of round. Left image: average experimental results13. Right image: numerical simulation results. Results are averages over 25 repetitions. Results This binary clas- sification is a simplification but it allows us to group behaviors instead of treating them as a continuous variable. This is useful to understand the system behavior in terms of well-defined behavioral types and gave useful results when applied to the experimental data13. pp p Given that we introduced an amount of cheater agents approximately equal to the experimentally observed quantity (fch = 0.5), it is again not surprising that the simulated population behavior is qualitatively similar to the experimental results with human subjects. It can be observed, however, that the simulation results are more concentrated, a phenomenon that can be attributed to the average artificial agent behavior compared to the more SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 5 www.nature.com/scientificreports/ Figure 4. Simulated cooperation indices per individual type in small systems. Frequency of reliable and cheater players for real (left) and observable (right) cooperation index in the simulated FR treatment. Results are averages over 25 runs. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Figure 4. Simulated cooperation indices per individual type in small systems. Frequency of reliable and cheater players for real (left) and observable (right) cooperation index in the simulated FR treatment. Results are averages over 25 runs. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). idiosyncratic human players which have a more spread-out distribution in the scatter plot. In both cases, cheaters cooperate less on average. idiosyncratic human players which have a more spread-out distribution in the scatter plot. In both cases, cheaters cooperate less on average. Frequency of cooperation. We continue the comparison between human agents and artificial agents behavior by showing the histograms giving the fraction of the population that has a given average cooperation index in the FR treatment for reliable and cheater players respectively. This is shown in Fig. 4 where simulation results are reported. Results Comparing them with the laboratory results in13 one can see that the general patterns are similar in both cases, although the distributions for the simulated population are more centered between 1 and 2 for the true cooperation index distribution (left panel) and between 2 and 4 for observable cooperation index distribution. This is essentially a consequence of the less erratic behavior of the agents. Scaling up the population size. All the results shown until now were for a population size of 20, the same size that was used in the laboratory experiment13. This is interesting enough but one is let with the question of whether a larger number of participants would give rise to fundamentally different behavior. We want also to stress that human subjects were aware of the fact that they were playing against other people in the room, putting them in a situation of a small-scale experiment. However, the same experimental protocol can be easily extended to a larger population. We thus assume that participants’ incentives and consequent behavior should not com- pletely change when playing in a larger pool of people. Managing a large number of subjects is difficult to do in a laboratory setting, although today there exist web-based systems that allow hundreds of people to participate in an experiment. Yet, those experiments are hard to set up, control, and analyze, not to speak of the financial aspects involved. Thus, numerical simulation provides a cheap means to explore untried possibilities. h In what follows, we report results for simulations performed with 500 agents that interact during 100 rounds in the simulated FR treatments. Figure 5 depicts the average cooperation results. Compared with the laboratory results for 20 participants (left panel), it is clear that the trend is maintained and the fluctuations are lower in the larger simulated population. In particular, it is reassuring to see that nothing odd happens when more players interact during more rounds; rather, the behavior becomes more stable and statistically reliable (right panel). We also conducted simulations with 1000 agents with basically the same results that we omit for the sake of brevity.i g y y Now, comparing player type frequencies in the large populations in the FR treatment, we find very similar trends for the real cooperation index, as shown in Fig. SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 Results 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Simulation data are averages over 25 runs. Figure 5. Size and time horizon effects. Comparing average cooperation in populations of size 20 (left) and size 500 (right). Blue curves: real cooperation index. Red curves: visible cooperation index. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Results are averages over 25 runs of the simulated system. Figure 5. Size and time horizon effects. Comparing average cooperation in populations of size 20 (left) and size 500 (right). Blue curves: real cooperation index. Red curves: visible cooperation index. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Results are averages over 25 runs of the simulated system. Figure 6. Simulated cooperation indices per individual type in larger systems. Real (a) and visible (b) cooperation index frequency for reliable and cheater players in the large population, i.e. 500 agents. See also Fig. 4 for comparison with the same results on the small simulated system. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Simulation data are averages over 25 runs. Figure 6. Simulated cooperation indices per individual type in larger systems. Real (a) and visible (b) cooperation index frequency for reliable and cheater players in the large population, i.e. 500 agents. See also Fi 4 f i ith th lt th ll i l t d t P t l th Figure 6. Simulated cooperation indices per individual type in larger systems. Real (a) and visible (b) cooperation index frequency for reliable and cheater players in the large population, i.e. 500 agents. See als Fig. 4 for comparison with the same results on the small simulated system. Parameters values are the same those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Simulation data are averages over 25 runs. in the particular case studied here. Results This means that using the typical 15 to 25 participants in a laboratory experi- ment, numbers that are often dictated by logistic and financial limitations, does not seem to impair the qualitative nature of the results. On the other hand, if one can afford many more participants, the simulations suggest that the results are more stable and their statistical significance is higher. Results 6 (left panel), while visible cooperation frequencies (right panel) seem to experience a shift towards the right of the x-axis and cheaters essentially stay around cooperation index 3, instead of being mainly distributed between indices 3 and 4 as in the smaller population (see Fig. 4). In the following Fig. 7 we show the scatterplots of the points purchased per round by each individual against the individual’s cooperation frequency in large simulated populations. The correlation patterns are similar to what happens for smaller system sizes (see Fig. 3): we observe cheaters cooperating less in the average but that in the large population case the density of points in the two regions is much higher and points are less scattered around. Thus, it appears that using more agents in the simulations really gives crisper and more stable patterns of behavior. h g g y g Regarding the evolution of the degree distribution we have noticed that in the small population case the net- work quickly saturates and becomes an almost complete graph. This behavior is very close to the trend observed in the experiment13. In the large population case the trend is the same and the degree growth rate is even faster in the large population. g p p From the previous results for larger populations we can infer that using more agents does indeed improve the stability of the dynamical systems and the associated statistics since there are far less fluctuations. Nevertheless, it is also clear that the small and the large systems basically show the same trends in all measured quantities, at least SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 6 www.nature.com/scientificreports/ ntificreports/ Figure 5. Size and time horizon effects. Comparing average cooperation in populations of size 20 (left) and size 500 (right). Blue curves: real cooperation index. Red curves: visible cooperation index. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Results are averages over 25 runs of the simulated system. Figure 6. Simulated cooperation indices per individual type in larger systems. Real (a) and visible (b) cooperation index frequency for reliable and cheater players in the large population, i.e. 500 agents. See also Fig. 4 for comparison with the same results on the small simulated system. Parameters values are the same as those of Fig. Conclusions Our main objective in the present study was to design a numerical simulation model of a system where reputation can be faked, based on artificial agents since such a model can be suitably parameterized and can be run quickly and repeatedly, substituting the need for actual experiments. Our agent model does not try to faithfully reproduce the idiosyncrasies of particular human agents, it rather strives to represent the rules of typical agents such that the collective behavior of the agents’ interactions results in a global dynamics that is qualitatively in agreement with the experimental observations. To validate our model design, we first compared the numerical simulation results with the same system size as in the laboratory experiment. Having thus obtained a good qualitative fit, we then studied much larger systems over longer time horizons, that would make them either unfeasible or difficult to study in a laboratory with human participants. The main results we obtained is that larger populations essentially behave in the same qualitative manner as the small one, except that all results have smaller fluctuations, both because the populations are larger and also because one can easily and quickly perform many repetitions of the virtual experiment before taking the averages. SCIentIfIC REPOrTS | (2018) 8:9093 | DOI:10.1038/s41598-018-27544-5 7 www.nature.com/scientificreports/ tificreports/ Figure 7. Individual players’ average behavior (cheating/cooperation) in larger systems. As in Fig. 3, we represent individuals by the number of points they purchased per round (x axis) and their cooperation frequency (y axis), for a population of 500 agents in a simulated FR treatment. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). Figure 7. Individual players’ average behavior (cheating/cooperation) in larger systems. As in Fig. 3, we represent individuals by the number of points they purchased per round (x axis) and their cooperation frequency (y axis), for a population of 500 agents in a simulated FR treatment. Parameters values are the same as those of Fig. 2 (fch = 0.5, ρ = .0 3 D ch , ρ = .0 25 R rel , F = 0.95). This result has two interesting implications. Conclusions First, it justifies the use of classroom-size laboratory experiments, at least in this case, and suggests that people might behave in a large system by just keeping the links that have a reasonable observable reputation and making new links to similar ones, leading to a growth of the mean degree. This is a clear-cut prediction that raises the question as to whether real people, with limited attention and cogni- tive capabilities can actually behave in that manner. We envisage that the way information about the (very many) other participants can be key to the verification of this prediction. Second, large scale simulations suggest that the observation could exhibit less fluctuations compared to those of small size experiment. This seems to indicate that it could be better, in terms of the statistical significance of the results, to run a large system than many instances of smaller ones, something that again requires experimental verification. In this sense, it has to be kept in mind that, following the findings about static PD experiments32, we have proposed a model where payoffs do not play any role. It then goes without saying that it would be important to check the accuracy of this assumption by repeating the experiments in small size systems with different payoffs; if the model is valid in these other setups, we would then have a very general manner to describe quite a large range of experiments.i y g g g Another point about the comparison of our model with other experimental setups relates to one of the findings of our large scale simulations, namely the rapid growth of the number of links in the system. Such large growth rates are possible only because link creation and deletion are free in the model. However, actual socio-economic networks have mean degrees that do not exceed 15 in most measured cases (see, for instance33). This is because in the real social world link creation, and even link cutting, are not free. They often imply a cost, either economical or of other types. Moreover, issues such as time and attention span limitations prevent actors to engage in too many simultaneous contacts. It would certainly be interesting to modify the network dynamics part of our model so as to take these factors into account. 1. Nowak, M. A. & Sigmund, K. Evolution of indirect reciprocity by image scoring. Nature 393, 573–577 (1998). 2. Panchanathan, K. & Boyd, R. Indirect reciprocity can stabilize cooperation without the second-order free rider problem. Nature 432, 499–502 (2004). 3. Brandt, H. & Sigmund, K. Indirect reciprocity, image scoring, and moral hazard. Proceedings of the National Academy of Sciences 102, 2666–2670 (2005). 4. Nowak, M. A. & Sigmund, K. Evolution of indirect reciprocity. Nature 437, 1291–1298 (2005). Conclusions Likewise, concepts such as the degree distribution function, the mean distance, or the clustering coefficient would not make much sense for our very dense final population graphs. However, our main purpose here was to create a numerical counterpart of the experimental setting we used in13. The experiments we are proposing here would allow us to extend our model to those, more realistic situations. h To conclude, we stress that, by design, the main limitation of our approach is that it cannot be applied to other situations as it has been purposedly tailored to the setting described in the experiment. On the other hand, using general game-theoretical models such as learning or replicator dynamics would certainly have prevented us from approximately matching the human behavior in the experiment. Another advantage of the specialized agent system is that simulations may also be used to suggest further experiments to be tried out as we have done above. We are thus led to argue that the parallel use of experiments with people and of suitably designed agent simulations greatly enhances the scope of both laboratory experiments and agent-based simulations. Eventually, the interaction of models and experiments should lead to a better understanding of the behavior of a large class of people, and the discrepancies could be classified by looking at the differences with this average behavior. That would be a real contribution to advancing the behavioral sciences. We hope that the success of the model we are presenting here stimulates further work along these lines. www.nature.com/scientificreports/ Prisoner’s Dilemma (Universi p p ( y f g 29. Axelrod, R. The Evolution of Cooperation (Basic Books, 1984).h 29. Axelrod, R. The Evolution of Cooperation (Basic Books, 1984).h h f p and, D. G. The promise of mechanical turk: How online labor markets can help theorists run behavioral experiments. Journal of Theoretical Biology 299, 172–179 (2012). h f p 30. Rand, D. G. The promise of mechanical turk: How online labor markets can help theorists run behavioral experiments. Journ Theoretical Biology 299, 172–179 (2012).h h 30. Rand, D. G. 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Cuesta, J. A., Gracia-Lázaro, C., Ferrer, A., Moreno, Y. & Sánchez, A. Reputation drives cooperative behaviour and network formation in human groups. Scientific Reports 5, 7843 (2014).hf g p fi p 2. Gallo, E. & Yan, C. The effects of reputational and social knowledge on cooperation. Proceedings of the National Academy of Science 112, 3647–3652 (2015). 13. Antonioni, A., Sánchez, A. & Tomassini, M. Cooperation survives and cheating pays in a dynamic network structure with unreliable reputation. Scientific Reports 6, 27160 (2016).f i 4. Eguíluz, V. M., Zimmermann, M. G. & Cela-Conde, C. J. & San Miguel, M. Cooperation and the emergence of role differentiation in the dynamics of social networks. American Journal of Sociology 110, 977–1008 (2005). in the dynamics of social networks. American Journal of Sociology 110, 977–1008 (2005). 5. Santos, F. C., Pacheco, J. M. & Lenaerts, T. Cooperation prevails when individuals adjust their social ties. PLoS Computationa Biology 2 1284 1291 (2006) 5. Santos, F. C., Pacheco, J. M. & Lenaerts, T. Cooperation prevails when individuals adjust their social ties. Author Contributions All authors conceived the study. P.L. wrote the code to run computer simulations and performed data analysis. Al uthors discussed the results, drew conclusions and wrote the manuscript. Acknowledgementsh g This work was partially supported by the EU through FET-Proactive Project DOLFINS (contract no. 640772, AS) and FET-Open Project IBSEN (contract no. 662725, A. S.), and by the Ministerio de Econom a y Competitividad of Spain (grant no. FIS2015-64349-P, A.S.) (MINECO/FEDER, UE). A.A. gratefully acknowledges the financial support of the Swiss National Science Foundation under Grants No. P2LAP1-161864 and P300P1-171537. References 4. Nowak, M. A. & Sigmund, K. Evolution of indirect reciprocity. Nature 437, 1291–1298 (2005). 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Perc, M., Gómez-Gardeñes, J., Szolnoki, A., Floría, L. M. & Moreno, Y. Evolutionary dynamics of group interactions on structured populations: A review. Journal of the Royal Society Interface 10, 20120997 (2013). 21. Rand, D. G., Arbesman, S. & Christakis, N. A. Dynamic social networks promote cooperation in experiments with humans. Proceedings of the National Academy of Sciences 108, 19193–19198 (2011). Proceedings of the National Academy of Sciences 108, 19193–19198 ( g f y f 2. Wang, J., Suri, S. & Watts, D. J. Cooperation and assortativity with dynamic partner updating. Proceedings of the National Academy of Sciences 109, 14363–14368 (2012). f ( ) 23. Fehl, K., van der Post, D. J. & Semmann, D. J. Co-evolution of behavior and social network structure promotes human cooperation. Ecology Letters 14, 546–551 (2011). 24. Antonioni, A., Cacault, M. P., Lalive, R. & Tomassini, M. Know thy neighbor: Costly information can hurt cooperation in dynamic networks. PLoS ONE 9, e110788 (2014).i 5. Nax, H., Perc, M., Szolnoki, A. & Helbing, D. Stability of cooperation under image scoring in group interactions. Scientific Report 5, 12145 (2015).h 26. Rainie, L. & Wellman, B. Networked. The New Social Operating System (MIT Press, Cambridge, MA, 2012).h 26. Rainie, L. & Wellman, B. Networked. The New Social Operating System (MIT Press, Cambridge, MA, 2012).h Rainie, L. & Wellman, B. Networked. The New Social Operating Syste 26. Rainie, L. & Wellman, B. Networked. The New Social Operating System (MIT Press, Cambridge, MA, 2012).h h 27. Kendall, L. The Handbook of Internet Studies (Wiley-Blackwell, 2011). h 27. Kendall, L. The Handbook of Internet Studies (Wiley-Blackwell, 2011). h 28. Rapoport, A. & Chammah, A. M. Competing Interests: The authors declare no competing interests. Competing Interests: The authors declare no competing interests. Competing Interests: The authors declare no competing interests. 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Hydrodynamic Optimization for Design of a Submersible Axial-Flow Pump with a Swept Impeller
Energies
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  Received: 7 April 2020; Accepted: 9 June 2020; Published: 12 June 2020 Abstract: Submersible pumps are now in high demand due to the sporadic occurrence of recent torrential rains. The current study was carried out to investigate the hydraulic characteristics of a submersible axial-flow pump with a swept impeller and to optimize the impeller and diffuser shapes of the pump to enhance the hydraulic performance. Three-dimensional Reynolds-averaged Navier–Stokes equations were solved with the shear stress transport turbulence model. The governing equations were discretized using the finite volume method, and unstructured tetrahedral and hexahedral meshes were used in the grid system. The optimal grid system was selected through a grid dependency test. A performance test for the submersible axial-flow pump was carried out experimentally, and the results of the numerical analysis were validated against the experimental results. The hydraulic efficiency and the total head were used as objective functions. For the first optimization, a multi-objective optimization was carried out to simultaneously improve the objective functions through a hybrid multi-objective evolutionary algorithm coupled with a response surface approximation by varying the swept angle and pitch angle of the blades of the rotating impeller. The second multi-objective optimization was performed using two design variables, i.e., the inlet angle and the length of the diffuser vanes, to simultaneously increase the objective functions. Clustered optimum designs in the Pareto optimal solutions yielded significant increases in the objective function values as compared with the reference design. Keywords: submersible axial-flow pump; sweep angle; pitch angle; diffuser inlet and outlet angle; diffuser length www.mdpi.com/journal/energies Hydrodynamic Optimization for Design of a Submersible Axial-Flow Pump with a Swept Impeller Youn-Sung Kim 1,2, Man-Woong Heo 3, Hyeon-Seok Shim 2, Bong-Soo Lee 4, Dong-Hwan Kim 3 and Kwang-Yong Kim 2,* 1 FLUXYS Pump Company, Paju-si, Gyeonggi-do 10847, Korea; fluxys.pump@gmail.com 2 Department of Mechanical Engineering, Inha University, Incheon 22212, Korea; shs_8341@inha.edu 3 Coastal Development and Ocean Energy Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Korea; mwheo@kiost.ac.kr (M.-W.H.); dhk@kiost.ac.kr (D.-H.K.) 4 Korea Testing Certification, Gunpo-si, Gyeonggi-do 15809, Korea; bs7624@ktc.re.kr * Correspondence: kykim@inha.ac.kr; Tel.: +82-32-860-7317 1 FLUXYS Pump Company, Paju-si, Gyeonggi-do 10847, Korea; fluxys.pump@gmail.com 2 Department of Mechanical Engineering, Inha University, Incheon 22212, Korea; shs_8341@inha.edu 3 Coastal Development and Ocean Energy Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Korea; mwheo@kiost.ac.kr (M.-W.H.); dhk@kiost.ac.kr (D.-H.K.) 4 Korea Testing Certification, Gunpo-si, Gyeonggi-do 15809, Korea; bs7624@ktc.re.kr * Correspondence: kykim@inha.ac.kr; Tel.: +82-32-860-7317   energies Article Hydrodynamic Optimization for Design of a Submersible Axial-Flow Pump with a Swept Impeller Youn-Sung Kim 1,2, Man-Woong Heo 3, Hyeon-Seok Shim 2, Bong-Soo Lee 4, Dong-Hwan Kim 3 and Kwang-Yong Kim 2,* 1 FLUXYS Pump Company, Paju-si, Gyeonggi-do 10847, Korea; fluxys.pump@gmail.com 2 Department of Mechanical Engineering, Inha University, Incheon 22212, Korea; shs_8341@inha.edu 3 Coastal Development and Ocean Energy Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Korea; mwheo@kiost.ac.kr (M.-W.H.); dhk@kiost.ac.kr (D.-H.K.) 4 Korea Testing Certification, Gunpo-si, Gyeonggi-do 15809, Korea; bs7624@ktc.re.kr * Correspondence: kykim@inha.ac.kr; Tel.: +82-32-860-7317 Received: 7 April 2020; Accepted: 9 June 2020; Published: 12 June 2020   energies Article Hydrodynamic Optimization for Design of a Submersible Axial-Flow Pump with a Swept Impeller Youn-Sung Kim 1,2, Man-Woong Heo 3, Hyeon-Seok Shim 2, Bong-Soo Lee 4, Dong-Hwan Kim 3 and Kwang-Yong Kim 2,* 1 FLUXYS Pump Company, Paju-si, Gyeonggi-do 10847, Korea; fluxys.pump@gmail.com 2 Department of Mechanical Engineering, Inha University, Incheon 22212, Korea; shs_8341@inha.edu 3 Coastal Development and Ocean Energy Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Korea; mwheo@kiost.ac.kr (M.-W.H.); dhk@kiost.ac.kr (D.-H.K.) 4 Korea Testing Certification, Gunpo-si, Gyeonggi-do 15809, Korea; bs7624@ktc.re.kr * Correspondence: kykim@inha.ac.kr; Tel.: +82-32-860-7317 Received: 7 April 2020; Accepted: 9 June 2020; Published: 12 June 2020   energies 1. Introduction Submersible axial-flow pumps have been used in Korea, since the early 1980s, for pumping out the water at drainage pumping stations. In recent years, due to the frequent occurrence of torrential rain, the demand for equipping a higher capacity pump system has been steadily and significantly increasing. Nowadays, the system has been used in various applications, such as drainage pumping stations and irrigation water supply facilities. In addition, recently, as continuity of water resource use has been emphasized, industries related to reuse water and desalination have been continuously growing. In general, the submersible axial-flow pump is composed of a submersible motor, the inlet guide vanes (IGVs), a rotating impeller, and a diffuser. The design of axial-flow pumps considers the discharging flow rate and the head to determine the impeller rotational speed and the discharging diameter, and the best efficiency at the design point is taken into account to determine the power and the rotation speed of the motor. Submersible pumps used in drainage pumping stations operate for Energies 2020, 13, 3053; doi:10.3390/en13123053 www.mdpi.com/journal/energies 2 of 18 Energies 2020, 13, 3053 a relatively short period of time and have a long downtime. As a result, foreign substances such as soil and sludge are likely to be deposited inside the impeller or cling to the surface of the impeller blade. This can lead to a reduction of pump efficiency and clogging, which can be major causes of failures, such as confinement of an impeller or breaking of a motor. Therefore, recent studies have focused on improving the internal flow during the rotation and increasing the impeller surface flow rate to remove the foreign substances that adhere to the blade surface, by changing the shape of the impeller. This has required an understanding of the characteristics of submersible pumps by performing systematic analysis. Kim et al. [1] analyzed the effects of the IGV angle on the hydraulic performance of a submersible axial-flow pump and confirmed that the incidence loss was reduced at all ranges of flow rates in accordance with an increase in the IGV angle and, particularly, that this angle imparted a substantial influence on increasing the efficiency in the high flow rate region. Pessoa and Prado [2] experimentally carried out an investigation on the two-phase flow characteristics inside a submersible pump. Shi et al. [3] suggested fundamental theories and methodologies for the design of a multiphased submersible pump. 1. Introduction Moreover, Barrios and Prado [4] experimentally studied the detailed characteristics of the motion of bubbles and turbulence inside a submersible pump using visualization techniques. Multistage electrical submersible pump performances with different viscosities of oil used as working fluid were numerically analyzed by Zhu et al. [5]. They found that the boosting pressure decreased as much as 30–40% by increasing the oil viscosity from 10 to 100 cp and compared their numerical results with the corresponding experimental data under the water flow. Pineda et al. [6] investigated a problem that can result from a submersible pump in the oil and gas industry, viz., water/air two-phase flow, by a numerical analysis using the volume-of-fluid model. Additionally, Zhu et al. [7] performed experimental measurements to study the pressure surging phenomenon in a two-phase flow loop with a fourteen-stage radial type electrical submersible pump. Stel et al. [8] numerically identified the effects of the number of stages of submersible pumps on their performances. They also investigated the restriction caused by a reverse flow at the interface between the impeller and the diffuser. Chaudhari et al. [9] carried out a numerical analysis to predict the effects of the inlet, outlet, and the number of blades of the impeller on the head of a submersible mixed type pump. Zhou et al. [10] described the design methodology of a new type of diffuser, viz., a three-dimensional surface return diffuser for enhancing hydraulic performance of a submersible pump used in deep wells. Roclawski et al. [11] numerically and experimentally analyzed the performance characteristics of a modified submersible centrifugal pump stage which was designed by decreasing the diameter of the casing. Thus, numerous investigations to understand the flow characteristics of the submersible pumps have been carried out numerically and experimentally. In addition, high-performance designs of various pumps using optimization techniques have been of immense interest. Ling et al. [12] performed a parametric study to investigate the effects of the IGV configuration on the hydraulic performance of a multiphase submersible pump. They improved the hydraulic efficiency and the total head by using a design optimization technique. Song et al. [13] performed a multi-objective design optimization that simultaneously optimized the efficiency, vibration, and the sum of radial forces in a single-channel submersible pump. Si et al. 1. Introduction [14] proposed a matrix method for the optimization of the results of the orthographic experiment using the parameters, outlet width, number of impeller blade, and inlet setting angle of the guide vane, to enhance the hydraulic performances of a multistage pump. Suh et al. [15] performed a multi-objective optimization to simultaneously increase the efficiency and the pressure of the second stage of a multiphase pump. In order to prevent the problems of sludge deposition in advance, a couple of methods have been introduced [16–18]. Lee [16] suggested a sludge adhesion preventing device that was installed inside the pump and utilized the static electricity generated by the friction between the flow of water and the copper and carbon compound. Yeom [17] circumferentially installed jet nozzles on the casing of a submersible pump to inject fresh water and air to invoke the bubble jet effect that could improve the sludge removal. Joseph [18] developed a strainer equipped with plural angled slots, which considered 3 of 18 which Energies 2020, 13, 3053 the sludge remov the angle of impeller vanes, to throw any debris offfrom a fluid intake. Kliger [19] introduced an impeller with backswept blades in order to prevent the clogging of solids and reported that the backswept blades of the impeller helped to push the solids to the periphery while the impeller rotated. The swept impeller of the submersible pump evenly distributed the fluid flow from the hub to the shroud by improving the internal flow inside the blade passage. Kim et al. [20] performed a parametric study and analyzed the effects of geometric parameters of the swept impeller on the total efficiency and the head of a submersible axial-flow pump. introduced an impeller with backswept blades in order to prevent the clogging of solids and reported that the backswept blades of the impeller helped to push the solids to the periphery while the impeller rotated. The swept impeller of the submersible pump evenly distributed the fluid flow from the hub to the shroud by improving the internal flow inside the blade passage. Kim et al. [20] performed a parametric study and analyzed the effects of geometric parameters of the swept impeller on the total efficiency and the head of a submersible axial-flow pump. 1. Introduction Although some studies on traditional submersible pumps have been carried out over the last decades there is a lack of studies on the submersible axial flow pumps with swept blades that enable p p Although some studies on traditional submersible pumps have been carried out over the last decades, there is a lack of studies on the submersible axial-flow pumps with swept blades that enable the impeller to self-clean using the fluid flow evenly distributed in the blade passages. Understanding the hydrodynamic characteristics of the diffuser, as well as the rotating impeller, is crucial to concretely design a submersible axial-flow pump with a swept impeller. decades, there is a lack of studies on the submersible axial-flow pumps with swept blades that enable the impeller to self-clean using the fluid flow evenly distributed in the blade passages. Understanding the hydrodynamic characteristics of the diffuser, as well as the rotating impeller, is crucial to concretely design a submersible axial-flow pump with a swept impeller. In this study, three-dimensional Reynolds-averaged Navier–Stokes (RANS) analysis was performed to understand the internal flow characteristics of a submersible axial-flow pump with a In this study, three-dimensional Reynolds-averaged Navier–Stokes (RANS) analysis was performed to understand the internal flow characteristics of a submersible axial-flow pump with a swept impeller. A hydrodynamic optimization of the submersible pump was carried out in two stages through a hybrid multi-objective evolutionary algorithm (MOEA) coupled with a response surface approximation (RSA). Firstly, a multi-objective optimization was performed to simultaneously increase the objective functions, viz., the total efficiency and the head with the sweep and pitch angles as design variables. Secondly, the inlet angle and the length of the diffuser vanes of the pump installed with the optimum impeller were optimized to simultaneously improve the objective functions. The performance characteristics of the submersible axial-flow pump with the optimum impeller and diffuser vanes were also experimentally investigated through a performance test. The results of this study could contribute to the development of the serialization of the submersible pump with the swept impeller because there is no systematic design basis available for this pump type. performed to understand the internal flow characteristics of a submersible axial-flow pump with a swept impeller. A hydrodynamic optimization of the submersible pump was carried out in two stages through a hybrid multi-objective evolutionary algorithm (MOEA) coupled with a response surface approximation (RSA). 1. Introduction Firstly, a multi-objective optimization was performed to simultaneously increase the objective functions, viz., the total efficiency and the head with the sweep and pitch angles as design variables. Secondly, the inlet angle and the length of the diffuser vanes of the pump installed with the optimum impeller were optimized to simultaneously improve the objective functions. The performance characteristics of the submersible axial-flow pump with the optimum impeller and diffuser vanes were also experimentally investigated through a performance test. The results of this study could contribute to the development of the serialization of the submersible pump with the swept impeller because there is no systematic design basis available for this pump type. 3. Numerical Methods To analyze the hydraulic characteristics of the submersible axial-flow pump with the changes in the configuration of diffuser vanes, an incompressible steady three-dimensional flow analysis was carried out using a commercial CFD code ANSYS CFX-16.0® [21]. The computational domain for the flow analysis is presented in Figure 1. For the analysis of turbulence, the k-ω SST (shear stress transport) model [22] was used. The k-ω SST model combines the advantages of the k-ω and the k-ε models by using the k-ω model in the region near the wall and the k-ε model in the bulk-flow region. The working fluid was single-phase water at 25 ◦C, and the total pressure and the mass flow rate were assigned at the inlet and outlet boundaries of the computation domain, respectively. The stage model was applied at the interface between the rotational and stationary domains, and solid surfaces were considered to be smooth and no-slip wall conditions were applied there. The grid system was composed of tetrahedral meshes in the IGV domain and hexahedral meshes in the impeller, diffuser, suction, and discharge columns domains. The normalized distance of the first grid from the wall (y+) was maintained to be <2 to apply the low Reynolds number SST model. To find the optimal number of the grid system, a grid dependency test was carried out with the number of grids in a range of 1,500,000–12,000,000 in a previous study [20]. As the result, the optimal number of meshes for the computation were determined to be approximately 3,800,000. For convergence criteria, the root-mean-square (RMS) residual values for all governing equations were set to be less than 10−5. The variations in the performance parameters were maintained less than 0.5% during 100 time steps. The computations were performed using an Intel Core i7 CPU with 3.6 GHz unit and MPICH, which subdivided a task into 8 for the parallel computation. The computation took approximately 12 h for a single analysis, and the time varied depending on the geometry and the convergence criteria. g The feasibility of the numerical analysis was verified by comparing the numerical analysis results with experimental data in the previous study [20], where a parametric study of the submersible pump with a conventional impeller was performed. The total efficiency and head values of the numerical analysis showed good agreements with the experimental data with relative errors of 1.6% and 0.7%, respectively, at the design point. 2. Submersible Axial-Flow Pump Model 2. Submersible Axial-Flow Pump Model Figure 1 illustrates the submersible axial-flow pump model of this work. The pump is composed of the suction and discharge columns, IGV, the rotating impeller, and the stationary diffuser domains. A motor shape was neglected in this numerical simulation. The numbers of IGVs and rotating impeller blades are commonly four. The impeller of the submersible axial-flow pump has a diameter of 550 mm and a tip clearance of 1 mm, and the pump rotates at 700 rpm. The diffuser has six vanes and the diameters are 550 and 710 mm at the inlet and the outlet, respectively. The designed flow coefficient and the head coefficient are 0.047 and 0.031, respectively. Detailed design specifications are given in Table 1. Figure 1 illustrates the submersible axial-flow pump model of this work. The pump is composed of the suction and discharge columns, IGV, the rotating impeller, and the stationary diffuser domains. A motor shape was neglected in this numerical simulation. The numbers of IGVs and rotating impeller blades are commonly four. The impeller of the submersible axial-flow pump has a diameter of 550 mm and a tip clearance of 1 mm, and the pump rotates at 700 rpm. The diffuser has six vanes and the diameters are 550 and 710 mm at the inlet and the outlet, respectively. The designed flow coefficient and the head coefficient are 0.047 and 0.031, respectively. Detailed design specifications are given in Table 1. Figure 1. Computational domain and grid system. Figure 1. Computational domain and grid system. Figure 1. Computational domain and grid system. Figure 1. Computational domain and grid system. 4 of 18 Energies 2020, 13, 3053 Table 1. Design specification of submersible axial-flow pump. Table 1. Design specification of submersible axial-flow pump. Parameter Value Flow coefficient, Φ = Q/ωD3 0.047 Head coefficient, Ψ = gH/ω2D2 0.031 Rotational speed (rpm) 700 Impeller diameter (mm) 550 Tip clearance (mm) 1 Diffuser outlet diameter (mm) 710 Number of IGVs (EA) 4 Number of impeller blades (EA) 4 Number of diffuser vanes (EA) 6 3. Numerical Methods The neglect of the motor shape could have affected these errors. Optimization Techniques 5. Optimization Techniques Op i i a io ec iques Multi-objective optimizations were carried out to simultaneously enhance the total efficie d the head of the submersible axial pump with the swept impeller. The definitions of the t i d th h d id d t b th bj ti f ti f ll Multi-objective optimizations were carried out to simultaneously enhance the total efficiency and the head of the submersible axial pump with the swept impeller. The definitions of the total efficiency and the head considered to be the objective functions are as follows: he objective functions are as follows: 𝜂= 𝜌𝑔𝑄𝐻 (2𝜋𝑇𝑅 60 ) = 𝑃𝑜𝑢𝑡−𝑃𝑖𝑛 𝜌𝑔 η = ρgQH  2πTR 60  (1) H = Pout −Pin ρg (2) (1) (2) 𝑃𝑖𝑛 𝑔 ρg 𝜌𝑔 ere, ρ, g, Q, and H mean the density of the working fluid, the acceleration by gravity, the flow ra d the head, respectively; and T, R and P are the torque, rotational speed of the impeller, and where, ρ, g, Q, and H mean the density of the working fluid, the acceleration by gravity, the flow rate, and the head, respectively; and T, R and P are the torque, rotational speed of the impeller, and the total pressure, respectively. al pressure, respectively. The multi-objective optimization was carried out in two stages for the impeller and the diffu nes, through the hybrid MOEA coupled with the RSA surrogate model. The aim of the first st he multi-objective optimization was to simultaneously improve the objective functions with o design variables related to the swept angle and the pitch angle of the impeller blades. Then, ond stage of the multi-objective optimization based on the first optimization results w formed by the same method. The overall optimization procedures adopted in this work cribed in the flow chart presented in Figure 3 First design variables and objective functions w The multi-objective optimization was carried out in two stages for the impeller and the diffuser vanes, through the hybrid MOEA coupled with the RSA surrogate model. The aim of the first stage of the multi-objective optimization was to simultaneously improve the objective functions with the two design variables related to the swept angle and the pitch angle of the impeller blades. Then, the second stage of the multi-objective optimization based on the first optimization results was performed by the same method. 4. Experimental Apparatus The hydrodynamic performance characteristics of the pump prototype model were measured following the KS B 6320 standard [23] in the current study. A schematic diagram of the experimental setup for the performance test is shown in Figure 2. The submersible axial pump was vertically installed at the bottom of the pipe inside the water tank, and the pressure gauge, volume control valve, discharge pipe, and the flow meter were installed to measure the performance data. The length of the discharge pipe was 100 times the inlet diameter of the flow meter distancing from the valve, and the flow rate of the pump could be controlled by opening or closing the flow control valve. The water 5 of 18 the val Energies 2020, 13, 3053 he discharge pipe discharged from the pump flows back into the water tank, passed the distributing plate and circulates. The uncertainties of measurement (pressure and efficiency) in the experiment range were ±0.306 m and ±1%, respectively (confidence level 95.45% and k = 2). ter discharged from the pump flows back into the water tank, passed the distributing plate a ulates. The uncertainties of measurement (pressure and efficiency) in the experiment range w 306 m and ±1%, respectively (confidence level 95.45% and k = 2). Figure 2. Schematic of experimental apparatus. Figure 2. Schematic of experimental apparatus. igure 2. Schematic of experimental apparatus Figure 2. Schematic of experimental apparatus. Optimization Techniques 5. Optimization Techniques In the present study, these design 6 of 18 6 of Energies 2020, 13, 3053 nergies 2020, 13, x FOR P points were used as sampling points in space for the design variables of the swept impeller and the diffuser vanes. esign points were used as sampling points in space for the design variables of the swept impell nd the diffuser vanes. design points were used as sampling points in space for the design variables of the swept impeller and the diffuser vanes. Figure 3. Overall optimization procedure. Figure 4 Design points of Latin hypercube sampling (LHS) for two design variables Figure 3. Overall optimization procedure. Figure 3. Overall optimization procedure. Figure 4. Design points of Latin hypercube sampling (LHS) for two design variables. Figure 4. Design points of Latin hypercube sampling (LHS) for two design variables. Figure 3 O erall optimization procedure Figure 3. Overall optimization procedure. Figure 3. Overall optimization procedure. Figure 3. Overall optimization procedure Figure 3. Overall optimization procedure. Figure 3. Overall optimization procedure. Figure 3. Overall optimization procedure Figure 3. Overall optimization procedure. Figure 3. Overall optimization procedure. Figure 3. Overall optimization procedure Figure 3. Overall optimization procedure. Figure 3. Overall optimization procedure. i 4 D i i t f L ti h b li (LHS) f t d i i bl Figure 4. Design points of Latin hypercube sampling (LHS) for two design variables. Figure 4. Design points of Latin hypercube sampling (LHS) for two design variables. Figure 4. Design points of Latin hypercube sampling (LHS) for two design variables. The RSA model was used to construct the surrogate model. The RSA model is a methodolog hat makes a polynomial function based on the discrete responses obtained by numerical calculation detailed explanation of the RSA model is presented in Myers and Montgomery [25]. The presen work adopted a second-order polynomial for the response function and the constructed respon The RSA model was used to construct the surrogate model. The RSA model is a methodology that makes a polynomial function based on the discrete responses obtained by numerical calculations. A detailed explanation of the RSA model is presented in Myers and Montgomery [25]. The present work adopted a second-order polynomial for the response function, and the constructed response model for each objective function was formulated as follows: The RSA model was used to construct the surrogate model. Optimization Techniques 5. Optimization Techniques The RSA model is a methodology that makes a polynomial function based on the discrete responses obtained by numerical calculations. A detailed explanation of the RSA model is presented in Myers and Montgomery [25]. The present work adopted a second-order polynomial for the response function, and the constructed response model for each objective function was formulated as follows: function was formulated as follows: 𝑦(𝑥) = 𝛽0 + ∑ 𝛽𝑖𝑥𝑖 𝑁 + ∑ 𝛽𝑖𝑥𝑖 2 𝑁 + ∑ 𝛽𝑖𝑗𝑥𝑖𝑥𝑗 𝑁 (3) 𝑦(𝑥) = 𝛽0 + ∑ 𝛽𝑖𝑥𝑖 𝑁 𝑖=1 + ∑ 𝛽𝑖𝑥𝑖 2 𝑁 𝑖=1 + ∑ 𝛽𝑖𝑗𝑥𝑖𝑥𝑗 𝑁 𝑖<𝑗 (3) he number of design variables the vector of design variables and the vector y(x) = β0 + XN i=1 βixi + XN i=1 βix2 i + XN i<j βijxixj (3) (3) (3) 𝑦( ) 𝛽0 ∑ 𝛽𝑖 𝑖 𝑖=1 ∑ 𝛽𝑖 𝑖 𝑖=1 ∑ 𝛽𝑖𝑗 𝑖𝑗 𝑖<𝑗 (3 where N, x, and β are the number of design variables, the vector of design variables, and the vecto f unknown constant coefficients, respectively. The accuracy of this response function is evaluate where N, x, and β are the number of design variables, the vector of design variables, and the vector of unknown constant coefficients, respectively. The accuracy of this response function is evaluated using the R2adj value [25]. A hybrid MOEA was used to obtain POSs. In this algorithm, the approximate global POSs are where N, x, and β are the number of design variables, the vector of design variables, and the vector of unknown constant coefficients, respectively. The accuracy of this response function is evaluated using the R2adj value [25]. sing the R2adj value [25]. A hybrid MOEA was used to obtain POSs. In this algorithm, the approximate global POSs ar nitially obtained for each objective function using the real-coded fast and elitist NSGA-II which wa uggested by Deb [26]. Here, the “real code” means that the crossover and the mutation are achieve n real space to get a response from NSGA-II. These initially guessed POSs obtained by NSGA-II ar efined by searching local optimal solutions using the sequential quadratic programming (SQP lgorithm [27]. The SQP is a gradient-based optimization technique based on Newton’s method. Th y g , pp g initially obtained for each objective function using the real-coded fast and elitist NSGA-II which was suggested by Deb [26]. Optimization Techniques 5. Optimization Techniques The overall optimization procedures adopted in this work are described in the flow chart presented in Figure 3. First, design variables and objective functions were selected, and the ranges of the design variables were set up based on a parametric study. cribed in the flow chart presented in Figure 3. First, design variables and objective functions w ected, and the ranges of the design variables were set up based on a parametric study. The design space was filled with the sampling points obtained by the design of experime OE) technique. Values of the objective functions were calculated at the sampling points, a rogate models were constructed based on these calculated values. The Pareto optimal soluti The design space was filled with the sampling points obtained by the design of experiments (DOE) technique. Values of the objective functions were calculated at the sampling points, and surrogate models were constructed based on these calculated values. The Pareto optimal solutions (POSs) were finally obtained using the MOEA. POSs were the objective functions that could not be improved in value without degrading some of the others. OSs) were finally obtained using the MOEA. POSs were the objective functions that could not proved in value without degrading some of the others. Latin hypercube sampling (LHS) [24] was used to select design (sampling) points in the des ce as a DOE technique. LHS uses an m x N matrix where m and N are the number of levels mination and the number of design variables, respectively. Each N column of the ma taining m level rows is randomly paired to form a Latin hypercube Accordingly LHS genera Latin hypercube sampling (LHS) [24] was used to select design (sampling) points in the design space as a DOE technique. LHS uses an m × N matrix where m and N are the number of levels of examination and the number of design variables, respectively. Each N column of the matrix containing m level rows is randomly paired to form a Latin hypercube. Accordingly, LHS generates a group of random sample points and ensures that it effectively fills the entire design space. Figure 4 shows the design points selected by the LHS for two design variables. 6.1. Multi-Objective Optimization of the Impeller To simultaneously improve the total effic t i ll th h b id MOEA l d ith To simultaneously improve the total efficiency and the head of the submersible pump with the swept impeller, the hybrid MOEA coupled with the RSA surrogate model was employed in the multi-objective optimization procedure. wept impeller, the hybrid MOEA coupled with the RSA surrogate model was employed in the mul bjective optimization procedure. Figure 5 presents the definition of the sweep (θ) and pitch (βr) angles of the swept impell h i h l (θ d β ) f h θ d β f h f h l d d i Figure 5 presents the definition of the sweep (θ) and pitch (βr) angles of the swept impeller. Changes in the angles (θc and βc) from the θand βr of the reference shape were selected as two design variables based on the results of the previous study [20] which investigated the effects of the geometric parameters on the hydrodynamic performances of the submersible pump. Figure 5a shows the meridional plane of the swept impeller, and θindicates the angle of inclination in the chord direction between the rotating axis and the line connecting the 25% chord of hub and the shroud of the blade. hanges in the angles (θc and βc) from the θ and βr of the reference shape were selected as two desi ariables based on the results of the previous study [20] which investigated the effects of t eometric parameters on the hydrodynamic performances of the submersible pump. Figure 5a show e meridional plane of the swept impeller, and θ indicates the angle of inclination in the cho rection between the rotating axis and the line connecting the 25% chord of hub and the shroud e blade. Figure 5. Design variables of the swept impeller Kim et al. [20]. Figure 5. Design variables of the swept impeller Kim et al. [20]. Figure 5. Design variables of the swept impeller Kim et al. [20 Figure 5. Design variables of the swept impeller Kim et al. [20]. In the optimization procedure, the setup of the feasible design space formed by ranges of t esign variables is important in predicting the optimum points. In this study, the design space w stablished based on results of a preliminary parametric study [20] and is presented in Table xteen design points were generated within the design space using LHS. Optimization Techniques 5. Optimization Techniques Here, the “real code” means that the crossover and the mutation are achieved in real space to get a response from NSGA-II. These initially guessed POSs obtained by NSGA-II are refined by searching local optimal solutions using the sequential quadratic programming (SQP) algorithm [27]. The SQP is a gradient-based optimization technique based on Newton’s method. The local searching approach proceeds as follows: the first objective function is optimized, and the second objective function is regarded as an equality constraint. This local search is repeated for the second A hybrid MOEA was used to obtain POSs. In this algorithm, the approximate global POSs are initially obtained for each objective function using the real-coded fast and elitist NSGA-II which was suggested by Deb [26]. Here, the “real code” means that the crossover and the mutation are achieved in real space to get a response from NSGA-II. These initially guessed POSs obtained by NSGA-II are refined by searching local optimal solutions using the sequential quadratic programming (SQP) algorithm [27]. The SQP is a gradient-based optimization technique based on Newton’s method. The local searching approach proceeds as follows: the first objective function is optimized, and the 7 of 18 7 of Energies 2020, 13, 3053 ergies 2020, 13, x FOR P second objective function is regarded as an equality constraint. This local search is repeated for the second objective function regarding the first objective function as an equality constraint. The solutions obtained by these procedures are merged with the initial NSGA-II solutions, then, the dominated and duplicated solutions are removed to obtain the improved global POSs. btained by these procedures are merged with the initial NSGA-II solutions, then, the dominated a uplicated solutions are removed to obtain the improved global POSs. Results and Discussion 6.1. Multi-Objective Optimization of the Impeller To simultaneously improve the total effic t i ll th h b id MOEA l d ith And the RANS analy as carried out to evaluate the objective functions at the discrete design points In the optimization procedure, the setup of the feasible design space formed by ranges of the design variables is important in predicting the optimum points. In this study, the design space was established based on results of a preliminary parametric study [20] and is presented in Table 2. Sixteen design points were generated within the design space using LHS. And the RANS analysis was carried out to evaluate the objective functions at the discrete design points. j g p able 2. Ranges of the design variables of the swept impeller. Variables θc, Deg. βc, Deg. Lower bound −8 −4 Table 2. Ranges of the design variables of the swept impeller. Variables θc, Deg. βc, Deg. Lower bound −8 −4 Upper bound +6 +4 bl f h d bl f h ll Table 2. Ranges of the design variables of the swept impeller. Upper bound +6 +4 Regarding the results of the multi-objective optimization, the functional forms of the RSA mod or the two objective functions can be expressed in terms of the design variables normalized betwe Regarding the results of the multi-objective optimization, the functional forms of the RSA model for the two objective functions can be expressed in terms of the design variables normalized between 0 and 1 as shown in the following equations: j p g hown in the following equations: 𝜂= 75.6895 −4.73059𝜃𝑐−0.513506𝛽𝑐+ 1.76209𝜃𝑐𝛽𝑐−1.82734𝜃𝑐 2 −3.25551𝛽𝑐 2 (4 4 93110 + 0 044064𝜃+ 1 05809𝛽+ 0 250351𝜃𝛽+ 0 104467𝜃2 0 600793𝛽2 η = 75.6895 −4.73059θc −0.513506βc + 1.76209θcβc −1.82734θ2 c −3.25551βc2 (4) H = 4.93110 + 0.044064θc + 1.05809βc + 0.250351θcβc + 0.104467θ2 c −0.600793βc2 (5) (4) (4 2 (5) Energies 2020, 13, 3053 8 of 18 Figure 6 shows the global POSs, the reference design, the sixteen design points and the three representative clustered optimum designs (CODs). As objective function values for the total efficiency and the head are to be simultaneously maximized, a trade-offcorrelation was obviously shown between those values. A higher total efficiency was observed at a lower total head, and vice versa. Energies 2020, 13, x FOR PEER REVIEW 8 of 17 shown between those values. A higher total efficiency was observed at a lower total head, and vice versa. 6.1. Multi-Objective Optimization of the Impeller To simultaneously improve the total effic t i ll th h b id MOEA l d ith The values of the design variables and objective functions corresponding to the reference design and the three CODs extracted from the global POSs are listed in Table 3. Both the values of the two design variables of COD 2 are increased as compared with those of the reference design. Additionally, a decrease of θc and an increase of βc are confirmed as compared with those of the reference design and COD 1 and also with COD 3. Meanwhile, enhancement of both the objective functions is observed for all the CODs. The total efficiencies of CODs 1–3 are relatively increased by 7.51%, 2.69%, and 0.01%, respectively, as compared with the reference design. In the case of COD 1, the greatest increase in the total efficiency is observed. The relative increases of 0.19%, 5.97%, and 9.25% in the total head of CODs 1–3 were shown, respectively, as compared with the reference design. It is noticeable that the combination effect between the two design variables of the swept impeller contributes to the enhancement of the objective function values. The objective function values predicted using the hybrid MOEA show less than 1% discrepancies, except for the total efficiency (1.39%) for COD 2 as compared with the results of the RANS analysis. The values of the design variables and objective functions corresponding to the reference design and the three CODs extracted from the global POSs are listed in Table 3. Both the values of the two design variables of COD 2 are increased as compared with those of the reference design. Additionally, a decrease of θc and an increase of βc are confirmed as compared with those of the reference design and COD 1 and also with COD 3. Meanwhile, enhancement of both the objective functions is observed for all the CODs. The total efficiencies of CODs 1–3 are relatively increased by 7.51%, 2.69%, and 0.01%, respectively, as compared with the reference design. In the case of COD 1, the greatest increase in the total efficiency is observed. The relative increases of 0.19%, 5.97%, and 9.25% in the total head of CODs 1–3 were shown, respectively, as compared with the reference design. It is noticeable that the combination effect between the two design variables of the swept impeller contributes to the enhancement of the objective function values. 6.1. Multi-Objective Optimization of the Impeller To simultaneously improve the total effic t i ll th h b id MOEA l d ith The low total pressure in this region is improved as a consequence of the optimization and the improved total pressure presents the reason for the increased efficiency without having loss of the total head. In addition, it is observed that the total pressure distributions (red allow) near the pressure side of the swept impeller are also improved in COD 1. gies 2020, 13, x FOR PEER REVIEW 9 o tribution near the leading edge is improved in COD 1. The low total pressure in this region proved as a consequence of the optimization and the improved total pressure presents the rea the increased efficiency without having loss of the total head. In addition, it is observed that al pressure distributions (red allow) near the pressure side of the swept impeller are also improv COD 1. Figure 7. Total pressure coefficient contours at 50% span of the impeller. Figure 7. Total pressure coefficient contours at 50% span of the impeller. gure 7 Total pressure coefficient contours at 50% span of the impelle Figure 7. Total pressure coefficient contours at 50% span of the impeller. The relative total pressure coefficient (CRT) contours on the meridional plane for the refere COD 1 impellers are presented in Figure 8. The CRT is calculated using the relative total press ead of the total pressure in Equation (6). In both cases, the relative total pressure is dependent radial position because the relative total pressure is associated with the relative velocity W. D 1, the relative total pressure values near 70% span and the leading edge are improved mpared with the reference model. The relative total pressure values of COD 1 are improv ctively by flow redistribution near the shroud where the high relative total pressures occur. Th reased local relative total pressures enhance the total pressure rises by the rotor resulting in The relative total pressure coefficient (CRT) contours on the meridional plane for the reference and COD 1 impellers are presented in Figure 8. The CRT is calculated using the relative total pressure instead of the total pressure in Equation (6). In both cases, the relative total pressure is dependent on the radial position because the relative total pressure is associated with the relative velocity W. For COD 1, the relative total pressure values near 70% span and the leading edge are improved as compared with the reference model. 6.1. Multi-Objective Optimization of the Impeller To simultaneously improve the total effic t i ll th h b id MOEA l d ith The objective function values predicted using the hybrid MOEA show less than 1% discrepancies, except for the total efficiency (1.39%) for COD 2 as compared with the results of the RANS analysis. Figure 6. Results of Pareto optimal solutions (POSs) for the swept impeller. Figure 6. Results of Pareto optimal solutions (POSs) for the swept impeller. Figure 6. Results of Pareto optimal solutions (POSs) for the swept impeller. Figure 6. Results of Pareto optimal solutions (POSs) for the swept impeller. Table 3. Results of the multi-objective optimization of the swept impeller. Table 3. Results of the multi-objective optimization of the swept impeller. Table 3. Results of the multi-objective optimization of the swept impeller. Description Reference Design COD 1 COD 2 COD 3 Design variables θc - −5.87 +3.39 −3.38 βc - +0.31 +3.51 +3.35 Hybrid MOEA η (%) - 75.25 73.04 70.06 H (m) - 5.24 5.52 5.72 RANS analysis η (%) 70.15 75.42 72.04 70.16 H (m) 5.19 5.20 5.50 5.67 Discrepancy (%) η (%) - 0.23 1.39 0.95 H (m) - 0.74 0.44 0.85 Increment (%) η - 7.51 2.69 0.01 H - 0.19 5.97 9.25 Table 3. Results of the multi-objective optimization of the swept impeller. Description Reference Design COD 1 COD 2 COD 3 Design variables θc - −5.87 +3.39 −3.38 βc - +0.31 +3.51 +3.35 Hybrid MOEA η (%) - 75.25 73.04 70.06 H (m) - 5.24 5.52 5.72 RANS analysis η (%) 70.15 75.42 72.04 70.16 H (m) 5.19 5.20 5.50 5.67 Discrepancy (%) η (%) - 0.23 1.39 0.95 H (m) - 0.74 0.44 0.85 Increment (%) η - 7.51 2.69 0.01 H - 0.19 5.97 9.25 Energies 2020, 13, 3053 Energies 2020, 13, 3053 9 of 18 Figure 7 shows the total pressure coefficient (CT) contours at 50% span of the swept impellers for the reference and COD 1. CT is defined as follows: Cr = P −Pin 1 2ρV2 (6) 9 (6) where P is total pressure and Pin is total pressure averaged at the inlet of the computational domain, and V is the tip speed of the rotating impeller. In the reference design, the low total pressure region (red dashed circle) is widely distributed near the leading edge of the impeller. This total pressure distribution near the leading edge is improved in COD 1. 6.1. Multi-Objective Optimization of the Impeller To simultaneously improve the total effic t i ll th h b id MOEA l d ith Relative total pressure coefficient contours on the meridional plane of the impeller. 020, 13, x FOR PEER REVIEW ws that this vortex generation in the diffuser passages is suppressed by the ation of the impeller. It is noticeable that the improvement in the hydrodynamic perfo ubmersible pump is caused by this suppression of the vortex generation in the s. (a) Reference impeller (b) COD 1 Figure 8. Relative total pressure coefficient contours on the meridional plane of the impeller. igure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impellers Figure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impellers. Table 4. Rotor performances of optimum swept impellers. Description RANS Analysis Increment (%) η (%) H (m) η (%) H (m) Reference design 85.83 6.36 - - COD 1 86.56 6.41 0.84 0.87 COD 2 86.01 6.50 0.21 2.25 COD 3 83.46 6.78 −2.76 6.72 es 2020, 13, x FOR PEER REVIEW shows that this vortex generation in the diffuser passages is suppressed by the mization of the impeller. It is noticeable that the improvement in the hydrodynamic perf e submersible pump is caused by this suppression of the vortex generation in the ages. (a) Reference impeller (b) COD 1 Figure 8. Relative total pressure coefficient contours on the meridional plane of the impeller. Figure 8. Relative total pressure coefficient contours on the meridional plane of the impeller. es 2020, 13, x FOR PEER REVIEW shows that this vortex generation in the diffuser passages is suppressed by the mization of the impeller. It is noticeable that the improvement in the hydrodynamic perf e submersible pump is caused by this suppression of the vortex generation in the ages. (a) Reference impeller (b) COD 1 Figure 8. Relative total pressure coefficient contours on the meridional plane of the impeller. Table 4. Rotor performances of optimum swept impellers. (a) Reference impeller (a) Reference impeller igure 8. Relative total pressure coefficient contours on the meridional plane of the impe Figure 8. Relative total pressure coefficient contours on the meridional plane of the impelle igure 8. Relative total pressure coefficient contours on the meridional plane of the impe ive total pressure coefficient contours on the meridional plane of the impelle lative total pressure coefficient contours on the meridional plane of the impeller. 6.1. Multi-Objective Optimization of the Impeller To simultaneously improve the total effic t i ll th h b id MOEA l d ith The relative total pressure values of COD 1 are improved effectively by flow redistribution near the shroud where the high relative total pressures occur. These increased local relative total pressures enhance the total pressure rises by the rotor, resulting in the high head rise of COD 1 (Table 4). reased local relative total pressures enhance the total pressure rises by the rotor, resulting in h head rise of COD 1 (Table 4). Table 4. Rotor performances of optimum swept impellers. Description RANS Analysis Increment (%) Figure 9 shows the comparison of the incidence angles of the diffuser for the reference and COD 1 impellers. In both cases, high incidence angles of about 25◦occur near the diffuser shroud. The diffuser of the submersible pump with the COD 1 impeller has the incidence angles of less than 8◦below 75% span. However, the diffuser with the reference impeller has higher incidence angles than those with the COD 1, and shows a very high incidence angle of around 49◦near the hub. This incidence angle 10 of 18 Energies 2020, 13, 3053 leads to generate a large vortex in the diffuser passage as shown in Figure 10a; Figure 10b shows that this vortex generation in the diffuser passages is suppressed by the design optimization of the impeller. It is noticeable that the improvement in the hydrodynamic performance of the submersible pump is caused by this suppression of the vortex generation in the diffuser passages. g p g pp y g p oticeable that the improvement in the hydrodynamic performance of the submersible pu d by this suppression of the vortex generation in the diffuser passages. Table 4. Rotor performances of optimum swept impellers. Description RANS Analysis Increment (%) η (%) H (m) η (%) H (m) Reference design 85.83 6.36 - - COD 1 86.56 6.41 0.84 0.87 COD 2 86.01 6.50 0.21 2.25 COD 3 83.46 6.78 −2.76 6.72 020, 13, x FOR PEER REVIEW ws that this vortex generation in the diffuser passages is suppressed by the ation of the impeller. It is noticeable that the improvement in the hydrodynamic perfo ubmersible pump is caused by this suppression of the vortex generation in the s. (a) Reference impeller (b) COD 1 Figure 8. Relative total pressure coefficient contours on the meridional plane of the impeller. igure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impellers Figure 8. 6.2. Multi-Objective Optimization of the Diffuser 6 2 Multi-objective Optimization of the Diffuser The inlet angle (βs1) and the length (Ls) of the diffuser of the submersible axial-flow pump are defined as shown in Figure 11. In the second-stage optimization, change in the angle (βc1) from the inlet angle of the reference diffuser and change in the length (Lc = Ls/Lsref) normalized with that of the reference diffuser are optimized to simultaneously maximize the total efficiency and the head of the submersible axial-flow pump with the COD 1 impeller. When the length of the diffuser is changed, the blade angle is not changed at the normalized position of the diffuser. j p f ff The inlet angle (βs1) and the length (Ls) of the diffuser of the submersible axial-flow pump are defined as shown in Figure 11. In the second-stage optimization, change in the angle (βc1) from the inlet angle of the reference diffuser and change in the length (Lc = Ls/Lsref) normalized with that of the reference diffuser are optimized to simultaneously maximize the total efficiency and the head of the submersible axial-flow pump with the COD 1 impeller. When the length of the diffuser is changed, the blade angle is not changed at the normalized position of the diffuser Figure 11. Inlet angle (βs1) and length (Ls) of the diffuser of the submersible axial-flow pump. Figure 11. Inlet angle (βs1) and length (Ls) of the diffuser of the submersible axial-flow pump. Figure 11. Inlet angle (βs1) and length (Ls) of the diffuser of the submersible axial-flow pump. Figure 11. Inlet angle (βs1) and length (Ls) of the diffuser of the submersible axial-flow pump. On the basis of the results of the parametric study from the previous study by Heo et al. [28]], the range of design variables were determined, as shown in Table 5. The sixteen design points were extracted within the range of the design variables through the LHS, as shown in Figure 4. Then, the objective function values were evaluated at the design points by solving the RANS equations. On the basis of the results of the parametric study from the previous study by Heo et al. [28], the range of design variables were determined, as shown in Table 5. The sixteen design points were extracted within the range of the design variables through the LHS, as shown in Figure 4. Then, the objective function values were evaluated at the design points by solving the RANS equations. Table 5. 6.1. Multi-Objective Optimization of the Impeller To simultaneously improve the total effic t i ll th h b id MOEA l d ith ive total pressure coefficient contours on the meridional plane of the impelle Figure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impeller igure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impeller Figure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impellers. igure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impeller igure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impeller Figure 9. Comparison of incidence angles of the diffuser for the reference and COD 1 impellers. 11 of 18 Energies 2020, 13, 3053 i C (a) Reference impeller (b) COD 1 Figure 10. Streamlines in the passage of the diffuser. Figure 10. Streamlines in the passage of the diffuser. ies 2020, 13, x FOR PEER REVIEW (a) Reference impeller (b) COD 1 Figure 10. Streamlines in the passage of the diffuser. Figure 10. Streamlines in the passage of the diffuser. EVIEW 6.2. Multi-Objective Optimization of the Diffuser 6.2. Multi-objective Optimization of the Diffuser 6.2. Multi-Objective Optimization of the Diffuser 6 2 Multi-objective Optimization of the Diffuser Ranges of the design variables for the diffuser. Variables βc1, Deg. Lc( =Ls/Lsref) Lower bound −9 0.9 Upper bound 20 1 3 Table 5. Ranges of the design variables for the diffuser. Variables βc1, Deg. Lc (=Ls/Lsref) Lower bound −9 0.9 Upper bound 20 1.3 Table 5. Ranges of the design variables for the diffuser Table 5. Ranges of the design variables for the diffuser. Energies 2020, 13, 3053 12 of 18 The following expressions in terms of the normalized design variables are the functional forms for the RSA model. The following expressions in terms of the normalized design variables are the functional forms for the RSA model. η = 77.7222 −1.21262βc1 + 0.480914Lc + 2.49158βc1Lc −0.339219β2 c1 −0.875502Lc2 (7) H = 5.41609 −0.348995βc1 −0.133129Lc + 0.216645βc1Lc + 0.141180β2 c1 + 0.0628439Lc2 (8) (7) (8) Figure 12 presents the global POSs, COD 1, the sixteen design points, and the three CODs, viz., COD 4, COD 5, and COD 6. The values of design variables and objective functions with respect to these reference design, COD 1 and CODs 4–6, are listed in Table 6. COD 5 and COD 6 have decreased βc1s as compared with the reference design, while the βc1 of COD 4 increased. CODs 4–6 show larger values of Ls than that of the reference design. CODs 4–6 show superior results to the COD 1 for both the objectives. In addition, CODs 4–6 show improved total efficiencies as much as 1.30%, 0.77%, and 1.52%, and 2.88%, 3.08%, and 4.42% increases in the total head, respectively. Consequently, the highest values of both the objective functions are observed from COD 6 which shows the smallest discrepancies between the predicted objective function values and the corresponding values of the RANS analysis among the CODs 4–6. Therefore, COD 6 is selected as the final optimum design. rgies 2020, 13, x FOR PEER REVIEW 12 o Figure 12. Results of POSs for the diffuser. Figure 12. Results of POSs for the diffuser. igure 12 Results of POSs for the diffuser Figure 12. Results of POSs for the diffuser. bl 6 R lt f th lti bj ti ti i ti f th diff Table 6. Results of the multi-objective optimization of the diffuser. Table 6. Results of the multi-objective optimization of the diffuser. (compared to COD 1) (%) H - - 2.88 3.08 4.42 Figure 13 presents the total pressure coefficient contours at 50% span of the impeller and fuser for the reference design, COD 1, and COD 6. In the case of the reference design, the low t ssure region is widely spread in the passages of the diffuser. These regions are improved throu multi-objective optimization of the swept impeller, as shown in Figure 13b. It is noticeable flow downstream of the impeller affects the flow field of the diffuser and the flow passage of Figure 13 presents the total pressure coefficient contours at 50% span of the impeller and the diffuser for the reference design, COD 1, and COD 6. In the case of the reference design, the low total pressure region is widely spread in the passages of the diffuser. These regions are improved through the multi-objective optimization of the swept impeller, as shown in Figure 13b. It is noticeable that the flow downstream of the impeller affects the flow field of the diffuser, and the flow passage of the diffuser is also improved through the design optimization. COD 6 shows further improvement of the 6.2. Multi-Objective Optimization of the Diffuser 6 2 Multi-objective Optimization of the Diffuser Description Reference Design COD 1 COD 4 COD 5 COD Design variables βc1 - - +3.00 −2.96 −8.7 Lc - - +1.14 +1.14 +1.1 Hybrid MOEA η (%) - 75.25 77.41 77.22 76.8 H (m) - 5.24 5.36 5.39 5.43 RANS analysis η (%) 70.15 75.42 76.40 76.00 76.5 H (m) 5.19 5.20 5.35 5.36 5.43 Discrepancy (%) η (%) - - 1.33 1.61 0.35 H (m) - - 0.11 0.57 0.11 Increment η 1 30 0 77 1 52 j p Description Reference Design COD 1 COD 4 COD 5 COD 6 Design variables βc1 - - +3.00 −2.96 −8.70 Lc - - +1.14 +1.14 +1.13 Hybrid MOEA η (%) - 75.25 77.41 77.22 76.84 H (m) - 5.24 5.36 5.39 5.43 RANS analysis η (%) 70.15 75.42 76.40 76.00 76.57 H (m) 5.19 5.20 5.35 5.36 5.43 Discrepancy (%) η (%) - - 1.33 1.61 0.35 H (m) - - 0.11 0.57 0.11 Increment (compared to COD 1) (%) η - - 1.30 0.77 1.52 H - - 2.88 3.08 4.42 (compared to COD 1) (%) H - - 2.88 3.08 4.42 Figure 13 presents the total pressure coefficient contours at 50% span of the impeller and fuser for the reference design, COD 1, and COD 6. In the case of the reference design, the low t ssure region is widely spread in the passages of the diffuser. These regions are improved throu multi-objective optimization of the swept impeller, as shown in Figure 13b. It is noticeable t flow downstream of the impeller affects the flow field of the diffuser and the flow passage of Figure 13 presents the total pressure coefficient contours at 50% span of the impeller and the diffuser for the reference design, COD 1, and COD 6. In the case of the reference design, the low total pressure region is widely spread in the passages of the diffuser. These regions are improved through the multi-objective optimization of the swept impeller, as shown in Figure 13b. It is noticeable that the flow downstream of the impeller affects the flow field of the diffuser, and the flow passage of the diffuser is also improved through the design optimization. 6.2. Multi-Objective Optimization of the Diffuser 6 2 Multi-objective Optimization of the Diffuser COD 6 shows further improvement of the (compared to COD 1) (%) H - - 2.88 3.08 4.42 Figure 13 presents the total pressure coefficient contours at 50% span of the impeller and fuser for the reference design, COD 1, and COD 6. In the case of the reference design, the low t ssure region is widely spread in the passages of the diffuser. These regions are improved throu multi-objective optimization of the swept impeller, as shown in Figure 13b. It is noticeable fl d t f th i ll ff t th fl fi ld f th diff d th fl f Figure 13 presents the total pressure coefficient contours at 50% span of the impeller and the diffuser for the reference design, COD 1, and COD 6. In the case of the reference design, the low total pressure region is widely spread in the passages of the diffuser. These regions are improved through the multi-objective optimization of the swept impeller, as shown in Figure 13b. It is noticeable that the flow downstream of the impeller affects the flow field of the diffuser, and the flow passage of the diffuser is also improved through the design optimization. COD 6 shows further improvement of the Energies 2020, 13, 3053 13 of 18 13 of 18 total pressure in the passage of the diffuser. However, the high total pressure region observed near the trailing edge of the diffuser is slightly diminished for COD 6. total pressure in the passage of the diffuser. However, the high total pressure region observed near the trailing edge of the diffuser is slightly diminished for COD 6. The pressure coefficient contours at 50% span of the diffuser for the reference design, COD 1 and COD 6, are presented in Figure 14. The pressure coefficient is defined by using the static pressure instead of the total pressure in Equation (6). For the reference design, the pressure is increased along the pressure surface of the diffuser vanes and decreased from the 80% chord of the diffuser vanes. This decreasing pressure is improved for COD 1 as a result of optimization of the swept impeller. In addition, through the design optimization of the diffuser, the pressure distribution in the passages of the diffuser gradually increases from the leading edge to the trailing edge of the diffuser vane for COD 6. 6.2. Multi-Objective Optimization of the Diffuser 6 2 Multi-objective Optimization of the Diffuser Figure 15 presents the comparison between the velocity distributions of CODs 1 and 6 at 50% span of the diffuser vane. The velocity is normalized by the velocity averaged at the inlet of each diffuser. The velocity distributions of COD 6 show generally larger values than those of COD 1. The velocities along the suction side of the diffuser vane of COD 6 decrease drastically from 40% normalized length, and have lower values than those of COD 1 from 65% normalized length. However, near the trailing edge of the diffuser, the normalized velocity of COD 6 becomes similar to that of COD 1. This decrease in the velocity for COD 6 is due to the recovery of the static pressure. The sufficient recovery of the static pressure in COD 6 results in higher total pressure than that in COD 1. On the pressure side of COD 6, the velocity remains nearly constant as the velocity averaged at the inlet. Energies 2020, 13, x FOR PEER REVIEW 13 of 17 Energies 2020 13 x FOR PEER REVIEW 13 of 17 Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 14. Static pressure coefficient contours at 50% span of the diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. g Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 14. Static pressure coefficient contours at 50% span of the diffuser. Figure 14. Static pressure coefficient contours at 50% span of the diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 13. Total pressure coefficient contours at 50% span of the impeller and diffuser. Figure 14. Static pressure coefficient contours at 50% span of the diffuser. 6.2. Multi-Objective Optimization of the Diffuser 6 2 Multi-objective Optimization of the Diffuser g p p p Figure 14. Static pressure coefficient contours at 50% span of the diffuser. Figure 14. Static pressure coefficient contours at 50% span of the diffuser. gure 14. Static pressure coefficient contours at 50% span of the diffuse gure 14. Static pressure coefficient contours at 50% span of the diffuse Figure 14. Static pressure coefficient contours at 50% span of the diffuser. 14 of 18 Energies 2020, 13, 3053 Fi Figure 15. Velocity distributions at 50% span of the diffuser vane. Figure 15. Velocity distributions at 50% span of the diffuser vane. Energies 2020, 13, x FOR PEER REVIEW 6.3. Performance Test Figure 15. Velocity distributions at 50% span of the diffuser vane. Figure 15. Velocity distributions at 50% span of the diffuser vane. Test In order to analyze the three-dimensional flow structure near the diffuser, the absolute helicity contours on the isosurface of the vorticity of 22 s−1 are compared among the reference, COD 1, and COD 6, as shown in Figure 16. In the case of the reference diffuser, the vorticity increases along the streamwise direction, as shown in Figure 16a. Although CODs 1 and 6 have these vorticity regions at the inlet, they decrease as the flow proceeds. In particular, COD 6 has a relatively small vorticity region at the inlet of the diffuser. These phenomena can explain the total pressure contours, also shown in Figure 13 In order to analyze the three-dimensional flow structure near the diffuser, the absolute helicity contours on the isosurface of the vorticity of 22 s−1 are compared among the reference, COD 1, and COD 6, as shown in Figure 16. In the case of the reference diffuser, the vorticity increases along the streamwise direction, as shown in Figure 16a. Although CODs 1 and 6 have these vorticity regions at the inlet, they decrease as the flow proceeds. In particular, COD 6 has a relatively small vorticity region at the inlet of the diffuser. These phenomena can explain the total pressure contours, also shown in Figure 13. The performance test for the submersible axial-flow pump with the swept impeller and the diffuser of COD 6 was performed to verify the validity of the present multi-objective optimization results. Figure 17 shows the experimental apparatus (left picture) schematized in Figure 2 and the optimum axial-flow pump (right picture) based on COD 6. 6.3. Performance Test The performance test for the submersible axial-flow pump with the swept impeller and the diffuser of COD 6 was performed to verify the validity of the present multi-objective optimization results. Figure 17 shows the experimental apparatus (left picture) schematized in Figure 2 and the optimum axial-flow pump (right picture) based on COD 6. (c) COD 6 The results of the performance test and the comparison with the RANS analysis are presented in Figure 18 and Table 7. The RANS analysis predicted the higher efficiency and the lower head as much as 3.46% and 0.69 m as compared with the experiment, respectively, at the design point. Figure 16. Absolute helicity contours on the vorticity region of 22 s−1 in the diffuser domain. igure 17. Experimental apparatus (left) and submersible axial-flow pump (right Figure 17. Experimental apparatus (left) and submersible axial-flow pump (right). 13, x FOR PEER REVIEW ure 17. Experimental apparatus (left) and submersible axial-flow pump (right Figure 17. Experimental apparatus (left) and submersible axial-flow pump (right). , x FOR PEER REVIEW gure 17. Experimental apparatus (left) and submersible axial-flow pump (right) Figure 17. Experimental apparatus (left) and submersible axial-flow pump (right). 13, x FOR PEER REVIEW Figure 18. Comparison between the results of the experiment and RANS analysis for COD 6. Figure 18. Comparison between the results of the experiment and RANS analysis for COD 6. Figure 18. Comparison between the results of the experiment and RANS analysis for COD 6. Figure 18. Comparison between the results of the experiment and RANS analysis for COD 6. Table 7. Results of the performance test at the design point. Objective Functions Exp. RANS Discrepancy η (%) 73.11 76.57 3.46 H (m) 6.12 5.43 0.69 Table 7. Results of the performance test at the design point. Objective Functions Exp. RANS Discrepancy η (%) 73.11 76.57 3.46 H (m) 6.12 5.43 0.69 Table 7. Results of the performance test at the design point. Table 7. Results of the performance test at the design point. 6.2. Multi-Objective Optimization of the Diffuser 6 2 Multi-objective Optimization of the Diffuser The results of the performance test and the comparison with the RANS analysis are presented in Figure 18 and Table 7. The RANS analysis predicted the higher efficiency and the lower head as much as 3.46% and 0.69 m as compared with the experiment, respectively, at the design point. (a) Reference diffuser (b) COD 1 (c) COD 6 Figure 16. Absolute helicity contours on the vorticity region of 22 s−1 in the diffuser domain. Figure 16. Absolute helicity contours on the vorticity region of 22 s−1 in the diffuser domain. (b) COD 1 (b) COD 1 (a) Reference diffuser (a) Reference diffuser Figure 16. Absolute helicity contours on the vorticity region of 22 s−1 in the diffuser domain. Figure 16. Absolute helicity contours on the vorticity region of 22 s−1 in the diffuser domain. Energies 2020, 13, 3053 15 of 18 15 of 18 7. Conclusions 7. Conclusions A submersible axial-flow pump with a swept impeller was optimized to simultaneously improve the total efficiency and the head, which were considered as two objective functions. A submersible axial-flow pump with a swept impeller was optimized to simultaneously improve the total efficiency and the head, which were considered as two objective functions. p y , j Two stage optimizations were carried out sequentially through a hybrid MOEA coupled with a RSA model. The first multi-objective optimization was performed to simultaneously improve two b f h d bl h d h l f h ll Two stage optimizations were carried out sequentially through a hybrid MOEA coupled with a RSA model. The first multi-objective optimization was performed to simultaneously improve two 16 of 18 16 of 18 Energies 2020, 13, 3053 objective functions with two design variables, i.e., the sweep and pitch angles of the swept impeller. The first optimization of the swept impeller achieved 7.51% and 0.19% increases in the total efficiency and the head, respectively, as compared with the reference design. Although the shape of the rotor was designed through the first design optimization, it was confirmed that the design of the rotor resulted in an improvement of the diffuser’s performance rather than the performance of the rotor by changing the shape of the rotor. Consequently, the overall performance of the pump was improved. Then, the second multi-objective optimization was carried out to simultaneously improve the total efficiency and the head using the COD 1 impeller obtained from the first optimization. The inlet angle and the length of the diffuser vane were considered as two design variables. The final selected optimum pump design (COD 6) showed improvements of 9.03% and 4.61% in the total efficiency and the head, respectively, as compared with the reference design. In the second design optimization process, the design improved the static pressure recovery through the shape design of the diffuser. As a result, the total head and total efficiency increased in the optimum design. y p g The results of the RANS analysis for COD 6 with the optimum swept impeller and diffuser designs obtained from the present optimizations were validated against the performance test results performed in this work. 7. Conclusions 7. Conclusions The numerical results showed reasonable agreements with the experimental data throughout the whole range of the flow coefficient with relative discrepancies of 3.46% and 0.69 m for the total efficiency and the head, respectively, at the design point. Author Contributions: Y.-S.K. presented the main idea of the swept impeller of submersible axial flow pump; Y.-S.K. and M.-W.H. contributed to the overall composition and writing of the manuscript; M.-W.H. and D.-H.K. analyzed the proposed swept impeller and performed numerical analysis; H.-S.S. and B.-S.L. performed experiments and analyzed the data; K.-Y.K. revised and finalized the manuscript. All authors have read and agreed to the published version of the manuscript. Funding: The research was supported by a grant (no. S2765307) from the Korea Technology and Information Promotion Agency (TIPA) that is funded by the Ministry of SMEs and Startups (MSS) and a grant (17IFIP-B089065-04) from the Industrial Facilities & Infrastructure Research Program (IFIP) funded by the Ministry of Land, Infrastructure and Transport of the Korean government. The authors gratefully acknowledge this support. Conflicts of Interest: The authors declare there is no conflict of interest. nterest: The authors declare there is no conflict of inter Nomenclature CODs Clustered optimum solutions H Acceleration by gravity g Total head Lc Length normalized with Ls of reference Ls Length of diffuser vane P Total pressure Pin Total pressure at the inlet POSs Pareto optimum solutions Q Fluid flow rate R Rotational speed of impeller T Torque βc Angle changed from βr of reference βc1 Angle changed from βs1 of reference βs1 Inlet angle of diffuser vane βr Pitch angle of impeller η Total efficiency θ Sweep angle of impeller θc Angle changed from θ of reference ρ Density ϕ Flow coefficient ψ Head coefficient k Coverage factor V Rotating tip speed of the rotor 17 of 18 Energies 2020, 13, 3053 17 of 18 References Numerical investigation of the flow in a multistage electric submersible pump. J. Pet. Sci. Eng. 2015, 136, 41–54. [CrossRef] . Chaudhari, S.C.; Yadav, C.O.; Damor, A.B. 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Indigenous Development of a Submersible Axial Flow Pump (45kW Class) With a Self-Cleaning Backswept Impeller; Korea Technology and Information Promotion Agency: Daejeon, Korea, 2018; No. S2522342. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). 26. Deb, K. Multi-Objective Optimization Using Evolutionary Algorithms, 1st ed.; John Wiley & Sons Inc.: Chichester, UK, 2001. 26. Deb, K. Multi-Objective Optimization Using Evolutionary Algorithms, 1st ed.; John Wiley & Sons Inc.: Chichester, UK, 2001. 27. MATLAB. The Language of Technical Computing; Release 14; Math Work Inc.: Natick, MA, USA, 2004. 28. FLUXYS Pump Company. Indigenous Development of a Submersible Axial Flow Pump (45kW Class) With a Self-Cleaning Backswept Impeller; Korea Technology and Information Promotion Agency: Daejeon, Korea, 2018; No. S2522342. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access 27. MATLAB. The Language of Technical Computing; Release 14; Math Work Inc.: Natick, MA, USA, 2004 28. FLUXYS Pump Company. Indigenous Development of a Submersible Axial Flow Pump (45kW Class) With a Self-Cleaning Backswept Impeller; Korea Technology and Information Promotion Agency: Daejeon, Korea, 2018; No. S2522342. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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<i>Treponema denticola</i>dentilisin triggered TLR2/MyD88 activation upregulates a tissue destructive program involving MMPs via Sp1 in human oral cells
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Permalink https://escholarship.org/uc/item/1dx785v1 ISSN 1553-7366 Authors Ganther, Sean Radaic, Allan Malone, Erin et al. Publication Date 2021 DOI 10.1371/journal.ppat.1009311 Peer reviewed Title Treponema denticola dentilisin triggered TLR2/MyD88 activation upregulates a tissue destructive program involving MMPs via Sp1 in human oral cells UC San Francisco Previously Published Works UC San Francisco Previously Published Works Powered by the California Digital Library University of California eScholarship.org Treponema denticola dentilisin triggered TLR2/MyD88 activation upregulates a tissue destructive program involving MMPs via Sp1 in human oral cells Sean GantherID1, Allan RadaicID1, Erin MaloneID1, Pachiyappan Kamarajan1, Nai-Yuan Nicholas Chang1, Christian Tafolla1, Ling Zhan1, J. Christopher FennoID2, Yvonne L. KapilaID1* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, United States of America, 2 Department of Biological and Material Sciences & Prosthodontics, School of Dentistry, University of Michigan, Ann Arbor, Michigan, United States of America * Yvonne.Kapila@ucsf.edu * Yvonne.Kapila@ucsf.edu OPEN ACCESS Periodontal disease is driven by dysbiosis in the oral microbiome, resulting in over-repre- sentation of species that induce the release of pro-inflammatory cytokines, chemokines, and tissue-remodeling matrix metalloproteinases (MMPs) in the periodontium. These chronic tissue-destructive inflammatory responses result in gradual loss of tooth-support- ing alveolar bone. The oral spirochete Treponema denticola, is consistently found at sig- nificantly elevated levels in periodontal lesions. Host-expressed Toll-Like Receptor 2 (TLR2) senses a variety of bacterial ligands, including acylated lipopolysaccharides and lipoproteins. T. denticola dentilisin, a surface-expressed protease complex comprised of three lipoproteins has been implicated as a virulence factor in periodontal disease, pri- marily due to its proteolytic activity. While the role of acylated bacterial components in induction of inflammation is well-studied, little attention has been given to the potential role of the acylated nature of dentilisin. The purpose of this study was to test the hypothe- sis that T. denticola dentilisin activates a TLR2-dependent mechanism, leading to upregu- lation of tissue-destructive genes in periodontal tissue. RNA-sequencing of periodontal ligament cells challenged with T. denticola bacteria revealed significant upregulation of genes associated with extracellular matrix organization and degradation including poten- tially tissue-specific inducible MMPs that may play novel roles in modulating host immune responses that have yet to be characterized within the context of oral disease. The Gram- negative oral commensal, Veillonella parvula, failed to upregulate these same MMPs. Dentilisin-induced upregulation of MMPs was mediated via TLR2 and MyD88 activation, since knockdown of expression of either abrogated these effects. Challenge with purified dentilisin upregulated the same MMPs while a dentilisin-deficient T. denticola mutant had no effect. Finally, T. denticola-mediated activation of TLR2/MyD88 lead to the nuclear translocation of the transcription factor Sp1, which was shown to be a critical regulator of all T. denticola-dependent MMP expression. Taken together, these data suggest that Citation: Ganther S, Radaic A, Malone E, Kamarajan P, Chang N-YN, Tafolla C, et al. (2021) Treponema denticola dentilisin triggered TLR2/MyD88 activation upregulates a tissue destructive program involving MMPs via Sp1 in human oral cells. PLoS Pathog 17(7): e1009311. https://doi.org/10.1371/journal.ppat.1009311 Editor: D. Scott Samuels, University of Montana, UNITED STATES Author summary Periodontal disease is driven by dysbiosis of the oral microbiome, which interacts with host tissues and thereby induces the release of pro-inflammatory cytokines, chemokines, and tissue-remodeling matrix metalloproteinases (MMPs), leading to destruction of the periodontal tissues. Even after clinical intervention, patients with severe periodontal dis- ease are left with a persistent pro-inflammatory transcriptional profile throughout the per- iodontium. The oral spirochete, Treponema denticola is consistently found at elevated levels in periodontal lesions and is associated with several pathophysiological effects driv- ing periodontal disease progression. The T. denticola surface-expressed protease complex (dentilisin) has cytopathic effects consistent with periodontal disease pathogenesis. To date, few direct links have been reported between dentilisin and the cellular and tissue processes that drive periodontal tissue destruction at the transcriptional and/or epigenetic levels. Here, we utilize wild type and dentilisin-deficient T. denticola as well as purified dentilisin to characterize dentilisin-dependent activation of intracellular pathways con- trolling MMP expression and activity. Our results define a role for dentilisin in initiating this signal cascade. Also, our study identified tissue-specific inducible MMPs that may play novel roles in modulating as-yet uncharacterized host responses in periodontal dis- ease. Lastly, T. denticola dentilisin stimulates tissue-destructive cellular processes in a TLR2/MyD88/Sp1-dependent fashion. Taken together, our study provides new insights into the molecular mechanisms underpinning periodontal disease progression which could lead to the development of more efficacious therapeutic treatments. Competing interests: The authors have declared that no competing interests exist. Editor: D. Scott Samuels, University of Montana, UNITED STATES Kirschstein National Research Service Award (NRSA) Institutional Research Training Grant (T32DE007306) to SG (https://www.nih.gov/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Editor: D. Scott Samuels, University of Montana, UNITED STATES Received: January 13, 2021 Accepted: May 26, 2021 Published: July 13, 2021 Copyright: © 2021 Ganther et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: January 13, 2021 Accepted: May 26, 2021 Published: July 13, 2021 Copyright: © 2021 Ganther et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: © 2021 Ganther et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: The data underlying the results presented in the study are available from (https://figshare.com/collections/T_denticola_ dentilisin_triggered_TLR2_MyD88_activation_ upregulates_a_tissue_destructive_program_ involving_MMPs_via_Sp1_in_human_oral_cells/ 5262821). Dentilisin-induced upregulation of MMPs was mediated via TLR2 and MyD88 activation, since knockdown of expression of either abrogated these effects. Challenge with purified dentilisin upregulated the same MMPs while a dentilisin-deficient T. denticola mutant had no effect. Finally, T. denticola-mediated activation of TLR2/MyD88 lead to the nuclear translocation of the transcription factor Sp1, which was shown to be a critical regulator of all T. denticola-dependent MMP expression. Taken together, these data suggest that dentilisin_triggered_TLR2_MyD88_activation_ upregulates_a_tissue_destructive_program_ involving_MMPs_via_Sp1_in_human_oral_cells/ 5262821). Funding: This work was supported by funding from Research Project Grant funding from the NIH (R01 DE025225) to YLK and JCF (https://www.nih. 1 / 29 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells T. denticola dentilisin stimulates tissue-destructive cellular processes in a TLR2/MyD88/ Sp1-dependent fashion. T. denticola dentilisin stimulates tissue-destructive cellular processes in a TLR2/MyD88/ Sp1-dependent fashion. gov/); Ruth L. Kirschstein Individual Predoctoral NRSA for MD/PhD and other Dual Degree Fellowships (F30 DE027598) to EM (https://www. nih.gov/), and the Ruth L. Kirschstein National Research Service Award (NRSA) Institutional Research Training Grant (T32DE007306) to SG (https://www.nih.gov/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. gov/); Ruth L. Kirschstein Individual Predoctoral NRSA for MD/PhD and other Dual Degree Fellowships (F30 DE027598) to EM (https://www. nih.gov/), and the Ruth L. Introduction Periodontitis or Periodontal Disease is characterized as a chronic oral inflammatory disease that compromises the integrity of the tooth-supporting tissues, which include the gingiva, peri- odontal ligament and alveolar bone, and are collectively known as the periodontium. In its severe form, which afflicts 8.5% of adults in the United States [1], periodontitis may cause tooth loss, and also affect systemic health by increasing the patients’ risk for atherosclerosis, adverse pregnancy outcomes, rheumatoid arthritis, aspiration pneumonia and cancer [2–5]. Additionally, patients with chronic forms of periodontal disease are left with a non-resolving pro-inflammatory transcriptional profile throughout the periodontium, even after clinical intervention, leading to tissue-destruction and tooth loss [6–8]. This suggests that previously uncharacterized cellular and molecular mechanisms underlying periodontal disease patho- physiology may explain why many patients do not respond to the conventional treatment schema. The periodontal ligament (PDL) has two primary functions: 1) to absorb and respond to mechanical stresses, and 2) to provide vascular supply and nutrients to the cementum, alveolar bone and the PDL itself. Osteoblasts, osteoclasts, cementoblasts and endothelial cells make up the PDL and reside on the surface of the lamina dura and endosteal surfaces of the alveolar bone and cementum [9,10]. The most prominent cell type are human periodontal ligament fibroblasts (hPDL), which specialize in mechanosensing and tissue remodeling through robust expression of various hydrolytic enzymes such as matrix metalloproteinases (MMPs)[10,11]. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 2 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells They also function as immune-like cells demarcated by the production of inflammatory cyto- kines, chemokines and expression of pattern recognition receptors (PRRs), such as toll-like receptors (TLRs), which are responsible for monitoring the local environment for signs of dan- ger in the form of highly conserved microbial molecules present during periodontal disease [12–15]. When TLR signaling is left unchecked, downstream genes, such as MMPs can become significantly upregulated and constitutively activated, thereby contributing to the overall destruction of the periodontium by degrading extracellular matrix (ECM) proteins, such as collagen and fibronectin [11,16–20]. Although the role of MMPs has been primarily ascribed to turnover of the ECM, the great number of new substrates discovered for MMPs in the last few years suggest they are capable of regulating many signaling pathways, cell behaviors and diseases through novel mechanisms [21]. Introduction Therefore, PDL cells likely play a significant role in initiating and exacerbating tissue degradation and suggest that pharmacological anti-inflam- matory treatment of periodontal disease should target dysregulated MMP activity and levels in the PDL tissues. The pathogenic processes of periodontal disease are primarily due to the host response, which propagates the destructive responses initiated by microbes [22–24]. While a large focus has been placed on species such as Porphyromonas gingivalis, Fusbacterium nucleatum, and Aggrigatibacter actinomycetemcomitans, recent metagenomic and metatranscriptomic studies have implicated the Gram negative-oral spirochete, T. denticola with advanced or aggressive forms of periodontal dis- ease and recurrence of disease [25–40]. Interactions between bacteria, viruses and host cells have been associated with shifts from health to disease in oral tissues as well [41–44]. Greatly increased numbers of T. denticola levels in periodontal disease vs health has been well-documented in the literature for >40 years [45]. Our lab has readily demonstrated that T. denticola was ~15-fold higher in the subgingival biofilm of periodontal lesions [46]. Addition- ally, elevated T. denticola biofilm levels combined with elevated MMP levels in host tissues dis- play robust combinatorial characteristics in predicting advanced periodontal disease severity [46,47]. Further, Lee et al. and colleagues demonstrated that T. denticola infection was suffi- cient to induce alveolar bone resorption in a mouse model of periodontal disease [48]. Thus, clinical data regarding the increased presence of T. denticola in periodontal lesions, together with basic and in vivo studies involving the role of T. denticola products suggest that it plays a pivotal role in driving periodontal disease progression. Among the various T. denticola effector molecules that have been described, its acylated chymotrypsin-like protease complex (CTLP), more recently called dentilisin, is a major viru- lence factor which facilitates numerous cytopathic effects that align with periodontal disease pathophysiology [30,49,50]. A few examples including adhesion, degradation of endogenous ECM-substrates [35], tissue penetration [51], complement evasion [52], ectopic activation of host MMPs [39] and degradation of host chemokines and cytokines, such as IL-1β and IL-6, primarily due to its potent proteolytic activity [38]. However, as in other spirochetes, con- served lipid moieties of the protease complex recognized by host TLR2 receptor complexes may contribute to activation of innate immune responses [53]. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 T. denticola upregulates genes associated with ECM and degradation in hPDL cells To better understand the extent to which T. denticola influences host transcriptomes in an unbi- ased and gene-centric context, we challenged three healthy patient replicates of hPDL cells with wild-type Td-WT for 2 hours. The cells were then incubated for an additional 3 or 22 hours (5 and 24-hours, respectively) before extracting total RNA for sequencing. Unchallenged hPDL cells were used as a negative control. The results are shown in Fig 1. In order to include moderately up- or downregulated genes in the analysis, genes below our cutoff criterion with a significant dif- ference (p < 0.05) were examined. Differential expression analysis revealed a large overlap in gene expression between the control and 5-hour incubation groups (289 genes), whereas the control and 24-hour incubation groups showed significantly less overlap (165 genes) (Fig 1A). Hierarchi- cal clustering analysis was carried out with the log10 (FPKM+1) of union differential expression genes of all comparison groups under different experimental conditions. Essentially, experimental groups which have more unique clusters diverge further away from the control group. The 24-hour incubation group clustered away from the 5-hour incubation and control groups (Fig 1B). For the gene ontology analysis, we utilized the mean FPKM values for each gene across experimental groups. Gene clusters at or above a 0.05 adjusted p-value were delineated as statically significant increases. ECM (~6-fold change), collagen degradation (~2-fold change) and degrada- tion of the ECM (~2-fold change) amongst the top 20 significantly enriched biological processes (Fig 1C). Downregulated GO and KEGG Terms can be found in S1 Fig. KEGG pathway analysis revealed ECM-Receptor (~4-fold change), Notch (~2-fold change), endocytosis (~2-fold change) and protein digestion (~2-fold change) signaling amongst the top 20 enriched signaling pathways upon T. denticola challenge (Fig 1D). Interestingly, Membrane-type matrix metalloproteinase 4 (MMP-17), Stromelysin-3 (MMP-11) and Epilysin (MMP-28) were consistently clustered with various GO terms associated with ECM remodeling and catabolism and have not been associated with periodontal disease to date. Although RNA-seq analysis revealed increases in MMP-2 and MMP-14 read counts, they were not found to be statistically significant. Both genes, however, have been found to be chronically upregulated in hPDL fibroblasts upon T. denticola challenge for up to 12 days in vitro [46]. T. denticola upregulates genes associated with ECM and degradation in hPDL cells Additionally, while the primary functions of these enzymes have been associated with tissue turnover, both MMP-2 and MMP-14 participate in the active degradation of various cytokines [57], chemokines [57], ECM proteins [58] and various intracellular substrates [21,59,60] expressed by hPDL cells expressed during periodontal disease infections, delineating their potentially important role in driving periodontal induced tissue destruction. Next, we sought to determine if this upregulation of tissue destructive genes is common among pathogens and commensal bacteria. Introduction Because predominant host responses to lipoproteins are believed to be to their lipid moieties, most studies have focused on diacylated lipopeptide, Pam2CSK4, and triacylated lipopeptide, Pam3CSK4, which mimic bacterial lipoproteins for their potent immunostimulatory and osteoclastogenic activities by preferentially activating TLR2-dependent pathways [53–55]. Recent studies have demon- strated that synthetic di- and tri-acylated lipopeptides which preferentially activate TLR2/6 and TLR2/1-dependent pathways respectively, are sufficient to induce alveolar bone loss in mice [54,56], broadening the avenues of investigation into the role of lipoproteins underpin- ning the pathogenesis of periodontal disease. However, studies which utilize endogenously expressed bacterial lipopeptides are greatly lacking. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 3 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells While a clear role for dentilisin in the context of periodontal disease has been delineated at the protein level, its ability to influence host ECM metabolism in a gene-centric context has yet to be characterized. Thus, the aim of this study was to determine the extent to which T. denti- cola and its highly expressed acylated dentilisin protease complex influence the transcriptional regulation of MMPs through TLR2-dependent pathways in hPDL cells. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 MMPs are not upregulated by commensal oral Gram-negative Veillonella parvula To determine if the induction of these MMPs was specific to T. denticola, we utilized Veillo- nella parvula, a Gram-negative anaerobic oral commensal that is prevalent in the gut and oral PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 4 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 1. Differential expression analysis of T. denticola challenged hPDL cells. Total RNA was extracted from healthy patient-derived hPDL cells challenged with Td-WT bacteria at a MOI of 50 for 2-hours in media free of supplements followed by 3 and 22-hours in media supplemented with 10% FBS, 1% Pen Strep and 1% Amphotericin B. Mean FPKM values were used for downstream analysis (n = 3 patient replicates). A) Overlapping and differentially expressed genes between control, 5-hour and 24-hour incubation groups visualized using a Venn diagram. B) Hierarchical clustering analysis was used to determine similarity of transcriptome profiles based on differential expression as a heatmap. Red (Upregulation) to blue (Downregulation) color gradient of heatmap represents normalized gene expression as row Z-scores. C) Top 20 enriched Gene Ontology terms of hPDL cells challenged for 2-hours followed by a 22-hour incubation using the Reactome nomenclature. Statistical significance was assessed using a Kolmogorov- Smirnov test followed by Benjamini-Hochberg correction (p<0.05). D) Top 20 enriched signaling pathways of hPDL cells challenged for 2-hours followed by a 22-hour incubation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Statistical significance was assessed using a Kolmogorov-Smirnov test followed Benjamini- Hochberg correction (p<0.05). Fig 1. Differential expression analysis of T. denticola challenged hPDL cells. Total RNA was extracted from healthy patient-derived hPDL cells challenged with Td-WT bacteria at a MOI of 50 for 2-hours in media free of supplements followed by 3 and 22-hours in media supplemented with 10% FBS, 1% Pen Strep and 1% Amphotericin B. Mean FPKM values were used for downstream analysis (n = 3 patient replicates). A) Overlapping and differentially expressed genes between control, 5-hour and 24-hour incubation groups visualized using a Venn diagram. B) Hierarchical clustering analysis was used to determine similarity of transcriptome profiles based on differential expression as a heatmap. Red (Upregulation) to blue (Downregulation) color gradient of heatmap represents normalized gene expression as row Z-scores. C) Top 20 enriched Gene Ontology terms of hPDL cells challenged for 2-hours followed by a 22-hour incubation using the Reactome nomenclature. MMPs are not upregulated by commensal oral Gram-negative Veillonella parvula Statistical significance was assessed using a Kolmogorov- Smirnov test followed by Benjamini-Hochberg correction (p<0.05). D) Top 20 enriched signaling pathways of hPDL cells challenged for 2-hours followed by a 22-hour incubation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Statistical significance was assessed using a Kolmogorov-Smirnov test followed Benjamini- Hochberg correction (p<0.05). Fig 1. Differential expression analysis of T. denticola challenged hPDL cells. Total RNA was extracted from healthy patient-derived hPDL cells challenged with Td-WT bacteria at a MOI of 50 for 2-hours in media free of supplements followed by 3 and 22-hours in media supplemented with 10% FBS, 1% Pen Strep and 1% Amphotericin B. Mean FPKM values were used for downstream analysis (n = 3 patient replicates). A) Overlapping and differentially expressed genes between control, 5-hour and 24-hour incubation groups visualized using a Venn diagram. B) Hierarchical clustering analysis was used to determine similarity of transcriptome profiles based on differential expression as a heatmap. Red (Upregulation) to blue (Downregulation) color gradient of heatmap represents normalized gene expression as row Z-scores. C) Top 20 enriched Gene Ontology terms of hPDL cells challenged for 2-hours followed by a 22-hour incubation using the Reactome nomenclature. Statistical significance was assessed using a Kolmogorov- Smirnov test followed by Benjamini-Hochberg correction (p<0.05). D) Top 20 enriched signaling pathways of hPDL cells challenged for 2-hours followed by a 22-hour incubation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Statistical significance was assessed using a Kolmogorov-Smirnov test followed Benjamini- Hochberg correction (p<0.05). https://doi.org/10.1371/journal.ppat.1009311.g001 cavity and is not associated with oral diseases [61]. hPDL cells were challenged with wild-type T. denticola or V. parvula bacteria for 2 hours at 50 MOI followed by a 22-hour incubation period in α-MEM media free of antibiotics and supplemented with 10% FBS. V. parvula chal- lenge did not induce the upregulation of MMPs 2, 11, 14, 17 or 28 (Fig 2). By contrast, T. den- ticola elicited a ~2-fold upregulation or more of all target MMP genes (Fig 2). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 T. denticola dentilisin mediates the upregulation of various MMPs in hPDL cells Among the various TLR2 stimulatory bacterial ligands, lipoproteins are considered a major virulence factor because of their strong immunostimulating capacity [55,62,63]. Interestingly, while differential innate immune responses have been reported depending on the acylation status and tissue type [63–65], both di- and triacylated synthetic lipopeptides have PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 5 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 2. T. denticola upregulates MMPs in hPDL cells while V. parvula does not. (A-E) RT-qPCR for MMP-2, MMP-11, MMP- 14, MMP-17 and MMP-28 mRNA expression of healthy hPDL cells challenged with V. parvula (ATCC 10790) and Td-WT bacteria at a MOI of 50 for 2-hours, followed by a 22-hour incubation in media supplemented with 10% FBS and 1% Pen/Strep and 1% Amphotericin B. Expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a One-Way ANOVA followed by Post-Hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 5). p < .05 versus control. p < .01 versus control. p < .001 versus control. Fig 2. T. denticola upregulates MMPs in hPDL cells while V. parvula does not. (A-E) RT-qPCR for MMP-2, MMP-11, MM Fig 2. T. denticola upregulates MMPs in hPDL cells while V. parvula does not. (A-E) RT-qPCR for MMP-2, MMP-11, MMP- 14, MMP-17 and MMP-28 mRNA expression of healthy hPDL cells challenged with V. parvula (ATCC 10790) and Td-WT bacteria at a MOI of 50 for 2-hours, followed by a 22-hour incubation in media supplemented with 10% FBS and 1% Pen/Strep and 1% Amphotericin B. Expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a One-Way ANOVA followed by Post-Hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 5). p < .05 versus control. p < .01 versus control. p < .001 versus control. https://doi org/10 1371/journal ppat 1009311 g002 Fig 2. T. denticola upregulates MMPs in hPDL cells while V. parvula does not. (A E) RT qPCR for MMP 2, MMP 11, MMP 14, MMP-17 and MMP-28 mRNA expression of healthy hPDL cells challenged with V. parvula (ATCC 10790) and Td-WT bacteria at a MOI of 50 for 2-hours, followed by a 22-hour incubation in media supplemented with 10% FBS and 1% Pen/Strep and 1% Amphotericin B. Expression of each gene was normalized to that of GAPDH. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 T. denticola dentilisin mediates the upregulation of various MMPs in hPDL cells Statistical significance was determined using a One-Way ANOVA followed by Post-Hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 5). p < .05 versus control. p < .01 versus control. p < .001 versus control. https://doi.org/10.1371/journal.ppat.1009311.g002 https://doi.org/10.1371/journal.ppat.1009311.g002 demonstrated the ability to sufficiently drive alveolar and long bone resorption in mice through TLR2/MyD88 dependent mechanisms [54,56]. We investigated whether purified den- tilisin can drive MMP gene regulation in hPDL cells and the results can be seen in Fig 3. hPDL cells were challenged with dentilisin purified from T. denticola ATCC 35405 at a final concen- tration of 1 μg/mL for 2-hours in MEM-media supplemented 1% P/S. Enzymatic activity of dentilisin protein was verified by collecting conditioned media from dentilisin stimulated hPDL cells as described above and analyzing samples using gelatin zymography (S2 Fig). While, dentilisin enzymatic activity (98 kDa) increased in a dose dependent manner, MMP-2 enzymatic activity (72 kDa) concomitantly increased in a statistically significant manner (~2.0-fold) across all 3 experimental conditions. Total RNA from hPDL cells (unchallenged and challenged with T. denticola strains or puri- fied dentilisin) was extracted, processed for cDNA synthesis and rendered to RT-qPCR. Cells stimulated with purified dentilisin resulted in statistically significant increases in all MMP tar- gets with MMP-17 being the most responsive (Fig 3). Similarly, hPDL cells challenged with T. denticola 35405 (Td-WT) resulted in statistically significant increases across all MMP targets (~2–2.5-fold) (Fig 3). By contrast, hPDL cells challenged with dentilisin-deficient T. denticola (Td-CF522) resulted in no statistically significant upregulation across all MMP targets com- pared to the control group (Fig 3). 6 / 29 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 3. T. denticola surface-expressed dentilisin mediates the upregulation of MMP 2, 11, 14, 17 and 28 mRNA levels in hPDL cells. (A-E) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of healthy hPDL cells challenged with isogenic Td-CF522 bacteria, Td-WT bacteria and purified dentilisin. Cells were stimulated at an MOI of 50 and a final concentration of of 1 μg/mL. Cells were challenged for 2-hours in alpha-MEM media supplemented with 10% FBS followed by a 22-hour incubation in alpha-MEM media with 10% FBS, 1% PenStrep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a One-Way ANOVA followed by Tukey’s Post-Hoc multiple comparisons. T. denticola dentilisin mediates the upregulation of various MMPs in hPDL cells Bars represent mean ± SEM (n = 4). p < .01 versus control. p < .001 versus control. Fig 3. T. denticola surface-expressed dentilisin mediates the upregulation of MMP 2, 11, 14, 17 and 28 mRNA levels in -expressed dentilisin mediates the upregulation of MMP 2, 11, 14, 17 and 28 mRNA levels in hPDL cells. (A-E) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of healthy hPDL cells challenged with isogenic Td-CF522 bacteria, Td-WT bacteria and purified dentilisin. Cells were stimulated at an MOI of 50 and a final concentration of of 1 μg/mL. Cells were challenged for 2-hours in alpha-MEM media supplemented with 10% FBS followed by a 22-hour incubation in alpha-MEM media with 10% FBS, 1% PenStrep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a One-Way ANOVA followed by Tukey’s Post-Hoc multiple comparisons. Bars represent mean ± SEM (n = 4). p < .01 versus control. p < .001 versus control. https://doi.org/10.1371/journal.ppat.1009311.g003 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 shRNA knockdown of TLR2 inhibits T. denticola-induced upregulation of MMPs 2, 14 17 and 28 in hPDL cells while synergistically increasing MMP 11 expression Bars represent mean ± SEM (n = 3). #p < .05 versus scramble control group. ##p < .01 versus scramble control group. ###p < .001 versus scramble control group. p < .05 versus TLR2 shRNA equivalent group. p < .001 versus TLR2 equivalent shRNA group. https://doi org/10 1371/journal ppat 1009311 g004 Fig 4. Suppression of TLR2 inhibits T. denticola-stimulated upregulation of MMPs 2, 14, 17 and 28 while exacerbating MMP 11 expression in hPDL Fig 4. Suppression of TLR2 inhibits T. denticola-stimulated upregulation of MMPs 2, 14, 17 and 28 while exacerbating MMP 11 expression in hPDL cells. A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against TLR2 in healthy hPDL cells. Cells transduced with ibits T. denticola-stimulated upregulation of MMPs 2, 14, 17 and 28 while exacerbating MMP 11 expression in hPDL Fig 4. Suppression of TLR2 inhibits T. denticola-stimulated upregulation of MMPs 2, 14, 17 and 28 while exacerbating M Fig 4. Suppression of TLR2 inhibits T. denticola-stimulated upregulation of MMPs 2, 14, 17 and 28 while exacerbating MMP 11 expression in hPDL cells. A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against TLR2 in healthy hPDL cells. Cells transduced with scrambled shRNA vectors were used as a control. Statistical significance was determined using an unpaired t-test. Bars represent ± SEM of mean value (n = 3 clones). p < .05 versus control. B-F) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of scrambled shRNA control and TLR2 shRNA hPDL cells challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha-MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a Two-Way ANOVA followed by post-hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 3). #p < .05 versus scramble control group. ##p < .01 versus scramble control group. ###p < .001 versus scramble control group. p < .05 versus TLR2 shRNA equivalent group. p < .001 versus TLR2 equivalent shRNA group. cells. A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against TLR2 in healthy hPDL cells. Cells transduced with scrambled shRNA vectors were used as a control. shRNA knockdown of TLR2 inhibits T. denticola-induced upregulation of MMPs 2, 14 17 and 28 in hPDL cells while synergistically increasing MMP 11 expression Thus, after determining dentilisin plays an important role as a regulator of MMP expression in host hPDL cells, we sought to establish a direct link between TLR2 activation and MMP gene regulation. TLRs, particularly TLR2, and to a much lesser extent TLR4, regulate important immune responses to periodontal bacteria in vivo and in vitro [34,66–72]. TLR2 has been iden- tified as a receptor for an array of ligands comprising T. denticola bacteria, including lipotei- choic acid, beta barrel proteins, and acylated lipopeptides, such as dentilisin [73,74]. Thus, to examine the role of TLR2 and MMP transcriptional regulation in hPDL cells, we generated a primary hPDL TLR2 knockdown cell line using shRNA targeted against the TLR2 gene and transduced using lentiviral particles. Basal TLR2 expression was reduced ~60% across 3 clonal replicates as validated using RT-qPCR; reduction was found to be statistically significant using an unpaired t-test (Fig 4A). Next, TLR2 knockdown cells were challenged with either purified dentilisin or wild-type T. denticola bacteria. MMP 2, 11, 14, 17 and 28 expression increased upon stimulation with both purified dentilisin and Td-WT in the shRNA control group (Fig 4B–4F). Compared with hPDL cells transfected with the scrambled shRNA control, induction of expression of MMPs 2, 14, 17 and 28 was suppressed in TLR2-deficient hPDL cells PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 7 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 4. Suppression of TLR2 inhibits T. denticola-stimulated upregulation of MMPs 2, 14, 17 and 28 while exacerbating MMP 11 expression in hPDL cells. A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against TLR2 in healthy hPDL cells. Cells transduced with scrambled shRNA vectors were used as a control. Statistical significance was determined using an unpaired t-test. Bars represent ± SEM of mean value (n = 3 clones). p < .05 versus control. B-F) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of scrambled shRNA control and TLR2 shRNA hPDL cells challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha-MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a Two-Way ANOVA followed by post-hoc Tukey’s multiple comparisons. shRNA knockdown of TLR2 inhibits T. denticola-induced upregulation of MMPs 2, 14 17 and 28 in hPDL cells while synergistically increasing MMP 11 expression Statistical significance was determined using an unpaired t-test. Bars represent ± SEM of mean value (n = 3 clones). p < .05 versus control. B-F) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of scrambled shRNA control and TLR2 shRNA hPDL cells challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha-MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a Two-Way ANOVA followed by post-hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 3). #p < .05 versus scramble control group. ##p < .01 versus scramble control group. ###p < .001 versus scramble control group. p < .05 versus TLR2 shRNA equivalent group. p < .001 versus TLR2 equivalent shRNA group. https://doi.org/10.1371/journal.ppat.1009311.g004 https://doi.org/10.1371/journal.ppat.1009311.g004 challenged with T. denticola or dentilisin, while MMP 11 was significantly upregulated in T. denticola-challenged TLR2-deficient hPDL cells. After determining TLR2 activation plays an integral role in the regulation of MMP expression, we next sought out to determine which downstream mediator is required to propagate this signal. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 shRNA knockdown of MyD88 inhibits T. denticola-stimulated upregulation of MMPs 2, 11, 14, 17 and 28 in hPDL cells All TLRs signal through MyD88 with the exception of TLR3 and TLR4 which utilize TIRAP [75]. However, numerous recent reports suggest that MyD88-independent TLR2 pathways may also contribute to periodontal disease progression [76]. Thus, to determine if T. denticola- induced TLR2 activation requires MyD88 to regulate targeted MMPs, we generated an hPDL MyD88 knockdown cell line, achieving approximately ~60% reduction in MyD88 basal expres- sion across 3 validated clonal replicates (Fig 5A). MyD88-deficient hPDL cells were stimulated with either Td-WT or purified dentilisin as described above. In the negative shRNA control group, all MMP targets showed increased mRNA levels following challenge with both Td-WT and dentilisin (Fig 5B–5F). By contrast, MyD88-deficient cells challenged with Td-WT bacte- ria and purified dentilisin revealed unanimous depression of all MMP targets as compared to the respective scrambled shRNA control samples (Fig 5B–5F). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 8 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 5. Suppression of MyD88 inhibits T. denticola-stimulated upregulation of MMP 2, 11, 14, 17 and 28 in hPDL cells. A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against MyD88 in healthy hPDL cells. Cells transduced with scrambled shRNA vectors were used as a control. Statistical significance was determined using an unpaired t-test. Bars represent ± SEM of mean values (n = 3 clones). p < .05 versus control. B-F) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of scrambled shRNA control and MyD88 shRNA hPDL cells challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha-MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a Two-Way ANOVA followed by post-hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 3). #p < .05 versus scramble control group. ###p < .001 versus scramble control group p < .05 versus MyD88 shRNA equivalent group. p < .01 versus MyD88 shRNA equivalent group. p < .001 versus MyD88 shRNA equivalent group. htt //d i /10 1371/j l t 1009311 005 Fig 5. Suppression of MyD88 inhibits T. denticola-stimulated upregulation of MMP 2, 11, 14, 17 and 28 in hPDL cells. shRNA knockdown of MyD88 inhibits T. denticola-stimulated upregulation of MMPs 2, 11, 14, 17 and 28 in hPDL cells A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against MyD88 in healthy hPDL cells. Cells transduced with scrambled shRNA vectors were used as a control. Statistical significance was determined using an unpaired t-test. Bars represent ± SEM of mean values (n = 3 clones). p < .05 versus control. B-F) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of scrambled shRNA control and MyD88 shRNA hPDL cells challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha-MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a Two-Way ANOVA followed by post-hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 3). #p < .05 versus scramble control group. ###p < .001 versus scramble control group p < .05 versus MyD88 shRNA equivalent group. p < .01 versus MyD88 shRNA equivalent group. p < .001 versus MyD88 shRNA equivalent group. https://doi org/10 1371/journal ppat 1009311 g005 ppression of MyD88 inhibits T. denticola-stimulated upregulation of MMP 2, 11, 14, 17 and 28 in hPDL cells. A) RT-qPC https://doi.org/10.1371/journal.ppat.1009311.g005 https://doi.org/10.1371/journal.ppat.1009311.g005 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 shRNA knockdown of TLR2/MyD88-dependent signaling inhibits nuclear translocation of transcription factor Sp1 in hPDL cells stimulated with T. denticola or dentilisin One of the many downstream targets of TLR/MyD88 signaling is the transcription factor Spec- ificity Protein 1 (Sp1). Sp1 regulates a variety of genes associated with cell cycle, pro-inflamma- tion and tissue-destruction, including MMPs 2, 11, 14 17 and 28. Interestingly, Larsson and colleagues have readily demonstrated that mRNA levels of Sp1 are consistently upregulated at periodontally involved sites in humans [77]. Thus, to determine if T. denticola influences Sp1 expression in the PDL, hPDL cells were challenged with Td-WT and Td-CF522 bacteria at a multiplicity of infection of 50 for 2-hours followed by a 22-hour incubation period in media. Cells were collected and used for western blot analysis utilizing a monoclonal antibody against total Sp1 protein. Total Sp1 protein expression levels increased in the groups challenged with Td-WT at 50 MOI compared to controls and were statistically significant (Fig 6). By contrast, challenge with Td-CF522 failed to recapitulate this effect (Fig 6). Transcription factors are activated post-translationally by TLR signaling, often at the step of nuclear translocation leading to the induction of the primary response genes [78]. After find- ing that T. denticola increases total Sp1 protein expression, we investigated whether T. denti- cola or dentilisin are able to induce nuclear translocation of Total Sp1 via TLR2 and MyD88 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 9 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 6. Healthy hPDL cells were challenged with A) Td-WT and B) isogenic Td-CF522 bacteria at an MOI of 50 as previously described. Whole cell lysates were generated and used for Western Blot analysis utilizing total anti-Sp1 antibodies. Total Sp1 protein expression was normalized against GAPDH protein expression as a loading control. Statistical significance was determined using a paired t-test. Bars represent mean ± SD (n = 3). p < .01 versus control. https://doi org/10 1371/journal ppat 1009311 g006 Fig 6. Healthy hPDL cells were challenged with A) Td-WT and B) isogenic Td-CF522 bacteria at an MOI of 50 as previously described. Whole cell lysates were generated and used for Western Blot analysis utilizing total anti-Sp1 antibodies. Total Sp1 protein expression was normalized against GAPDH protein expression as a loading control. Statistical significance was determined using a paired t-test. Bars represent mean ± SD (n = 3). p < .01 versus control. https://doi.org/10.1371/journal.ppat.1009311.g006 activation in hPDL cells and the results can be seen on Figs 7 and 8. shRNA knockdown of TLR2/MyD88-dependent signaling inhibits nuclear translocation of transcription factor Sp1 in hPDL cells stimulated with T. denticola or dentilisin TLR2, MyD88-deficient and shRNA control cells were stimulated with purified dentilisin, Td-WT or Td-CF522 as pre- viously described. Protein localization was assessed using primary antibodies against Sp1 and a secondary antibody conjugated to an Alexa 488 fluorophore and subjected to confocal micros- copy. shRNA control hPDL cells challenged with Td-CF522 resulted in an increased Sp1 pro- tein signal compared to the control group but remained localized to the cytoplasm (Fig 7A). In contrast, shRNA control hPDL cells stimulated with purified dentilisin and Td-WT bacteria resulted in an increased Sp1 signal and translocation to the nucleus (Fig 7A). hPDL cells defi- cient in TLR2 and MyD88 and challenged with the Td-CF522 resulted in similar results as the shRNA control group (Figs 7 and 8). However, when challenged or stimulated with purified dentilisin and Td-WT bacteria, both TLR2 and MyD88 deficient cells inhibited the transloca- tion of Sp1 into the nucleus (Figs 7 and 8A). Thus, after determining both TLR2 and MyD88 play an integral role in the translocation of Sp1 in our system, we sought out to determine if Sp1 is required or sufficient to regulate target MMPs. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Knockdown of transcription factor Sp1 inhibits T. denticola/dentilisin- stimulated upregulation of MMPs 2, 11, 14, 17 and 28 in hPDL cells Promoter characterization and luciferase promoter activity assays have identified Sp1 as a reg- ulator of most MMPs and TLRs, through interactions with other transcription factors and cis- regulatory elements such as distal enhancers [79–84]. Thus, it is possible that Sp1 may function as a critical regulator in response to T. denticola challenge. To answer this question, shRNA vectors against the Sp1 gene were used to transduce healthy patient-derived hPDL cells using lentiviral particles as previously described. Cells transfected with scrambled shRNA were used as a negative control. Average basal Sp1 mRNA levels were decreased ~40% across three clones as assessed using RT-qPCR (Fig 9A). These shRNA control and Sp1 deficient hPDL cells were PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 10 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 7. Knockdown of TLR2-dependent signaling inhibits translocation of transcription factor Sp1 in both T. denticola- and dentilisin-stimulated hPDL cells. A-B) Healthy hPDL cells were challenged with Td-WT and isogenic Td-CF522 bacteria at an MOI of 50 as previously described. Whole cell lysates were generated and used for Western blot analysis utilizing total Sp1-specific antibodies. Total Sp1 protein expression was normalized using GAPDH as a loading control. Statistical significance was determined using a paired t-test. Bars represent mean ± SD (n = 3). p < .01 versus control. C) Scrambled shRNA control and TLR2 shRNA hPDL cells were challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha-MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. Cells were stained with Hoescht 33342 (Blue) and total Sp1-specific antibodies (Green), and subjected to confocal microscopy. Scale bar represents 10 μm. Fig 7. Knockdown of TLR2-dependent signaling inhibits translocation of transcription factor Sp1 in both T. denticola- and dentilisin-stimulated hPDL cells. A-B) Healthy hPDL cells were challenged with Td-WT and isogenic Td-CF522 bacteria at an MOI of 50 as previously described. Whole cell lysates were generated and used for Western blot analysis utilizing total Sp1-specific antibodies. Total Sp1 protein expression was normalized using GAPDH as a loading control. Statistical significance was determined using a paired t-test. Bars represent mean ± SD (n = 3). p < .01 versus control. Knockdown of transcription factor Sp1 inhibits T. denticola/dentilisin- stimulated upregulation of MMPs 2, 11, 14, 17 and 28 in hPDL cells C) Scrambled shRNA control and TLR2 shRNA hPDL cells were challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha-MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. Cells were stained with Hoescht 33342 (Blue) and total Sp1-specific antibodies (Green), and subjected to confocal microscopy. Scale bar represents 10 μm. https://doi.org/10.1371/journal.ppat.1009311.g007 then challenged with purified dentilisin at 1 μg/mL concentration or Td-WT bacteria at an MOI of 50 followed by RNA isolation and RT-qPCR as previously described. Control shRNA hPDL cells stimulated or challenged with purified dentilisin and Td-WT bacteria resulted in the statistically significant upregulation of MMPs 2, 11, 14, 17 and 28 (Fig 9B–9F). By contrast, Sp1 deficient hPDL cells under the same conditions suppressed the upregulation of all MMP targets (Fig 9B–9F). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Discussion Data from this study extends our earlier reports that short term exposure to dentilisin leads to sustained upregulation of tissue destructive processes at both the transcriptional and transla- tional levels. Specifically, we demonstrated that T. denticola surface-expressed dentilisin plays a direct role in activating TLR2/MyD88-dependent pathways resulting in the subsequent upre- gulation of MMPs in hPDL cells. Additionally, we have identified the transcription factor Sp1 as an important downstream target that is activated as a result of TLR2/MyD88 activation, PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 11 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 8. Knockdown of MyD88-dependent signaling inhibits translocation of transcription factor Sp1 in both T. denticola- and dentilisin-stimulated hPDL cells. A) Scrambled shRNA control and MyD88 shRNA hPDL cells were challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha- MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. Cells were stained with Hoescht 33342 (Blue) and total Sp1-specific antibodies (Green) and subjected to confocal microscopy. Scale bar represents 10 μm. Scale bar represents 10 μm. https://doi.org/10.1371/journal.ppat.1009311.g008 Fig 8. Knockdown of MyD88-dependent signaling inhibits translocation of transcription factor Sp1 in both T. denticola- and dentilisin-stimulated hPDL cells. A) Scrambled shRNA control and MyD88 shRNA hPDL cells were challenged or stimulated with Td-CF522, purified dentilisin or Td-WT at an MOI of 50 and concentration of 1 μg/mL for 2-hours in alpha- MEM media with no supplementation followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. Cells were stained with Hoescht 33342 (Blue) and total Sp1-specific antibodies (Green) and subjected to confocal microscopy. Scale bar represents 10 μm. Scale bar represents 10 μm. https://doi.org/10.1371/journal.ppat.1009311.g008 https://doi.org/10.1371/journal.ppat.1009311.g008 leading to its translocation into the nucleus and mediating the upregulation of various MMPs (Fig 10). Our RNA-Seq analysis revealed specific gene expression patterns that are associated with distinct pathologic features presented clinically [16], reported in in vivo studies [85] and previous studies from our lab [39,46]. Additionally, our present data expands on this finding demonstrating T. denticola’s ability to drive a tissue-destructive gene profile after a brief expo- sure. Discussion denticola-stimulated upregulation of MMP 2, 11, 14, 17 and 28 in hPDL cells. A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against Sp1 in healthy hPDL cells. Cells transduced with scrambled shRNA vectors were used as a control. Statistical significance was determined using an unpaired t-test. Bars represent ± SEM of mean values (n = 3 clones). p < .01 versus control. B-F) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of scrambled shRNA control and Sp1 shRNA hPDL cells challenged or stimulated with purified dentilisin at a concentration of 1 μg/mL or Td-WT at an MOI of 50 for 2-hours in alpha-MEM media supplemented with 10% FBS and no antibiotics followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a Two-Way ANOVA followed by post-hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 3). #p < .05 versus scramble control group. ##p < .01 versus scramble control group. ###p < .001 versus scramble control group. p < .05 versus Sp1 shRNA equivalent group. p < .01 versus Sp1 shRNA equivalent group. p < .001 versus Sp1 shRNA equivalent group. https://doi.org/10.1371/journal.ppat.1009311.g009 expressed by hPDL including IL-1β, IL-6, TNF-α, CXCL12, IL-8 and MCP protein family members [57]. Lastly, although MMPs are classically viewed as extracellular and localized to the cell surface, they have also been found in every cellular compartment [21]. Compelling evi- dence has revealed MMP-14 moonlighting as a transcription factor independent of its catalytic activity, regulating >100 genes associated with inflammation and bacterial clearance [21,93]. Therefore, it is possible that MMP-14 regulates other MMPs or initiates a forward feed-back loop to regulate itself. Taken together, these data suggest that dysregulation of MMP-2 and MMP-14 play a key role in modulating numerous host responses during periodontal infections. While MMPs 2 and 14 have been linked to periodontal disease progression, MMPs 11, 17 and 28 have yet to be described in this disease context [17]. Our gene ontology analysis places all within the various collagen and ECM catabolic processes (Fig 1C). Similar to many other MMPs, clear roles for MMP-17 (also called MT4-MMP) have been described within the con- text of cancer [94]. However, identifying a specific role in tissue homeostasis and in other dis- eases has been challenging. Discussion While the 5-hour incubation group clustered with the control group, the 24-hour incuba- tion group clustered away from the control group illustrating T. denticola’s ability to mediate large-scale transcriptional changes within 24-hours after infection (Fig 1B). leading to its translocation into the nucleus and mediating the upregulation of various MMPs (Fig 10). Our RNA-Seq analysis revealed specific gene expression patterns that are associated with distinct pathologic features presented clinically [16], reported in in vivo studies [85] and previous studies from our lab [39,46]. Additionally, our present data expands on this finding demonstrating T. denticola’s ability to drive a tissue-destructive gene profile after a brief expo- sure. While the 5-hour incubation group clustered with the control group, the 24-hour incuba- tion group clustered away from the control group illustrating T. denticola’s ability to mediate large-scale transcriptional changes within 24-hours after infection (Fig 1B). PDLs insert into the cementum of the tooth root through Sharpey’s fibers which are pri- marily comprised of fibrillar collagen [86,87]. While most collagen is degraded by collagenases such as MMP-1, MMP-8 and MMP-13, MMP-2 (gelatinase B) and MMP-14 are the predomi- nately expressed species in human PDLs and they are able to actively degrade fibrillar collagen [88,89]. MMP proteolytic cascades can also lead to widespread periodontal tissue destruction due to cooperative MMP activation [90]. A myriad of MMP-14 substrates have been identified including complement components [91] and fibrinogens [92] as well as being a potent activa- tor of other MMPs such as pro-enzymatic MMP-2[90]. Additionally, both MMP-2 and MMP- 14 participate in the active degradation of various cytokine and chemokine substrates PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 12 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Fig 9. Stable Suppression of Sp1 inhibits T. denticola-stimulated upregulation of MMP 2, 11, 14, 17 and 28 in hPDL cells. A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against Sp1 in healthy hPDL cells. Cells transduced with scrambled shRNA vectors were used as a control. Statistical significance was determined using an unpaired t-test. Bars represent ± SEM of mean values (n = 3 clones). p < .01 versus control. Discussion B-F) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of scrambled shRNA control and Sp1 shRNA hPDL cells challenged or stimulated with purified dentilisin at a concentration of 1 μg/mL or Td-WT at an MOI of 50 for 2-hours in alpha-MEM media supplemented with 10% FBS and no antibiotics followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a Two-Way ANOVA followed by post-hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 3). #p < .05 versus scramble control group. ##p < .01 versus scramble control group. ###p < .001 versus scramble control group. p < .05 versus Sp1 shRNA equivalent group. p < .01 versus Sp1 shRNA equivalent group. p < .001 versus Sp1 shRNA equivalent group. e Suppression of Sp1 inhibits T. denticola-stimulated upregulation of MMP 2, 11, 14, 17 and 28 in hPDL cells. A) RT-qPC Fig 9. Stable Suppression of Sp1 inhibits T. denticola-stimulated upregulation of MMP 2, 11, 14, 17 and 28 in hPDL cells. A) RT-qPCR validation of stable gene suppression using shRNA vectors targeted against Sp1 in healthy hPDL cells. Cells transduced with scrambled shRNA vectors were used as a control. Statistical significance was determined using an unpaired t-test. Bars represent ± SEM of mean values (n = 3 clones). p < .01 versus control. B-F) RT-qPCR for MMP-2, MMP-11, MMP-14, MMP-17 and MMP-28 mRNA expression of scrambled shRNA control and Sp1 shRNA hPDL cells challenged or stimulated with purified dentilisin at a concentration of 1 μg/mL or Td-WT at an MOI of 50 for 2-hours in alpha-MEM media supplemented with 10% FBS and no antibiotics followed by a 22-hour incubation in alpha-MEM media supplemented with 10% FBS, 1% Pen/Strep and 1% Amphotericin B. The expression of each gene was normalized to that of GAPDH. Statistical significance was determined using a Two-Way ANOVA followed by post-hoc Tukey’s multiple comparisons. Bars represent mean ± SEM (n = 3). #p < .05 versus scramble control group. ##p < .01 versus scramble control group. ###p < .001 versus scramble control group. p < .05 versus Sp1 shRNA equivalent group. p < .01 versus Sp1 shRNA equivalent group. p < .001 versus Sp1 shRNA equivalent group. Fig 9. Stable Suppression of Sp1 inhibits T. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Discussion The GPI- anchored MMP-17 has minimal catalytic activity against ECM substrates only showing affinity for fibrin/fibrinogen, gelatin and pro-TNF-alpha ligands PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 13 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells [94,95]. To date, analysis of MMP-17 null mice has revealed a weak phenotype associated with water retention that is regulated by processes in the hypothalmus [96]. Additionally, MMP-17 Fig 10. Model of proposed mechanism. T. denticola activates host expressed TLR2 receptors via surface-expressed dentilisin. Subsequent downstream activation of MyD88 and translocation of the transcription factor Sp1 lead to the upregulation of MMPs 2, 11, 14, 17 and 28 in human periodontal ligament cells. Grey colored icons represent genes that were identified through RNA- sequencing and analysis but were not directly validated. https://doi.org/10.1371/journal.ppat.1009311.g010 Fig 10. Model of proposed mechanism. T. denticola activates host expressed TLR2 receptors via surface-expressed dentilisin. Subsequent downstream activation of MyD88 and translocation of the transcription factor Sp1 lead to the upregulation of MMPs 2, 11, 14, 17 and 28 in human periodontal ligament cells. Grey colored icons represent genes that were identified through RNA- sequencing and analysis but were not directly validated. https://doi.org/10.1371/journal.ppat.1009311.g010 https://doi.org/10.1371/journal.ppat.1009311.g010 [94,95]. To date, analysis of MMP-17 null mice has revealed a weak phenotype associated with water retention that is regulated by processes in the hypothalmus [96]. Additionally, MMP-17 mediates C-terminal processing of ADAMTS4, one of the aggrecanases that are thought to play a role in arthritis [97]. Pro-MMP-11 (also called Stromelysin-3) contains a unique pro- peptide motif for intracellular calcium activation by furin and has also demonstrated rather [94,95]. To date, analysis of MMP-17 null mice has revealed a weak phenotype associated with water retention that is regulated by processes in the hypothalmus [96]. Additionally, MMP-17 mediates C-terminal processing of ADAMTS4, one of the aggrecanases that are thought to play a role in arthritis [97]. Pro-MMP-11 (also called Stromelysin-3) contains a unique pro- peptide motif for intracellular calcium activation by furin and has also demonstrated rather PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 14 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells restricted substrate specificity [98,99]. Identified MMP-11 ECM substrates include the laminin receptor, fibronectin, elastin and the native alpha3 chain of collagen [100]. All of these are con- stituent ECM proteins found to be upregulated by T. Discussion denticola challenge (Fig 1C), highlighting MMP-11 as a potentially unique response regulator underpinning periodontal disease progression. MMP-28 overexpression in vitro lead to increased MMP-2 and MMP-14 mRNA levels, con- stitutive MMP-2 activation, and revealed e-cadherin as a high-affinity substrate for proteaso- mal degradation in lung carcinoma cells [101,102]. Our data aligned with these findings as MMP-28 was the most upregulated MMP (~2-fold change) within the proteinaceous ECM gene ontology term and was not expressed in control groups, suggesting that MMP-28 may play a multifaceted role in exacerbating MMP-2 and MMP-14 mRNA upregulation while directly contributing to their constitutive activation. Taken together, the multi-dimensionality of MMPs and their varied localizations highlight their role as integral host factors that, in addi- tion to modulating homeostatic tissue turnover, also respond to bacterial challenge through a web of complex interactions. Spirochetes express a wide range of novel and structurally diverse lipoproteins that help define how these unique microbes interact with their environments [103,104]. All lipoproteins are acylated on the N-terminal cysteine residue, and many spirochete lipoproteins are localized to the outer membrane [55]. Compelling reports have demonstrated the importance of specific lipoprotein acyl groups as drivers of both pro and anti-inflammatory cytokine responses in various experimental infection models over the last few decades [65,103]. However, thorough characterization of acylation of T. denticola lipoproteins including dentilisin has yet to be done. Therefore, due to the availability and access to numerous other T. denticola dentilisin isogenic mutants, we decided to investigate the role of dentilisin proteolyitic activity in the context of host gene regulation, an area which has yet to be explored in oral tissues. Of the vari- ous available dentilisin mutants, we chose to utilize CF522 which expresses PrcA (one of the three lipoproteins of the dentilisin complex), but lacks PrtP, the actual protease. Planned future studies will include an otherwise native “catalytically dead” isogenic T. denticola dentilisin mutant strain carrying single base changes in each of the triad of PrtP catalytic residues (Asp203, His258, and Ser447). In our study, stimulation with purified dentilisin lead to the upregulation of MMPs 2, 11, 14, 17 and 28. By contrast, challenging hPDL cells with isogenic Td-CF522 (which lacks the proteolytic PrtP subunit)[105] had no effect (Fig 4). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Discussion denticola infection or treatment with dentilisin. ECM degradation is a key event in the early stages of periodontal disease, generating frag- ments that can act as danger-associated molecular patterns (DAMPs) such as fragmented aggrecan, fibronectin, biglycan, decorin and low molecular weight hyaluronic acid [108]. Our lab has readily demonstrated that dentilisin mediates MMP-2-dependent degradation of Fibronectin in patient derived hPDL cell cultures [35], with specific fragments (i.e. 29, 40, 68 and 120 kDa) capable of modulating various cellular processes including apoptosis, prolifera- tion and proteinase expression through integrin signaling [109–113]. Dongsheng and col- leagues reported that fibronectin was able to activate TLR2/4 to stimulate an innate immune response in macrophages through cross-talk between TLR2, TLR4 and integrin signaling, lead- ing to upregulation of pro-inflammatory genes [114]. Interestingly, while the upregulation of integrins α10 and β4 associated with collagen and laminin interactions were detected, integrins responsible for sensing full-length or fragmented fibronectin did not change. These data sug- gest that T. denticola dentilisin-induced fibronectin fragmentation may play a role in activating and amplifying TLR2-dependent signaling resulting in the differential expression of MMPs. Several other pathways modulate TLR-signaling, fostering tissue-specific outcomes. Syner- gistic cooperation between the Notch pathway and acute TLR-induced signals in the activation of canonical and non-canonical Notch target genes has been characterized as an integral path- way governing the regulation of innate and adaptive immunity [115–118]. Consistent with this, our KEGG pathway analysis revealed Notch signaling (~2-fold change) as the second most enriched pathway resulting from T. denticola challenge in hPDL cells 22-hours post-chal- lenge (Fig 1D). However, mechanisms by which TLRs induce Notch ligand expression and indirectly activate Notch signaling are not well understood and are in many cases, contradic- tory [119–121]. Although inflammatory pathways include a core set of genes that are activated in response to inflammatory stimuli, they differ extensively depending on the cell and tissue type and on the intensity of the trigger [78]. Examples include nuclear factor-κB (NF-κB)[78,122], inter- feron-regulatory factor (IRF) proteins [123] and Kruppel-Like family transcription factors such as Sp1[124,125]. While increased Sp1 levels have been implicated as a factor in periodon- tal disease progression in previous studies, a thorough characterization of its role in PDL tis- sues has not been reported. Many MMPs, including MMPs 2, 11, 14, 17 and 28, have multiple GC boxes in their proximal promoters that bind Sp1 and potentially other GC-binding pro- teins [83]. Discussion Thus, while we originally hypothesized dentilisin lipid moieties to be the causative drivers of TLR2 activation, our data suggest dentili- sin protease activity may be an integral factor responsible for the induction of various MMPs in oral tissues. However, the exact mechanism of action remains to be determined. We plan to pursue the issue of relative contributions of dentilisin acylation and proteolytic activity in future studies. Although both TLR2 and TLR4 have been implicated in periodontal disease progression, various studies utilizing knockout mice and in vitro systems suggest that TLR2 plays the most direct role is in sensing various components produced by periodontal pathogens that drive alveolar bone destruction [32,34,85,106]. However, the precise roles, whether protective or destructive, played by TLR2 in periodontal inflammation and disease are poorly understood, particularly in the context of T. denticola infection. Once a bacterial ligand binds, a conforma- tional change is thought to occur that brings the two Toll/interleukin-1 (IL-1) receptor (TIR) domains on the cytosolic face of each receptor into closer proximity, creating a new platform on which to build a signaling complex through various adaptor molecules [107]. Thus, avail- ability of intracellular adaptors can accommodate rather distinct signaling patterns as a result of TLR activation [74]. Because MyD88 is the predominant mediator for almost all TLRs with PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 15 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells the exception of TLR3 and TLR4, we sought out to determine its role in regulating MMP expression in PDL tissues first. MyD88 deficient hPDL cells stimulated with Td-WT or purified dentilisin resulted in uni- versal suppression of all MMP targets compared to the shRNA control group (Fig 5). Interest- ingly, while shRNA knockdown of MyD88 resulted in a statistically significant downregulation of MMP-2 in the negative control group (Fig 5B), this was not observed for any other MMP targets as well as in any TLR2 knockdown groups. Similarly, TLR2 deficiency (in hPDL cells under the same experimental conditions) was sufficient to suppress all MMP targets with the exception of MMP-11 (Fig 4). Thus, our data suggests that T. denticola utilizes a TLR2/MyD88-dependent pathway to regulate MMPs 2, 14, 17 and 28 in PDL tissues. A pos- sible explanation for this differential response is that MMP-11 may be more highly regulated by an alternative pathway that is indirectly activated as a result of T. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Discussion For example, the Sp1 binding site in the human MMP-14 promoter is crucial in maintaining expression of this gene, since introducing mutations reduces promoter activity by approximately 90%[126]. Sp1 has also demonstrated the capacity to affect cis-regulatory ele- ments that are highly susceptible to cell stimulation [127], potentially explaining how constitu- tively expressed MMPs (such as MMP-2 and MMP-14) are still subject to upregulation upon PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 16 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells T. denticola stimulation. Swingler et al. 2010 reported that Sp1 transcription factors are acety- lated in response to HDAC inhibitors, bind to the conserved GT-box of the MMP28 promoter, potentially working in conjunction with p300/CREB to upregulate mRNA expression [80]. T. denticola stimulation. Swingler et al. 2010 reported that Sp1 transcription factors are acety- lated in response to HDAC inhibitors, bind to the conserved GT-box of the MMP28 promoter, potentially working in conjunction with p300/CREB to upregulate mRNA expression [80]. When healthy hPDL cells were challenged with wild-type T. denticola, total Sp1 protein expression increased compared to the control group (Fig 6A). In contrast, this effect was inhibited in hPDL cells challenged with isogenic mutant Td-CF522 (Fig 6B). This led us to determine if this increase in Sp1 protein expression was combined with increased Sp1 translo- cation to the nucleus. To answer this question, TLR2- and MyD88-knockdown patient-derived hPDL cells lines were generated and challenged with wild-type T. denticola, Td-CF522 and purified dentilisin. shRNA-control cells stimulated with dentilisin and challenged with Td- WT resulted in Sp1 protein localizing to the nucleus, while TLR2 and MyD88 suppression under the same conditions inhibited this effect (Figs 7 and 8). Interestingly, a slight increase in cytoplasmic Sp1 was noted in shRNA control, TLR2 and MyD88 knockdown groups when challenged with the Td-CF522 isogenic mutant, suggesting that other factors expressed by T. denticola may influence Sp1 expression, whereas dentilisin preferentially regulates its post- translational activation. While shRNA-control hPDL cells stimulated with Td-WT and dentili- sin resulted in the upregulation of MMPs 2, 11, 14, 17 and 28, this effect was suppressed in Sp1-deficient hPDL cells under the same conditions (Fig 9). Taken together, these data suggest that the transcription factor Sp1 is an important downstream early response gene that is post- translationally activated as a consequence of TLR2/MyD88 activation, mediating T. Discussion denticola- induced upregulation of several MMPs in hPDL cells. This study has potential limitations, most of which we intend to address in future studies. Because our samples are generated from a small number of human patient tissues, genetic varia- tion may lead to heavily variegated responses. Due to a low sample size, our RNA-Seq in partic- ular may be subject to read count bias and confounding that may have influenced our results. The Pearson’s correlation reflects the linear relationship between two variables accounting for differences in their mean and SD. The more similar the expression profiles for all transcripts are between two samples, the higher the correlation coefficient will be. As shown in S3 Fig, our samples clustered well, suggesting that dispersion effects are low across the 3 biological repli- cates. In addition, comprehensive analyses have shown that data sets with very low dispersions, a power of 0.8 is easily reached with very low sample size and sequencing depth [128]. While our results provide a strong support for mechanisms of action underpinning periodontal dis- ease, other systemic factors could potentially modulate true phenotypic effects. As such, simula- tion of similar experimental conditions in an animal model is planned in future studies. Studies that focus on the effects of unchecked TLR signaling and its contributions to dysre- gulation of tissue destructive genes in periodontal ligament connective tissues are lacking. Considering the limitations of the study, to the best of our knowledge this study is the first associating dentilisin with TLR2 activation using an in vivo isogenic mutant bacteria in con- junction with purified product from its parent strain. Additionally, we also identified poten- tially tissue-specific inducible MMPs that that may play novel roles in modulating host immune responses that have yet to be characterized in the context of periodontal disease. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Purification of T. denticola dentilisin The dentilisin protease complex was purified from the detergent phase of Triton X-114 extracts of an isogenic T. denticola mutant that lacks Msp,the dominant outer membrane pro- tein, as described previously. Briefly, following overnight Triton X-114 treatment, cells were pelleted, the supernatants were phase-separated, the detergent phase was re-extracted twice, precipitated in acetone, then subjected to preparative SDS-PAGE electrophoresis. Fractions of interest, eluted in detergent-free buffer, were concentrated by ultrafiltration, subjected to buffer exchange into PBS containing 0.1% CHAPS {3-[(-[(3-cholamidopropyl)-dimethylam- monio]-1-propanesulfonate} and concentrated again [35]. Aliquots of purified dentilisin were stored at -80˚C. Activity of purified dentilisin samples was monitored periodically, using the chromogenic substrate succinyl-L-alanyl-L-alanyl-L-prolyl-L-phenylalanine-p-nitroanilide (SAAPFNA) as described previously [50]. Anaerobic bacterial cultures T. denticola ATCC 35405 (Td-WT) and its isogenic Td-CF522 dentilisin-deficient mutant Td- CF522 were grow in in Oral Treponeme Enrichment Broth (OTEB; Anaerobe Systems, USA) at 37˚C) grown in tanks filled with an anaerobic gas mixture [131]. Veilonella parvula ATCC 10790 was grown under the same anaerobic conditions as T. denticola in brain heart infusion (BHI) media supplemented with 0.075% sodium thioglycolate, 0.1% Tween 80 and 1% of 85% lactic acid and pH adjusted to 6.5–6.6 using 1 M NaOH. Ethics statement Approval to conduct human subjects’ research, including protocols for the collection and use of human teeth and PDL tissue was obtained from the University of California San Francisco Institutional Review Board (#16–20204; reference #227030). Consent was not obtained due to anonymity of the samples. 17 / 29 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Human PDL cell cultures As described previously, the primary culture of PDL cells was conducted via the direct cell out- growth method by isolating cells from the PDL tissue around the middle third of extracted healthy human teeth [129,130]. Cells were maintained in Minimum Eagle Medium-α (MEM-α) (Gibco, USA) augmented with 10% fetal bovine serum (FBS) (Gibco, USA), 1% pen- icillin/streptomycin (P/S), and 1% amphotericin B (Gibco, USA) in a Steri Cycle 370 incubator (Thermo-Fisher Scientific, USA) with a humid atmosphere containing 95% air and 5% CO2 at 37˚C. Cell outgrowths were passaged before reaching confluency. Only cells passaged three to seven were used for experimentation. Cells were validated by morphological assessment and gene expression of confident biomarkers such as Periostin. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) Total hPDL RNA was extracted and purified using the RNeasy mini kit (Cat# 74134, Qiagen, Germany) according to the manufacturer’s instructions and quantified using a NanoDrop UV-Vis Spectrophotometer (Thermo Scientific, USA). Reverse transcription of the RNA into cDNA was then performed using the SuperScript III cDNA synthesis kit (Cat #11754050, Invi- trogen, USA). Samples were analyzed on a Bio-Rad MyCycler Thermal Cycler according to manufacturers protocol. All cDNA samples were diluted to 5 ng/mL working concentrations and stored at -20˚C. cDNA samples were probed for target gene expression via RT-qPCR using PowerUp SYBR Green Master Mix (Applied Biosystems, USA) and primer sequences (Table 1) on a QuantStudio 3 platform (Applied Biosystems, USA). The relative expression lev- els of target genes were plotted as fold change compared with untreated or negative controls. The 2-ΔΔCT method was used to determine relative change in target gene expression, and gene expression was normalized against GAPDH expression. RNA-Seq RNA was extracted from ~9.5x105 hPDL cells challenged with wild-type T. denticola (as described above using a RNeasy Mini Kit and following the manufacturers protocol (Qiagen, Germany). The quality of the extracted RNA was assessed using a Nanodrop UV-Vis Spectro- photometer (Thermo-Fisher Scientific, USA) and by calculating the percentage of RNA frag- ments with size > 200 bp (DV200) using an Agilent 2100 Bioanalyzer. The RNA was used for first and second strand synthesis, polyA tail bead capture, and sequencing adapter ligation using a TruSeq RNA Library Prep Kit v2 (Illumina, USA). Libraries were sent to Novogene Genomic Services (Davis, USA) for paired-end sequencing on a HiSeq 4000 instrument (150 bp paired-end reads) (Illumina, USA) and analysis. The mean gene expression across all repli- cates were used for data visualization. Analysis was conducted using the opensource statistical software called R [133] and figures were produced using the Grammar of Graphics Plot 2 (GGplot2) [134] software package. Bacterial challenging of hPDL cells ~9x105 healthy hPDL cells were seeded on 6 cm plates. On the next day, these cells were chal- lenged with either T. denticola, Td-CF522 or V. parvula, as previously described by Ateia et al. [46]. Briefly, the bacteria were centrifuged at 4000 RPM for 15 minutes and the supernatant was removed. The pelleted bacterial cells were then resuspended in antibiotic-free MEM-α (without phenol red) at an optical density (OD) of 0.1 at 600 nm using a Spectramax M2 microplate spectrophotometer (Molecular Devices, USA). It has been previously established that an OD of 0.1 at 600nm is equivalent to 2.4x108 CFU/ml for T. denticola [131] and 2x108 CFU/mL for V. parvula strains [132]. Next, hPDL cells were challenged with the bacteria at 50 multiplicity of infection (MOI), whereas the control group was challenged with antibiotic-free MEM-α. Next, the cells were incubated for 2h at 37˚C and 5% CO2, washed twice with Phos- phate Buffer Saline (PBS) (Gibco, USA) and incubated again at 37˚C and 5% CO2 overnight in antibiotic-free MEM-α. On the next day, cells were either harvested for RNA isolation, or gen- eration of cell lysates and stored at -80˚C for further investigations. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 18 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells https://doi.org/10.1371/journal.ppat.1009311.t001 Gelatin zymography Supernatant collected from dentilisin stimulated hPDL cells were quantified and normalized to an albumin standard using the Pierce BCA protein assay kit (Cat# 23225, Thermo Scientific, USA) according to the manufacturers protocol. Equivalent protein concentrations from sam- ples were mixed with nonreducing sample buffer (0.25 M tris-base, 40% glycerol, 0.8% sodium dodecyl sulfate (SDS), and 0.05% bromophenol blue stain in distilled deionized water/ddH2O at pH 6.8) and loaded into 8% polyacrylamide gels that were co-polymerized with 0.4% SDS and 0.2% gelatin. Samples were electrophoretically resolved on gelatin-containing gels at 125 V for 110 min at 4˚C using a Power Pack supply (Bio-Rad, USA) Next, gels were washed in a series of buffers to facilitate re-constitution of endogenous protein and stained with Coomassie Blue as previously described [46]. Briefly, Gels were then washed twice for 15 min under con- tinuous agitation using renaturation/washing buffer (2.5% v/v Triton-X100 and 0.05 M Tris- base in ddH2O at pH 7.5) to eliminate SDS and promote the renaturation of MMP enzymes. Subsequently, gels were incubated in developing/incubation buffer (0.05MTris-base, 0.15Mso- dium chloride, 0.01Mcalcium chloride, and 0.02% sodium azide in ddH2O at pH 7.5) for 30 min under agitation, and then the buffer was replaced and gels incubated for 16–20 hr at 37˚C. After that, gels were stained using filtered Coomassie Brilliant blue stain for 1 or 2 hr under agitation. Destaining of the gels was performed using a methanol/acetic acid destaining buffer (40% methanol and 10% acetic acid in ddH2O) until the bands on the gel appeared clear. Zymograms were scanned using an Hp Officejet 6700, and the densitometry of gelatinolytic activity represented by the clear bands was analyzed using Fiji software [135]. Brightness and contrast levels of zymogram images were slightly adjusted for publication only. Stimulation of hPDL cells using purified dentilisin A BCA protein assay kit (CAT # 23227 Thermo Scientific, USA) was used to determine puri- fied dentilisin sample concentrations as described above. Assessment of enzymatic activity was determined using gelatin zymography as described below. ~9.5x105 cells were seeded on 6 cm plates. Purified dentilisin was added to MEM-α media with no serum and 1% P/S at a final concentration of 1 μg/mL and added to healthy hPDL cell cultures for 2-hours. The treated Table 1. RT-qPCR forward and revers primer pairs. Table 1. RT-qPCR forward and revers primer pairs. Gene Forward Primer Reverse Primer GAPDH 5’-TTGAGGTCAATGAAGGGGTC-3’ 5’-GAAGGTGAAGGTCGGAGTCA-3’ MMP-2 5’-TTTCCATTCCGCTTCCAGGGCAC-3’ 5’- TCGCACACCACATCTTTCCGTCACT-3’ MMP-11 5’ CGATGCTGCTGCTGCTGCTCCAG-3’ 5’-TGGCGTCACATCGCTCCATACCTTTAG-3’ MMP-14 5’ TGAGGATCTGAATGGAAATGAC-3’ 5’-CATAAAGTTGCTGGATGCCC-3’ MMP-17 5-CACCAAGTGGAACAAGAGGAACCT-3’ 5-TGGTAGTACGGCCGCATGATGGAGTGTGCA-3’ MMP-28 5’-CACCTCCACTCGATTCAGCG-3’ 5’-AAAGCGTTTCTTACGCCTCA-3’ MyD88 5’-TCTCTGTTCTT GAACGTGCGGACA-3’ 5’-TTTGGCAATCCTCCTCA ATGCTGG-3’ Periostin 50-CCAGCAGACACACCTGTTGG-30 50-CCTTGAACTTTTTTGTTGGC-30 Sp1 50-TAATGGTGGTGGTGCCTTT-30 50-GAGATGATCTGCCAGCCATT-30 TLR2 5’-ATCCTCCAATCAGGCTTCTCT-3’ 5’-ACACCTCTGTAGGTCACTGTTG-3’ https://doi org/10 1371/journal ppat 1009311 t001 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 19 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells cells were washed with PBS and incubated overnight in MEM-α media free of FBS and supple- mented with 1% P/S. Next, the Supernatant (conditioned media) was collected and total RNA was extracted using an RNeasy Mini kit (Cat# 74134, Qiagen, Germany). The resulting samples were stored at −80˚C until analyzed further in downstream applications. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Statistical analysis Statistical analysis of differentially expressed genes in RNA-Seq data was assessed using a Kol- mogorov-Smirnov test followed by Benjamini-Hochberg correction (p<0.05) using R open source software [133]. All other data was analyzed using GraphPad Prism Version 8 software (San Diego, USA). Results were evaluated by a one-way ANOVA when comparing more than two groups with a single independent variable while a two-way ANOVA was used to compare more than two groups with 2 independent variables. Western blot and gelatin zymography data was analyzed using a paired or unpaired t-test, respectively. Western blot analyses Cell lysates generated from shRNA lentiviral infection were normalized to an albumin stan- dard as described above. These samples were then subjected to SDS-PAGE 4–12% polyacryl- amide gels (Invitrogen, USA) and transferred to polyvinylidene difluoride (PVDF) membranes (EMD Millipore, USA) using a Turbo Blot transfer system and PowerPac Basic power supply (Bio-Rad, USA). The membranes were exposed to a rabbit polyclonal anti-Sp1 (Cat# PA5-29165, Invitrogen, Carlsbad, CA, USA) primary antibody diluted 1:500 in Tris- buffered saline, 0.1% Tween 20 (TBST) solution overnight at 4˚C followed by a horseradish peroxidase-conjugated mouse anti-rabbit IgG secondary antibody (Cat# sc-235, Santa Cruz, Dallas, TX, USA) diluted 1:3000 in TBST for 1 hour at room temperature with agitation. West- ern blots using anti-GAPDH antibodies (Cat# sc-32233, Santa Cruz Biotechnology, USA) were used to confirm equal protein loading. Blots were developed using the Super Signal West Pico kit (ThermoFischer Scientific, USA), scanned for digitization using an Officejet 6700 scanner (Hewlett-Packard, USA) and analyzed using Fiji software [135]. Cell lysates generated from shRNA lentiviral infection were normalized to an albumin stan- dard as described above. These samples were then subjected to SDS-PAGE 4–12% polyacryl- amide gels (Invitrogen, USA) and transferred to polyvinylidene difluoride (PVDF) Lentiviral shRNA knockdown ~6x104 hPDL cells were seeded on 96-well plates. 48 hours later, these cells were infected with either TLR2, MyD88, or Sp1 targeted short hairpin RNA (shRNA) constructs via lentiviral par- ticles according to the kits instructions (Cat# sc-40256-V, Cat# sc-44313-V and Cat# sc- 29487-V, Santa Cruz Biotechnology, USA,). Control samples were transduced using nonspe- cific scrambled shRNA control constructs (Cat# sc-108060, Santa Cruz Biotechnology, USA). hPDL cells were concomitantly permeabilized using Polybrene reagent at a final concentration of 5 μg/mL (EMD Millipore, USA). Approximately 10 hours after infection, cells were washed and incubated overnight in complete MEM-α media supplemented with 10% FBS, 1% Pen- Strep and 1% Amphotericin B. A pol III promoter drives expression of a silencing cassette con- taining a puromycin resistance gene used for selection [136]. As a result, a short hairpin RNA complex is exported into the cytoplasm, processed by Dicer and assembled into the RISC com- plex [136]. Degradation of targeted mRNA transcripts is mediated by unwinding the siRNA duplex leading to a stable reduction in gene expression. Selection of clones with successfully integrated knockdown constructs was accomplished by treating infected hPDL cells with puro- mycin (Calbiochem, USA) at a final concentration of 5 μg/mL for 24-hours in supplemented MEM- α media. This media was then exchanged for supplemented MEM-α media containing 1 μg/mL puromycin until single cell colonies were isolated. Finally, cell colonies were expanded and validated via RT-qPCR and/or Western Blot. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 20 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells Confocal microscopy Approximately 8x104 hPDL cells were seeded into 4-well glass bottom wells. Cells were chal- lenged with purified dentilisin, wild-type T. denticola or isogenic Td-CF522 mutant bacteria as described above. Cells were washed with PBS before being fixed using 4% paraformaldehyde for 10 minutes at room temperature. Next, cells were incubated for 20 minutes with 0.1 M gly- cine in PBS, washed with PBS and permeabilized with 0.2% Triton X-100 in PBS for 2 minutes at room temperature. Cells were incubated in a 10% serum/PBS blocking buffer for 5 minutes at room temperature followed by a 60-minute incubation in a rabbit sourced polyclonal anti- Sp1primary antibody diluted 1:500 in 10% serum/PBS solution. Next, cells were washed 3 times with PBS followed by incubation in 10% serum/PBS blocking buffer for 1 minute at room temperature followed by incubation in anti-rabbit, mouse secondary antibody conju- gated to Alexa 488 fluorophore for 30 minutes at 37˚C (1:3000 dilution) and Hoescht 33342 nuclear staining (1:2000 Dilution) in 10% serum/PBS solution. Finally, cells were washed 3 times with PBS, imaged using an SP8 confocal microscope (Leica, Germany) and analyzed using Fiji [135]. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 Acknowledgments We would like to thank Charles Le for his technical assistance recovering and maintaining Vei- lonella parvula bacterial stocks and Dr. Ryutaro Kuraji as creator of the artwork used as the striking image for this work. Supporting information S1 Fig. A) Top 20 downregulated Gene Ontology terms of hPDL cells challenged for 2-hours followed by a 22-hour incubation using the Reactome nomenclature. Statistical significance was assessed using a Kolmogorov-Smirnov test followed by Benjamini-Hochberg correction (p<0.05). B) Top 20 downregulated signaling pathways of hPDL cells challenged for 2-hours followed by a 22-hour incubation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Statistical significance was assessed using a Kolmogorov-Smirnov test PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1009311 July 13, 2021 21 / 29 PLOS PATHOGENS Treponema denticola dentilisin-dependent upregulation of MMPs in oral cells S2 Fig. Assessment of purified dentilisin enzymatic activity after stimulation with purified dentilisin. Healthy hPDL cells were challenged with purified dentilisin at increasing concen- trations (1, 3 and 5 μg/mL) for 2-hours followed by a 22-hour incubation in MEM-α media free of FBS and supplemented with 1% P/S. Conditioned media from these cells were used to assess the enzymatic activity of Active MMP-2 (64-kDa) and Dentilisin (98 kDa) using gelatin zymography followed by densitometry analysis using Fiji. Statistical significance was deter- mined using a One-Way ANOVA. Bars represent ± SD of mean values (n = 3). p < .001 versus control. S3 Fig. Assessing inter- and intragroup gene expression variability across sample repli- cates. 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Q aQ ‘ – Ñ <–L Q   Q ˜ L < Ñ D Q „‘–Ñ ¯< „Ñ ‫ ݿ‬%OOļ͏Фwଵ Ñ · ‫ߢ ݞ‬wwļwŬଵ փརᙕ Ր‫ڬ‬ᄻ޼ୢᙕ ʮÙᙕ Ȇ ̡ͤ˕Ùᙕ л፡ୣఱၚდఱ‫ڬ‬gሠᙕ ֟ᄻၚᐋఱሠఱၚར‫ڬ‬෹ᙕ Րఱ෹ఱ፡‫ڬ‬ᄻᒥᙕ σࡂ໪ఱརఱሠ፡ᄺ‫ڬ‬፡ఱၚརᙕ Ўၚᎍར޺ఱ෺ᙕ დᄺၚ޺෹‫ڬ‬ఱ໪ࣰࡁᙕ ‫ڬ‬ᙕ ሠᑋࣰࣰდఱར૥ᙕ ᄺࣰਰၚᄻ໪ᙕ ၚਰᙕ ᄻᎍᄻ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂĹୣၚືࡂఱར૥űᙕ ӂརᙕ ‫ڬ‬ᙕ ࡂᄺ‫ڬ‬໪‫ڬ‬፡ఱ޺ᙕ ‫ݯ‬ᄺࣰ‫ڬ‬ඬᙕ ᑋఱ፡ୣᙕ ‫ڬ‬རᙕ ୢఱሠ፡ၚᄺఱࣽᙕ ፡‫ڬ‬ར૥෹ࣰᙕ ၚਰᙕ ື‫ڬ‬རࡂᙕ ፡ࣰརᎌᄺࣰᙕ ޺ၚརࡂఱ፡ఱၚཧሠÙᙕ ፡ୣࣰᙕ ໪ఱ෹ఱ፡‫ڬ‬ᄻᒥᙕ ૥ၚᐋࣰᄻར໪ࣰར፡ᙕ ࡂࣰ޺෺‫ڬ‬ᄺࣰࡂᙕ ‫ڬ‬෺෺ᙕ ᄺᎌᄻ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂሠᙕ ፡ၚᙕ ‫ࣰݯ‬ᙕ ፡ୣࣰᙕ ޺ၚື෹ࣰ޼፡ఱᐋࣰᙕ დᄻၚდࣰᄻ፡ᒥᙕ ၚਰᙕ ፡ୣࣰᙕ л፡ୣఱၚდఱ‫ڬ‬རᙕ დࣰၚდ෹ࣰ  ฿ ΢ ᙕ ୣఱᄺࣰࡂᙕ ෺‫ݯڬ‬ၚᄺᙕ ፡ၚᙕ ޺ᎍ෺፡ఱᐋ‫ڬ‬፡ࣰᙕ ୣၚ෹ࡂఱར૥ሠᙕ ፡ၚᙕ ‫ࣰݯ‬ᙕ დᄺၚୣఱ‫ݯ‬ఱ፡ࣰࡂɹ ΢ᙕ ‫ڬ‬རࡂᙕ ෺ၚ޺‫ڬ‬෹ᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར፡ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬፡ൈၚརሠᙕ ፡ၚᙕ ‫ࣰݯ‬ᙕ ፡ୣࣰᙕ ޺ୣၚሠࣰརᙕ ໪ࣰ‫ڬ‬རሠᙕ ਰၚᄻᙕ ‫ݯ‬ᎍఱ෹ࡂఱར૥ᙕ ‫ڬ‬ᙕ རࣰᑋᙕ ‫ڬ‬૥ᄺ‫ڬ‬ᄻఱ‫ڬ‬རᙕ ሠ፡ᄺᎍ޺፡ᎍᄺࣰűᙕ ؉ୣఱሠᙕ დᄺၚ޺෺‫ڬ‬໫‫ڬ‬፡ఱၚརᙕ ᑋ‫ڬ‬ሠᙕ ‫ݯ‬ᎍ፡ᙕ ၚརࣰᙕఱརᙕ ‫ ڬ‬ሠࣰᄻఱࣰሠᙕ ၚਰᙕ໪ࣰ‫ڬ‬ሠᎍᄺࣰሠᙕ ࡂࣰሠఱ૥རࣰࡂᙕ ፡ၚᙕఱ໪ე෹ࣰ໪ࣰར፡ᙕ፡ୣࣰᙕ ࡂࣰ޺ఱሠఱၚརᙕ ፡‫ڬ‬ඬࣰརᙕ ၚརᙕ Хࣰ޺ࣰ໪‫ࣰݯ‬ᄺᙕ Ȇ ʈ Ü ᙕ Ȇ ̡ͤʰÜᙕ ፡ၚᙕ ࣰሠ፡‫ݯڬ‬෹ఱሠୢᙕ л፡ୣఱၚდఱ‫ڬ‬ᙕ ‫ڬ‬ሠᙕ ‫ڬ‬ᙕ ሠၚ޺ఱ‫ڬ‬෺ఱሠ፡ᙕ ሠ፡‫ڬ‬፡ࣰኬűᙕ ׂࣰ෹‫ڬ‬፡ࣰࡂᙕ დᄺၚ޺෹‫ڬ‬ላ‫ڬ‬፡ఱၚརሠᙕ ეᄺၚᐋఱࡂࣰᙕ ਰၚᄻᙕ ፡ୣࣰᙕ ར‫ڬ‬፡ఱၚར‫ືڬ‬ఱᓯ‫ڬ‬፡ఱၚརᙕ ၚਰᙕ ໪‫ڬ‬རᒥᙕ ‫ݯ‬ᎍሠఱརࣰሠሠᙕ ‫޼ڬ‬፡ఱᐋఱ፡ఱࣰሠˊᙕ ‫ڬ‬ཧࡂᙕ ၚਰᙕ ᎍᄺ‫ڬݯ‬རᙕ ෺‫ڬ‬རࡂሠᙕ ‫ڬ‬རࡂᙕ  ࣰᒈ፡ᄻ‫ ڬ‬ᙕ ୢၚᎍሠࣰሠ˗ᘫᙕ ؉ୣࣰሠࣰᙕ ໪ࣰ‫ڬ‬ሠᎌᄻࣰሠᙕ ᄻࣰდᄻࣰሠࣰར፡ᙕ ‫ڬ‬ᙕ ᄻࣰᐋၚືᎍ፡ఱၚར‫ڬ‬ᄺᒥᙕࡂࣰე‫ڬ‬ᄻ፡ᎍᄺࣰᙕ ਰᄺၚ໪ᙕ ፡ୣࣰᙕ ޺ၚརሠ፡‫ڬ‬ར፡ᙕ ሠᎍეეၚᄺ፡ᙕ ਰၚᄺᙕ დၚ෹ఱ፡ఱ޼‫ືڬ‬෹ᒥᙕ დၚᑋࣰᄻਰᎍືᙕ ෹‫ڬ‬རࡂį‫ڬݯ‬ሠࣰࡂᙕ დᄺၚᐋఱར޺ఱ‫ڬ‬෹ᙕ ‫ڬ‬རࡂᙕ ར‫ڬ‬፡ఱၚར‫ڬ‬෹ᙕ ࣰ෹ఱ፡ࣰሠᙕ ეᄺၚᐋఱࡂࣰࡂᙕ ‫ݯ‬ᒥᙕ ፫ୣࣰᙕ ຾‫ڬ‬፡ࣰᙕ Ҕ‫ڬ‬ఱ෹ࣰᙕ ‫ࣰכ‬෺෺‫ڬ‬ሠሠఱࣰgሠᙕ ૥ၚᐋࣰᄺཧ໪ࣰར፡űᙕ ؉ୣࣰᒥᙕ ᄺࣰሠ፡ᙕ ၚཧᙕ ፡ୣࣰᙕ ეၚ෹ఱ፡ఱ޺‫ڬ‬෺ᙕ დୣఱ෺ၚሞၚეୣᒥÙᙕ ࣰᒈეᄺࣰሠሜࣰࡂᙕ ఱརᙕ ፡ୢࣰᙕ ׂᎍᄻ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄺၚ޺෹‫ڬ‬ላ‫ڬ‬፡ఱၚརÙᙕ ፡ୣ‫ڬ‬፡ᙕ ఱ፡ᙕ ఱሠᙕ ࣰሠሠࣰར፡ఱ‫ڬ‬෺ᙕ ፡ၚᙕ ਰᎍརࡂ‫ڬ‬໪ࣰར፡‫ڬ‬෺෺ᒥᙕ ‫ڬ‬෺፡ࣰᄺᙕ ፡ୣࣰᙕ ࣰᒈఱሠ፡ఱར૥ᙕ ‫ڬ‬૥ᄻ‫ڬ‬ᄻఱ‫ڬ‬རᙕ ᄻࣰ෹‫ڬ‬፡ఱၚརሠᙕ ሠၚᙕ ፡ୣ‫ڬ‬፡ᙕ ፡ୣࣰᙕл፡ୣఱၚდఱ‫ڬ‬རᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར፡ᙕ ໪‫ڬ‬ሠሠࣰሠᙕ ᑋୣఱ޺ୢᙕ ୣ‫ڬ‬ᐋࣰᙕ ე‫ڬ‬ఱࡂᙕ ሠၚᙕ ໪ᎍ޺ୣᙕఱརᙕሠᑋࣰ‫ڬ‬፡ᙕ‫ڬ‬ሠᙕఱརᙕ‫ݯ‬෹ၚၚࡂᙕ ፡ၚᙕ໪‫ڬ‬ఱར፡‫ڬ‬ఱརᙕ ‫ڬ‬རᙕࣰᒈ፡ᄺ‫ڬ‬ᐋ‫ڬ‬૥‫ڬ‬ར፡ᙕਰࣰᎍࡂ‫ڬ‬෹ᙕ ޺෹‫ڬ‬ሠሠᙕ ໪‫ڬ‬ᒥᙕ ‫ࣰݯ‬ᙕ෹ఱ‫ࣰݯ‬ᄺ‫ڬ‬፡ࣰࡂᙕ ਰᄺၚ໪ᙕ ‫ڬ‬૥ࣰĶၚ෹ࡂᙕ ਰࣰᎍࡂ‫ڬ‬෹ᙕ ၚდდᄻࣰሠሠఱၚརÙᙕ ఱརආᎍታ፡ఱ޺ࣰÙᙕ დၚᐋࣰᄺ፡ᒥÙᙕ ‫ڬ‬རࡂᙕ ࡂఱሠࣰ‫ڬ‬ሠࣰᙕ ų ų ᙕĬ˽Pᙕ ؉ୣࣰᒥᙕ ‫ڬ‬ఱ໪ᙕ ፡ၚᙕ ෹‫ڬ‬ᒥᙕ ፡ୢࣰᙕ ‫ڬݯ‬ሠవሠᙕ ਰၚᄺᙕ ‫ڬ‬ᙕ རࣰᑋᙕ ሠၚ޺ఱၚįࣰ޺ၚརၚ໪ఱ޺Ĺდၚ෹ఱ፡ఱ޺‫ڬ‬෹ᙕ ၚᄺࡂࣰᄺᙕ ఱརᙕ л፡ୣఱၚეఱ‫ڬ‬Ùᙕ ‫ڬ‬෺፡ୣၚᎍ૥ୣᙕ ‫ڬ‬፡ᙕ დᄺࣰሠࣰར፡ᙕ ፡ୢࣰᙕ ར‫ڬ‬፡ᎍᄺࣰᙕ ၚਰᙕ ፡ୣࣰᙕ རࣰᑋᙕ ၚᄺࡂࣰᄻᙕ ఱሠᙕ ਰ‫ڬ‬ᄻᙕ ਰᄻၚ໪ᙕ ޼෹ࣰ‫ڬ‬ᄻűᙕ ؉ୣఱሠᙕ ‫ڬ‬ᄻ፡ఱ޺෺ࣰᙕ ᑋఱ෺෺ᙕ ᄺࣰᐋఱࣰᑋᙕ ፡ୣࣰᙕ ໪‫ڬ‬ඈၚᄻᙕეᄻၚᐋఱሠఱၚརሠᙕ ၚਰᙕ፡ୣࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄺၚ޺෹‫ڬ‬ላ‫ڬ‬፡ఱၚརᙕ ఱ፡ሠࣰ෹ਰ ΢ᙕ დᄻၚᐋఱࡂࣰᙕ ሠၚ໪ࣰᙕ ఱ໪ეᄺࣰሠሠఱၚཧሠᙕ ၚਰᙕ ፡ୢࣰᙕ ఱ໪დືࣰ໪ࣰར፡‫ڬ‬፡ఱၚརᙕ ࣰᒈდࣰᄺఱࣰར޺ࣰᙕ ᑋఱ፡ୢᙕ ፡ୣ‫ڬ‬፡ᙕ დᄻၚ޺෹‫ڬ‬ላ‫ڬ‬፡ఱၚརᙕ ࡂᎍᄺఱར૥ᙕ ఱ዁ሠᙕ ਰఱᅆሠ፡ᙕ ᒥࣰ‫ڬ‬ᄺγᙕ ‫ڬ‬རࡁᙕ ᄻࣰᐋఱࣰᑋᙕ ‫ڬ‬ᙕ ໪ၚᄻࣰᙕ ᄻࣰ޺ࣰར፡ᙕ დᄻၚ޺෺‫ڬ‬ላ‫ڬ‬፡ఱၚརᙕ ᑋୣఱ޺ୢᙕ ᄻࣰდᄺࣰሠࣰར፡ሠᙕ ‫ڬ‬ᙕ დᄻၚརၚᎍཧ޺ࣰࡂᙕ ޺ୣ‫ڬ‬ར૥ࣰᙕ ਰᄻၚ໪ᙕ፡ୢࣰᙕ ෹‫ڬ‬རࡂᙕ፡ၚᙕ፡ୢࣰᙕ፡ఱ෹෹ࣰᄻ ᙕ ޼ၚར޺ࣰე፡ᙕၚਰᙕ፡ୢࣰᙕׂᎍᄻ‫ڬ‬෹ᙕԴ‫ڬ‬རࡂሠᙕ֟ᄻၚ޺෹‫ڬ‬ላ‫ڬ‬፡ఱၚརűᙕ )ɕ @ɕS ɕ2„ Eɕ- ɕɕɕ2 ɕ ֟ᄻఱၚᄻᙕ ፡ၚᙕ ፡ୢࣰᙕ ׂࣰᐋၚ෹ᎍ፡ఱၚརÙᙕ ፡ᑋၚᙕ დᄺఱར޺ఱე‫ڬ‬෹ᙕ ᐋఱࣰᑋሠᙕ ၚརᙕ ෺‫ڬ‬རࡂᙕ ᄻࣰਰၚᄺ໪ᙕ ࣰᒈఱሠ፡ࣰࡂᙕ ‫ڬ‬໫ၚཧ૥ᙕ ፡ୣၚሠࣰᙕ ᑋୣၚᙕ დᎍᄺდၚᄻ፡ࣰࡂᙕ ፡ၚᙕ ਰ‫ڬ‬ᐋၚᄻᙕ ‫ڬ‬ᙕ ޺ୣ‫ڬ‬ར૥ࣰᙕ ఱརᙕ ፡ᄺ‫ࡂڬ‬ఱ፡ఱၚར‫ڬ‬෹ᙕ ሠᒥሠ፡ࣰ໪ሠ ͸ᙕ ‫ڬ‬རᙕ ၚਰਰఱ޺ఱ‫ڬ‬෹ ᙕ ෹ఱརࣰᙕ ‫ڬ‬རࡂᙕ ‫ڬ‬ᙕ ሠ፡ᎌࡁࣰར፡ ᙕ ෹వརࣰűᙕ ؉ୢࣰᙕ ၚਰਰఱ޺ఱ‫ڬ‬෹ᙕ ෹ఱརࣰᙕ ᑋ‫ڬ‬ሠᙕ ࡂࣰᐋࣰ෹ၚეࣰࡂᙕ ਰၚ෹ືၚᑋఱར૥ᙕ ፡ୣࣰᙕ ‫ݯڬ‬ၚᄺ፡ఱᐋࣰᙕ ޺ၚᎍეᙕ ࡂgः፡‫ڬ‬፡ᙕ ၚਰᙕ Ȇ ͛˸ǧƅᙕ ӂ፡ᙕ ࣰ໪ეୣ‫ڬ‬ሠఱᓯࣰࡂᙕ ፡ୣࣰᙕ ࡂࣰᐋࣰືၚე໪ࣰར፡ᙕ ၚਰᙕ ‫ ڬ‬ሠࣰᄻఱࣰሠᙕ ၚਰᙕ ໪ၚࡂࣰሠ፡ᙕ෺ࣰ૥ఱሠ෹‫ڬ‬፡ఱᐋࣰᙕეᄺၚეၚሠ‫ືڬ‬ሠÙᙕ ᑋୣవ޺ୢᙕ ࡂࣰ‫ڬ‬෹፡ᙕ ᑋఱ፡ୣᙕ ፡ࣰརᎌᄺࣰᙕ ᄺࣰਰၚᄺ໪ᙕ ఱརᙕ ፡ୣࣰᙕ རၚᄹ፡ୣࣰᄺརᙕ ୣఱ૥ୣ෹‫ڬ‬རࡂሠÙᙕ ፡ୣࣰᙕ ሠၚij޺‫ڬ‬෺෺ࣰࡂᙕ ޺ၚ໫ı ଵ %ଵ 3 ™ç ଵ Ⱦଵ 3 "IJ ଵ K ଵ ଵ 3ÿ™ଵ x) ଵ Kଵ O ™ଵ g &ଵ 3 ™ç ଵ ƷĪଵ @ ଵ ‫ݤ‬ଵ |4&ଵ % Lଵ @ଵ ǣ Ë&ଵ w  ଵ Ŭ ଵ @6 ଵ ŕ ଵ wLଵ ô+ଵ ǣ% ™ଵô& |4 Ë & ଵ  K  ଵ âO ™ଵg ଵ 3 ™Ň IJ ƺ Lଵ ôଵ O ™ଵ g ଵ 3 ™Ň &ଵ % Lଵ 6ଵ ǣ4Ë L ଵ gIJç  ଵ V ଵ  ଵ ç &ଵ  Ī  L ଵ K ଵ ଵ )çଵ ) ଵ ଵ ö  ଵ  ơ ଵ çଵ Kଵ ™"™IJ ¹ଵ %™ ଵ ଵ  IJÿIJ ଵ  ଵ IJଵ ଵ  ™ଵ )ଵ  ଵ K ଵ ଵ ™ ଵ   ÿ &ଵ )IJଵ ଵ   IJ ଵ ™Ɩଵ K ଵ ଵ   ଵ  "&ଵ IJ ଵ )ଵ   ™Ɩଵ    ଵ ଵ ™Ɩଵ ଵ ™™ଵ  ™ଵ ™ ଵ V ଵ   ଵ K Īଵ Îଵ Ɩଵ " ଵ  ଵ ଵ  ଵ ÿଵ ଵ   IJଵ Kଵ ଵ " ç ଵ ଵ K ଵ ଵ  ÿ &ଵ K ଵ Vç™ଵ ଵ ଵ KKǷ )IJଵ  ଵ Kଵ ଵ  )´ ଵ )ଵ ™ଵ   ଵ ™ÿ ଵ ଵ " ™ଵ ଵ ଵ  ͠™  ™ଵ Ň˃Lଵ @ଵ H†ଵ Gç&ଵ Q IJIJ  ƒ ଵ Gଵ ȑ Ɩଵ G ଵ ȑ ଵ xKKଵ k ଵ ` ଵ ǣg &ଵ |4Ë&ଵ  L ଵ  @  L ଵ 6ଵ %ଵ 3 ™Ň ଵ ଵ 3 "IJ ଵ K  ଵ   ଵ x) ଵ   ଵ ȑ ™ଵ ÿƖଵ ଵ Ŭ"   ଵ Kଵ   ଵ C֓ଵ  K ଵ 3   &ଵ 3 ͨŇ ଵ w ,ଵ ô + ଵKଵ |4 &ଵ Ʒ IJ ଵ Ŭ ଵ @6 ଵ ŕ ଵ w  L ଵ ôôଵ ǣC ଵ & ଵ |4Ë L ଵ 4ଵ %ଵ 3ਵ™Ň ଵ ଵ 3 " ଵ K ଵ y" ç ଵ x) IJଵ Kଵ Ŧ ÿଵ g ଵ  ଵ QV ଵ Ŧ ÿଵ `ધ&ଵ 3 ™Ň ଵ wLଵ 6|ଵ Kଵ |4&ଵ w IJ ଵŬ ଵ@6 ଵŕ ଵƷĪଵ 6 ଵ ǣȽ™Ɩଵ ô+&ଵ $‫܌‬oLଵ +ଵ O ™ଵgX ଵ 3 ™Ň &ଵ  çÿ™Lଵ ɛǧʈᙕ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb ໪ᎌར‫ڬ‬ເOᙕ ፡ࣰརᎌᄹࣰᙕ ᄹࣰ૥఼ၚརΣᙕ ‫ڬ‬૥ᄹ఼޼ᎌ෹፡ᎌᄹ‫ڬ‬ขᙕ ፡ࣰར‫ڬ‬ར޼ᒦᙕ ᄹࣰਲ਼ၚᄹ໪ ΢ᙕ ޼‫ڬࡂڬ‬ሠ፡ᄹ‫ڬ‬෹ᙕ ሠᎌᄺᐋࣰᒥᙕ ‫ڬ‬རࡂᙕ ፡ఱࣰࣘᙕ ᄹࣰ૥ఱሠ፡ᄹ‫ڬ‬፡ఱၚར ΢ᙕ ෹‫ڬ‬རࡁᙕ ፡‫ڬ‬ᒈᙕ ᄹࣰਭၚᄹ໪Ùᙕ ఱར޼෹ᎌࡁఱར૥ᙕ დᄹၚ૥ᄹࣰሠሠఱᐋࣰᙕ ፡‫ڬ‬ᒈ‫ڬ‬፡ఱၚརᙕ ၚਭᙕ ᎌརᎌ፡ఱ෹ఱᓱࣰࡂᙕ ෹‫ڬ‬རࡂሠ ΢ᙕ ‫ڬ‬རࡁᙕ ‫ݯڬ‬ၚ෹ఱ፡ఱၚརᙕ ၚਭᙕ ፡ୣࣰᙕ დᄹ‫޼ڬ‬፡ఱ޼ࣰᙕ ၚਭᙕ ૥ᄺ‫ڬ‬ར፡ఱར૥ᙕ ૥ၚᐋࣰᄹར໪ࣰར፡ᙕ ෹‫ڬ‬རࡁᙕ ఱརᙕ ఱརࡁఱᐋఱࡂᎌ‫ڬ‬෹ᙕ ၚᑌརࣰᄺሠୣఱდᙕ ፡ၚᙕ დၚ෹ఱ፡ఱ޼‫ڬ‬෹෹ᒦᙕ ෹ၚᒦ‫ڬ‬෹ᙕ დࣰᄹሠၚརሠ̫ᘩᙕ ؉ୣࣰᙕ ໪ၚሠ፡ᙕ ᄹ‫ࡁڬ‬ఱ޺‫ڬ‬෹ᙕ ၚਭਭఱ޼ఱ‫ڬ‬෹ᙕ დᄺၚდၚሠ‫ڬ‬෹ᙕ ޺‫ڬ‬໪ࣰᙕ ఱརᙕ Ȇ ̡ͤʆÙᙕ ᑌୣࣰརᙕ ፡ୣࣰᙕ Րఱརఱሠ፡ᄹᒥᙕ ၚਭᙕ Դ‫ڬ‬རࡁᙕ ׂࣰਭၚᄺ໪ᙕ ‫ڬ‬རࡁᙕ σࡁ໪ఱརఱሠ፡ᄺ‫ڬ‬፡ఱၚརᙕ ᎌᄺ૥ࣰࡂᙕ ޺ၚརሠఱࡂࣰᄺ‫ڬ‬፡ఱၚརᙕ ၚਭᙕ ࣰᒈდᄺၚდᄺఱ‫ڬ‬፡సၚརᙕ ‫ڬ‬རࡂᙕ ᄹࣰࡁఱሠ፡ᄺఱ‫ݯ‬ᎌ፡ఱၚརᙕ ၚਭᙕ ୣၚ෹ࡂఱར૥ሠᙕ ఱརᙕ ࣰᒈ޼ࣰሠሠᙕ ၚ਱ᙕ ‫ڬ‬ᙕ ޼ࣰఱ෹ఱར૥͉ᘳᙕ ӂརᙕ ਭ‫޺ڬ‬፡Ùᙕ ୣၚᑌࣰᐋࣰᄻÙᙕ ‫ڬ‬ᙕ ޼ၚ໪‫ݯ‬ఱར‫ڬ‬፡ఱၚརᙕ ၚਭᙕ ֟‫ڬ‬ᄹ෹ఱ‫ڬ‬໪ࣰར፡‫ڬ‬ᄹᒥᙕ ၚდდၚሠఱ፡ఱၚརᙕ ‫ڬ‬རࡂᙕ ෹‫޺ڬ‬ඬᙕ ၚਭᙕ დၚ෹ఱ፡ఱ޺‫ڬ‬෹ᙕ ᑌఱ෹෹ᙕ ၚརᙕ ፡ୣࣰᙕ თ‫ڬ‬ᄺ፡ᙕ ၚ਱ᙕ ፡ୣࣰᙕ ࣰᒈࣰ޼ᎌ፡ఱᐋࣰᙕ ໪ࣰ‫ڬ‬ར፡ᙕ ፡ୣ‫ڬ‬፡ᙕ ᐋࣰᄺᒦᙕ ෹ఱ፡፡෹ࣰᙕ ၚਭᙕ ᑌୣ‫ڬ‬፡ᙕ ᑌ‫ڬ‬ሠᙕ დᄺၚდၚሠࣰࡂᙕ ᑌ‫ڬ‬ሠᙕ ࣰᐋࣰᄺᙕ ࣰར‫޼ڬ‬፡ࣰࡁᙕ ఱར፡ၚᙕ ෹‫ڬ‬ᑌ͝ᘩᙕ ӂརᙕ ፡ୣࣰᙕ დၚ෺ఱ፡ఱ޼‫ڬ‬෺ᙕ ޺ఱᄺ޺ᎌ໪ሠ፡‫ڬ‬ར޺ࣰሠᙕ ၚਭᙕ ፡ୣࣰᙕ ໪ၚར‫ڬ‬ᄹ޺ୣᒦÙᙕ ሠఱ૥རఱਭఱ޺‫ڬ‬ར፡ᙕ ෹‫ڬ‬རࡂᙕᄹࣰਭၚᄺ໪ᙕ ሠࣰࣰ໪ࣰࡂᙕ፡ၚᙕ‫ࣰݯ‬ᙕ‫ڬ‬རᙕఱ໪დၚሠሠఱ‫ݯ‬ఱ෹ఱ፡ᒦŶᙕ Ӂརᙕ ޼ၚར፡ᄹ‫ڬ‬ሠ፡ᙕ ፡ၚᙕ ፡ୣࣰᙕ ၚਭਭఱ޼ఱ‫ڬ‬෹ᙕ ෹ఱརࣰÙᙕ ፡ୣࣰᙕ ሠ፡ᎌࡂࣰར፡ᙕ ෺ఱརࣰᙕ ࡂᎌᄺఱར૥ᙕ ፡ୣࣰᙕ ෹‫ڬ‬ሠ፡ᙕ ਭࣰᑌᙕ ᒥࣰ‫ڬ‬ᄺሠᙕ ၚਭᙕ ፡ୣࣰᙕ ໪ၚར‫ڬ‬ᄺ޺ୣᒥᙕ ᑌ‫ڬ‬ሠᙕ ࡂఱᄹࣰ޼፡ᙕ ‫ڬ‬རࡂᙕ ᄹ‫ࡂڬ‬ఱ޼‫ڬ‬෹űᙕ ‫כ‬፡ᎌࡁࣰར፡ሠᙕ ᐋఱ૥ၚᄹၚᎌሠ෹ᒥᙕ ሠᎌდდၚᄹ፡ࣰࡁᙕ ፡ୣࣰᙕ ਱ఱᄺሠ፡ᙕ ‫ڬ‬૥ᄺఱ޺ᎌ෹ᔜ ፡ᎌᄹ‫ڬ‬෹ᙕ፡ࣰར‫ڬ‬ར޼ᒦᙕ ᄺࣰਭၚᄺ໪ᙕ ‫ݯ‬ఱ෹෹ᙕᑌୣࣰརᙕఱ፡ᙕ޼‫ڬ‬໪ࣰᙕ‫ࣰݯ‬ਭၚᅆࣰᙕ ֟‫ڬ‬ᄹ෹ఱ‫ڬ‬໪ࣰར፡ᙕ ఱརᙕ Ȇ ͤ˸˕Ùᙕ ‫ڬ‬རࡁᙕდ‫ڬ‬ᄺ፡ఱ޺ᎌ෺‫ڬ‬ᄺ෺ᒥᙕ ᑌఱ፡ୣᙕ ፡ୣࣰᙕ ਭၚᄹ໪‫ڬ‬፡ఱၚརᙕ ၚ਱ᙕ ፡ୣࣰᙕ ‫ز‬རఱᐋࣰᄺሠఱ፡ᒦᙕ ‫כ‬፡ᎌࡂࣰར፡ሠᙕ ‫ز‬རఱၚརᙕ ၚਭᙕ σࡂࡂఱሠᙕ σ‫ڬݯڬݯ‬ᙕ ఱརᙕ Ȇ ͤ˸̡ᙕ ෹‫ڬ‬རࡁᙕ ፡ၚᙕ ፡ୣࣰᙕ ፡ఱ෹෹ࣰᄺ ᙕ ‫ڬ޼ࣰݯ‬໪ࣰᙕ ፡ୣࣰᙕ ሠ෹ၚ૥‫ڬ‬རᙕ ၚਭᙕ ፡ୣࣰᙕ ሠ፡ᎌࡂࣰར፡ᙕ ໪ၚᐋࣰ໪ࣰར፡űᙕ ؉ୣࣰᙕ རࣰ޺ࣰሠሠ‫ڬ‬ᄹᒦᙕ ޺ၚᄹၚ෹෹‫ڬ‬ᄹᒦᙕ ᑌ‫ڬ‬ሠᙕ ፡ୣ‫ڬ‬፡ᙕ ‫ݯڬ‬ሠࣰར፡ࣰࣰᙕၚᑌརࣰᄹሠᙕ ሠୣၚᎌ෹ࡂᙕ ‫ࣰݯ‬ᙕ ࡁࣰდᄺఱᐋࣰࡁᙕ ၚਭᙕ፡ୣࣰఱᄹᙕ ᄹఱ૥ୣ፡ሠᙕ ፡ၚᙕ ෺‫ڬ‬རࡁᙕ ၚᄺᙕ፡ၚᙕ ఱ፡ሠᙕ਱ᄹᎌఱ፡ሠŶᙕ ӂསᙕ Ȇ ̟͛ʰÜᙕ ‫ڬ‬ሠᙕ ፡ୣࣰᙕ თၚᑌࣰᄹᙕ ၚ਱ᙕ Ҕ‫ڬ‬ఱ෹ࣰᙕ ‫ࣰכ‬෹෹‫ڬ‬ሠሠఱࣰhሠᙕ ᄹࣰ૥ఱ໪ࣰᙕ ᑌ‫ڬ‬རࣰࡂᙕ ‫ڬ‬རࡂᙕ ໪ఱ෺ఱ፡‫ڬ‬ᄺᒥᙕ ૥ᄺၚᎌდሠᙕ ໪ၚᐋࣰࡂᙕ ፡ၚᙕ ਱ఱ෹෹ᙕ ፡ୣࣰᙕ ᐋ‫޼ڬ‬ᎌᎌ໪ȈǬÙᙕ ሠఱ૥རఱ਱ఱ޼‫ڬ‬ར፡ᙕᄹᎌᄺ‫ڬ‬෹ᙕ෹‫ڬ‬རࡂᙕᅆࣰਭၚᄹ໪ᙕ‫ڬ޼ࣰݯ‬໪ࣰᙕდၚ෹ఱ፡ఱ޺‫ڬ‬෹෹ᒦᙕᄺࣰ‫ڬ‬෹ఱሠ፡ఱ޺ᙕ ਱ၚᄹᙕ ፡ୣࣰᙕ ਱ఱᄺሠ፡ᙕ ፡ఱ໪ࣰűᙕυᙕ ޼ఱᐋఱ෹ఱ‫ڬ‬རᙕ޼‫ݯڬ‬ఱརࣰ፡ᙕਭၚᄺ໪ࣰࡁᙕ ၚརᙕ ፡ୣࣰᙕ ‫ࡂڬ‬ᐋఱ޼ࣰᙕ ၚ਱ᙕ ፡ୣࣰᙕ໪ఱ෹ఱ፡‫ڬ‬ᄺᒦᙕ፡ၚၚඬᙕᎌდᙕ ፡ୣࣰᙕ ໪ၚሠ፡ᙕ ᄹ‫ࡂڬ‬ఱ޺‫ڬ‬෹ᙕ ၚ਱ᙕ ፡ୣၚሠࣰᙕ დᄹၚᙕდ ၚሠᙕ‫ ڬ‬෹ሠᙕ ࣰ‫ڬ‬ᄹ෹ఱࣰᄹᙕ ࡁࣰᐋࣰ෹ၚდࣰࡂᙕ ‫ݯ‬ᒦᙕ ፡ୣࣰᙕ Րఱརఱሠ፡ᄺᒦᙕ ၚਭᙕ Դ‫ڬ‬རࡂᙕ ׂࣰਭၚᄹ໪ᙕ ‫ڬ‬རࡂᙕ σࡂ໪ఱརఱሠ፡ᄹ‫ڬ‬፡ఱၚརŶᙕ ӂརᙕ σდᄺఱ෹ᙕ Ȇ ̟͛ʰᙕ ፡ୣࣰᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰਭၚᄺ໪ᙕ დၚ෹ఱ޼ᒥᙕ ᑌ‫ڬ‬ሠᙕ ሠ፡‫ڬ‬፡ࣰࡁᙕ ፡ၚᙕ ‫ࣰݯ‬ᙕ‫ڬ‬ሠᙕਭၚ෹෹ၚᑌሠ ͸ᙕ Ҕၚ෹ࡂఱར૥ሠᙕఱརᙕࣰᒈ޼ࣰሠሠᙕၚਭᙕᑌୣᙕ‫ ڬ‬፡ᙕఱሠᙕ ޼ၚརሠఱࡂࣰᄹࣰࡂᙕ ‫ڬ‬ᙕ ᄹࣰ‫ڬ‬ሠၚར‫ݯڬ‬෹ࣰᙕ ෹ఱ໪ఱ፡ᙕၚਭᙕ፡ୣࣰᙕ ၚᑌརࣰᄹhሠᙕ ޼‫ڬ‬დ‫޼ڬ‬ఱ፡ᒦᙕ ፡ၚᙕ ࡂࣰᐋࣰ෹ၚდᙕ ᑌఱ෹෹ᙕ ‫ࣶݯ‬ᙕ ፡‫ڬ‬ඬࣰརᙕ ၚᐋࣰᄺᙕ ‫ݯ‬ᒦᙕ ፡ୣࣰᙕ ѿၚᐋࣰᄺར໪ࣰར፡ᙕ ‫ڬ‬རࡁᙕ ᑌఱ෹෺ᙕ ‫ࣰݯ‬ᙕ ࡂఱሠ፡ᄹఱ‫ݯ‬ᎌ፡ࣰࡁᙕ ፡ၚᙕ ፡ୣၚሠࣶᙕ ᑌୣၚᙕ ᑌఱ෹෹ᙕ ໪‫ڬ‬ඬࣰᙕ ፡ୣࣰఱᄹᙕ ෺ఱᐋఱར૥ᙕ ‫ݯ‬ᒥᙕ ᑌၚᄹඬఱར૥ᙕ ၚརᙕ ፡ୣࣰᙕ ෹‫ڬ‬རࡂ฿Ȉű ᙕ Ѝၚ໪დࣰརሠ‫ڬ‬፡ఱၚརᙕᑌ‫ڬ‬ሠᙕ ፡ၚᙕ ‫ࣰݯ‬ᙕ დ‫ڬ‬ఱࡂᙕਭၚᄹᙕ ࣰᒈდᄺၚდᄹఱ‫ڬ‬፡ࣰࡂᙕ෹‫ڬ‬རࡂŶᙕ ժࣰ‫ڬ‬ᄹ෹ᒦᙕ ‫ڬ‬ᙕ ᒦࣰ‫ڬ‬ᄻᙕ ᑌ‫ڬ‬ሠᙕ ፡ၚᙕ თ‫ڬ‬ሠሠÙᙕ ୣၚᑌࣰᐋࣰᄹÙᙕ ‫ࣰݯ‬ਭၚᄹࣰᙕ დᄹၚ໪ᎌ෺૥‫ڬ‬፡ఱၚརᙕ ၚਭᙕ ፡ୣࣰᙕ ׂᎌᄺ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡁሠᙕ ֟ᄹၚ޼෹‫ڬ‬໪‫ڬ‬፡ఱၚརŶᙕ Րࣰ‫ڬ‬རᑌୣఱ෹ࣰᙕ ፡ୣࣰᙕ ޼ၚར፡ᄹၚ෹෹ఱར૥ᙕ ໪ఱ෹ఱ፡‫ڬ‬ᄺᒦᙕ ૥ᄺၚᎌდᙕ ‫ڬ޼ࣰݯ‬໪ࣰᙕ ఱར޺ᄹࣰ‫ڬ‬ሠఱར૥෺ᒥᙕ ሠၚ޼ఱ‫ڬ‬෺ఱሠ፡ᙕఱརᙕ ఱ፡ሠᙕ ၚᄹఱࣰར፡‫ڬ‬፡ఱၚརÙᙕ ፡ୣࣰᙕ ෹ࣰ‫ࣰࡂڬ‬ᄹሠୣఱთᙕ ޼ୣ‫ڬ‬ར૥ࣰࡁᙕ సརᙕ ፡ୣࣰᙕ Րఱརఱሠ፡ᄹᒦᙕ ၚਭᙕ Դ‫ڬ‬རࡁᙕ ׂࣰਭၚᄺ໪ᙕ ‫ڬ‬རࡁᙕ σࡂ໪ఱརసሠ፡ᄹ‫ڬ‬፡ఱၚརȈɚÙᙕ ‫ڬ‬རࡂᙕ ሠᎌ޼޼ࣰሠሠసᐋࣰᙕ ࡁᄹ‫ڬ‬਱፡ሠᙕ ၚਭᙕ ፡ୣࣰᙕ ෹ࣰ૥ఱሠ෺‫ڬ‬፡ఱၚརᙕ ‫ڬ޺ࣰݯ‬໪ࣰᙕ ໪ၚᄺࣰᙕ ‫ڬ‬རࡁᙕ ໪ၚᄹࣰᙕ ᄹࣰሠ፡ᄺఱ޼፡ఱᐋࣰᙕ ၚ਱ᙕ დᄹఱᐋ‫ڬ‬፡ࣰᙕ ෹‫ڬ‬རࡂᙕ ၚᑌརࣰᄺሠୣఱდŶᙕ ѣఱར‫ڬ‬෹෹ᒦᙕ ፡ୣࣰᙕ རၚ፡ఱၚརሠᙕ ‫ݯ‬ၚ፡ୣᙕ ၚਭᙕ ޺ၚར፡ఱརᎌࣰࡁᙕ დᄺఱᐋ‫ڬ‬፡ࣰᙕ ၚᑌརࣰᄹሠఙసდᙕ ၚ਱ᙕ ᄹᎌᄹ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂÙᙕ ᑌఱ፡ୣᙕ ‫ڬ‬ᙕ ޼ࣰఱ෹ఱར૥Ùᙕ ‫ڬ‬རࡁᙕ ၚ਱ᙕ ޼ၚ໪დࣰརሠ‫ڬ‬፡ఱၚརᙕ ਭၚᄹᙕ ࣰᒈდᄺၚდᄺఱᔝ ‫ڬ‬፡ࣰࡁᙕ෹‫ڬ‬རࡁᙕᑌࣰᄹࣰᙕ ‫ڬݯڬ‬རࡁၚརࣰࡂᙕ ఱརᙕ਱‫ڬ‬ᐋၚᄺᙕၚਭᙕ ఱ໪໪ࣰࡁఱ‫ڬ‬፡ࣰÙᙕ ᎌར޺ၚ໪დࣰརሠ‫ڬ‬፡ࣰࡂᙕ დᎌ‫ݯ‬෺ఱ޺ᙕ ၚᑌརࣰᄺሠୣఱდᙕ ၚ਱ᙕ ‫ڬ‬෹෹ᙕ ᄺᎌᄹ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡁŶᙕ ‫ز‬རࡁࣰᄹᙕ ፡ୣఱሠᙕ རࣰᑌᙕ ሠ޺ୣࣰ໪ࣰÙᙕ ፡ୣᄺࣰࣰᙕ ໪‫ڬ‬፡፡ࣰᄺሠᙕ ‫ڬ‬ᄹࣰᙕ ၚਭᙕ დ‫ڬ‬ᄺ፡ఱ޺ᎌ෺‫ڬ‬ᄺᙕ ఱར፡ࣰᄺࣰሠ፡ ͸ ᙕ ፡ୣࣰᙕ፡ࣰརᎌᄹࣰᙕሠᒦሠ፡ࣰ໪ᙕ‫ݯ‬ᎌఱ෹፡ᙕᎌდၚརᙕ፡ୣࣰᙕ‫ڬݯ‬ሠࣰᙕၚ ਱ ᙕდᎌ‫ݯ‬෺ఱ޺ᙕ ၚᑌརࣰᄹሠୣఱდÙᙕ ፡ୣࣰᙕდᄺၚᐋఱሠఱၚརሠᙕ ໪‫ࣰࡁڬ‬ᙕਭၚᅊᙕ ޼ၚ໪დࣰརሠ‫ڬ‬፡ఱၚསᙕ ਱ၚᄹᙕ ࣰᒈდᄺၚდᄺఱ‫ڬ‬፡ࣰࡂᙕ ‫ڬ‬ሠሠࣰ፡ሠᙕ ၚ፡ୣࣰᄺᙕ ፡ୣ‫ڬ‬རᙕ ፡ୣࣶᙕ ෹‫ڬ‬རࡁᙕ ఱ፡ሠࣰ෹ਭÙᙕ ‫ڬ‬རࡂᙕ ᎌሠࣰᙕ ၚਭᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར፡ᙕ‫ڬ‬ሠሠၚ޼ఱ‫ڬ‬፡ఱၚརሠ ᙕ ‫ڬ‬ሠᙕ፡ୣࣰᙕ໪ࣰ‫ڬ‬རሠᙕ਱ၚᄹᙕ޺ၚརሠ፡ᄹᎌ޼፡ఱར૥ᙕརࣰᑌᙕ‫ڬ‬૥ᄹ‫ڬ‬ᄹఱ‫ڬ‬རᙕდ‫ڬ‬፡፡ࣰᄺརሠűᙕ ®ଵ #ଵ `Êଵ 8uaଵ ƹăUଵ OãB ଵ uଵ QuBu _ଵ %ଵ Nଵ #U*ଵ uଵ wBȄ8"?B  đ aଵ Rଵ sNă%ଵ ğ)ଵ O"u)ଵ 2$tŎD$ଵ ¬  $Do ĵଵ Ò,ଵ NBଵ Ǚଵ 8 Ê ଵ mu'ଵ ğUଵ Uଵ 3ଵ uଵ k u?ଵ QuBuଵ ¬%“ଵ Gଵ w?Uaଵ $4o ĵଵ Uଵ Ò Ê ଵ H£aଵ âQB _ଵ wuBu5Bଵ Bãଵ O?ଵ ğUଵ 3B? Baଵ  $4 đ “ଵ su"u*ଵ Bãଵ mu£Buଵ ăUଵ Gଵ Nଵ w)aଵ wBÊଵ 6$ଵ ¬Ò*ƑC£ଵ  ®4oěଵ Rଵ Haଵ BÊଵ uěଵ Bଵ $Êଵ ଵ NBଵǙଵ muଵaଵ Běଵ £uÊଵ Bଵ ®aଵ  ş ଵŎěଵ Dଵ #ଵ ?*ଵ GB Baଵ BÊଵ uଵ BଵŎÊଵ ଵ ĥwƦଵNuଵ ԁଵ3B?u£*ଵ 8uB đ aଵ QBuଵ `Uaଵ %u?ଵ a ଵ $6ěଵ  2 ଵ H·ଵ BÊଵ uÊଵ Bଵ $ěଵ Tŵ{ʍ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb )ɕ ".'0 ؉ୣࣰᙕ ዁ࣰརᎌᅆࣰᙕ ቚᒥቚ዁ࣰ໪ᙕ ၚਰᙕ ዁ୣࣰᙕ ׂᎌᅆ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂቚᙕ ֟ᅆၚ޺෺‫ڬ‬໪‫ڬ‬዁ఱၚརᙕ ఱቚᙕ རၚ዁ᙕ ᑋఱ዁ୣၚᎌ዁ᙕ ޺ၚ໪ე෹ఱ޻‫ڬ‬዁హၚརƅᙕ σ෹዁ୣၚᎌ૥ୣᙕ‫ڬ‬෹෺ᙕᅆᎌᄹ‫ڬ‬෹ᙕ෹‫ڬ‬རࡂᙕహቚᙕ޺ၚ෹෹ࣰ޺዁ఱᐋࣰ෹ᒥᙕၚᑋརࣰࡂᙕ‫ݯ‬ᒦᙕ዁ୣࣰᙕл዁ୣఱၚეహ‫ڬ‬རᙕეࣰၚე෹ࣰÙᙕ዁ఱ዁෹ࣰᙕࡂၚࣰቚᙕརၚ዁ᙕ ቚࣰࣰ໪ᙕ ዁ၚᙕ ‫ࣰݯ‬ᙕ ᐋࣰቚ዁ࣰࡂᙕ ఱརᙕ ዁ୣࣰᙕ ቚ዁‫ڬ‬዁ࣰÙᙕ ਭၚᅆᙕ ዁ୣࣰᙕ ར‫ڬ‬዁ఱၚར‫ڬ‬෹ᙕ ૥ၚᐋࣰᅆར໪ࣰར዁ᙕ ఱቚᙕ ૥ఱᐋࣰརᙕ ዁ୣࣰᙕ ეၚᑋࣰᄹᙕ ዁ၚᙕ ࣰᒈეᅆၚეᅆఱ‫ڬ‬዁ࣰᙕ ෹‫ڬ‬རࡂᙕ ‫ࣰݯ‬෹ၚར૥ఱར૥ᙕ ዁ၚᙕ ეࣰ‫ڬ‬ቚ‫ڬ‬ར዁ᙕ ‫ڬ‬ቚቚၚ޻ఱ‫ڬ‬዁హၚརቚȇʌ  ƅᙕ թၚᅆᙕ ఱቚᙕ ዁ୣࣰᅆࣰᙕ హརᙕ ዁ୣࣰᙕ ෹ࣰ૥ఱቚ෹‫ڬ‬ᔥ ዁హၚརᙕ ‫ڬ‬རᒦᙕ ࣰᒈე෹ఱ޺ఱ዁ᙕ ቚ዁‫ڬ‬዁ࣰ໪ࣰར዁ᙕ ዁ୣ‫ڬ‬዁ᙕ ዁ఱ࡬ࣰᙕ ዁ၚᙕ ෺‫ڬ‬རࡂᙕ ఱቚᙕ ᐋࣰቚ዁ࣰࡂᙕ ఱརᙕ ዁ୣࣰᙕ ეࣰ‫ڬ‬ቚ‫ڬ‬ར዁ᙕ ‫ڬ‬ቚቚၚ޺ఱ‫ڬ‬዁ఱၚརቚÙᙕ ‫ڬ‬෹዁ୣၚᎌ૥ୣᙕ ዁ୣࣰᙕ ‫ڬ‬ቚቚၚ޺ఱ‫ڬ‬዁ఱၚརቚhᙕ ਱ᎌར޺዁ఱၚརቚᙕ ᑋఱ዁ୣᙕ ᅆࣰ૥‫ڬ‬ᅆࡂᙕ ዁ၚᙕ ෹‫ڬ‬རࡂᙕ ࡂఱቚ዁ᅆఱ‫ݯ‬ᎌ዁ఱၚརᙕ ቚᎌ૥૥ࣰቚ዁ᙕ ‫ڬ‬ቚᙕ ໪ᎌ޺ୣȇʲᘩᙕ ٝୣఱ෹ࣰᙕ ቚᎌ޺ୣᙕ ᄯᎌࣰቚ዁ఱၚརቚᙕ ‫ڬ‬ቚᙕ ዁ၚᙕ ዁ୣࣰᙕ ར‫ڬ‬዁ᎍᅆࣰᙕ ၚਰᙕ ዁ୣࣰᙕ ᎌ෹዁హ໪‫ڬ‬዁ࣰᙕ ዁ఱ࡬ࣰᙕ ໪‫ڬ‬ᒥᙕ ‫ࣰݯ‬ᙕ ᅆ‫ڬ‬዁ୣࣰᄹᙕ ዁ୣࣰၚᄹࣰ዁ఱ޺‫ڬ‬෹Ùᙕ዁ୢࣰᅆࣰᙕ‫ڬ‬ᅆࣰᙕ ‫ڬ‬෹ቚၚᙕᎌར޺ࣰᅆ዁‫ڬ‬ఱར዁ఱࣰቚᙕ ᅆࣰ૥‫ڬ‬ᅆࡂఱར૥ᙕ዁ୣࣰᙕ໪ၚᅆࣰᙕეᅆ‫޺ڬ‬዁ఱ޺‫ڬ‬෹ᙕᄯᎌࣰቚ዁ఱၚརᙕ ၚਰᙕ዁ୣࣰᙕ ෺ࣰ૥‫ڬ‬෹ᙕ ეၚቚహ዁హၚརᙕ ၚਰᙕ ޺ᎌ෹዁హᐋ‫ڬ‬዁ၚᅆቚƅᙕ ٝఱ዁ୣᙕ ෹హ໪ఱ዁ࣰࡂᙕ ࣰᒈ޺ࣰე዁ఱၚརቚȇ˗Ùᙕ ዁ୣࣰᙕ ޺ᎌ෹዁ఱᐋ‫ڬ‬዁ၚᅆÙᙕ హਰᙕ ਰၚᄹ໪ࣰᅆ෺ᒥᙕ ‫ڬ‬ᙕ ዁ࣰར‫ڬ‬ར዁ᙕ ၚᅆᙕ ‫ڬ‬ᙕ ୣఱᅆࣰࡂᙕ ෹‫ݯڬ‬ၚᅆࣰᅆÜᙕ ఱቚᙕ ޺ၚརਰఱᅆ໪ࣰࡂᙕ ఱརᙕ ‫ڬ‬ᙕ རၚརį዁ᅆ‫ڬ‬རቚਰࣰᅆ‫ݯڬ‬෹ࣰᙕ ეၚቚቚࣰቚቚၚᅆᒥᙕ ᄹహ૥ୣ዁ ᙕ ၚᐋࣰᅆᙕ ዁ୣࣰᙕ ෹‫ڬ‬རࡂᙕ ୣࣰᙕ ዁ఱ෹෺ቚᙕ ၚᅆÙᙕ ეᅆࣰቚᎍ໪‫ݯڬ‬෹ᒥÙᙕ ᎌቚࣰቚᙕ ਰၚᅆᙕ ૥ᅆ‫ڬ‬ᓯహར૥ȇ̂¸ ƅᙕ ؉ୣ౺ቚᙕ ეၚቚቚࣰቚቚၚᄹᒥᙕ ᄹహ૥ୣ዁ᙕ ޺ၚར዁ఱརᎌࣰቚᙕ ၚར෹ᒦᙕ ቚၚᙕ ෹ၚར૥ᙕ ‫ڬ‬ቚᙕ ዁ୣࣰᙕ ޺ᎌ෹዁ఱᐋ‫ڬ‬዁ၚᅆᙕ ၚᅆᙕ ޺ࣰᅆ዁‫ڬ‬ఱརᙕ ቚᎌ޺޺ࣰቚቚၚᅆቚᙕ ᑋၚᅆඬᙕ ዁ୣࣰᙕ ე‫ڬ‬ᄹ዁ఱ޻ᎌ෺‫ڬ‬ᅆᙕ ୣၚ෹ࡂఱར૥ȇ̫Ùᙕ ‫ڬ‬རࡂᙕ ఱརᙕ ‫ڬ‬རᒦᙕ ࣰᐋࣰར዁ᙕ ఱརᙕ ዁ୣࣰᙕ ቚၚᎌ዁ୣࣰᅆརᙕ ეᅆၚᐋఱར޺ࣰቚᙕ ዁ୣࣰᙕ ׂᎌᅆ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂቚᙕ ֟ᅆၚ޺෹‫ڬ‬໪‫ڬ‬ᔥ ዁హၚརᙕቚ዁‫ڬ‬዁ࣰቚᙕ ዁ୣ‫ڬ‬዁ᙕ዁ୣࣰᙕდၚቚቚࣰቚቚၚᅆᒥᙕ ᅆఱ૥ୣ዁ᙕ ࣰᒈఱቚ዁ቚᙕ ၚར෹ᒥᙕ ᎌར዁హ෹ᙕ ეࣰ‫ڬ‬ቚ‫ڬ‬ར዁ᙕ ‫ڬ‬ቚቚၚ޺ఱ‫ڬ‬዁హၚརቚᙕ ‫ڬ‬෹෹ၚ዁ᙕ዁ୣࣰ൉ᇰᙕ ෹‫ڬ‬རࡂቚᙕ ዁ၚᙕ޺ᎌ෹዁ఱᐋ‫ڬ‬዁ၚᅆቚᙕఱརᙕ ᅆၚᎌ૥ୣ෹ᒥᙕ ࣰᄯᎌ‫ڬ‬෹ᙕ ე‫ڬ‬ᅆ޺ࣰ෹ቚȇ͉ᘫᙕ թၚᙕ ቚᎌࠟᙕ ‫ڬ‬෹෹ၚ዁໪ࣰར዁ᙕ హቚᙕ ዁ၚᙕ ࣰᒈ޺ࣰࣰࡂᙕ ዁ࣰརᙕ ୣࣰ޺዁‫ڬ‬ᅆࣰቚȇ͝ᘶᙕ քར޺ࣰᙕ ቚᎌ޺ୣᙕ ᅆࣰࡂఱቚ዁ᅆఱ‫ݯ‬ᎌ዁ఱၚརᙕ ၚ޺޺ᎌᅆቚÙᙕ ዁ୣࣰᙕ ‫ڬ‬෹෹ၚ዁዁ࣰࣰቚᙕ ‫ڬ‬ეე‫ڬ‬ᅆࣰར዁෺ᒥᙕ ‫ڬ‬ᅆࣰᙕ ዁ၚᙕ ஄‫ڬ‬ᐋࣰᙕ ዁ୣࣰᙕቚ‫ڬ‬໪ࣰᙕቚၚᅆ዁ᙕၚਰᙕეၚቚቚࣰቚቚၚᅆᒦᙕᅆఱ૥ୣ዁ᙕ‫ڬ‬ቚᙕఱቚᙕቚეࣰ޺ఱਰఱࣰࡂᙕਰၚᄻᙕ዁ୣࣰᙕეᅆࣰįᅆࣰࡂహቚ዁ᅆఱ‫ݯ‬ᎌ዁ఱၚརᙕეୣ‫ڬ‬ቚࣰɚǭᘳᙕ ؉ࣰར‫ڬ‬ར዁ቚᙕ ‫ڬ‬རࡂᙕ ୣఱᅆࣰࡂᙕ෹‫ݯڬ‬ၚᅆࣰᅆቚᙕ ‫ڬ‬ᅆࣰᙕ རၚ዁ÙᙕୣၚᑋࣰᐋࣰᅆÜᙕ ዁ୣࣰᙕ ၚར෹ᒥᙕ ၚརࣰቚᙕ ޺ၚརਰఱᅆ໪ࣰࡂᙕఱརᙕეၚቚቚࣰቚቚၚᅆᒥᙕ ᅆఱ૥ୣ዁ቚŶᙕ ׂࣰቚఱࡂࣰར዁ ᙕ ෹‫ڬ‬རࡂၚᑋརࣰᅆቚᙕ ᑋୣၚᙕ ୣ‫ڬ‬ᐋࣰᙕ ෹ࣰ‫ڬ‬ቚࣰࡂᙕ ‫ڬ‬෹෹ᙕ ዁ୣࣰఱᅆᙕ ෹‫ڬ‬རࡂᙕ ୣ‫ڬ‬ᐋࣰᙕ ዁ୣࣰᙕ ᅆఱ૥ୣ዁ᙕ ዁ၚᙕ ዁‫ڬ‬ඬࣰᙕ ეၚቚቚࣰቚቚఱၚརᙕ ၚਰᙕ ‫ڬ‬ᙕ ቚୣ‫ڬ‬ᇜࣰᙕ ࣰᄯᎌ‫ڬ‬෹ᙕ ዁ၚᙕ ዁ୣ‫ڬ‬዁ᙕ ၚਰᙕ ዁ୢࣰᙕ ዁ࣰར‫ڬ‬ར዁ቚɚȇᘩᙕ ֟ᅆࣰቚᎌ໪‫ݯڬ‬෹ᒥᙕ ෹‫ڬ‬རࡂၚᑋརࣰᅆቚᙕ ᑋୣၚᙕ ᑋࣰᅆࣰᙕ ޺ᎌ෹዁ఱᐋ‫ڬ‬዁ఱར૥ᙕ ዁ୣࣰఱᅆᙕ ၚᑋརᙕ ე‫ڬ‬ᅆ޺ࣰ෹ቚᙕ ‫ڬ‬ᅆࣰᙕ ‫ڬ‬෹ቚၚᙕ ޺ၚརਰఱᅆ໪ࣰࡂᙕ ఱརᙕ ეၚቚቚࣰቚቚၚᄹᒦᙕ ᅆహ૥ୣ዁ቚÙᙕ ‫ڬ‬෹዁ୣၚᎌ૥ୣᙕ ਰၚᅆᙕ ዁ୣࣰᙕ ቚၚᎌ዁ୣࣰᅆརᙕ დᅆၚᐋహར޺ࣰቚᙕ ዁ୣఱቚᙕ ఱቚᙕ རၚ዁ᙕ ໪‫ࣰࡂڬ‬ᙕ ࣰᒈე෹ఱ޺ఱ዁ᙕ ఱརᙕ ዁ୣࣰᙕ ෹ࣰ૥ఱቚ෹‫ڬ‬዁ఱၚརƅᙕ σརࡂᙕ ਰၚᅆᙕ  ޺ၚ໪໪ᎌར‫ڬ‬෹ ᙕ ‫ڬ‬རࡂᙕ རၚ໪‫ࡂڬ‬ఱ޺ᙕ ෹‫ڬ‬རࡂቚᙕ ეၚቚቚࣰቚቚၚᅆᒥᙕ ᅆఱ૥ୣ዁ቚᙕ ‫ڬ‬ᅆࣰᙕ ޺ၚརਰఱᅆ໪ࣰࡂᙕ ᅆࣰቚეࣰ޻ᔣ ዁ఱᐋࣰ෹ᒦᙕ ਰၚᅆᙕ ෹‫ڬ‬རࡂቚᙕ ዁ୣࣰᙕ ޺ᎌ෹዁ఱᐋ‫ڬ‬዁ၚᅆቚᙕ ეᅆࣰቚࣰར዁෹ᒦᙕ ዁ఱ෹෹ᙕ ‫ڬ‬རࡂᙕ ਰၚᅆᙕ ዁ୣၚቚࣰᙕ ዁ୣࣰᙕ རၚ໪‫ࡂڬ‬ቚᙕ ეᅆࣰቚࣰར዁෹ᒥᙕ ᎌቚࣰᙕ ਰၚᅆᙕ ૥ᅆ‫ڬ‬ᓯఱར૥ɚɚÜᙕ ࣰᒈ޺ࣰდ፬ᙕ ዁ୣ‫ڬ‬዁ᙕ ޺ᎌ෹዁ఱᐋ‫ڬ‬዁ၚᅆቚᙕ ఱརᙕ ޺ၚ໪໪ᎌར‫ڬ‬෹ᙕ ዁ࣰརᎌᅆࣰᙕ ‫ڬ‬ᅆࣰ‫ڬ‬ቚᙕ ᑋୣၚᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ࣰࣰݯ‬རᙕ ዁ࣰར‫ڬ‬ར዁ቚᙕ ၚਰᙕ ቚၚ໪ࣰᙕ ෹‫ڬ‬རࡂᙕ ‫ڬ‬རࡂᙕ ၚᑋརࣰᅆቚᙕ ၚਭᙕ ၚ዁ୣࣰᅆᙕ ෹‫ڬ‬རࡂᙕ ĸ ‫ڬ‬ᙕ ᐋࣰᅆᒦᙕ ޺ၚ໪໪ၚརᙕ ቚఱ዁ᎌ‫ڬ‬዁ఱၚརᙕ ఱརᙕ ዁ୣࣰቚࣰᙕ ‫ڬ‬ᅆࣰ‫ڬ‬ቚᙕ ĸ ‫ڬ‬ᅆࣰᙕ རၚ዁ᙕ ޺ၚརਰఱᅆ໪ࣰࡂᙕ ఱརᙕ დၚቚቚࣰቚቚၚᅆᒦᙕ ᅆస૥ୣ዁ቚᙕ ၚᐋࣰᅆᙕ ෹‫ڬ‬རࡂᙕ ዁ୣࣰᒥᙕ ୣ‫ڬ‬ᐋࣰᙕ ޺ᎌ෹዁ఱᐋ‫ڬ‬዁ࣰࡂᙕ‫ڬ‬ቚᙕ዁ࣰར‫ڬ‬ར዁ቚɚʅᘫᙕ ϴᒦᙕ ዁ୣࣰᙕ ࣰቚ዁‫ݯڬ‬෹ఱቚୣ໪ࣰར዁ᙕ ၚਰᙕ ዁ୣఱቚᙕ རࣰᑋᙕ ෹‫ڬ‬རࡂᙕ ዁ࣰརᎌᅆࣰᙕ ቚᒥቚ዁ࣰ໪ᙕ ‫ڬݯ‬ቚࣰࡂᙕ ᎌეၚརᙕ ეᎍ‫ݯ‬෹ఱ޺ᙕ ၚᑋརࣰᄹቚୣఱეᙕ ‫ڬ‬རࡂᙕ ეᅆఱᐋ‫ڬ‬዁ࣰᙕ ޺ᎌ෹዁ఱᐋ‫ڬ‬዁ఱၚརᙕ ᅆఱ૥ୣ዁ቚÙᙕ ዁ୣࣰᙕ л዁ୣఱၚეఱ‫ڬ‬རᙕ ૥ၚᐋࣰᅆར໪ࣰར዁ᙕ ୣ‫ڬ‬ቚᙕ ఱརᙕ ዁ୣࣰၚᅆᒥᙕ ቚᑋࣰე዁ᙕ ‫ڬ‬ᑋ‫ڬ‬ᒦᙕ ‫ݯ‬ၚ዁ୣᙕ዁ୣࣰᙕၚეეᅆࣰቚቚఱᐋࣰᙕ ዁ࣰར‫ڬ‬ར޺ᒦᙕ ቚᒥቚ዁ࣰ໪ᙕ ᑋୣహ޺ୣᙕ ეᅆࣰᐋ‫ڬ‬ఱ෹ࣰࡂᙕఱརᙕ ዁ୣࣰᙕ ቚၚᎌ዁ୣࣰᄹརᙕ ਰᅆࣰࣰୣၚ෹ࡂᙕ ᅆࣰ૥ఱၚརቚᙕ ‫ڬ‬རࡂᙕ ዁ୣࣰᙕ ࡂࣰቚ޺ࣰར዁ᙕ ၚᅆᙕ ᐋఱ෺෹‫ڬ‬૥ࣰį‫ڬݯ‬ቚࣰࡂᙕ ዁ࣰᙕར ᎌᅆᙕࣰ ቚᙕ ၚਭᙕ ዁ୣࣰᙕ རၚᅆ዁ୣࣰᅆརᙕ ୣఱ૥ୣ෹‫ڬ‬རࡂቚƅᙕ ؉ୣࣰᙕ ቚၚᎌ዁ୣࣰᅆརᙕ ෹‫ڬ‬རࡂቚᙕ ᑋࣰᅆࣰᙕ ෹‫ڬ‬ᅆ૥ࣰ෺ᒥᙕ  ޺ၚརᄯᎌࣰቚ዁ ᙕ ෹‫ڬ‬རࡂቚÙᙕ ᑋୣఱ޺ୣᙕ ਰࣰ෺෹ᙕ ᎌརࡂࣰᅆᙕ རၚᅆ዁ୣࣰᅆརÙᙕ ໪ၚቚ዁෹ᒥᙕ ‫כ‬ୣၚ‫ڬ‬རÙᙕ ޺ၚར዁ᅆၚ෹ᙕ ‫ڬ‬ਰ዁ࣰᅆᙕ ዁ୣࣰᙕ ᐋఱ޺዁ၚᅆఱࣰቚᙕ ၚਰᙕ ዁ୣࣰᙕ ‫ڬ‬ᅆ໪ఱࣰቚᙕ ၚਰᙕ Րࣰརఱ෹ࣰඬᙕ ӂӂᙕ ఱརᙕ ዁ୣࣰᙕ ෹‫ڬ‬዁዁ࣰᄹᙕ –@ଵ O?ଵ ğ ଵ 3 Bɀ B“ଵ % ,ଵ – ® ଵ Z –  ȍ ଵ – 6 ଵ O?ଵ ğ ଵ 3Bɀ B'ଵ %  , ଵ – Ȏ ଵZ – o , ଵ – 4 ଵ O™ଵ ğ ଵ 3B? Bˋଵ %  , ଵ +ଵ ¬2o ଵ ӳ B ଵ V ™“ଵ ଵ VBଵ ଵ   ଵ ǘଵ  ଵ Bଵ B   ଵ ǘFଵ (ଵ  ଵ ? ଵ B ଵ ଵ ǘB ଵ ǘଵ Bଵ Bଵ  ¾ଵ ଵ B ଵ ™"?BB ,ଵ –+ଵ O ?ଵ ğ ଵ 3Bɀ B“ଵ % ,ଵ +ଵ Z–oaଵ % ,ଵ –,ଵ Gଵ Bଵ Bଵ  ଵ Bଵ ?*ଵ Bଵ ƹ™ ž‘? àଵ  ,ଵ k ,ଵ ଵ %,ଵ ®,ଵ –®ଵ Gଵ B ଵ  ଵ ଵ  "ƒ"ଵ öଵ B  ଵ ? ˆଵ O ?ଵ ă ଵ 3 B? B(aଵ %,ଵ 4,ଵ ļ ଵ 1ଵ ଵ Bଵ ଵ ""B aଵ ଵ B? ଵ ଵ ?*ଵ Bଵ   ଵ ™?B ଵ*ଵ ଵ ଵ BƒB,ଵ – R ଵ O ?ଵ ğ ଵ 3Bɀ Baଵ %,ଵ 6ଵ ZDž ,ଵ –ଵ O?ଵ ğ ଵ 3Bɀ Baଵ %,ଵ 6ଵ Z@o , ଵ 2 Ȏ ଵs B ?*ଵ ଵ Ǽଵ    ଵ ଵ ǘ ?*ଵ  ଵ ଵ ଵ ѿ  ̳ ΄ଵ H“ଵ ö   ଵ ଵ Bଵ ® ĵ ଵ % ଵ `)“ଵ Q 1B _ଵ ȲB ଵ % B*ଵ Bଵ O"B?Bଵ ¬ğB B“ଵ –®4oaଵ ,ଵ – 2t – @ , ଵ G1ଵ "ଵ B Bଵ )1ଵ ଵ "?ଵ ?)ଵ ã 'ଵ )1ଵ Bଵ Bଵ ¾ଵ ଵ 1B?  ଵ Bଵ ଵ ଵ BBଵ Bଵ  "Bଵ Bãଵ ଵ ? ,ଵ #ଵ N"?ଵ NBଵ BãଵŠ 1B“ଵ %ƭ,ଵ –@Dìଵ 2–ଵ O?ଵ ğ ଵ 3 B?ŇB(aଵ % ,ଵ +ଵ Z–o,ଵ `Bǘଵ ଵ ଵ Bଵ ଵ Bଵ ǘଵ 1ଵ ଵ "ଵ ¾?ଵ 1B? ଵ ଵ ? aଵ ଵ ଵ ଵ ଵ BKଵ ĥ   đଵ B ଵ Bଵ ǘBଵ ଵ ? ଵ ??ଵ B ଵଵ ? ,ଵ 22ଵ O?ଵ ğ ଵ 3Bɀ ƒBaଵ %,ଵ –ଵ  ଵ %,ଵ 26,ଵ 2šଵ Oଵ ğ ଵ 3Bɀ ƒBaଵ % ěଵ 22ଵ Z2oěଵ ɝǯ˥ᙕ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb ე‫ڬ‬ᄺ዁ᙕ ၚਰᙕ ዁ୣࣰᙕ རసརࣰ዁ࣰࣰར዁ୣᙕ ޺ࣰར዁ᎍᄺᒥɚʲƅᙕ Ӆརᙕ ໪‫ڬ‬རᒥᙕ ၚਰᙕ ዁ୣࣰሠࣰᙕ ሠၚᎍ዁ୣࣰᄺརᙕ ‫ڬ‬ᄺࣰ‫ڬ‬ሠÙᙕ శ዁ᙕ ‫ڬ‬ეეࣰ‫ڬ‬ᄺሠᙕ ࣰਰਰࣰ޺዁సᐋࣰᙕ ޺ၚར዁ᄺၚ෹ᙕ ၚਰᙕ ෹‫ڬ‬རࡂᙕ ‫ڬ‬རࡂᙕ ෹‫ڬ‬རࡂᙕ ᄺࣰᐋࣰརᎍࣰሠᙕ ᑋ‫ڬ‬ሠᙕ ࣰሠ዁‫ݯڬ‬෹ఱሠୣࣰࡂᙕ ၚར෹ᒥᙕ ‫ڬ‬ሠᙕ ᄺࣰ޺ࣰར዁෹ᒥᙕ ‫ڬ‬ሠᙕ ዁ୣࣰᙕ Ȇ ͤʆǯ‫ף‬ɚ˖ᘩᙕ ѿఱᐋࣰརᙕ ዁ୣࣰᙕ ၚᄺఱ૥ఱརᙕ ၚਰᙕ ዁ୣࣰᙕ ሠᒥሠ዁ࣰ໪Ùᙕ ዁ୣࣰᙕ ࣰ዁ୣརఱ޺ᙕ ‫ڬ‬རࡂᙕ ޺ᎍ෹዁ᎍᄺ‫ڬ‬෹ᙕ ࡂసਰਰࣰᄺࣰར޺ࣰሠᙕ ‫ࣰݯ‬዁ᑋࣰࣰརᙕ ዁ୣࣰᙕ ዁ࣰར‫ڬ‬ར዁ሠᙕ ‫ڬ‬རࡂᙕ ዁ୣࣰᙕ ෹‫ڬ‬རࡂ෹ၚᄺࡂሠÙᙕ ‫ڬ‬རࡂᙕ ዁ୣࣰᙕ ୣఱ૥ୣᙕ ᄺࣰར዁ሠᙕ ࡂࣰ໪‫ڬ‬རࡂࣰࡂᙕ సརᙕ ໪ၚሠ጖ᙕၚਰᙕ዁ୣࣰᙕ ሠୣ‫ڬ‬ᄺࣰį޺ᄺၚეეఱར૥ᙕ ‫ڬ‬ᄺᄺ‫ڬ‬ར૥ࣰ໪ࣰར዁ሠÙᙕ ᑋసࡂࣰሠეᄺࣰ‫ࡂڬ‬ᙕ ‫ࣰ޺޺ڬ‬ე዁‫ڬ‬ར޺ࣰᙕၚਰᙕ዁ୣࣰᙕ ᄺࣰਰၚᄺ໪ሠᙕ ‫ݯ‬ᒥᙕ ޺ᎍ෹዁సᐋ‫ڬ‬዁ၚᄺሠᙕᑋ‫ڬ‬ሠᙕ዁ၚᙕ‫ࣰݯ‬ᙕࣰᒈეࣰ޺጖ࣰࡂűᙕ ؉ୣࣰᙕሠఱ዁ᎍ‫ڬ‬዁ఱၚརᙕసሠᙕࣰར዁ఱᄺࣰ෹ᒥᙕࡂఱਰਰࣰᄺࣰར዁ᙕసརᙕ጖ୣࣰᙕརၚᄺ዁ୣࣰᄺརᙕୣఱ૥ୣ෹‫ڬ‬རࡂሠÙᙕᑋୣࣰᄺࣰᙕ໪ၚሠ዁ᙕ޺ᎍ෹዁ఱᐋ‫ڬ‬዁ၚᄺሠᙕ ୣ‫ࡂڬ‬ᙕ ෹‫ڬ‬རࡂᙕ ୣࣰ෹ࡂᙕ ఱརࡂఱᐋఱࡂᎍ‫ڬ‬෹෹ᒥÙᙕ ‫ݯ‬ᎍ዁ᙕ ሠᎍ‫ݯ‬ආࣰ޺዁ᙕ ዁ၚᙕ ޺ࣰᄺ዁‫ڬ‬ఱརᙕ ૥ᄺၚᎍეᙕ ޺ၚར዁ᄺၚ෹ሠɚ˽ ΢ᙕ ᑋୣࣰᄺࣰᙕ ዁ୣࣰᙕ ෹‫ڬ‬རࡂᙕ ጖ࣰརᎍᄺࣰᙕ ሠᒥሠ዁ࣰ໪ሠᙕ ᑋࣰᄺࣰᙕ ࡂᒥར‫ڬ‬໪ఱ޺ᙕ ၚརࣰሠᙕ ఱར጖ࣰᄺᑋၚᐋࣰརᙕ ఱརᙕ ዁ୣࣰᙕ ‫ڬݯ‬ሠఱ޺ᙕ ਰ‫ݯڬ‬ᄺఱ޺ᙕ ၚਰᙕ ෹ၚ޺‫ڬ‬෹ᙕ ሠၚ޺స‫ڬ‬෹ᙕ ‫ڬ‬རࡂᙕ ეၚ෹ఱ዁ఱ޺‫ڬ‬෹ᙕ ၚᄺ૥‫ڬ‬རఱᓱ‫ڬ‬዁సၚརɚ̫ ΢ᙕ ᑋୣࣰᄺࣰᙕ ୣసሠ዁ၚᄺఱ޺‫ڬ‬෹෹ᒥᙕ ዁ୣࣰᄺࣰᙕ ୣ‫ڬ‬ሠᙕ ‫ࣰࣰݯ‬རᙕ ࣰརၚᄺ໪ၚᎍሠᙕ ሠᎍሠეఱ޺ఱၚརᙕ ၚਰᙕ ዁ୣࣰᙕ ໪ၚ዁ఱᐋࣰሠᙕ ၚਰᙕ ޺ࣰར዁ᄺ‫ڬ‬෹ᙕ ૥ၚᐋࣰᄺར໪ࣰར዁ᙕ ዁‫ڬ‬໪ეࣰᄺఱར૥ᙕ ᑋస዁ୣᙕ ෹‫ڬ‬རࡂᙕ ዁ࣰརᎍᄺࣰɚ͉ ΢ᙕ ‫ڬ‬རࡂᙕ ᑋୣࣰᄺࣰᙕ ਰᄺ‫ڬ‬૥໪ࣰར዁‫ڬ‬዁ఱၚརᙕ ၚਰᙕ ୣၚ෹ࡂఱར૥ሠÙᙕ ᅆ‫ڬ‬዁ୣࣰᄺᙕ ዁ୣ‫ڬ‬རᙕ ၚეეᄺࣰሠሠసᐋࣰᙕ ዁ࣰར‫ڬ‬ར޺ᒥᙕ ޺ၚརࡂఱ዁సၚརሠÜᙕ ୣ‫ڬ‬ሠᙕ ‫ڬ‬ეეࣰ‫ڬ‬ᄺࣰࡂᙕ ጖ၚᙕ ໪‫ڬ‬རᒥᙕ ጖ၚᙕ ‫ࣰݯ‬ᙕ ዁ୣࣰᙕ ໪‫ڬ‬ඈၚᄺᙕ ෹‫ڬ‬རࡂᙕ ዁ࣰརᎍᄺࣰᙕ ޺ၚརሠ዁ᄺ‫ڬ‬ఱར዁ᙕ ᎍეၚརᙕ ఱར޺ᄺࣰ‫ڬ‬ሠࣰࡂᙕ ‫ڬ‬૥ᄺస޺ᎍ෹጖ᎍᄺ‫ڬ‬෹ᙕ ეᄺၚࡂᎍ޺዁ఱᐋఱ዁ᒥƶᙕ Ҕࣰᄺࣰᙕ ᑋఱࡂࣰሠეᄺࣰ‫ࡂڬ‬ᙕ ‫ࣰ޺޺ڬ‬ე዁‫ڬ‬ར޺ࣰᙕ ‫ݯ‬ᒥᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ሠÙᙕ ໪ᎍ޺ୣᙕ ෹ࣰሠሠᙕ ‫ݯ‬ᒥᙕ ዁ୣࣰᙕ ෹ၚ޺‫ڬ‬෹ᙕ ૥ࣰར዁ᄺᒥÙᙕ ޺ၚᎍ෹ࡂᙕ རၚ዁ᙕ ‫ࣰݯ‬ᙕ ࣰᒈეࣰ޺዁ࣰࡂƅᙕ ϴᒥᙕ ዁ᒥఱར૥ᙕ ეᄺఱᐋ‫ڬ‬጖ࣰᙕ ޺ᎍ෹዁సᐋ‫ڮ‬዁ఱၚརᙕ ᄺఱ૥ୣ዁ሠᙕ ዁ၚᙕ ࣰᒈఱሠ዁ఱར૥ᙕ ‫ڬ‬෹෹ၚ޺‫ڬ‬዁ఱၚརሠÙᙕ ዁ୣࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄺၚ޺෹‫ڬ‬໪‫ڬ‬዁ఱၚརᙕ ਰᄺࣰࣰᓱࣰሠᙕ ᑋୣ‫ڬ‬዁ᙕ ୣ‫ࡂڬ‬ᙕ ‫ࣰࣰݯ‬རᙕ ‫ڬ‬ᙕ ࡂᒥར‫ڬ‬໪ఱ޺ᙕ ሠᒥሠ዁ࣰ໪űᙕ ѣᎍᄺ዁ୣࣰᄺᙕ ఱ዁ᙕ ეᄺၚୣఱ‫ݯ‬ఱ጖ሠᙕ ‫ڬ‬෹෹ᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ၚ‫ݯ‬෹ఱ૥‫ڬ‬዁ఱၚརሠᙕ ዁ၚᙕ ე‫ڬ‬ᒥᙕ ࡂᎍࣰሠᙕ ዁ၚᙕ ෹ၚ޺‫ڬ‬෹ᙕ ၚਰਰఱ޺ఱ‫ڬ‬෹ሠᙕ ၚᅆᙕ ᄺࣰეᄺࣰሠࣰར዁‫ڬ‬዁ఱᐋࣰሠᙕ ၚਰᙕ ዁ୣࣰᙕ ෹‫ڬ‬རࡂࣰࡂᙕ ૥ࣰར዁ᄺᒥɚ͡űᙕ ‫כ‬ᎍ޺ୣᙕ ࡂᎍࣰሠÙᙕ ਰၚᄺᙕ ࣰᒈ‫ڬ‬໪ე෹ࣰᙕ ૥ᎍ෹጖ᙕ ᑋୣఱ޺ୣᙕ ᄺࣰეᄺࣰሠࣰར጖ࣰࡂᙕ ጖ᄺఱ‫ݯ‬ᎍ዁ࣰᙕ ე‫ڬ‬ఱࡂᙕ ‫ݯ‬ᒥᙕ ‫ڬ‬ᙕ ዁‫ڬ‬ᒈე‫ڬ‬ᒥࣰᄺᙕ ዁ၚᙕ ‫ڬ‬ᙕ ეᄺఱᐋ‫ڬ‬጖ࣰᙕ ఱརࡂఱᐋఱࡂᎍ‫ڬ‬෹ᙕ ‫ڬ‬ሠᙕ ‫ڬ‬ሠሠఱ૥རࣰࣰᙕ ၚਰᙕ ዁ୣࣰᙕ ሠ጖‫ڬ‬጖ࣰÙᙕ ‫ڬ‬ᄺࣰᙕ ‫ڬ‬ᙕ ᄺࣰ໪ར‫ڬ‬ར዁ᙕ ၚਰᙕ ዁ୣࣰᙕ ਰࣰᎍࡂ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ዁ࣰརᎍᄺࣰᙕ ሠᒥሠ዁ࣰ໪ᙕ ᑋୣఱ޺ୣᙕ ୣఱሠ጖ၚᄺఱ޺‫ڬ‬෹෹ᒥᙕ ეᄺࣰᐋ‫ڬ‬స෹ࣰࡂᙕ ఱརᙕ ዁ୣࣰሠࣰᙕ རၚᄺ዁ୣࣰᄺརᙕ ‫ڬ‬ᄺࣰ‫ڬ‬ሠʅǭᘪᙕ ‫כ‬ᎍ޺ୣᙕ ე‫ڬ‬ᒥ໪ࣰར዁ሠᙕ ᑋࣰᄺࣰᙕ సརᙕ ეᄺఱར޺ఱე෹ࣰᙕ ‫ݯڬ‬ၚ෹ఱሠୣࣰࡂᙕ ዁ࣰརᙕ ᒥࣰ‫ڬ‬ᄺሠᙕ ‫ڬ‬૥ǪʅȇÙᙕ ‫ݯ‬ᎍ዁ᙕ ዁ୣࣰᒥᙕ ሠࣰࣰ໪ᙕ ఱརᙕ ਰ‫޺ڬ‬዁ᙕ ዁ၚᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ࣰࣰݯ‬རᙕ ޺ၚར዁సརᎍࣰࡂᙕ సརᙕ ეᄺ‫޺ڬ‬጖ఱ޺ࣰᙕ సརᙕ ሠၚ໪ࣰᙕ ‫ڬ‬ᄺࣰ‫ڬ‬ሠʅɚᘩᙕ ϴᒥᙕ ၚར޺ࣰᙕ ‫ڬ‬૥‫ڬ‬ఱརᙕ ‫ݯڬ‬ၚ෹ఱሠୣఱར૥ᙕ ሠᎍ޺ୣᙕ ე‫ڬ‬ᒥ໪ࣰར዁ሠÙᙕ ጖ୣࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄺၚ޺෹‫ڬ‬ላ‫ڬ‬጖ఱၚརᙕ ‫ڬ‬዁዁ࣰ໪ე጖ሠᙕ ዁ၚᙕ ࣰ෹ఱ໪ఱར‫ڬ‬዁ࣰᙕ ე‫ڬ‬ᄺ዁ᙕ ၚਰᙕ ዁ୣࣰᙕ ࣰ޺ၚརၚ໪స޺ᙕ ‫ڬݯ‬ሠࣰᙕ ၚਰᙕ ዁ୣࣰᙕ ᄺᎍᄺ‫ڬ‬෹ᙕ ࣰ෹ఱ዁ࣰሠᙕ సརᙕ རၚᄺ዁ୣࣰᄺརᙕ ‫ڬ‬ᄺࣰ‫ڬ‬ሠƅᙕ ‫כ‬ఱ໪ఱ෹‫ڬ‬ᄺ෹ᒥÙᙕ ‫ݯ‬ᒥᙕ ਰ‫ڬ‬ఱ෹ఱར૥ᙕ ጖ၚᙕ ఱར޺෹ᎍࡂࣰᙕ ‫ڬ‬རᒥᙕ ሠ‫ڬ‬ᐋఱར૥ᙕ ეᄺၚᐋఱሠఱၚརᙕ ਰၚᄺᙕ ޺ୣᎍᄺ޺ୣᙕ ෹‫ڬ‬རࡂሠÙᙕ ዁ୣࣰᙕ ෹ࣰ૥ఱሠ෹‫ڬ‬዁ఱၚརᙕ ‫ڬ‬዁዁ࣰ໪ე዁ሠᙕ ዁ၚᙕ ࣰ෹ఱ໪ఱར‫ڬ‬዁ࣰᙕ ໪ᎍ޽ୣᙕ ၚਰᙕ ዁ୣࣰᙕ ෹‫ڬ‬རࡂįᄺࣰ෹‫ڬ‬዁ࣰࡂᙕ ࣰ޺ၚརၚ໪ఱ޺ᙕ ‫ڬݯ‬ሠࣰᙕ ၚਰᙕ ዁ୣࣰᙕ л዁ୣఱၚეఱ‫ڬ‬རᙕփᄺ጖ୣၚࡂၚᒈᙕЎୣᎍᄺ޺ୣʅʅᘩᙕ :ñʍ €<8  < ɕ σ෹዁ୣၚᎍ૥ୣᙕ ᎍརࡂࣰᄺᙕ ዁ୣࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄺၚ޽෹‫ڬ‬ላ‫ڬ‬጖ఱၚརᙕ རၚᙕ ޺ၚ໪ეࣰརሠ‫ڬ‬዁ఱၚརᙕ ఱሠᙕ ዁ၚᙕ ‫ࣰݯ‬ᙕ ე‫ڬ‬సࡂᙕ ਰၚᄺᙕ ࣰᒈეᄺၚეᄺఱ‫ڬ‬዁ࣰࡂᙕ ෹‫ڬ‬རࡂʅʲÙᙕ ეᄺၚᐋఱሠసၚརᙕ ఱሠᙕ ໪‫ࣰࡂڬ‬ᙕ ਰၚᄺᙕ  ਰ‫ڬ‬ఱᄺᙕ ޺ၚ໪ეࣰརሠ‫ڬ‬ወఱၚར ᙕ ਰၚᄺᙕ ໪ၚᐋ‫ݯڬ‬෹ࣰᙕ ეᄺၚეࣰᄺ጖ఱࣰሠᙕ ‫ڬ‬རࡂᙕ ეࣸᄺ໪‫ڬ‬རࣰར዁ᙕ ᑋၚᄺඬሠᙕ ၚརᙕ ጖ୣࣰᙕ ෹‫ڬ‬རࡂʅ˖ᘳᙕ ؉ᄺࣰࣰᙕ ޺ᄺၚეሠÙᙕ ఱར޺෹ᎍࡂఱར૥ᙕ ޽ၚਰਰࣰࣰÙᙕ ‫ڬ‬ᄺࣰᙕ ÇDžଵ [˴:ଵ 1ଵ "7)ଵ 1 ଵ 17ଵ 7 :7 ଵ V070ଵ )ଵ ĥ0ଵ 70 1:70ଵ Ïଵ  ଵ )7ԫ1ଵ ଵ 17 :7 ଵ ÏÏ707 7 ƺଵ : 1:ଵ 10ଵ ̲ଵ ǀ 70ଵ Ïଵ  70ଵ ѝ ƺ Ðଵ ଵ 8ଵ g"70Ðଵ y: :ଵ Q 177 _ଵ G1ଵ Q"  7ଵ Ïଵ ଵ C 7 107ଵ #7 *ଵ ¬È17Ðଵ ʖ į|DžʌÐଵ ଵ ÇüÐଵ 7 ଵ Ç4ଵ ľଵ ¤ଵ gV0 :Ðଵ g0 ଵ x)0:17Ðଵ G00˥*ଵ 0 ଵ #7 ଵ x:075 70ଵ 70ଵ ଵ ı7Ÿ7ଵ ¤:ଵ Z˖¤8sଵ  7ѻ 70ଵ 0   ଵ 4DÐଵ ʖ į|Dʌ Ðଵ   ଵ |Džଵ Çüଵ x: 70:7 *ଵ ԫ17ଵ )ଵ 1ଵ 0 ž ଵ :7 ଵ :ଵ 1ଵ "7 Ǐ ଵ 7ଵ Ďଵ 1ଵ 0: 1ଵ 0 ଵ :ଵ "ଵ  *ଵ 0ଵ 7଱:ଵ  :ଵ Ïଵ : 70ଵ  ଵ Wū‚Ƽ 70ଵ  ଵ :70Ðଵ C 7 ଵ Ç|ଵ #ଵ ¤ଵ ‫ݾ‬0Ðଵ Ž0 ଵ G0:ଵ  0ଵ 1ଵ ¤ :ଵ ²ଵ ‫ ݣ‬17 _ ଵ Gଵ 8* μ˥ଵ ²ଵ ˖ ‘ଵ Ӭ˥0 ଵ ¬˖17Ðଵ į|© Ë ¿ ଵ Çĩଵ #   ଵ`0Ðଵ 7 ଵ  ଵ ēଵ 2|ĖÇ2ü¿ଵ Çįଵ O: ଵ g0 ଵ 3:   70Ðଵ ¤: ଵ Ç ʖ  ଵ © D ଵ [:ଵ V 07"ଵ :Ï:0ଵ ଵ 1ଵ ૂ7 0ଵ Ïଵ ĥÏ  7 àଵ 70ଵ Q 177Ðଵ ଵ żଵ ˖10Ðଵ ĥQ 177 _ଵ ଵ ľ:"*ଵ 0ଵ 1ଵ QV7 0ଵ Ïଵ ଵ [  ଵ 30 :* à Ðଵ G1ଵ ż:0 ଵ Ïଵ C :0ଵ ¤Ï:70ଵ #  7ଵ ଵ üü4Ċü|Çଵ ¬ ʖ į|DžËଵ © ʖ ଵ ¤ଵ 3:   μ0ଵ ଵ ¤ 0 ଵ 1ଵ ğ0 ଵ GVଵ 3: ɔ  70ଵ Ïଵ ʖįDžDžÐଵ 3: ɔ  70ଵ qଵ Ç©Dଵ  Ï ଵ ʖ įüüÐଵ ¤: ‫ڙ‬ଵ Çଵ ¬ʌÐଵ q:7 ଵy૝ ଵÇ4 1ଵ Ʊ:ଵqଵ įଵ ¬¤ʌଵ ¬C:1ଵ| Ð ଵ ʖįüüʌ ଵ ©Çଵ È10ଵ Ǚଵ ı70 :Ðଵ ଵ 7 ଵ 0 ଵ |Ðଵ ΍ଵ ĩÇଵ ©©ଵ Ď0ଵ 1ଵ Ï:ɥ0 ଵ ଵ )1:ଵ  :€*ଵ :7"ଵ 17:ଵ  :7 ଵ  00ଵ *ଵ 1ଵ  7" 70ଵ Ïଵ 1:1ଵ 0 Ðଵ È10ଵ Ǚଵ ı70 :Ðଵ 7 ଵ  ଵ   ଵ Dž ʖ ĭଵ 1ଵ  :*Ǐ 7" :ଵ 7ଵ 0Ï7:  ଵ 70ଵ 17ଵ :*ଵ :71 ଵ 7Æଵ 0*ଵ  1:ଵ  7" :  ଵ ©Džଵ O: ଵ ğ0 ଵ 3:   70Ðଵ ¤ :  ଵ ©ଵ ¬©ʌ  ଵ ©4ଵ O: ଵ ğ ଵ 3:   7Ðଵ ¤: ଵ ©ଵ ¬ © ʌ Ð ଵ ¤: ଵ |ଵ ¬Çʌଵ ɔ 0 ଵ ଵ ¤: ଵ üଵ ¬DžË ଵ G1ଵ 7  70ଵ 0 70ଵ 0  ଵ :"770ଵ V 77 *ଵ V::7 70ଵ ĥ " ଵ :: 7 ƺଵ  0 ଵ ĥ: 00 ଵ ):ƍଵ 0ଵ 1ଵ 0 à Ðଵ  11ଵ 1ଵ  :ଵ 1 ଵ :1ଵ ଵ "7) ଵ ଵ : ଵ Ïଵ ĥ ଵ :: ଵ 0  ƺଵ 0 70 75 ଵ *ଵ ¤: 7 ଵ ©ଵ ºƨÁÛȀ  ଵ  ଵ ଵ ɛǯ˸ᙕ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb ࣰᒈე෹హࠒఱ዁෹ᒥᙕ ࣰᒈ޺෹ᎍࡂࣰࡂᙕ ਰᄻၛ໪ᙕ ޺ၛ໪ეࣰརሠ‫ڬ‬዁హၛརʅ˽ᘪᙕ ؉ஙࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄺၚ޺෹‫ڬ‬ላ‫ڬ‬዁హၛརᙕ ეᄺၛᐋహࡂࣰሠᙕ ዁ங‫ڬ‬዁ᙕ ዁ஙࣰᙕ Ցహརహሠ዁ࣰᄺᙕ ၛਰᙕԴ‫ڬ‬རࡂᙕׂࣰਰၛᄺ໪ᙕ ‫ڬ‬རࡂᙕσࡂ໪హཀྵహሠ዁ᄺ‫ڬ‬዁హၛརᙕ žརၛᑋᙕ ዁ஙࣰᙕ Րఱརఱሠ዁ࣰᄺᙕ ၚਰᙕ Դ‫ڬ‬རࡂሠᙕ ‫ڬ‬རࡂᙕ‫ࣰכ‬዁዁෹ࣰ໪ࣰར዁¸ᙕ ሠங‫ڬ‬෹෹ᙕ ࡂࣰ዁ࣰᄺ໪ఱརࣰᙕ዁ஙࣰᙕ ޺ၛ໪ეࣰརሠ‫ڬ‬዁హၛརᙕ዁ၚᙕ ‫ࣰݯ‬ᙕე‫ڬ‬హࡂᙕఱརᙕ ᄺࣰሠეࣰ޺዁ᙕၛਰᙕ໪ၛᐋ‫ݯڬ‬෹ࣰᙕ ეᄺၛეࣰᄺ዁హࣰሠᙕ ‫ڬ‬རࡂᙕ ეࣰᄺ໪‫ڬ‬རࣰར዁ᙕ ᑋၛᄺඬሠᙕ ၛརᙕ  ෹‫ڬ‬ᄺ૥ࣰįሠ޺‫ڬ‬෹ࣰ ᙕ ਰ‫ڬ‬ᄻ໪ሠʅ̫Üᙕ ‫ݯ‬ᎍ዁ᙕ ሠᎍ‫ݯ‬ሠࣰᄯᎍࣰར዁ᙕ ෹ࣰ૥హሠ෹‫ڬ‬዁హၛརᙕ ࣰሠ዁‫ݯڬ‬෹హሠஙࣰሠᙕ ‫ڬ‬ᙕ Ўၛ໪ეࣰརሠ‫ڬ‬዁హၛརᙕ Ўၛ໪໪ఱሠሠహၛཀྵᙕ ᑋహ዁ஙᙕ ૥ࣰརࣰᄺ‫ڬ‬෹ᙕ ეၛᑋࣰᄺሠᙕ ዁ၛᙕ ਰహᒈᙕ ዁ஙࣰᙕ ޺ၛ໪ეࣰརሠ‫ڬ‬዁హၛརᙕეᄺၛᐋఱࡂࣰࡂᙕ ਰၛᅆᙕహརᙕ ෹ࣰ૥హሠ෹‫ڬ‬዁హၛརᙕ ࣰᒈეᄺၛეᄺహ‫ڬ‬዁ఱར૥ᙕ ‫ݯ‬ᎍሠఱརࣰሠሠࣰሠÙᙕ ᄻᎍᄺ‫ڬ‬෹ᙕ ‫ڬ‬རࡂᙕ ᎏᄺ‫ڬݯ‬རᙕ ෹‫ڬ‬རࡂሠÜᙕ ‫ڬ‬རࡂᙕ ეᄺఱᐋ‫ڬ‬዁ࣰᙕ ሠ޺ஙၛၛ෹ሠʅ͉ᘾᙕ ؉ஙహሠᙕ ෹ࣰ૥ఱሠ෹‫ڬ‬዁హၛརᙕ ޺ၛར዁‫ڬ‬హརሠᙕ རၚᙕ ਰᎍᄻ዁ஙࣰᄺᙕ ሠ዁‫ڬ‬རࡂ‫ڬ‬ᄺࡂሠᙕ ਰၚᄻᙕ ਰఱᒈఱར૥ᙕ޺ၛ໪ეࣰརሠ‫ڬ‬዁హၛར Σᙕ హརሠ዁ࣰ‫ࡂڬ‬Ùᙕ ዁ஙࣰᙕ ޺ၛ໪໪హሠሠహၛརᙕ ఱሠᙕఱརሠ዁ᄻᎍ޺዁ࣰࡂᙕ዁ၛᙕ རࣰ૥ၛ዁హ‫ڬ‬዁ࣰᙕ ‫ڬ‬རࡂᙕ ᄻࣰ‫޺ڬ‬ஙᙕ ‫ڬ‬૥ᄺࣰࣰ໪ࣰར዁ሠᙕ ᑋహ዁ஙᙕ ޺ၛ໪ეࣰརሠ‫ڬ‬዁హၛརᙕ ޺෹‫ڬ‬హ໪‫ڬ‬ར዁ሠᙕ ű ű ű ᙕ‫ڬ‬ሠᙕ ዁ၛᙕ ዁ஙࣰᙕ ‫ڬ‬໪ၛᎍར዁ᙕ ၛਰᙕ ޺ၛ໪ეࣰརሠ‫ڬ‬዁ఱၛརᙕ ე‫ڬ‬ᒥ‫ݯڬ‬෹ࣰᙕ ‫ڬ‬རࡂᙕ ዁ஙࣰᙕ ໪‫ڬ‬རརࣰᅆᙕ ၛਰᙕ ე‫ڬ‬ᒥ໪ࣰར዁ᙕ ዁ஙࣰᄺࣰၛਰʅ͡ ű P ᙕ ѿహᐋࣰརᙕ ዁ஙࣰᙕ ޺ၛ໪ეᄺࣰஙࣰརሠఱᐋࣰᙕ ޺ங‫ڬ‬ᄺ‫޺ڬ‬ᔜ ዁ࣰᅆᙕ ၛਰᙕ ዁ஙࣰᙕ ཀྵ‫ڬ‬዁హၛཀྵ‫ڬ‬෹హᓯ‫ڬ‬዁హၛཀྵሠÙᙕ л዁ஙఱၛეఱ‫ڬ‬gሠᙕ ሠၛ޺హ‫ڬ‬෹హሠ዁ᙕ ეஙహ෹ၛሠၛეஙᒥÜᙕ ‫ڬ‬ཀྵࡂᙕ ዁୥ࣰᙕ ޺ၛᎍཀྵ዁ᄺᒥሠᙕ ᐋࣰᄺᒥᙕ ෹హ໪హ዁ࣰࡂᙕ ਰహར‫ڬ‬ཀྵ޺హ‫ڬ‬෹ᙕ ᄺࣰሠၛᎍᄺ޺ࣰሠÙᙕ ዁ஙࣰᙕ ਰ‫ڬ‬హᄺᙕ ޺ၛ໪ეࣰརሠ‫ڬ‬዁ఱၚར ᙕ ეᄺၚᐋఱሠఱၛརᙕ ၛਰᙕ ዁ஙࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ Դ‫ڬ‬ཀྵࡂሠᙕ ֟ᅆၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛཀྵᙕ హሠᙕᎍར෹ఱඬࣰ෹ᒥᙕ዁ၛᙕ ໪ࣰ‫ڬ‬ཀྵᙕ ޺෹‫ڬ‬హ໪‫ڬ‬ར዁ሠᙕ ᑋఱ෹෹ᙕ ᄺࣰ޺ࣰఱᐋࣰᙕఱ໪໪ࣰࡂఱ‫ڬ‬዁ࣰᙕ ე‫ڬ‬ᒥ໪ࣰར዁ᙕ ၛਭᙕ ዁ஙࣰᙕ ໪‫ڬ‬ᄺඬࣰ዁ᙕ ᐋ‫ڬ‬෹ᎏࣰᙕ ၛਰᙕ ዁ஙࣰహᄻᙕ ࣰᒈეᄺၛეᄺహ‫ڬ‬዁ࣰࡂᙕ ໪ၛᐋ‫ݯڬ‬෹ࣰᙕ ეᄺၛეࣰᄺ዁ఱࣰሠᙕ ‫ڬ‬རࡂᙕ ეࣰᄺ໪‫ڬ‬རࣰར዁ᙕ ᑋၚᄺඬሠᙕ ၛརᙕ ዁ஙࣰᙕ෹‫ڬ‬ཀྵࡂűᙕ ǂāȀ @ ɕ   ɕ ֶࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ‫ڬ‬ᄺࣰᙕ ਰᎍཀྵࡂ‫ڬ‬໪ࣰར዁‫ڬ‬෹ᙕ ዁ၛᙕ ዁ஙࣰᙕ л዁ஙఱၛეహ‫ڬ‬ཀྵᙕ ᄺᎍᄺ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᄺࣰਰၛᅆ໪ሠÙᙕ ਰၛᄺᙕ ዁୥ࣰᒥᙕ ‫ڬ‬ᄺࣰᙕ ዁ஙࣰᙕ ໪ࣰ‫ڬ‬རሠᙕ ዁ၛᙕ ໪ၛ‫ݯ‬హ෹హᓯࣰᙕ ዁ஙࣰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᄺᒥᙕ ‫ڬ‬རࡂᙕ ࣰརሠᎍᄺࣰᙕ ఱ໪ე෹ࣰ໪ࣰཀྵ዁‫ڬ‬዁హၛརᙕ ၛ੗ᙕ ዁୥ࣰᙕ རࣰᑋᙕ ෹‫ڬ‬རࡂᙕ ዁ࣰཀྵᎍᇱ਍ᙕ ሠᒥሠ዁ࣰ໪űᙕ ӂརࡂࣰࣰࡂÙᙕ ሠၛ໪ࣰᙕ ୥‫ڬ‬ᐋࣰᙕ ᐋహࣰᑋࣰࡂᙕ ዁ஙࣰ໪ᙕ ‫ڬ‬ሠᙕ ዁ஙࣰᙕ ‫ڬݯ‬ሠహ޺ᙕ ࣰ෹ࣰ໪ࣰཀྵ዁ሠᙕ హརᙕ ‫ڬ‬ᙕ ཀྵࣰᑋᙕ ෹ၛ޺‫ڬ‬෹ᙕ ૥ၛᐋࣰᄺར໪ࣰར዁ᙕ ሠ዁ᄺᎍ޺዁ᎍᄺࣰÙᙕ ၛᅆᙕ ‫ڬ‬ᙕ རࣰᑋᙕ ეၛეᎍ෹‫ڬ‬ᄻᙕ ეၛ෹హ዁హ޺‫ڬ‬෹ᙕ ე‫ڬ‬ᄺ዁ᒥÜᙕ ၛᄻᙕ ‫ݯ‬ၛ዁ஙűᙕ ؉ஙࣰహᄺᙕ ࡂࣰᐋࣰ෹ၛე໪ࣰར዁ᙕ ޺ࣰᄺ዁‫ڬ‬హར෹ᒥᙕ ᑍఱ෹෹ᙕ ‫ࣰݯ‬ᙕ ‫ڬ‬ᙕ ޺ᄺᎍ޺ఱ‫ڬ‬෹ᙕ ‫ڬ‬ሠეࣰ޺዁ᙕ ၚਰᙕ ᄻᎍᄺ‫ڬ‬෹ᙕ ሠၛ޺ఱ‫ڬ‬෹ᙕ ޺ங‫ڬ‬ར૥ࣰᙕ ఱརᙕ ዁ஙࣰᙕ རࣰᑋᙕ л዁ஙఱၛეహ‫ڬ‬རᙕၛᄺࡂࣰᅆűᙕ σ޺޺ၛᄺࡂహར૥ᙕ዁ၛᙕ዁ஙࣰᙕׂᎍᄺ‫ڬ‬෹ᙕԴ‫ڬ‬རࡂሠᙕ֟ᄺၚ޺෹‫ڬ‬ላ‫ڬ‬዁హၛརÙᙕ ໪ࣰ໪‫ࣰݯ‬ᄺሠஙఱეᙕ హརᙕ ዁ஙࣰᙕეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརᙕ ఱሠᙕᐋၛ෹ᎍཀྵ዁‫ڬ‬ᄺᒥᙕ ‫ڬ‬རࡂᙕ హሠᙕ ၛეࣰཀྵᙕ ዁ၛᙕ ਰၛᄺ໪ࣰᄺᙕ ዁ࣰར‫ڬ‬ར዁ሠÜᙕ ෹‫ڬ‬རࡂ෹ࣰሠሠᙕ ეࣰᄺሠၛརሠÜᙕ ‫ڬ‬རࡂᙕ ஙహᄻࣰࡂᙕ ‫ڬ‬૥ᄺహ޺ᎍ෹዁ᎍᄺ‫ڬ‬෹ᙕ ᑋၛᄺඬࣰᅆሠᙕ ၛਰᙕ ෹‫ڬ‬རࡂၛᑋརࣰᄺሠᙕ ᑋஙၚᙕ ங‫ࡂڬ‬ᙕ ෹ࣰሠሠᙕ ዁ங‫ڬ‬ཀྵᙕ ዁ࣰརᙕ ஙࣰ޺዁‫ڬ‬ᄻࣰሠᙕ ၚਰᙕ ෹‫ڬ‬རࡂʲǬᘩᙕ л‫޺ڬ‬ஙᙕ ‫ڬ‬ሠሠၛ޺ౝ‫ڬ‬዁హၛརᙕ ዁‫ڬ‬ඬࣰሠᙕ ‫ڬ‬ሠᙕ ‫ڬ‬ᙕ ૥ࣰၛ૥ᄺ‫ڬ‬ეஙహࣽᙕ ‫ڬݯ‬ሠࣰᙕ ዁ஙࣰᙕ ‫ڬ‬ᄺࣰ‫ڬ‬ᙕ ਰၛᄺ໪ࣰᄺ෹ᒥᙕ ᎍརࡂࣰᄻᙕ ‫ڬ‬ᙕ ޺ஙహඬ‫ڬ‬ᙕ ሠஙᎍ໪ʲȇÙᙕ ᑋஙၛᙕ ᑋ‫ڬ‬ሠᙕ ዁ஙࣰᙕ ෹ၛᑋࣰሠ዁ᙕ ၛਰਰహ޺హ‫ڬ‬෹ᙕ ఱརᙕ ዁ஙࣰᙕ ਰၛᄺ໪ࣰᄺᙕ ෹ၛ޺‫ڮ‬෹ᙕ ૥ၛᐋࣰᄺར໪ࣰཀྵ዁ᙕ ஙఱࣰᄺ‫ڬ‬ᄺ޺ஙᒥűᙕ ӂརᙕ ‫ࡂࡂڬ‬హ዁హၛརᙕ ዁ၛᙕ ዁ஙࣰሠࣰᙕ ‫ڬ‬ሠሠၚ޺హ‫ڬ‬዁ఱၛརሠᙕ ၛਰᙕ ዁ஙࣰᙕ ໪‫ڬ‬ሠሠᙕ ၛਰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ሠᙕ ዁ஙࣰ໪ሠࣰ෹ᐋࣰሠÙᙕ ეᅆၛᐋహሠహၛརᙕ ఱሠᙕ ໪‫ࣰࡂڬ‬ᙕ ਰၛᄺᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺హ‫ڬ‬዁ఱၛརሠᙕ ‫ڬ‬዁ᙕ ዁ஙࣰᙕ ሠᎍ‫ݯ‬įࡂహሠ዁ᄺహ޺዁ᙕ žᑋၛᄺࣰࡂ‫¸ڬ‬ᙕ ‫ڬ‬རࡂᙕ ࡂహሠ዁ᄺహࣽ዁ᙕ ž‫ڬ‬ᑋᄺ‫ڬ‬ආ‫¸ڬ‬ᙕ ෹ࣰᐋࣰ෹ሠÜᙕ హརᙕ ࣰ‫޺ڬ‬ஙᙕ ޺‫ڬ‬ሠࣰᙕ ޺ၛ໪ეၚሠࣰࡂᙕၛਰᙕࡂࣰ෹ࣰ૥‫ڬ‬዁ࣰሠᙕਰᄺၛ໪ᙕ዁ஙࣰᙕ‫ڬ‬ሠሠၛ޺హ‫ڬ‬዁హၛརሠᙕ‫ࣰݯ‬෹ၛᑋʲɚᘩᙕ dz1ଵ V dzଵ dz1*ଵ  ଵ 1ଵ ãuu uBଵ Bãଵ   ଵ )BJଵ ଵ â uu Bଵ )BJ'ଵ ) ଵ )͈'ଵ uuࣾଵ ଵ ɠ 1ଵ )BJଵ ଵ B ã ଵ  B'ଵ B0 'ଵ uJ'ଵ  ଵ Bଵ *ଵ B u Bଵ dz1Bã đ ,ଵ k,ଵ  ଵ % ,ଵ 2ଵ Ϣ$,ଵ ݊dz?*ଵ Bଵ uଵ ãBଵ 1ଵ VBu uBଵ Bãଵ B"ଵ uଵ dz1ଵ B"uuBଵ uଵ žଵ ã ଵ 1 ଵ 1ȶଵ ĥ 1ଵ ଵ B05ଵ ଵ  ė  ଵ Bଵ ଵ B٣B "ଵ ã ଵ Bଵ 1ଵ ଵ B ଵ Bଵ u, đଵ k,ଵ  ଵ % ,ଵ $ଵ ¬   ,ଵ %ଵ ĥ  Ǐ đଵ ã ଵ ଵ Bଵ )11ଵ uଵ 105ଵ Bଵ ଵ B0ଵ  1Bଵ Bãଵ ଵu ଵ ଵ 10ȶ,ଵ k,ଵ  ଵ ʚdzɒଵ 2ଵ ¬2 ěଵ ¤B 1ଵ uଵ ãBଵ 1ଵ VBu Bଵ Bãଵ B"ଵ uଵ 1ଵ B"B0ଵ 1 ଵ ଵ 0 ଵ â1ଵ1"ଵ 1ଵ ͚u1 ଵ Bଵ  ଵ u ଵ u  0 ଵ ଵ ଵ uଵ Bãଵ ã ଵ BVଵ Buଵ dzBଵ 1ଵ ?B)ଵ )u 1uଵ Ƽ ਑uBଵ 0B ଵ Vр0ଵ 1ଵ ȶଵ , , , đଵଵ Îଵ  ଵ % ଵ +ଵ Ϣ6 ,ଵ īƺƼ Oଵ ğ0ଵ 3BŇ uB'ଵ % ,ଵ Ŏଵ ¬Ŏଵ 0ଵ %dz,ଵ 2ଵ Ϣ ,ଵ Ŏ$ଵ Oଵ ğ0ଵ 3BŇ B'ଵ % ଵ +ଵ ¬2ଵ Ŏ R ଵ %ଵ 3BŇ uBଵ Bଵ 3B"uଵ ãBଵ dz1ଵ Š 1 dzଵ Bãଵ ଵ NB  uB0ଵ NB uuB'ଵ 3B  uBଵ wB,ଵ ®Dଵ Bãଵ $Å'ଵ wu ଵ y5 ଵ ŎÅ 1ଵ ̔ଵ wB,ଵ  6 ଵ ¬8 ଵ  Ŏ µଵ $ŝ,ଵ C ଵ Bãଵ 1ଵ B Bଵ )਱ଵ B0 ଵ u0ଵ Ȳ*ଵ  $+,ଵ Ŏଵ k,ଵ  ଵ % ,ଵ $ଵ ¬6 ,ଵ ȲBଵ 1ଵ u ଵ 0ଵ 1Bଵ )1Bଵ )ଵ "ଵ B ã ଵ V ଵ 1Bଵ u0ଵ ଵ ଵ 0ଵ 1"ଵ Bଵ B 1ଵ ¾ ଵ Bଵ Bãଵ u0B ଵ u"ଵ 1ãଵ Bãଵ 1uଵ "Bଵ ଵ ଵ "̸ଵ ଵ dzBଵ ଵ Vu  ଵ Bãଵ ½ 1,ଵ dȀ 2ÅDଵ ଵ B0 1ଵ ¬Ŧėଵ ¬Ȁ  DDଵ ‚ ½ 1,ଵ dȀ 2D$  , ଵ 6 D ଵ Oଵ ğ0ଵ ĸB  B0‫ع‬ଵ ʵ   ଵ  ‫ ړ‬ଵ ȲB ଵ B)0ଵ Bãଵ ଵ ¾0  uଵ Bãଵ   0  ଵ ȶଵ πBuଵ B 0 р  ଵ u u uB0ଵ óĽƼ B  ,ଵ ku,ଵ G1ଵ Bu uB0ଵ 1Ň"ଵ )ଵ 0B ଵ "ଵ ଵ Bu *ଵ *ଵ 1ଵ Oଵ ğଵ 3BŇ B0'ଵ  ଵ 1uଵ )ଵ B"uଵ *ଵ ଵ ଵ¾  ଵ u uB,ଵ %ଵ 3BŇ uBଵ Bଵ 3 B"uଵ ãBଵ 1ଵ ޽Œ(u5 uF(ଵ  ଵ NBBu uBଵ B ã ଵ 3 ଵ %Bu uB'ଵ 3BŇ Bଵ wB,ଵ ®  ଵ Bãଵ $Å 'ଵ wu ଵ y5 ଵ ŎȻ 1ଵ ̔ଵ wBଵ  Å ଵ ¬8 ࢷଵ 6'ଵ  $ŝଵ % ଵ 6ଵ % շଵ ăଵ 3B?  uBµଵ ¤dz,ଵ R ě ଵ G1ଵ u0u દ ଵ ଵ ãBଵ ଵ B uBଵ uଵ 1dzଵ 10ଵ 1 ,ଵ Î,ଵ ėB ଵ ãଵ Bઊଵ u0ࠧ ଵ 1ûଵ 1 ଵ B0uଵ Bã 0ଵ 1Ţଵ B ଵ 0ଵ ãBB),ଵ ð0 uՊଵ Ĝ1uଵ ė"uଵ ğu  'ଵ ĥĜଵ ńଵ 8"B  ଵ ė * đ 'ଵ %00Vଵ R ' ଵ ĥėBuଵ ȳu5 uBˈଵ ¬ã 'ଵ 8 ଵ $Å  ' ଵ ,ଵ 2R,ଵ ‫۽‬2ଵ Oଵ ğଵ 3B»  uB'ଵ % ,ଵ   , ଵ T†÷ʍ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb թᎍ໪ࣰᄹၛᎌሠᙕ ౝ໪დၛᄹ዁‫ڬ‬ར዁ᙕ ਰᎍར޺዁ౝၛརሠᙕ ‫ڬ‬ᄹࣰᙕ ‫ڬ‬ሠሠౝ૥རࣰࡂᙕ ‫ݯ‬ᒥᙕ ዁ୣࣰᙕ ׂᎍᄹ‫ڬ‬෹ᙕ ԰‫ڬ‬རࡂሠᙕ ֟ᄹၛ޺෹‫ڬ‬ሎ‫ڬ‬዁ౝၛཧᙕ ዁ၛᙕ ዁ୣࣰᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ౝ‫ڬ‬዁ౝၛརሠŵᙕ ؉ୣࣰሠࣰᙕ ఴར޺෺ᎌࡂࣰᙕ ዁ୣࣰᙕ ‫ࡂڬ‬໪ౝརౝሠ዁ᄹ‫ڬ‬዁ౝၛརᙕ ၛਰᙕ დᎍ‫ݯ‬෹ౝ޺ᙕ დᄹၛეࣰᄹ዁ᒮᙕ ᑋౝ዁ୣఴརᙕ ዁ୣࣰᙕ ‫ڬ‬ሠሠၛ޺ౝ‫ڬ‬዁ౝၛརgሠᙕ ‫ڬ‬ᄹࣰ‫ ڬ‬΢ᙕ ዁ୣࣰᙕ ࣰሠ዁‫ݯڬ‬෹ౝሠୣ໪ࣰར዁ᙕ ၛਰᙕ ޺ၛįၛდࣰᄹ‫ڬ‬዁ౝᐋࣰሠ ΢ᙕ ዁ୣࣰᙕ ޻ၛཧሠ዁ᄹᎍ޻዁఺ၛརᙕ ၛਰᙕ ሠ޺ୣၛၛ෹ሠÜᙕ ޺෺ౝརఴ޺ሠᙕ ‫ڬ‬རࡂᙕ ሠౝ໪ౝ෹‫ڬ‬ᄹᙕ ఴརሠ዁ౝ዁ᎌ዁ౝၛརሠ ΢ᙕ ‫ڬ‬ཧࡂᙕ ዁ୣࣰᙕ ᎍཧࡂࣰᄹ዁‫ڬ‬ඬౝར૥ᙕ ၛਰᙕ ᐋౝ෺෺‫ڬ‬૥ౝᓯ‫ڬ‬዁ౝၛཧᙕ დᄹၛ૥ᄹ‫ڬ‬໪ሠʲʅᘫᙕ փਰᙕდ‫ڬ‬ᄹ዁ౝ޺ᎌ෹‫ڬ‬ᄹᙕఴ໪დၛᄹ዁‫ڬ‬ར޺ࣰÜᙕ ዁ୣࣰᙕ ෹ࣰ૥ౝሠ෹‫ڬ‬዁ౝၛརᙕ ‫ڬ‬ར዁ఴ޺ౝდ‫ڬ‬዁ࣰሠᙕ ዁ୣ‫ڬ‬዁ᙕ ၛཧ޺ࣰᙕ დࣰᙕ‫ ڬ‬ሠ‫ڬ‬ར዁ሜᙕ ౝརᙕ ዁ୣࣰᙕ ሠၛᎍ዁ୣࣰᄹརᙕ ਰᄹࣰ਎ஜၛ෹ࡂᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ࣰࣰݯ‬རᙕ ޺ၛརਰౝᄹ໪ࣰࡂᙕ ఴརᙕ ዁ୣࣰౝᄹᙕ დၛሠሠࣰሠሠၛᄹᒥᙕ ᄹఴ૥ୣ዁ሠÙᙕ ෹‫ڬ‬རࡂᙕ ᑋౝ෹෹ᙕ ‫ࣰݯ‬ᙕ ᄹࣰࡂౝሠ዁ᄹఴ‫ݯ‬ᎍ዁ࣰࡂᙕ ዁ၛᙕ ਰ‫ڬ‬ᄹ໪ౝར૥ᙕ ਰ‫ڬ‬໪ౝ෹ౝࣰሠᙕ ౝརᙕ დ‫ڬ‬ᄹ޺ࣰ෹ሠᙕ  ‫ڬ‬ሠᙕ ਰ‫ڬ‬ᄹᙕ ‫ڬ‬ሠᙕ დၛሠሠౝ‫ݼ‬෺ࣰᙕ ű ű ű ᙕ ࣰᄯᎍ‫ڬ‬Ȍʲʲű ᙕ ‫כ‬ᎌ޺ୣᙕ ᄹࣰࡂౝሠ዁ᄹౝ‫ݯ‬ᎍ዁ౝၛརᙕ ౝሠᙕ ዁ၛᙕ ‫ࣰݯ‬ᙕ ޺‫ڬ‬ᄹᄹౝࣰࡂᙕ ၛᎍ዁ᙕ ၛརᙕ ዁ୣࣰᙕ ౝརౝ዁ౝ‫ڬ‬዁ఴᐋࣰᙕ ၛੁᙕ ዁ୣࣰᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ౝ‫ڬ‬዁ఴၛརᙕ ఴ዁ሠࣰ෹ਰÜᙕ ᑍൊ዁ୣᙕ ‫ڬ‬ሠሠౝሠ዁‫ڬ‬ཧ޺ࣰᙕ დᄺၛᐋఴࡂࣰࡂᙕ ‫ݯ‬ᒥᙕ ዁ୣࣰᙕ ૥ၛᐋࣰᄺར໪ࣰཧ዁ᙕ ၛཧແᒨᙕ ᑋୣࣰᄹࣰᙕ ሠၛ෹ౝ޺ఴ዁ࣰࡂʲ˗ᘫᙕ ѣᎍᄹ዁ୣࣰᄹ໪ၛᄹࣰÜᙕ ౝརᙕ ၛᄹࡂࣰᄹᙕ ዁ၛᙕ დᄹࣰᐋࣰར዁ᙕ ዁ୣࣰᙕ ޺ၛᎍᄹ዁ሠᙕ ਰᄹၛ໪ᙕ ‫ݯ‬෺ၛ޺ඬౝར૥ᙕ ఴ໪დ෺ࣰ໪ࣰར዁‫ڬ‬዁ౝၛརᙕ ၛਰᙕ ዁ୣࣰᙕ ᄹࣰਰၛᄹ໪ሠÜᙕ ዁ୣࣰᙕ ׂᎍᄹ‫ڬ‬෹ᙕ ԰‫ڬ‬རࡂሠᙕ ֟ᄹၛ޺෹‫ڬ‬ላ‫ڬ‬዁ౝၛརᙕ დᄹၛᐋఴࡂࣰሠᙕ ਰၛᄹᙕ ዁ᄹఴ‫ݯ‬ᎍར‫ڬ‬෹ሠᙕ ਱ၛᄹᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ౝ‫ڬ‬዁ౝၛརሠᙕ ‫ڬ‬རࡂᙕ ૥ఴᐋࣰሠᙕ ዁ୣࣰሠࣰᙕ ዁ᄹౝ‫ݯ‬ᎍར‫ڬ‬෹ሠᙕ ࣰᒈ޺෹ᎍሠౝᐋࣰᙕ ඊᎍᄹౝሠࡂౝ޺዁ౝၛ࿡ᙕ ၛᐋࣰᄹᙕ෹‫ڬ‬རࡂᙕࡂఴሠდᎍ዁ࣰሠʲ˽ᘩᙕ tȀ @ɕS ɕ@   Eɕ ɕ(  ɕ թၛᙕ ᄹࣰሠࣰ‫ڬ‬ᄹ޺ୣᙕ ૥ᄹၛᎍდᙕ ౝརᙕ л዁ୣౝၛდౝ‫ڬ‬ᙕ ୣ‫ڬ‬ሠᙕ ዁ၛᙕ ࡂ‫ڬ‬዁ࣰᙕ ‫ࣱࣱݯ‬ཧᙕ ‫ݯڬ‬෹ࣰᙕ ‫ڬ‬རࡂᙕ ᑋౝ෹෺ౝར૥ᙕ ዁ၛᙕ ეᄹࣰე‫ڬ‬ᄺࣰᙕ ‫ڬ‬ᙕ ޺ၛ໪დᄹࣰୣࣰརሠౝᐋࣰᙕ ‫ڬ‬ར‫ڬ‬෹ᒥሠౝሠᙕ ၛਰᙕ ዁ୣࣰᙕ ਰౝࣰ෺ࡂᙕ ࣰᒈდࣰᄹౝࣰར޺ࣰᙕ ࡂᎍᄹౝར૥ᙕ ዁ୣࣰᙕ ਰౝᄹሠ዁ᙕ ᒥࣰ‫ڬ‬ᄹᙕ ၛਰᙕ ዁ୣࣰᙕ ׂᎍᄹ‫ڬ‬෹ᙕ ԰‫ڬ‬ཧࡂሠᙕ ֟ᄹၛ޺෺‫ڬ‬ላ‫ڬ‬዁ౝၛརűᙕ ‫כ‬ᎍ޺ୣᙕ ‫ڬ‬ᙕ ዁‫ڬ‬ሠඬᙕ ౝሠᙕ ໪‫ࣰࡂڬ‬ᙕ დ‫ڬ‬ᄹ዁ౝ޻ᎍ෺‫ڬ‬ᄹ෹ᒥᙕ ࡂౝਰਰౝ޺ᎍ෹዁ᙕ ‫ڬ޻ࣰݯ‬ᎍሠࣰÙᙕ ‫ݓ‬ሠᙕ ෹ၛ޺‫ڬ‬෹ᙕ ၛਰਰౝ޻ౝ‫ڬ‬෹ሠᙕ ‫ڬ‬ᄹࣰᙕ ᄯᎍౝ޺ඬᙕ ዁ၛᙕ ޺ၛ໪໪ࣰར዁Ùᙕ ࣰᐋࣰརᙕ ᑋౝ዁ୣౝརᙕ ‫ڬ‬ᙕ ሠౝར૥෹ࣰᙕ ࡂ఺ሠ዁ᄺౝ޺዁ᙕ ዁ୣࣰᙕ ౝ໪დ෺ࣰ໪ࣰར዁‫ڬ‬዁ౝၛཧᙕ ࣰᒈდࣰᄹౝࣰར޺ࣰᙕ ୣ‫ڬ‬ሠᙕ ૥ᄹࣰ‫ڬ‬዁෹ᒥᙕ ࡂౝਰਰࣰᄹࣰࡂᙕ ਰᄹၛ໪ᙕ ე෺‫ࣰ޺ڬ‬ᙕ ዁ၛᙕ დ෹‫ࣰ޺ڬ‬űᙕ ؉ୣࣰᙕ Րౝརౝሠ዁ᄹᒥᙕ ၛਰᙕ ԰‫ڬ‬རࡂሠᙕ ‫ڬ‬ཧࡂᙕ ‫ࣰכ‬዁዁෹ࣰ໪ࣰར዁Ùᙕ ᑋୣౝ޺ୣᙕ ୣ‫ڬ‬ሠᙕ ᄹࣰდၛᄹ዁ሠᙕ ਰᄹၛ໪ᙕ ዁ୣࣰᙕ ਰౝࣰ෹ࡂᙕ ၛਰਰౝ޺ࣰᄹሠᙕ ‫ڬ‬ሠሠౝ૥རࣰࡂÙᙕ ౝརᙕ დᄹౝཧ޺ౝდ෺ࣰÙᙕ ዁ၛᙕ ࣰ‫޺ڬ‬ୣᙕ ࡂౝሠ዁ᄹఴ޺዁ᙕఴརᙕ ዁ୣࣰᙕ ޺ၛᎌར዁ᄹᒥʲȤÜᙕ ୣ‫ڬ‬ሠᙕ ໪ᎌ޺ୣᙕ ၛਰᙕ ዁ୣࣰᙕ ᄹ‫ڬ‬ᑋᙕ ໪‫ڬ‬዁ࣰᄹఴ‫ڬ‬෹ᙕ རࣰ޺ࣰሠሠ‫ڬ‬ᄹᒥᙕ ਰၛᄹᙕ ሠᎍ޺ୣᙕ ‫ڬ‬ᙕ ޺ၛ໪დᄹࣰୣࣰརሠౝᐋࣰᙕ ‫ڬ‬ར‫ڬ‬෹ᒥሠౝሠűᙕ ԰ၛ޺‫ڬ‬෹ᙕ ၛᄹ૥‫ڬ‬རౝᓯ‫ڬ‬዁ౝၛརሠᙕ ౝཧᙕ ሠၛ໪ࣰᙕ ޺‫ڬ‬ሠࣰሠᙕ დၛሠሠࣰሠሠᙕ ዁ୣࣰᙕ ᄹࣰሠၛᎍᄺ޺ࣰሠᙕ ዁ၛᙕ დᄹࣰდ‫ڬ‬ᄹࣰᙕ዁ୣၛᄹၛᎍ૥ୣᙕ‫ڬ‬ར‫ڬ‬෹ᒥሠࣰሠᙕਰၛᄹᙕ዁ୣࣰౝᄹᙕᄹࣰ૥ౝၛརሠűᙕ ЍσХ‫ز‬Ùᙕ ‫ڬ‬ᙕ ޺ၛ໪დࣰ዁ࣰར዁ᙕ ‫ڬ‬རࡂᙕ ᑋࣰӍ෹ᙕ ࡂࣰᐋࣰ෹ၛდᔦ ࣰࡂᙕ ၛᄹ૥‫ڬ‬རౝᓯ‫ڬ‬዁ౝၛརᙕ ࣰར૥‫ڬ‬૥ࣰࡂᙕ ఴརᙕ ޺ၛ໪დᄹࣰୣࣰརሠౝᐋࣰᙕ ᄹᎍᄹ‫ڬ‬෹ᙕ ࡂࣰᐋࣰ෹ၛდ໪ࣰར዁ᙕ ౝརᙕ ‫ڬ‬ᙕ ࡂౝሠ዁ᄹౝ޺዁ᙕ ౝརᙕ σᄹᎍሠሠఴᙕ დᄹၛᐋఴར޺ࣰʲ͉Üᙕ ୣ‫ڬ‬ሠᙕ ‫ڬ‬ᙕ დ෹‫ڬ‬རརౝར૥ᙕ ‫ڬ‬རࡂᙕ ࣰᐋ‫ڬ‬෹ᎍ‫ڬ‬዁ౝၛརᙕ ᎌརఴ዁ᙕ ᑋୣౝ޺ୣᙕ ୣ‫ڬ‬ሠᙕ ‫ࣱݯ‬૥ᎍརᙕ ዁ၛᙕ ૥‫ڬ‬዁ୣࣰᄹᙕ རࣰ޺ࣰሠሠ‫ڬ‬ᄹᒥᙕ ਰౝࣰ෹ࡂᙕ ࡂ‫ڬ‬዁‫ڬ‬űᙕ ؉ୣࣰᙕ ӂཧሠ዁ౝ዁ᎍ዁ࣰᙕ ၛਰᙕ Хࣰᐋࣰ෺ၛდ໪ࣰར዁ᙕ ׂࣰሠࣰ‫ڬ‬ᄹ޺ୣᙕ ‫ڬ‬዁ᙕ σࡂࡂౝሠᙕ σ‫ڬݯڬݯ‬ᙕ ‫ز‬རౝᐋࣰᄹሠౝ዁ᒥᙕ ఴሠᙕ ሠდၛརሠၛᄹౝར૥ᙕ ሠౝ໪ౝ෺‫ڬ‬ᄹᙕ ᄹࣰሠࣰ‫ڬ‬ᄺ޺ୣűᙕ ؉ୣࣰᙕ დᄹၛ‫ݯ‬෹ࣰ໪ሠᙕ ၛརࣰᙕ ࣰར޺ၛᎍཧ዁ࣰᄹሠᙕ ౝརᙕ ሠᎍ޺ୣᙕ ᄹࣰሠࣰ‫ڬ‬ᄹ޺ୣᙕ ౝརᙕ л዁ୣఴၛდౝ‫ڬ‬ᙕ ‫ڬ‬ᄹࣰᙕ ਰၛᄹ໪ౝࡂ‫ݯڬ‬෺ࣰʲ͡Ùᙕ ‫ڬ‬རࡂᙕ ዁ୣࣰᙕ ሠၛᄹ዁ᙕ ၛਰᙕ ࡁࣰ዁‫ڬ‬ౝ෹ࣰࡂᙕ ‫ڬ‬རࡂᙕ ᑋࣰ෹෹įሠᎍდდၛᄺ዁ࣰࡂᙕ ޺ၛ໪დᄹࣰୣࣰརሠౝᐋࣰᙕ‫ڬ‬ར‫ڬ‬෹ᒥሠౝሠᙕ ࡂࣰ‫ڬ‬ᄹᙕ ዁ၛᙕ ዁ୣࣰᙕ ୣࣰ‫ڬ‬ᄹ዁ᙕ ၛਰᙕ ዁ୣࣰᙕ ‫ࣰࡂڬ޺ڬ‬໪ౝ޺ᙕ ‫ڬ‬རࡂᙕ დࣰᄹచ‫ڬ‬ეሠᙕ ࣱᐋࣰརᙕ ᎍሠࣰਰᎍ෺ᙕ ਰၛᄹᙕ ዁ୣࣰᙕ ሠࣰᄹౝၛᎍሠᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰਰၛᄹ໪ࣰᄹ¸ᙕ ໪‫ڬ‬ᒥᙕ རࣰᐋࣰᄹᙕ ‫ڬ‬დდࣰ‫ڬ‬ᄹűᙕ Хࣰሠდౝ዁ࣰᙕ ዁ୣࣰᙕ རࣰ‫ڬ‬ᄺ෹ᒥᙕ ዁ၛ዁‫ڬ‬෹ᙕ ෹‫޺ڬ‬ඬᙕ ၛਰᙕ ਰౝࣰ෹ࡂᙕ ࡂ‫ڬ‬዁‫ڬ‬ᙕ ‫ڬ‬རࡂᙕ ዁ୣࣰᙕ ޺ၛརਰᎍሠౝར૥ᙕ ࣰᒈౝሠ዁ࣰར޺ࣰᙕ ౝརᙕ σࡂࡂౝሠᙕ σ‫ڬݯڬݯ‬ᙕ ‫ڬ‬རࡂᙕ ఴརᙕ ዁ୣࣰᙕ ޺ၛᎍར዁ᄹᒥሠౝࡂࣰᙕ ၛਰᙕ ໪‫ڬ‬རᒥᙕ ޺ၛརੁ෺ౝ޺዁ౝར૥ᙕ ᄹᎌ໪ၛᄹሠᙕ ‫ڬ‬ሠᙕ ዁ၛᙕ ዁ୣࣰᙕ ࣰਰਰࣰ޺዁ሠᙕ ၛਰᙕ ዁ୣࣰᙕ ᄹᎍᄹ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰਰၛᄹ໪ሠÙᙕ ‫ڬ‬རᙕ ‫ڬ‬዁዁ࣱ໫ე዁ᙕ ᑋౝ෹෹ᙕ‫ࣰݯ‬ᙕ໪‫ࣰࡂڬ‬ᙕୣࣰᄹࣰᙕ዁ၛᙕሠᎍ໪໪‫ڬ‬ᄹౝᓯࣰᙕ዁ୣࣰᙕ໪‫ڬ‬ඈၛᄹᙕਰࣰ‫ڬ‬዁ᎍᄹࣰሠᙕၛਰᙕდୣ‫ڬ‬ሠࣰᙕၛརࣰᙕეᄺ‫޻ڬ‬዁ౝ޻ࣰűᙕ ѣౝᄹሠ዁Üᙕ ዁ୣࣰᙕ დᄹၛࡂᎍ޺዁ఴၛརᙕ ࡂౝሠ‫ڬ‬ሠ዁ࣰᄹሠᙕ ਰᄹࣰࣰ෹ᒥᙕ ਰၛᄹࣰሠࣰࣰརᙕ ‫ݯ‬ᒥᙕ ሠၛ໪ࣰᙕ ၛ‫ݯ‬ሠࣰᄹᐋࣰᄺሠᙕ ‫ڬ‬ሠᙕ ‫ڬ‬ཧᙕ ౝ໪໪ࣰࡄౝ‫ڬ‬዁ࣱᙕ ޺ၛརሠࣰᄯᎌࣰར޺ࣰᙕ ၛਰᙕ዁ୣࣰᙕ ᄹࣰਰၛᄹ໪ሠᙕ ሠࣰࣰ໪ᙕᎍར෹ౝඬࣰ෹ᒥᙕ ዁ၛᙕ ୣ‫ڬ‬ᐋࣰᙕ ዁‫ڬ‬ඬࣰརᙕ დ෹‫˗ࣰ޺ڬ‬ǭᘩᙕ ؉ୣࣰᙕ ׂᎍᄹ‫ڬ‬෹ᙕ ԰‫ڬ‬ཧࣙሠᙕ ֟ᄹၛ޺෹‫ڬ‬ላ‫ڬ‬዁ౝၛརᙕ ᑍ‫ڬ‬ሠᙕ ౝሠሠᎍࣰࡂᙕ ౝརᙕ ࣰ‫ڬ‬ᄹ෹ᒥᙕ Ր‫ڬ‬ᄹ޺ୣÜᙕ ౝརᙕ ዁ୣࣰᙕ ሠࣰ‫ڬ‬ሠၛརᙕ ၛਰᙕ ዁ୣࣰᙕ ሠ໪‫ڬ‬෺෹ᙕ ᄹ‫ڬ‬ౝརሠ ᙕ ᑋୣࣱཧᙕ ሠၛᑋఴར૥ᙕ ዁‫ڬ‬ඬࣰሠᙕ დ෹‫ࣰ޺ڬ‬ᙕ ఴརᙕ л዁ୣౝၛდౝ‫ڬ‬űᙕ ؉ୣࣰᙕ ਰఴᄹሠ዁ᙕ ޺ၛར޺ࣰᄺརᙕ ᑋ‫ڬ‬ሠᙕ ዁ၛᙕ ૥ࣰ዁ᙕ ሠၛᑋౝར૥ᙕ ‫޻޺ڬ‬ၛ໫დ෹ౝሠୣࣱࡂᙕ ၛརᙕ ሠ޺ୣࣰࡂᎍ෹ࣰÜᙕ დ‫ڬ‬ᄹ዁ౝ޺ᎍ෺‫ڬ‬ᄹ෹ᒥᙕ ၛརᙕ ዁ୣࣰᙕ ෹‫ڬ‬ᄹ૥ࣰĹሠ޺‫ڬ‬෹ࣰᙕ ໪ࣰ޺ୣ‫ڬ‬རౝᓯࣰࡂᙕ ਰ‫ڬ‬ᄹ໪ሠᙕ ‫ࣰݯ‬ౝཧ૥ᙕ ዁‫ڬ‬ඬࣰརᙕ ၛᐋࣰᄺᙕ 6Ŏଵ O?ଵğ ଵ3B?ŇøB“ଵ %şଵ Dşଵ 66ଵ O?ଵ ğ ଵ 3B? B“ଵ %şଵ 6ଵ Z6o şଵ %?ଵ D ଵ Z ϥ ଵ Bãଵ 1ଵ ??Bଵ ?1Áଵ ଵ Vଵ B*ଵ B*ଵ * ଵ ãBଵ MB ş ଵ 6 Ȼ ଵ ń?ଵ ğMଵ 3B? øB“ଵ %   ş ଵ D ଵ ZΔo şଵ 6+ଵ O?ଵ ğMଵ 3B? B“ଵ %şଵ Dଵ Z6oଵ  ଵ %şଵ 2 R ş ଵ 6$ଵ O?ଵ ğ0Mଵ 3B? uB“ଵ %   ş ଵ 2 ଵ Z2oşଵ 6Rଵ ėଵ H  ଵ qû*“ଵ N%8s _ଵ %ଵ Š1Bଵ ŠV Á0ଵ ଵ 8Á"Á?Bଵ নଵ Ȳ ଵ ZėBû1B? “ଵ ’$ o ì ଵ 6  ଵė Á  ଵNB10ଵ Ǚଵ mu“ଵ B  ş ଵ   ş ଵBÁଵ $ “ ଵ ଵ  ଵ Ś , ଵ ȻDଵ NB1Áଵ Ǚଵ ɚ0“ଵ öşଵ    ş ଵ  B  Á ଵ$“ଵ ଵ  ş ଵ Dƛ “ ଵ    Á ଵ 1   ଵÁ?0ଵ BMBଵ 1Bଵ ã??ଵ )??ଵ ĥ BM?* đଵ ãB??B)ଵ ?Mଵ ÁãB ìଵ ɛǯͅᙕ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb ਭᄹၛ໪ᙕ დᄹఱᐋ‫ڬ‬዁ࣰᙕ ࣰཧ዁ᄹࣰდᄹࣰཧࣰᎍᄹሠŵᙕ ؉ୣఱሠᙕ ᑋ‫ڬ‬ሠᙕ ࡂၚརࣰᙕ ሠᎍ޺޺ࣰሠሠਭᎍӉ෹ᒥᙕ ਭၛᄹᙕ ໪ၚሠ዁ᙕ ၛਭᙕ ዁ୣࣰᙕ ෹‫ڬ‬ᄹ૥ࣰᙕ ਵ‫ڮ‬ᄹ໪ሠŵᙕ թၛᙕ დᄹၛ‫ݯ‬෹ࣰ໪ሠᙕ ᑋࣰᄹࣰᙕ ࣰᒈდࣰᄹఱࣰཧ޺ࣰࡂᙕ ఱཧᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ᙕ ਭ‫ڬ‬ᄹ໪ఱཧ૥ᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ሠÙᙕ ᑋୣࣰᄹࣰᙕ ዁ୣࣰᙕ ෹ࣰ૥ఱሠ෹‫ڬ‬ᔣ ዁ఱၛརᙕ ࡂఱࡂᙕ ཧၛ዁ᙕ ఱཧ዁ࣰᄹਭࣰᄹࣰᙕ ᑋఱ዁ୣᙕ დᄹࣰᐋఱၛᎍሠᙕ დ‫ڬ‬዁዁ࣰᄹཧሠᙕ ၚਭᙕ ၚ޺޺ᎍდ‫ڬ‬ཧ޺ᒥƹᙕ ؉ୣࣰᙕ ࡂࣰᙕ ਭ‫޺ڬ‬዁ၛᙕ ዁ࣰཧᙕ ୣࣰ޺዁‫ڬ‬ᄹࣰᙕ ෹ఱ໪ఱ዁ᙕ ୣ‫ࡂڬ‬ᙕ ෹ఱ዁዁෹ࣶᙕ ໪ࣰ‫ڬ‬ཧఱཧ૥ᙕ ਭၛᄹᙕ ໪ၚሠ዁ᙕ ޺ᎍ෹዁ఱᐋ‫ڬ‬዁ၛᄹሠÙᙕ ሠఱཧ޺ࣶᙕ ዁ୣࣰᙕ ‫ڬ‬ᐋࣰᄹ‫ڬ‬૥ࣰᙕ ୣၛໂࡂఱཧ૥ᙕ సሠᙕ ᑋࣰӉ෹ᙕ ‫ࣰݯ‬෹ၛᑋᙕ ዁ୣ‫ڬ‬዁ᙕ ෹ఱ໪స዁˚ŵᙕ Хఱሠᄹᎍდ዁ఱၛཧÙᙕ ᑋୣࣰᄹࣰᙕ ఱ዁ᙕ ዁ၚၚඬᙕ დ෹‫ࣰ޺ڬ‬Ùᙕ ሠࣰࣰ໪ሠᙕ ዁ၛᙕ ୣ‫ڬ‬ᐋࣰᙕ ޺ࣰཧ዁ࣰᄹࣰࡂᙕ ᎍდၛརᙕఱཧდᎍ዁ሠᙕ ሠၛ໪ࣰ዁ఱ໪ࣰሠᙕ ሠᎍდდ෹ఱࣰࡂᙕ‫ݯ‬ᒥᙕ෹‫ڬ‬ཧࡂ෹ၛᄹࡂሠÙᙕ ሠᎍ޺ୣᙕ ‫ڬ‬ሠᙕၛᒈघཧᙕ ‫ڬ‬རࡂᙕሠࣰࣰࡂ˖ɚᘩᙕ ѣၚᄹ዁ᎍఱ዁ၚᎍሠ෹ᒥᙕ ዁୩ࣰᙕᑋࣰ‫ڬ‬዁ୣࣰᄹᙕᑋ‫ڬ‬ሠᙕ‫ࣰݯ‬዁዁ࣰᄹᙕ዁ୣ‫ڬ‬རᙕ ‫ڬ‬ᐋࣰᄹ‫ڬ‬૥ࣰᙕ዁ୣᄹၚᎍ૥ୣᙕ໪ᎍ޺ୣᙕၛਭᙕ዁ୣࣰᙕ޺ၛᎍཧ዁ᄹᒥÙᙕ ‫ڬ‬ཧࡂᙕ዁ୣࣰᙕ ૥ၚᐋࣰᄹཧᔜ ໪ࣰར዁ᙕ დᎍ዁ᙕ ሠდࣰ޺ఱ‫ڬ‬෹ᙕ ࣰ໪დୣ‫ڬ‬ሠఱሠᙕ ၛཧᙕ ዁ୣࣰᙕ დᄹၛࡂᎍ޺዁ఱၚརᙕ ၚਭᙕ ਭၚၛࡂᙕ ޺ᄹၚდሠᙕ ၚཧᙕ ዁ୣၛሠࣰᙕ ෹‫ڬ‬ᄹ૥ࣰįሠ޺‫ڬ‬෹ࣰᙕ ໪ࣰ޺ୣ‫ڬ‬ཧఱᓯࣰࡂᙕ ࣰᒈķ޺ၛ໪໪ࣰᄹ޺ఱ‫ڬ‬෹ᙕ ਭ‫ڬ‬ᄹ໪ሠᙕ ᑋୣఱ޺ୣᙕ ਭၚᄹᙕ ዁ୣࣰᙕ ዁ఱ໪ࣰᙕ ‫ࣰݯ‬ఱཧ૥ᙕ ‫ڬ‬ᄹࣰᙕ ‫ࣰݯ‬ఱཧ૥ᙕ ᄹᎍཧᙕ ‫ڬ‬ሠᙕ ሠ዁‫ڬ‬዁ࣰᙕ ਭ‫ڬ‬ᄹ໪ሠŵᙕ σሠᙕ ‫ڬ‬ᙕ ᄹࣰሠᎍ෹዁Ùᙕ ఱ዁ᙕ‫ڬ‬დდࣰ‫ڬ‬ᄹሠᙕ ዁ୣࣰᄹࣰᙕ ୣ‫ڬ‬ሠᙕ རၚ዁ᙕ ‫ࣰࣰݯ‬རᙕ ‫ڬ‬ཧᒥᙕ ሠࣰᄹసၚᎍሠᙕ ࡂᄹၛდᙕ సརᙕ დᄹၛࡂᎍ޺዁ఱၚཧ˖ʅÙᙕ ‫ڬ‬෹዁ୣၚᎍ૥ୣᙕ ၚ੕ᙕ ޺ၚᎌᄹሠࣰᙕ ‫ڬ‬ᙕ Bcc1 E!m€6sz 1c6s ]cz ]6)6ssjIV  [6] zEy 16h~z6 ੈၜၚࡈᙕ ሠᎍდდ෹ఱࣰሠᙕ‫ڬ‬዁ᙕ‫ࣰ޺޺ڬ‬დ዁‫ڬ‬෹‫ࣰݯ‬ᙕდᄹఱ޺ࣰሠᙕᑋఱ෹෹ᙕᄹࣰ‫޺ڬ‬ୣᙕ዁ୣࣰᙕ޺ఱ዁ఱࣰሠᙕᑋୣࣰརᙕཧࣰࣰࡂࣰࡂ˖ʲᘪᙕ ‫޺ࣰל‬ၛཧࡂÙᙕ დᄹࣰࡂఱ޺዁‫ݯڬ‬෹ᒥᙕ ዁ୣࣰᙕ ᄹࣰਭၛᄹ໪ሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ఱརఱ዁ఱ‫ڬ‬෹෹ᒥᙕ ‫ࣰࣰݯ‬རᙕ ਭ‫ڬ‬ᄹᙕ ໪ၚᄹࣰᙕ ሠᎍ޺޺ࣰሠሠਭᎍ෹ᙕ ఱཧᙕ ዁ୣࣰᙕ ሠၛᎍ዁ୣᙕ ዁ୣ‫ڬ‬ཧᙕ ఱཧᙕ ዁ୣࣰᙕ ཧၛᄹ዁ୣŵᙕ ԰‫ڬ‬ཧࡂᙕ ዁ၚᙕ ዁ୣࣰᙕ ዁స෹෹ࣰᄹ ᙕ ‫ڬ‬ሠᙕ ‫ڬ‬ᙕ დୣఱ෹ၚሠၚდୣᒥᙕ ၚ‫ݯ‬ᐋఱၚᎍሠ෹ᒥᙕ ਭఱ዁ሠᙕ ໪ᎍ޺ୣᙕ ‫ࣰݯ‬዁዁ࣰᄹᙕ సཧᙕ ‫ڬ‬ཧᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ᙕ ᑋୣఱ޺ୣᙕ ୣ‫ڬ‬ሠᙕ ୣ‫ࡂڬ‬ᙕ ‫ڬ‬ᙕ ୣఱ૥ୣᙕ ᄹ‫ڬ‬዁ࣰᙕ ၚਭᙕ ዁ࣰཧ‫ڬ‬ཧ޺ᒥᙕ ᑋఱ዁ୣᙕ ୣࣰ‫ڬ‬ᐋᒥᙕ ࣰ޺ၚརၛ໪ఱ޺ᙕ ‫ݯ‬ᎍᄹࡂࣰཧሠᙕ დ෹‫ࡂࣰ޺ڬ‬ᙕ ᎍდၛཧᙕ ዁୩ࣰᙕ ዁ࣰཧ‫ڬ‬ར዁ሠᙕ ዁ୣ‫ڬ‬ཧᙕ సརᙕ ၛཧࣰᙕ ᑋୣఱ޺ୣᙕ ୣ‫ڬ‬ሠᙕ ཧၛ዁ᙕ ୣ‫ࡂڬ‬ᙕ ሠᎍ޺ୣᙕ ‫ڬ‬ᙕ დ‫ڬ‬዁዁ࣰᄹརŵᙕ ӂཧᙕ ሠၚ໪ࣰᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ሠᙕ ၚਭᙕ ዁ୣࣰᙕ ሠၛᎍ዁ୣᙕ ዁ࣰར‫ڬ‬ར዁ሠᙕ ୣ‫ࡂڬ‬ᙕ დᄹࣰᐋఱၛᎍሠ෹ᒥᙕ ‫ࣰࣰݯ‬ཧᙕ დၛ෹ఱ዁ఱ޺ఱᓯࣰࡂᙕ ‫ݯ‬ᒥᙕ ዁ࣰཧ‫ڬ‬ཧ዁ᙕ ࣰᐋఱ޺዁ఱၚཧሠᙕᑋୣఱ޺ୣᙕਭၛ෹෹ၛᑋࣰࡂᙕ ዁ୣࣰᙕ ఱཧ዁ᄹၚࡂᎍ޺዁ఱၚཧᙕ ‫ݯ‬ᒥᙕ დᄹఱᐋ‫ڬ‬዁ࣰᙕࣰཧ዁ᄹࣰდᄹࣰཧࣰᎍᄹሠᙕ ၛਭᙕ໪ࣰ޺୩‫ڬ‬རఱᓯࣰࡂᙕ ਭ‫ڬ‬ᄹ໪ఱཧ૥˖˖ᘩᙕ ѣᎍᄹ዁ୣࣰᄹ໪ၛᄹࣰÙᙕ ዁ୣࣰᙕ დᄹၛ໪ఱሠࣰᙕ ၛਭᙕ ᄹࣰࡂఱሠ዁ᄹఱ‫ݯ‬ᎍ዁ఱၛརᙕ ໪‫ڬ‬ᒥᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ࣰࣰݯ‬རᙕ ໪ၛᄹࣰᙕ ᑋࣰ෹޺ၛ໪ࣰᙕఱཧᙕ዁ୣࣰᙕሠၛ޺ఱ‫ڬ‬෹ᙕ޺ၛར዁ࣰᒈ዁ᙕၛਭᙕ዁ୣࣰᙕሠၚᎍ዁ୣࣰᄹརÙᙕ෹‫ڬ‬ᄹ૥ࣰ෹ᒥᙕ փᄹၛ໪ၛÙᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ሠᙕ ዁ୣ‫ڬ‬ཧᙕఱཧᙕ዁ୣ‫ڬ‬዁ᙕၛਭᙕ ዁ୣࣰᙕཧၛᄹ዁ୣࣰᄹཧÙᙕ ෹‫ڬ‬ᄹ૥ࣰ෹ᒥᙕσ໪ୣ‫ڬ‬ᄹ‫ڬ‬ᙕ‫ڬ‬ཧࡂᙕ؉ఱ૥ᄹࣰ‫ڬ‬ཧᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ሠŵᙕ փཧࣰᙕሠ዁ᎍࡂࣰར዁ᙕၚਭᙕሠၛ޺ఱ‫ڬ‬෹ᙕၛᄹ૥‫ڬ‬རఱᓯ‫ڬ‬዁ఱၛཧᙕ సཧᙕ л዁ୣఱၛდఱ‫ڬ‬ᙕ ޺ୣ‫ڬ‬ᄹ‫޺ڬ‬዁ࣰᄹసᓯࣰሠᙕ փᄹၛ໪ၚᙕ ሠၛ޺ఱࣰ዁ᒥᙕ ‫ڬ‬ሠᙕ ዁ୣࣰᙕ ‫ڬ‬ར዁ఱ዁ୣࣰሠఱሠᙕ ၛਭᙕ σ໪ୣ‫ڬ‬ᄹ‫ڬ‬ᙕ ሠၛ޺ఱࣰ዁ᒥᙕ ‫ڬ‬ሠᙕ ਭၛ෹෹ၚᑋሠ ͸ᙕ ٝୣࣰᄹࣰᙕ ዁ୣࣰᙕ σ໪ୣ‫ڬ‬ᄹ‫ڬ‬ᙕ ሠᒥሠ዁ࣰ໪ᙕ ఱሠᙕ ఛఱࣰᄹ‫ڬ‬ᄹ޺ୣస޺‫ڬ‬෹Ùᙕ ዁ୣࣰᙕ փᄹၚ໪ၛᙕ సሠᙕ ࣰ૥‫ڬ‬෹స዁‫ڬ‬ᄹఱ‫ڬ‬རŵᙕ ٝୣࣰᄹࣰᙕ዁ୣࣰᙕσ໪ୣ‫ڬ‬ᄹ‫ڬ‬ᙕఱሠᙕఱཧࡂఱᐋఱࡂᎍ‫ڬ‬෹ఱሠ዁ఱ޺Ùᙕ዁ୣࣰᙕփᄹၛ໪ၚᙕఱሠᙕሠၚ෹ఱࡂ‫ڬ‬ᄹఱሠ዁ఱ޺˖˽ŵPᙕ ѿၛᐋࣰᄹར໪ࣰར዁ᙕሠ዁‫ڬ‬዁ఱሠ዁ఱ޺ሠᙕ ၛརᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛཧᙕਭၚᄹ໪‫ڬ‬዁ఱၛཧᙕሠୣၚᑋᙕ዁ୣ‫ڬ‬዁ᙕసརస዁స‫ڬ‬෹෹ᒥᙕ ዁ୣࣰᙕᄹ‫ڬ‬዁ࣰᙕ ၛਭᙕਭၛᄹ໪‫ڬ‬዁ఱၛཧᙕᑋ‫ڬ‬ሠᙕ ໪ၛᄹࣰᙕ ᄹ‫ڬ‬დఱࡂᙕఱཧᙕ ዁ୣࣰᙕ ሠၛᎍ዁ୣࣰᄹརᙕ ୣఱ૥ୣ෹‫ڬ‬ཧࡂሠ˖̫Ùᙕ ‫ݯ‬ᎍ዁ᙕ዁ୣ‫ڬ‬዁ᙕ ዁ၚᑋ‫ڬ‬ᄹࡂᙕ ዁ୣࣰᙕ ࣰཧࡂᙕ ၛਭᙕ ዁ୣࣰᙕ ਭఱᄹሠ዁ᙕ ᒥࣰ‫ڬ‬ᄹᙕ ၚਭᙕ ዁ୣࣰᙕ ׂᎍᄹ‫ڬ‬෹ᙕ Դ‫ڬ‬ཧࡂሠᙕ ֟ᄹၚ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၚརᙕ ዁ୣࣰᙕ დ‫ࣰ޺ڬ‬ᙕ ᑋ‫ڬ‬ሠᙕ დఱ޺ඬఱཧ૥ᙕ ᎍდᙕ ఱཧᙕ ዁ୣࣰᙕ རၚᄹ዁ୣ˖͉ᘩᙕ Аఱᐋఱ෹ᙕ ࡂఱሠ዁ᎍᄹ‫ڬݯ‬ར޺ࣰሠᙕ సརᙕ ሠၛ໪ࣰᙕ დ‫ڬ‬ᄹ዁ሠᙕ ၚਭᙕ ዁ୣࣰᙕ ཧၛᄹ዁ୣᙕ ຬᏨᐋࣰᙕ ၚ‫ݯ‬ᐋసၚᎍሠ෹ᒥᙕ ୣ‫ࡂڬ‬ᙕ ‫ڬ‬རᙕ ఱཧୣఱ‫ݯ‬ఱ዁ఱཧ૥ᙕ స໪დ‫޺ڬ‬዁ŵᙕ ӂརᙕ ‫ڬ‬ᙕ ਭࣰᑋᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ሠᙕ ఱརᙕ σ໪ୣ‫ڬ‬ᄹ‫ڬ‬ᙕ ୣࣰ‫ڬ‬ᄹ዁෹‫ڬ‬ཧࡂ ᙕ დᄹၛᐋఱཧ޺ࣰሠᙕ ሠᎍ޺ୣᙕ ‫ڬ‬ሠᙕ ѿၛආආ‫ڬ‬໪ᙕ ‫ڬ‬ཧࡂᙕ ϴࣰ૥ࣰ໪ࡂఱᄹÙᙕ ఱ዁ᙕ ୣ‫ڬ‬ሠᙕ ‫ࣰࣰݯ‬ཧᙕ ཧࣰ޺ࣰሠሠ‫ڬ‬ᄹᒥᙕ ዁ၚᙕ ᑋఱ዁ୣࡂᄹ‫ڬ‬ᑋᙕ ෹ၛ޺‫ڬ‬෹ᙕ ෹‫ڬ‬ཧࡂᙕ ᄹࣰਭၚᄹ໪ᙕ ‫ࡂڬ‬ᐋసሠࣰᄹሠŵᙕ ϴᎍ዁ᙕ ࣰ෹ሠࣰᑋୣࣰᄹࣰᙕ ఱརᙕ ዁ୣࣰᙕ ཧၚᄹ዁ୣᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၚཧሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ࣰࣰݯ‬རᙕ ਭၛᄹ໪ࣰࡂᙕ ఱཧᙕ ሠఱᓯ‫ݯڬ‬෹ࣰᙕརᎍ໪‫ࣰݯ‬ᄹሠ˖͝Ùᙕ ‫ڬ‬ཧࡂᙕ዁ୣࣰᒥᙕ‫ڬ‬დდࣰ‫ڬ‬ᄹᙕ዁ၚᙕ‫ࣶݯ‬ᙕ૥సᐋఱར૥ᙕ ᄹఱሠࣰᙕ዁ၚᙕ ‫ڬ‬ᙕ ཧࣰᑋᙕ૥ᄹၛᎍდᙕၛਭᙕ ޺ၛ໪໪ᎍཧఱ዁ᒥᙕ ෹ࣰ‫ࣰࡂڬ‬ᄹሠŵᙕ σ޺޺ၛᄹࡂఱཧ૥ᙕ ዁ၛᙕ ‫ ڬ‬ᄹࣰ޺ࣰར዁ᙕਭఱࣰ෹ࡂᙕሠ዁ᎍࡂᒥᙕ ၚਭᙕሠၛ޺ఱ‫ڬ‬෹ᙕ ၚᄹ૥‫ڬ‬ཧఱᓯ‫ڬ‬዁ఱၛརᙕ ఱརᙕ؉ఱ૥ᄹ‫ڬ‬ఱᙕ დᄹၛᐋఱཧ޺ࣰÙᙕ ໪ၚሠ዁ᙕ໪ࣰ໪‫ࣰݯ‬ᄹሠᙕၛਭᙕ዁ୣࣰᙕ዁ᄹ‫ࡂڬ‬ఱ዁ఱၚཧ‫ڬ‬෹ᙕࣰ෹ఱ዁ࣰሠᙕ ୣ‫ڬ‬ᐋࣰᙕ‫ࣰࣰݯ‬ཧᙕࣰᒈდ෹ఱ޺ఱ዁෹ᒥᙕ ࣰᒈ޺Ȍᎍࡂࣰࡂᙕ ਭᄹၛ໪ᙕ ໪ࣰ໪‫ࣰݯ‬ᄹᔜ ሠୣఱდᙕ ఱརᙕდࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ᙕ‫ڬ‬ሠሠၛ޺స‫ڬ‬዁ఱၛཧᙕ ޺ၚ໪໪ఱ዁዁ࣰࣰሠ ͸ᙕ დᄹࣰᐋఱၛᎍሠᙕ ෹ၛ޺‫ڬ‬෹ᙕ ‫ࡂڬ‬໪ఱཧఱሠ዁ᄹ‫ڬ‬዁ၛᄹሠᙕ ž޺ୣసඬ‫ڬ‬ᙕ ሠୣᎍ໪½Ùᙕ დᄹࣰᐋఱၛᎍሠᙕ ෹ၚ޺‫ڬ‬෹ᙕ ආᎍࡂ૥ࣰሠᙕ ž‫ڬ‬዁‫ݯ‬స‫ڬ‬ᙕ ࡂ‫ڬ‬རᒥ‫½ڬ‬Ùᙕ ᄹᎍᄹ‫ڬ‬෹ᙕ རၛ‫ݯ‬෹ࣰሠÙᙕ ᄹస޺ୣᙕ დࣰၛდ෹ࣰᙕ žఱ෹෹įࡂࣰਭఱཧࣰࡂ½ᙕ ‫ڬ‬རࡂᙕ 4 ଵ N!ßଵ Ǚଵ m'ଵ öଵ ʨşଵ !ଵ |'ଵ ଵ ƌ ¿ Ƽ @ ĝ ଵ ø ଵ ßଵ Bଵ QßøBଵ ଵ ?"ଵ )Fଵ ßଵ  ଵ ଵ ßଵ ßଵ ã!ଵ Êଵ %iß!Ǽßଵ ßଵ ଵ ßଵ V I ଵ ଵ ßଵ Ǽ?Bଵ øଵ !*ଵ Bଵ i! ଵ  ଵ I0ଵ !ଵ 0 ଵ  I!aଵ ĹIଵ ğ ଵ 3B ø!aଵ %şଵ 6ଵ Z@oµଵ *ଵ ઋଵ øଵ ଵ ଵ ã̛ଵ"ଵ)ßଵ Ißଵ  ՞IÕB0ଵ ßଵ Bଵ Jଵ Êଵ 42ଵ C Ê ଵ x)*'ଵ âğ ଵ Ĺã! ଵ  ଵ 30ଵ %!!ଵ ଵ QßøB Ljଵ %ଵ 3 ø*ଵ %?*øƙଵ ¬ଵ ɅB ଵ ßଵ 00Iଵ øǼଵ Bãଵ ßଵ %ãø0ଵ ėIଵ %!øø!'ଵ ė0ଵ Ȳ0B'ଵ # ଵ |4oaଵ şଵ |Єଵ Bଵ ãBଵ %ãଵ  ଵ ßଵ Bଵ 4šଵ kଵ ãଵ ଵ  *ଵ  ଵ ଵ ßଵ s ଵ wB0ଵ Q!0! ଵ NB 0ଵ ß"ଵ Bଵ ȵଵ BV *ଵ ଵ ଵ Ǽଵ ßଵ ßଵ ß"ଵ ã!ଵ |6Ə|4Êଵ РÊଵ 8?Bµଵ âĹBଵ Bଵ 3Bଵ $%Ȁ ßଵ QßBଵ `"ଵ $%Ȁ +Rଵ Qşଵ N,ଵ ¬ |4Ə|+ଵ yǼ!o đଵ Ҕ8 ଵ 2š'ଵ –|4oaଵ  Ê ଵ 6Êଵ Gßଵ ଵ ଵ ଵ !ଵ )ßßଵ ßଵ |6‫|ڼ‬4ଵ ß"ଵ )ଵ ƹ"Ǽ àଵ !ଵ Ǽß*ଵ !)ଵ "ǼÊଵ 46ଵ %ଵ ßଵ  ଵ !ãଵ ßଵ ãଵ *ଵ !ãଵ ßଵ Ĺଵ ğ ଵ 3! ø!'ଵ ßଵ % ଵ %ଵ іଵ )ଵ V਒øǼଵ "ଵ ß!Ǽଵ !ãଵãã'ଵ ଵ ã"B ଵ Qß!ଵ Ǽ'ଵ Iଵ !ßଵ Ǽøଵ )ଵ ଵ Ǽ!B ଵ I*ěଵ 44ଵ ėଵ `!іଵ ‡̛Ħଵ âÎ"Ǽ!ଵ xଵ Cß5 ଵ Ȳ ଵ Ǚଵ ļଵ Qããଵ xଵ 3ଵ %Ǽø? ƙଵ ¬N%8sଵ Ii!ଵ wBଵ |6'ଵ |2o Êଵ 4+ଵ ğ"ø'ଵ BÊଵ ि Ê ଵ Bଵ 26aଵ ଵ ìଵ 2 R Ê ଵ 4|ଵ ėଵ ã !  ଵ ė ଵ |4ଵ    ଵ!"ø  ଵ ଵ ଟ)*'ଵ !ଵ øşଵ  B   ଵ42'ଵ ଵ B   ଵşଵ ‫ ܋‬ĩ ଵ C*ଵ !ãଵğ0ଵଵ ė ଵ øଵ ã!ଵ wB" ଵ |4ଵ ¬ଵ % ßo Êଵ 4ଵ mßଵ GǼଵ !"ଵ Bø!ଵ ଵ ଵ Ⱦଵ ßŢଵ ଵ ãB  ଵ ଵ âଵ  Jଵ  ƙ şଵ `ʾଵ Gßଵ ė"ଵ ğ  'ଵ BÊଵ Êଵ Bଵ 6'ଵ ଵ  Ê ଵ 2RÊଵ ?E https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb ᐋൈ෹෹‫ڬ‬૥ࣰᙕ ࣰ෹ࡂࣰᅆሠ̂ǭᘩᙕ ӂར዁ࣰᄺࣰሠ዁ఱར૥෹ᒥÙᙕ ୣၛᑋࣰᐋࣰᅆÙᙕ ఱརᙕ ؉ఱ૥ᅆ‫ڬ‬ఱᙕ დᄺၛᐋఱར޺ࣰᙕ დᅆఱࣰሠ዁ሠᙕ ୣ‫ڬ‬ᐋࣰᙕ རၛ዁ᙕ ‫ࣰࣰݯ‬རᙕ ࣰᒈ޺෹ᎍࡂࣰࡂᙕੁᅆၛ໫ᙕ෹ࣰ‫ࣰࡂڬ‬ᅆሠୣఱდᙕდၛሠఱ዁ఱၛརሠŶᙕ ӂརᙕᅆࣰ૥‫ڬ‬ᄺࡂᙕ ዁ၛᙕ ዁ୣࣰᙕ ዁ᑋၛᙕ ໫ၛሠ዁ᙕఱ໫დၛᄺ዁‫ڬ‬ར዁ᙕეၛሠఱ዁ఱၛརሠÚᙕ ޺ୣ‫ڬ‬ఱᄺ໫‫ڬ‬རᙕ ‫ڬ‬རࡂᙕ ሠࣰ޺ᄺࣰ዁‫ڬ‬ᅆᒥᙕ ၛਰᙕ ዁ୣࣰᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརÙᙕ ‫ڬ‬დდᅆၛᒈఱ໫‫ڬ‬዁ࣰ෹ᒥᙕ ዁ᑋࣱར዁ᒥᙕ ეࣰᄺ޺ࣰར዁ᙕ ၛਰᙕఱར޺ᎍ໫‫ࣰݯ‬ར዁ሠᙕఱརᙕ዁ୣࣰᙕ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕሠ዁ᎍࡂఱࣰࡂᙕᑋࣰᅆࣰᙕდᄺఱࣰሠ዁ሠ̂ȇᘩᙕ ӂརᙕ ዁ୣࣰᙕ རၛᅆ዁ୣÙᙕ ዁ୣࣰᙕ ໫‫ڬ‬ආၛᅆᙕ ੁᎍར޺዁ఱၛརᙕ ၛੁᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ‫޺޺ڬ‬ၛᄺࡂఱར૥ᙕ ዁ၛᙕ ዁ୣࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ ԰‫ڬ‬རࡂሠᙕ ֟ᅆၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛརᙕఱሠᙕ  ዁ၛᙕ ఱརࡂᎍ޺ࣰᙕ ‫ڬ‬རࡂᙕၛᄺ૥‫ڬ‬རఱᓯࣰᙕდࣰᙕ‫ ڬ‬ሠ‫ڬ‬ར዁ሠᙕ ఱར጖ၛᙕ ޺ၛıၛეࣰᄺ‫ڬ‬዁ఱᐋࣰᙕ ੁ‫ڬ‬ᄺ໪ሠ̂ɺƅ ᙕ ԰‫ڬ‬རࡂᙕ ᅆࣰࡂఱሠ዁ᅆఱ‫ݯ‬ᎍ዁ఱၛརᙕ ఱሠᙕ ޺෹ࣰ‫ڬ‬ᅆ෹ᒥᙕ རၛ዁ᙕ ‫ڬ‬໫ၛར૥ᙕ ዁ୣࣰᙕ ੁᎍར޺዁ఱၛརሠᙕ ૥ఱᐋࣰརᙕ ዁ၛᙕ རၛᄺ዁ୣࣱᄺརᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར጖ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠ̂ʌÙᙕ ᒥࣰ዁ᙕ ᑋୣࣰᄺࣰᙕ ሠᎍ޺ୣᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ᑋ‫ڬ‬ར዁ᙕ ዁ၛᙕ ޺‫ڬ‬ᄺᄺᒥᙕ ၛᎍ዁ᙕ ᅆࣰࡂോሠ጖ᄺൈ‫ݯ‬ᎍ጖ൈၛརᙕ ఱ዁ᙕ ఱሠᙕ ዁ୣࣳᙕ ૥ၛᐋࣰᅆར໪ࣰར዁gሠᙕ ᐋఱࣰᑋᙕ ዁ୣ‫ڬ‬዁ᙕ ዁ୣఱሠᙕ ఱሠᙕ დࣰᅆ໫ఱ዁጖ࣰࡂƅᙕ ӂརࡂࣱࣱࡂᙕ ዁ୣࣰᙕ Ցఱརఱሠ዁ᄺᒥᙕ ၛੁᙕ ԰‫ڬ‬རࡂሠᙕ ‫ڬ‬རࡂᙕ ‫ࣰל‬዁዁෹ࣰ໫ࣰར዁gሠᙕ ਰఱᅆሠ዁ᙕ ໫‫ڬ‬ආၛᅆᙕ ఱརᐋၛ෹ᐋࣰ໫ࣰར዁ᙕ ఱརᙕ ෹ၛ޺‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᅆࣰࡂఱሠ዁ᅆఱ‫ݯ‬ᎍ዁ൈၛརᙕ ఱሠᙕ დື‫ڬ‬རརࣰࡂᙕ ਰၛᄺᙕ ؉ఱ૥ᄺ‫ڬ‬ఱᙕდᅆၛᐋఱར޺ࣰŶᙕ σ෹዁ୣၛᎍ૥ୣᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ޺ၛįၛდࣰᅆ‫ڬ‬዁ఱᐋࣰሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ڬ‬ეე‫ڬ‬ᄺࣰར዁෹ᒥᙕ རၛ዁ᙕ ᒥࣰ዁ᙕ ‫ࣰࣰݯ‬རᙕ ၛᄺ૥‫ڬ‬རൈᓯࣰࡂᙕ ఱརᙕ ዁ୣࣰᙕ རၛᅆ጖ୣࣰᄺརᙕ დᅆၛᐋఱར޺ࣰሠÙᙕ ሠၛ໫ࣰᙕ ੁఱࣰ෹ࡂᙕ ᄺࣰეၛᄺ዁ሠᙕ ఱརࡂఱ޺‫ڬ‬዁ࣰᙕ ዁ୣ‫ڬ‬዁ᙕ ఱརᙕ ዁ୣࣰᙕ ఱརఱ዁ఱ‫ڬ‬෹ᙕ ሠ዁‫ڬ‬૥ࣱሠᙕ ሠၛ໪ࣰᙕ རၛᄺ዁ୣࣰᅆརᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ᅆࣰᄱᎍఱᄺࣰࡂᙕ ਰ‫ڬ‬ᄺ໫ࣰᄺሠᙕ ዁ၛᙕ ෹ఱ໫ఱ዁ᙕ ዁ୣࣰఱᄺᙕ ޺෹‫ڬ‬ఱ໫ሠᙕ ዁ၛᙕ ޺ᎍ෹዁ఱᐋ‫ڬ‬጖ൈၛརᙕ ᅆఱ૥ୣ዁ሠᙕ ዁ၛᙕ ෹‫ڬ‬རࡂᙕ ᑋఱ዁ୣೝརᙕ ዁ୣࣰᙕ ‫ݯ‬ၛᎍརࡂ‫ڬ‬ᄺൈࣰሠᙕ ၛશᙕ ‫ڬ‬ᙕ ሠఱར૥෹ࣰᙕ ‫ڬ‬ሠሠၛ޺ൈ‫ڬ‬጖ఱၛརƅᙕ ‫ל‬ᎍ޺ୣᙕ ‫޺ڬ‬዁ఱၛརÚᙕ ᑋୣఱ޺ୣᙕ ൈሠᙕ རၛ዁ᙕ ‫ڬ‬ᎍ዁ୣၛᅆఱᓯࣰࡂᙕ ‫ݯ‬ᒥᙕ ዁ୣࣰᙕ ෹ࣰ૥ఱሠ෹‫ڬ‬዁ఱၛར̂ʲÙᙕ ୣ‫ڬ‬ሠᙕ ዁ୣࣰᙕ ࣰੁਰࣰ޺዁ᙕ ၛਰᙕ ෹ఱ໫ఱ዁ఱར૥ᙕ ੁᄺ‫ڬ‬૥໪ࣰར዁‫ڬ‬዁ൈၛརᙕ ‫ڬ‬རࡂᙕ ᑋୣ‫ڬ‬዁ࣰᐋࣰᅆᙕ ‫ࡂڬ‬ᐋࣰᅆሠࣰᙕ ࣰ޺ၛརၛ໫ఱ޺ᙕ ࣰੁਰࣰ޺዁ሠᙕ ሠᎍ޺ୣᙕ ਰᄺ‫ڬ‬૥໫ࣰར዁‫ڬ‬዁ఱၛརᙕ ໫‫ڬ‬ᒥᙕ ୣ‫ڬ‬ᐋࣰᙕ ᎍეၛརᙕ ეᄺၛࡂᎍ޺ᔝ ዁ఱၛར̂˖ᘩᙕ ٝୣࣰᅆࣰᙕ ਰᅆ‫ڬ‬૥໫ࣰར዁‫ڬ‬዁ఱၛརᙕ ୣ‫ࡂڬ‬ᙕ ‫ࣰࣰݯ‬རᙕ ࡂࣰ‫ڬ‬෹዁ᙕ ᑋఱ዁ୣᙕ ‫ݯ‬ᒥᙕ ෹ࣰ‫ڬ‬ሠఱར૥ᙕ ‫ڬ‬ᄺᄺ‫ڬ‬ར૥ࣱ໪ࣰར዁ሠᙕ Ņ ਰ‫ڬ‬ᅆ໫ࣱᄺሠᙕ ᅆࣰར዁ఱར૥ᙕ ዁ၛᙕ ၛ዁ୣࣰᄺሠᙕ ዁ୣࣰఱᄺᙕ ࡂఱሠ዁‫ڬ‬ར዁ᙕ დ‫ڬ‬ᅆ޺ࣰ෹ሠᙕ ‫ڬ‬རࡂᙕ ᄺࣰར዁ఱར૥ᙕ ਰᄺၛ໫ᙕ ၛ዁ୣࣰᄺሠᙕ ე‫ݕ‬ᄺ޺ࣰ෹ሠᙕ ޺෹ၛሠࣰᅆᙕ ዁ၛᙕ ዁ୣࣰఱᅆᙕ ୣၛላࣰᙕ ‫ڬݯ‬ሠࣰᙕ İ ሠၛ໫ࣰᙕ རၛᅆ዁ୣࣰᄺརᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ᄺࣰეၛᄺ዁ࣰࡂ෹ᓧᙕ ୣ‫ڬ‬ᐋࣰᙕ ሠఱ໫დ෹ᒥᙕ ޺ၛརਰఱᅆ໫ࣰࡂᙕ ‫ڬ‬෹෹ᙕ ޺ᎍ෹዁ఱᐋ‫ڬ‬዁ၛᄺሠᙕ ఱརᙕ ዁ୣࣰఱᅆᙕ ࣰᒈఱሠ዁ఱར૥ᙕ ၛ޺޺ᎍდ‫ڬ‬ར޺ᒥŶᙕ ؉ୣఱሠᙕ ఱሠᙕ ࣰሠሠࣰར዁ఱ‫ڬ‬෹෹ᒥᙕ ᑋୣ‫ڬ‬዁ᙕ዁ୣࣰᙕׂᎍᅆ‫ڬ‬෹ᙕԴ‫ڬ‬རࡂሠᙕ֟ᅆၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛརᙕ ეᄺၛᐋఱࡂࣰሠᙕ ਰၛᅆᙕ዁ୣࣰᙕሠၛᎍ዁ୣ̂̂Ùᙕ ‫ݯ‬ᎍ዁ᙕརၛ዁ᙕ጖ୣࣰᙕརၛᄺ጖ୣ̻̂ᘰᙕ ؉ୣఱᅆࡂÙᙕ ዁ୣࣰᙕ Ցఱརఱሠ዁ᅆᒥᙕ ၛਰᙕ ԰‫ڬ‬རࡂሠᙕ ‫ڬ‬རࡂᙕ ‫ࣰל‬዁዁෹ࣰ໫ࣰར዁ᙕ ୣ‫ڬ‬ሠᙕ ୣ‫ࡂڬ‬ᙕ ఱརሠᎍੁੁఱ޺ఱࣰར዁ᙕ ᄺࣰሠၛᎍᄺ޺ࣰሠᙕ ዁ၛᙕ ሠࣰᅆᐋࣰᙕ ‫ڬ‬ሠᙕ ዁ୣࣰᙕ დᅆఱ໫‫ڬ‬ᅆᒥᙕ ‫ڬ‬૥ࣰར዁ᙕ ၛਰᙕ ޺ୣ‫ڬ‬ར૥ࣰᙕ ‫ڬ‬ሠᙕ ‫ڬ‬ར዁ఱ޺ఱე‫ڬ‬዁ࣰࡂᙕ ‫ݯ‬ᒥᙕ ዁ୣࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ ԰‫ڬ‬རࡂሠᙕ ֟ᅆၛ޺෹‫ڬ‬ላ‫ڬ‬ᔜ ዁ఱၛརŶᙕ ӂརሠ዁ࣰ‫ࡂڬ‬ᙕ ዁ୣࣰᙕ ໫‫ڬ‬ඈၛᅆᙕ ዁ୣᄺᎍሠ዁ᙕ ఱརఱ዁ఱ‫ڬ‬෹෹ᒥᙕ ޺‫ڬ‬໫ࣰᙕ ੁᅆၛ໫ᙕ ዁ୣࣰᙕ ᓯࣰ໫ࣰ޺ୣ‫ڬ‬Ùᙕ ‫ڬ‬ᙕ Хࣰᐋࣱ෹ၛე໫ࣰར዁ᙕ ؉ୣᄺၛᎍ૥ୣᙕ Ўၛįၛდࣰᅆ‫ڬ‬዁ఱၛརÙᙕ лར෹ఱ૥ୣ዁ࣰར໫ࣰར዁Ùᙕ ‫ڬ‬རࡂᙕ ٝၛᅆඬᙕ Ў‫ڬ‬໫დ‫ڬ‬ఱ૥ར ᙕ ఱརᙕ ᑋୣఱ޺ୣᙕ ሠၛᙕ໫ ࣰᙕ ሠఱᒈ዁ᒥᙕ ዁ୣၛᎍሠ‫ڬ‬རࡂᙕ ሠࣰ޺ၛརࡂ‫ڬ‬ᅆᒥᙕ ሠ޺ୣၛၛ෹ᙕ ሠ዁ᎍࡂࣰར዁ሠÙᙕ ᅆࣰ޺ࣰར጖ᙕ ሠࣰ޺ၛརࡂ‫ڬ‬ᄺᒥᙕ ሠ޺ୣၛၛ෹ᙕ ૥ᄺ‫ࡂڬ‬ᎍ‫ڬ‬጖ࣱማÚᙕ ‫ࡂဴڬ‬ᙕ ᎍརఱᐋࣰᅆሠఱ዁ᒥᙕሠ዁ᎍࡂࣰར዁ሠᙕ ୣ‫ڬ‬ᐋࣰᙕ‫ࣰࣰݯ‬རᙕሠࣰར዁ᙕ዁ၛᙕ዁ୣࣰᙕ޺ၛᎍར዁ᅆᒥሠఱࡂࣰᙕ዁ၛᙕ ࣰར૥‫ڬ‬૥ࣰᙕ ఱརᙕ ‫ڬ‬ᙕ ޺ᄺ‫ڬ‬ሠୣᙕეᄺၛ૥ᄺ‫ڬ‬໹ᙕ ၛਰᙕ ࣰࡂᎍ޺‫ڬ‬዁ఱၛརÙᙕ ࡂࣰᐋࣰ෹ၛდ໫ࣰར዁ᙕ ‫ڬ‬རࡂᙕდၛ෹ఱ዁ఱ޺ఱᓯ‫ڬ‬዁ఱၛརᙕ ၛੁᙕ ዁ୣࣰᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᄺᒥ͉̂ƅᙕ կၛᙕ ᄺၛ෹ࣰᙕ ੁၛᄺᙕ ጖ୣࣰሠࣰᙕ ሠ዁ᎍࡂࣰར዁ሠᙕ ᑋ‫ڬ‬ሠᙕ ‫ڬ‬ར዁ఱ޺ఱდ‫ڬ‬዁ࣰࡂᙕ ఱརᙕ ዁ୣࣰᙕ ׂᎍᅆ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄺၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛརᙕ ఱ጖ሠࣰ෹ਰÙᙕ ‫ݯ‬ᎍ዁ᙕ ෹‫ڬ‬རࡂᙕ ᄺࣱੁၛᄺ໪ᙕ ᑋၛᅆඬᙕ ఱሠᙕ ၛརࣰᙕ დၛఱར዁ᙕ ఱརᙕ ዁ୣࣰఱᅆᙕ ࣰఱ૥ୣ዁ᙕ დၛఱར዁ᙕ დᄺၛ૥ᄺ‫ڬ‬໫̂͡ᘩᙕ փੁᙕ ዁ୣࣰሠࣰᙕ ᐋ‫ڬ‬ᄺఱၛᎍሠᙕ ዁‫ڬ‬ሠඬሠÚᙕ ෹‫ڬ‬རࡂᙕ ᅆࣰੁၛᅆ໫ᙕ ᑋၛᄺඬᙕ ୣ‫ڬ‬ሠᙕ ‫ࣰࣰݯ‬རᙕ დ‫ڬ‬ᅆ‫ڬ‬໫ၛᎍར዁ᙕ ਰၛᅆᙕ ໫‫ڬ‬རᒥᙕ ᓯࣰ໫ࣰ޺ୣ‫ڬ‬ᙕ ე‫ڬ‬ᄺ዁ఱ޺ఱდ‫ڬ‬ར዁ሠƅᙕ ӂརࡂࣰࣰࡂᙕ ໫‫ڬ‬རᒥᙕ ሠࣰࣰ໫ᙕ ዁ၛᙕ ୣ‫ڬ‬ᐋࣰᙕ ૥ၛརࣰᙕ ‫ࣰݯ‬ᒥၛརࡂᙕ ࣰᒈდ෹‫ڬ‬ར‫ڬ‬዁ఱၛརᙕ ၛਰᙕ ዁ୣࣰᙕ ׂᎍᄺ‫ڬ‬෹ᙕ ԰‫ڬ‬རࡂሠᙕ ֟ᄺၛ޺෹‫ڬ‬໪‫ڬ‬጖ൈၛརᙕ ‫ڬ‬རࡂᙕ ‫ڬ‬ሠሠఱሠ዁‫ڬ‬ར޺ࣰᙕ ఱརᙕੁၛᅆ໫‫ڬ‬዁ఱၛརᙕၛਰᙕდࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ዁ၛᙕᎍར‫ڬ‬ᎍ዁ୣၛᄺఱᓯࣰࡂᙕ ‫޺ڬ‬዁ఱᐋൈ዁ఱࣱሠᙕ ሠᎍ޺୩ᙕ ‫ڬ‬ሠᙕ ዁ஒࠓᙕ ࡂఱሠ‫ڬ‬ᄺ໫ఱར૥ᙕ ‫ڬ‬རࡂᙕ ၛ޺޺‫ڬ‬ሠఱၛར‫ڬ‬෹෹ᒥᙕ ‫ڬ‬ᅆᅆࣰሠ዁ᙕ ၛᅆᙕ ඬఱ෹෹ఱར૥ᙕ ၛਰᙕ ੁၛᅆ໫ࣰᄺᙕ ෹‫ڬ‬རࡂ෹ၛᅆࡂሠƅᙕ Ўၛརሠൈࡂࣱᄺ‫ݯڬ‬෹ॠᙕ ‫ڬ‬ར዁‫ڬ‬૥ၛརఱሠ໫ᙕ ‫ࣰݯ‬዁ᑋࣰࣰརᙕ ᓯࣰ໫ࣰ޺ୣ‫ڬ‬ᙕ დ‫ڬ‬ᅆ዁ఱ޺ఱე‫ڬ‬ར዁ሠᙕ ‫ڬ‬རࡂᙕ ෹ၛ޺‫ڬ‬෹ᙕ დၛ෹ఱ޺ࣰᙕ ਰၛᄺ޺ࣰሠᙕ ୣ‫ڬ‬ሠᙕ ᅆࣰሠᎍ෹዁ࣰࡂÚᙕ ‫ڬ‬རࡂᙕ ఱ዁ᙕ ୣ‫ڬ‬ሠᙕ ‫ࣰࣰݯ‬རᙕ ዁ୣࣰᙕ დ‫ڬ‬዁዁ࣰᄺརᙕ ఱརᙕ ໫ၛሠ዁ᙕ ఱརሠ዁‫ڬ‬ར޺ࣰሠᙕ ੁၛᄺᙕ ዁ୣࣰᙕ ໫ఱ෹ఱ዁‫ڬ‬ᄺᒥᙕ ૥ၛᐋࣰᄺར໫ࣰར዁ᙕ ዁ၛᙕ ር᏶ეეၛᄺ፭ᙕ ዁ୣࣰᙕ დၛ෹ఱ޺ࣰᙕ ‫ڬ‬རࡂᙕ ᅆࣰሠ዁ᅆ‫ڬ‬ఱརᙕ ዁ୣࣰᙕ ሠ዁ᎍࡂࣰར዁ሠ̫ǭᘩᙕ ؉ୣఱሠᙕ დ‫ڬ‬዁዁ࣰᅆརᙕ ୣ‫ڬ‬ሠᙕ ޺ၛར዁ᄺఱ‫ݯ‬ᎍ዁ࣰࡂᙕ ጖ၛᙕ ጖ୣࣰᙕ ၰეࣱးᙕ ୣၛሠ዁ఱ෹ఱ዁ᒥᙕᑋఱ዁ୣᙕᑋୣఱ޺ୣᙕ໫ၛሠ጖ᙕሠ዁ᎍࡂࣰར዁ሠᙕ዁ၛࡂ‫ڬ‬ᒥᙕᅆࣰ૥‫ڬ‬ᄺࡂᙕ዁ୣࣰᙕ໫ఱ෹ఱ዁‫ڬ‬ᄺᒥᙕᅆࣰ૥ఱ໫ࣰƅᙕ +Dଵ kଵ ଵ   ଵ Ŏ   ଵ kυ ଵ ଵBଵVଵ ãB ଵ1ଵ B  Ⱥଵ üଵ kȺଵ ଵ   ଵ DžDLଵ +2ଵ ńଵ Žଵ 3B B'ଵ %¿ଵ 2Ŏ ,ଵ +Ŏଵ ńଵ Žଵ 3B Baଵ %ଵ Dଵ ¬   ଵ ଵ %ଵ 2ŎÊଵ +6ଵ ńଵğଵ3B B'ଵ %ଵ 2Ŏ Êଵ +4ଵ % 1B1ଵ 1ଵ ଵ BB ଵ ãã ଵ Bãଵ ã  Bଵ ଵ BK ଵ Bଵ 'ଵ ã̢ƕƕBଵ ̢* ीBଵ "ଵ Bଵ  5ଵ 1ଵ ëଵ B ã ଵ Bଵ Bଵ ã¿ଵ `B'ଵ öଵ ‘ɦଵ B ଵ 2$“ଵ ଵ  Ⱥ ଵ Dü'ଵ B ଵ Džଵ ++ଵ ńଵ Žଵ 3B Baଵ %¿ଵ +ଵ ¬   ¿ ଵ ü|ଵ ńଵ Žଵ 3BͳB'ଵ %   ¿ ଵ 22ìଵ +ƛଵ Î *'ଵ ૬ öଵ )ɦ1ଵ  ଵ Œଵ   ଵ B ଵ Bãଵ %ଵ )ଵ ȶଵ ̢Œଵ ɦɾଵ Œଵ ࠨ৞ଵ )Ŝƕऑଵ ଵ "B ଵ ଵ ߉Bଵ  BଵBãଵ 1ଵ ଵ ଵ   Ⱥ ƺଵଵ ʺ )*'ଵ B'ଵ ଵ B ଵ ÅÇÐଵ  ଵ   ଵ 6ìଵ ଊ +ଵ GŒଵ BƕŒଵ Bଵ ଵ ଵ ãBB) ƶଵ Œଵ ŒBB1*ଵ Bãଵ Š ŒBଵ B 'ଵ 11'ଵ ଵ ࢋ B ˌଵ ã 'ଵ ଵ  B"  'ଵ  ଵ ࠩBଵ ଵ Œଵ B Bଵ Bãଵ  B1‘ଵ мƕԡ‫ڔ‬ଵ |Dଵ ėଵȳ)*'ଵ Bଵ ӄଵ Bଵ42“ଵ ଵ ଵ $Ėƛ ଵ ɛȆǯᙕ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb )ɕ @ɕ&Kɕ&„ Eɕ &Kƒɕɕ  ɕȮ  ɕ փརᙕ Хࣰ޺ࣰ໪‫ࣰݯ‬ᄻᙕ Ȇ ʮ Ù ᙕ Ȇ ̡ͤ˕Ùᙕ ዁ୣࣰᙕ ֟ᄻၛᐋఱሠఱၛཧᙕ‫ ڬ‬෹ᙕ Րఱ෹ఱ዁‫ڬ‬ᄻᒥᙕ σࡂ໪ఱརఱሠ዁ᄻ‫ڬ‬዁ఱၛརᙕ Ўၛᎍཧ޺ఱ෹ᙕ ఱሠሠᎍࣰࡂᙕ ‫ڬ‬ᙕ ሠࣰ޺ၛཧࡂᙕ ეᄻၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛཧᙕ ၛརᙕ ᄻᎍᄻ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᄻࣰਰၛᄻ໪̫ȍᘳᙕ ؉ୣఱሠᙕ ෹ࣰ૥ఱሠ෹‫ڬ‬዁ఱၛཧÙᙕ ዁ୣࣰᙕ ࣰ֟‫ڬ‬ሠ‫ڬ‬ཧ዁ᙕ υሠሠၛ޺ఱ‫ڬ‬ᔝ ዁ఱၛརሠᙕ ֟ᄻၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛརÙᙕ ሠᎍ૥૥ࣰሠ዁ሠᙕ ‫ڬ‬ᙕ ࡂࣰ޺ఱࡂࣰࡂ෹ᒥᙕ ࡂఱਰਰࣰᄻࣰར዁ᙕ ‫ڬ‬዁዁ఱ዁ᎍࡂࣰᙕ ዁ၛᑋ‫ڬ‬ᄻࡂᙕ ෹‫ڬ‬རࡂᙕ ዁ࣰརᎍᄻࣰᙕ ዁ୣ‫ڬ‬ཧᙕ ࡂఱࡂᙕ ዁ୣࣰᙕ ׂᎍᄻ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄻၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛརŶᙕ ѿၛཧࣰᙕ ఱሠᙕ ዁ୣࣰᙕ ࣰ໪ეୣ‫ڬ‬ሠఱሠᙕ ၛཧᙕ ෹‫ڬ‬རࡂᙕ ዁ၛᙕ ዁ୣࣰᙕ ዁ఱ෹෹ࣰᄻ  Ùᙕ ᄻࣰࡂఱሠ዁ᄻఱ‫ݯ‬ᎍ዁ఱၛརᙕ ၛਰᙕ ෹‫ڬ‬རࡂሠᙕ ዁ၛᙕ ‫ࣰݯ‬ᙕ ޺ᎍ෹዁ఱᐋ‫ڬ‬዁ࣰࡂᙕ ‫ݯ‬ᒥᙕ ਰ‫ڬ‬ᄻ໪ఱར૥ᙕ ਰ‫ڬ‬໪ఱ෹ఱࣰሠᙕ ఱརᙕ ‫ڬ‬ᄦეᄻၛᒈఱᔝ ໪‫ڬ‬዁ࣰ෹ᒥᙕ ࣰᄯᎍ‫ڬ‬෹ᙕ ე‫ڬ‬ᄻ޺ࣰ෹ሠÙᙕ ‫ڬ‬ཧࡂᙕ ዁ୣࣰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརᙕ ‫ڬ‬ሠᙕ ‫ڬ‬ᙕ ໪ࣰ‫ڬ‬རሠᙕ ዁ၛᙕ ‫޺޺ڬ‬ၛ໪ე෹ఱሠୣᙕ ዁ୣఱሠᙕ ఱརࡂఱᐋఱࡂᎍ‫ڬ‬෹ఱሠ዁ఱ޺ᙕ ࣰརࡂŶᙕ ӂརᙕ ዁ୣࣰᙕ ࣰ֟‫ڬ‬ሠ‫ڬ‬ར዁ᙕ σሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ֟ᄻၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛཧᙕ ዁ୣࣰᙕ ᑋၛᄻࡂᙕ  ࡂఱሠ዁ᄻೊ‫ݼ‬ᎏᔝ ዁ఱၛར ᙕ ఱሠᙕ རࣰᐋࣰᄻᙕ ᎍሠࣰࡂÙᙕ ‫ڬ‬෹዁ୣၛᎍ૥ୣᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛཧሠᙕ ‫ڬ‬ᄻࣰᙕ ዁ၛᙕ ޺ၛར዁ఱཧᎍࣰᙕ ዁ၛᙕ ࣰᒈࣰᄻ޺ఱሠࣰᙕ ዁ୣࣰᙕ ੁᎍཧ޺዁ఱၛརሠᙕ ૥ఱᐋࣰརᙕ ዁ୣࣰ໪ᙕ ‫ݯ‬ᒥᙕ ዁ୣࣰᙕ ׂᎍᄻ‫ڬ‬෹ᙕ Դ‫ڬ‬རࡂሠᙕ ֟ᄻၛ޺෹‫ڬ‬໪‫ڬ‬዁ఱၛར̫ɚᘳᙕ փརࣰᙕ ၛਰᙕ ዁ୣࣰሠࣰᙕ ਰᎍར޺዁ఱၛརሠÙᙕ ੁၛᄻᙕሠၛᎍ዁ୣࣰᄻཧᙕਰၛᄻ໪ࣰᄻ෹ᒥᙕਰᄻࣰࣰୣၛ෹ࡂᙕ‫ڬ‬ᄻࣰ‫ڬ‬ሠÙᙕఱሠᙕ෹‫ڬ‬ཧࡂᙕࡂఱሠ዁ᄻఱ‫ݯ‬ᎍ዁ఱၛར̫ʅᘳᙕ Ӆརᙕ ዁ୣࣰᙕ ׂᎍᄻ‫ڬ‬෹ᙕԴ‫ڬ‬ཧࡂሠᙕ֟ᄻၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛཧᙕ ዁ୣࣰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ᙕ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛཧᙕ ᑋ‫ڬ‬ሠᙕ ዁ၛᙕሠࣰᄻᐋࣰᙕ዁ୣࣰᙕఱཧࡂఱᐋఱࡂᎍ‫ڬ‬෹ƅᙕ Ӆརᙕ ዁ୣࣰᙕ ࣰ֟‫ڬ‬ሠ‫ڬ‬ར዁ᙕσሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ֟ᄻၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛརᙕ ዁ୣࣰᙕ ఱརࡂఱᐋఱࡂᎍ‫ڬ‬෹ᙕ ఱሠᙕ ዁ၛᙕ ሠࣰᄻᐋࣰᙕ ዁ୣࣰᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརÚᙕ ‫ڬ‬ሠᙕ ᑋࣰӉ෹ᙕ ‫ڬ‬ሠᙕ ዁ୣࣰᙕ ሠࣰᄻᐋఱ޺ࣰᙕ ‫ڬ‬ཧࡂᙕ ეᄻၛࡂᎍ޺ࣰᄻᙕ ޺ၛįၛეࣰᄻ‫ڬ‬዁ఱᐋࣰሠᙕ ዁ၛᙕ ‫ࣰݯ‬ᙕ ࣰሠ዁‫ݯڬ‬෹ఱሠୣࣰࡂᙕ ‫ݯ‬ᒥᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠ ͸ᙕ  Ŷ Ŷ Ŷ ᙕ ఱ዁ᙕ ఱሠᙕ ཧࣰ޺ࣰሠሠ‫ڬ‬ᄻᒥᙕ ዁ၛᙕ ၛᄻ૥‫ڬ‬རఱᓯࣰᙕ ‫ڬ‬རࡂᙕ ࡂࣰᐋࣰ෹ၛეᙕ ޺ၛijၛეࣰᄻ‫ڬ‬዁ఱᐋࣰሠᙕ ఱཧᙕ ‫ڬ‬෹෹ᙕ ე෹‫ࣰ޺ڬ‬ሠᙕ ‫ڬ‬རࡂᙕ ‫ڬ‬዁ᙕ ‫ڬ‬෹෹ᙕ ෹ࣰᐋࣰ෹ሠᙕ ఱརᙕ ၛᄻࡂࣰᄻᙕ ዁ၛᙕ ෹‫ڬ‬ᒥᙕ ࡂၛᑋီᙕ ዁ୣࣰᙕ ਰၛᎍརࡂ‫ڬ‬዁ఱၛརᙕ ၛਰᙕ ሠၛ޺ఱ‫ڬ‬෹ఱሠ዁ᙕ ‫ڬ‬૥ᄻఱ޺ᎍ෹዁ᎍᄻࣰᙕ ሠၛᙕ ዁ୣ‫ڬ‬዁ᙕ ዁ୣࣰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᄻᒥᙕ ໪‫ڬ‬ᒥᙕ ‫ࣰݯ‬རࣰਰఱ዁ᙕ ਰᄻၛ໪ᙕ ආၛఱར዁ᙕ ෹‫ݯڬ‬ၛᎍᄻ̫ʲƅ P ᙕ ؉ୣఱሠᙕ རࣰᑋᙕ ࣰ໪ეୣ‫ڬ‬ሠఱሠᙕ ఱሠᙕ ე‫ڬ‬ᄻ዁ఱ޺ᎍ෹‫ڬ‬ᄻ෹ᒦᙕ ࣰᐋఱࡂࣰར዁ᙕᑋఱ዁ୣᙕ ᄻࣰ૥‫ڬ‬ᄻࡂᙕ ዁ၛᙕ ეᄻၛࡂᎍ޺ࣰᄻሠᙕ ޺ၛĶၛეࣰᄻ‫ڬ‬዁ఱᐋࣰሠƅᙕ փརࣰᙕ ၛਰᙕ ዁ୣࣰఱᄻᙕ ၛ‫ݯ‬ආࣰ޺ᔝ ዁ఱᐋࣰሠÙᙕਰၛᄻᙕࣰᒈ‫ڬ‬໪ე෹ࣰÙᙕఱሠᙕ  ዁ၛᙕ ეᎍ዁ᙕ዁ୣࣰᙕ໪‫ڬ‬ఱཧᙕఱརሠ዁ᄻᎍ໪ࣰར዁ሠᙕၛਰᙕეᄻၛࡂᎍ޺዁ఱၛཧᙕᎍརࡂࣰᄻᙕ዁ୣࣰᙕ޺ၛར዁ᄻၛ෹ᙕ ၛਰÙᙕ ‫ڬ‬རࡁᙕ ᑍୣࣰརᙕ རࣰ޺ࣰሠሠ‫ڬ‬ᄻᒥᙕ ዁ၛᙕ ૥ᄻ‫ࡂڬ‬ᎍ‫ڬ‬෹෹ᒥᙕ ዁ᄻ‫ڬ‬རሠਰࣰᄻᙕ ዁ୣࣰఱᄻᙕ ၛᑋརࣰᄻሠୣఱეᙕ ዁ၛÙᙕ ዁ୣࣰᙕ ሠၛ޺ఱࣰ዁ᒥ̫˖ƅ P ᙕ σརၛ዁ୣࣰᄻᙕ ఱሠᙕ  ዁ၛᙕ ࡂఱᐋఱࡂࣰᙕ ໪ࣰ໪‫ࣰݯ‬ᄻሠᙕ ఱར዁ၛᙕ ᑋၛᄻඬఱར૥ᙕ ૥ᄻၛᎍეሠᙕ ዁ ၛ ᙕ ࣰར‫ݯڬ‬෹ࣰᙕ ዁ୣࣰ໪ᙕ ዁ ၛ ᙕ ᑋၛᄻඬᙕ ޺ၛ෹෹ࣰ޺዁ఱᐋࣰ෹ᒥᙕਰၛᄻᙕ዁ୣࣰᙕሠၛ޺ఱࣰ዁ᒥᙕ Ŷ ŵ ŵ ̫̂ᙕ ᙕ ؉ୣࣰᙕ ࣰ֟‫ڬ‬ሠ‫ڬ‬ར዁ᙕ σሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ֟ᄻၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛརᙕ ዁ୣᎍሠᙕ ‫ڬ‬ར዁ఱ޺ఱე‫ڬ‬዁ࣰሠᙕ ዁ୣ‫ڬ‬዁ᙕ ࣰૹ‫ڬ‬෹ఱ዁‫ڬ‬ᄻఱ‫ڬ‬ཧᙕ ᐋ‫ڬ‬෹ᎍࣰሠᙕ ᑋఱ෹෹ᙕ ‫ࣰݯ‬ᙕ ᄻࣰਰ෹ࣰ޺዁ࣰࡂᙕ ఱརᙕ ޺ၛ෹෹ࣰ޺዁ఱᐋࣰᙕ ‫ڬ‬૥ᄻఱ޺ᎍ෹዁ᎍᄻ‫ڬ‬෹ᙕ ‫޺ڬ‬዁ఱᐋఱ዁ᒥÙᙕ ᄻ‫ڬ‬዁ୣࣰᄻᙕ ዁ୣ‫ڬ‬ཧᙕఱརᙕ ఱརࡂఱᐋఱࡂᎍ‫ڬ‬෹ᙕ ୣၛ෹ࡂఱར૥ሠᙕ ၛਰᙕ ࣰᄯᎍ‫ڬ‬෹ᙕ ሠఱᓯࣰÙᙕ ‫ڬ‬෹዁ୣၛᎍ૥ୣᙕ ఱརᙕ ޺ၛ෹෹ࣰ޺዁ఱᐋࣰᙕ ეᄻၛࡂᎍ޺዁ఱၛརᙕᄻࣰᑋ‫ڬ‬ᄻࡂሠᙕᑋఱ෹෹ᙕᐋ‫ڬ‬ᄻᒥᙕ ‫ڬ‬ሠᙕ ໪ࣰ໪‫ࣰݯ‬ᄻሠᙕᑋఱ෹෹ᙕ‫ࣰݯ‬ᙕ ე‫ڬ‬ఱࡂᙕ  ‫޺޺ڬ‬ၛᄻࡂఱར૥ᙕ ዁ၛᙕ ዁ୣࣰᙕ ᄯᎍ‫ڬ‬෹ఱ዁ᒥᙕ ‫ڬ‬རࡂᙕ ᄯᎍ‫ڬ‬ར዁ఱ዁ᒥᙕ ၛਰᙕ ዁ୣࣰఱᄻᙕ ᑋၛᄻඬ̫̫ ᙕ ѣᎍᄻ዁ୣࣰᄻ໪ၛᄻࣰÙᙕ ዁ୣࣰᙕ རࣰᑋᙕ෹ࣰ૥ఱሠ෹‫ڬ‬዁ఱၛརᙕეᎍ዁ሠᙕ ޺ၛཧሠఱࡂࣰᄻ‫ݯڬ‬෹ࣰᙕࣰ໪ეୣ‫ڬ‬ሠఱሠᙕၛརᙕఱࡂࣰၛ෹ၛ૥ఱ޺‫ڬ‬෹ᙕࡂࣰᐋࣰ෹ၛე໪ࣰར዁ᙕ ‫ڬ‬རࡂᙕეၛ෹ఱ዁ఱ޺‫ڬ‬෹ᙕ ޺ၛརሠ޺ఱၛᎍሠརࣰሠሠÙᙕ ‫ڬ‬ཧࡂᙕ ఱ዁ᙕ ࣰᒈე෹ఱ޺ఱ዁෹ᒥᙕ ఱར዁ᄻၛᙕࡂ ᎍ޺ࣰሠᙕ ዁ୣࣰᙕ ޺෹‫ڬ‬ሠሠᙕ ሠ዁ᄻᎍ૥૥෹ࣰᙕ ᑋఱ዁ୣఱཧᙕ ዁ୣࣰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ᄻᒥᙕ ఱརሠࣰ෹ਰŶᙕ ٝఱ዁ୣఱརᙕ ეᄻၛࡂᎍ޺ࣰᄻሠᙕ ޺ၛįၛეࣰᄻ‫ڬ‬዁ఱᐋࣰሠÙᙕ ఱ዁ᙕ ఱሠᙕ ‫ڬ‬རᙕ ၛ‫ݯ‬ආࣰ޺዁ఱᐋࣰᙕ  ዁ၛᙕ ૥ఱᐋࣰᙕ ეᄻఱၛᄻఱ዁ᒥᙕ ዁ၛᙕ ዁ୣࣰᙕ ఱཧ዁ࣰᄻࣰሠ዁ሠᙕ ၛਰᙕ ეၛၛᄻᙕ ‫ڬ‬རࡂᙕ ໪ఱࡂࡂ෹ࣰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ሠᙕ ‫ڬ‬རࡂᙕ ዁ၛᙕ ࣰརሠᎍᄻࣰᙕ ዁ୣ‫ڬ‬዁ᙕ ዁ୣࣰᙕ ෹ࣰ‫ࣰࡂڬ‬ᄻሠᙕୣ ఱეᙕ ၛਰᙕ ዁ୣࣰᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརᙕ ఱሠᙕ ࡂᄻ‫ڬ‬ᑋརᙕ ਰᄻၛ໪ᙕ ሠᎍ޺ୣᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ሠ̫͉  ŵᙕ ؉ୣఱሠᙕ ᄻࣰਰ෹ࣰ޺዁ሠᙕ ዁ୣࣰᙕ ᑋఱࡂࣰሠეᄻࣰ‫ࡂڬ‬ᙕ ᐋఱࣰᑋᙕ ‫ڬ‬໪ၛཧ૥ᙕ л዁ୣఱၛეఱ‫ڬ‬ཧᙕ ᄻ‫ࡂڬ‬ఱ޺‫ڬ‬෹ሠᙕ ዁ୣ‫ڬ‬዁ᙕ ዁ୣࣰᙕ ఱ໪໪ࣰࡂఱ‫ڬ‬዁ࣰᙕ ࡂ‫ڬ‬ཧ૥ࣰᄻᙕ ఱརᙕ ዁ୣࣰᙕ ᄻᎍᄻ‫ڬ‬෹ᙕ ෹‫ڬ‬ཧࡂᙕ ᄻࣰਰၛᄻ໪ᙕ ఱሠᙕ ޺ၛར዁ఱཧᎍ‫ڬ‬዁ఱၛཧᙕ ၛਰᙕ ‫ڬ‬ᙕ ޺෹‫ڬ‬ሠሠᙕ ၛਰᙕ  ᄻఱ޺ୣ ᙕ ეࣰᙕ‫ ڬ‬ሠ‫ڬ‬ཧ዁ሠᙕ ᑋୣၛᙕ ᑋఱ෹෹ᙕ ࣰᒈე෹ၛఱ዁ᙕ ዁ୣࣰᙕ ໪‫ڬ‬ሠሠᙕ ၛੁᙕ ეၛၛᄻࣰᄻᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ሠ̫͡ᘩᙕ ؐၛ૥ࣰ዁ୣࣰᄻᙕ ᑋఱ዁ୣᙕ ዁ୣࣰᙕ ሠ዁ᄻࣰར૥዁ୣࣰརఱར૥ᙕ ၛਰᙕ ዁ୣࣰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ཧ዁ᙕ ‫ڬ‬ሠሠၛ޺ఱ‫ڬ‬዁ఱၛརሠᙕ ዁ୣࣰᙕ རࣰᑋᙕ ෹ࣰ૥ఱሠ෹‫ڬ‬዁ఱၛརᙕ ዁‫ڬ‬ඬࣰሠᙕ ‫ڬ‬ᙕ རࣰᑋᙕ ᐋఱࣰᑋᙕ ၛਰᙕ ዁ୣࣰᙕ ᄻၛ෹ࣰᙕ ၛਰᙕ ዁ୣࣰᙕ ޺ࣰར዁ᄻ‫ڬ‬෹ᙕ ૥ၛᐋࣰᄻར໪ࣰར዁ƅᙕ ӂཧᙕ ዁ୣࣰᙕ ׂᎍᄻ‫ڬ‬෹ᙕ Դ‫ڬ‬ཧࡂሠᙕ ֟ᄻၛ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၛརᙕ ዁ୣࣰᙕ Րఱརఱሠ዁ᄻᒥᙕ ၛਰᙕ Դ‫ڬ‬ཧࡂሠᙕ ‫ڬ‬ཧࡂᙕ ‫ࣰכ‬዁዁෹ࣰ໪ࣰར዁ᙕ ž዁ୣࣰརᙕ ዁ୣࣰᙕ Րఱརఱሠ዁ᄻᒥᙕ ၛਰᙕ Դ‫ڬ‬རࡂᙕ ׂࣰਵၛᄻ໪ᙕ ‫ڬ‬རࡂᙕ σࡂ໪ఱརఱሠ዁ᄻ‫ڬ‬዁ఱၛར·ᙕ ᑋ‫ڬ‬ሠᙕ ዁ၛᙕ ‫ࣰݼ‬ᙕ ዁ୣࣰᙕ ሠᄦࣰ‫ڬ‬ᄻୣࣰ‫ࡂڬ‬Ùᙕ ‫ڬ‬෹዁ୣၛᎍ૥ୣᙕ ఱཧᙕ ეᄻ‫޺ڬ‬዁ఱ޺ࣰᙕ ໪ၛሠ዁ᙕ $ ଵ %ଵ 3BS Bଵ Bଵ 3B"ଵ Bଵ 1ଵ xX5Bଵ ଵ NBBiBଵ BKଵ 3Xଵ %BBaଵ 3Bɀ XBয়ଵ wBÊଵ $  ଵ B ଵ $4aଵ wଵ yX5ùଵ š41ଵ ԕXଵ ޹BÊଵ  4 ଵ ¬8 ଵ 6aଵ $4 aଵ 1ଵ ଵ â3Xଵ %BBଵ 3BSX B đଵÊଵ $2ଵ 3Xଵ %BBଵ 3BS XBцaଵ %Êଵ 4 Ê ଵ $šଵ OSଵ ğXଵ 3BɀX Baଵ %Êଵ Dଵ ¬   Ê ଵ $6ଵ 3ଵ %BBଵ 3BS XBরaଵ  SÊଵ $4ଵ 3Xଵ %BBଵ 3BiX Bцaଵ %Êଵ Rଵ ¬   Ê ଵ $+ଵ 3ଵ %BBଵ 3BiX Bцaଵ %   Ê ଵRଵ ¬2 Êଵ $$ଵ 3Xଵ %BXBଵ 3BiX Baଵ %Êଵ Rଵ ¬4 ‫ڕ‬ଵ $ƛଵ 3ଵ %BBଵ 3BS XBaଵ %Êଵ ƛଵ ¬š Ê ଵ 29g ଵ 1ଵ ଵ öଵ B Sଵ  Bଵ B ଵ â £1 ̳ଵ` ‫  ך‬S ̳ଵ  ଵ âBB đଵ XÊଵ %ଵ B Xiଵ Bࣟଵ 1ଵ 5 1ଵ XǿīMଵ Bଵ 1ଵ 1Bଵ 1ଵ  B Xiଵ BιBଵ 1Xଵ ଵ âBB àଵ Xଵ ଵ Š1BXଵ ଵ Bଵ )1ଵ ଵ Bଵ 1ଵ 1Xଵ B ଵ iмÊଵ %ଵ BBଵ B ଵ 1ଵ )BSଵ Bi*ଵ ଵ 5ଵ iXÊଵ $ଵ #ଵ % ଵ`)aଵ BȮଵ Êଵ Bଵ 2Daଵ Xଵ Êଵ  2t  Ŏ Ȯ ଵ &MMȀ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb ਰఱࣰ෹ࡂᙕఱ໪დ෹ࣰ໪ࣰར፡‫ڬ‬፡ఱၚརᙕᑋ‫ڬ‬ሠᙕ ෹ࣰࡂᙕ ‫ݯ‬ᒥᙕ ፡ୣࣰᙕ ᓱࣰ໪ࣰ޺ୣ‫ڬ‬ŵᙕ ӂརᙕ ፡ୣࣰᙕ ࣰ֟‫ڬ‬ሠ‫ڬ‬ར፡ᙕσሠሠၚ޺ఱ‫ڬ‬፡ఱၚརሠᙕ֟ᄹၚ޺෹‫ڬ‬ላ‫ڬ‬ᔝ ፡ఱၚརᙕ ޺ࣰར፡ᄹ‫ڬ‬෹ᙕ૥ၚᐋࣰᄹར໪ࣰར፡ᙕე‫ڬ‬ᄹ፡ఱ޺ఱე‫ڬ‬፡ఱၚརᙕ ఱሠᙕ ፡ၚᙕ ‫ࣰݯ‬ᙕ ‫޺ڬ‬ୣఱࣰᐋࣰࡂᙕეᄹఱ໪‫ڬ‬ᄹఱ෹ᒥᙕ ᐋఱ‫ڬ‬ᙕ ׂࣰᐋၚ෺ᎍ፡ఱၚརᔜ ‫ڬ‬ᄹᒥᙕ σࡂ໪ఱརఱሠ፡ᄹ‫ڬ‬፡ఱᐋࣳᙕ ‫ڬ‬རࡂᙕХࣰᐋࣰ෺ၚდ໪ࣰར፡ᙕЍၚ໪໪ఱ፡፡ࣰࣰሠ ᙕ ‫ڬ‬፡ᙕ፡ୣࣰᙕࡂఱሠ፡ᄹఱ޺፡Ùᙕሠᎍ‫ݯ‬ეᄹၚᐋఱར޺ࣰᙕ‫ڬ‬རࡂᙕ დᄹၚᐋఱར޺ఱ‫ڬ‬෹ᙕ ෹ࣰᐋࣰ෹ሠÙᙕ ‫ڬ‬རࡂᙕ ‫ڬ‬ᙕ ࣰ֟ᄹ໪‫ڬ‬རࣰར፡ᙕ Ѝࣰར፡ᄹ‫ڬ‬෹ᙕ Ѝၚ໪໪ఱ፡፡ࣰࣰᙕ ‫ڬ‬፡ᙕ ፡ୣࣰᙕ ར‫ڬ‬፡ఱၚར‫ڬ‬෹ᙕ ෺ࣰᐋࣰ෹Ͽ ၫ ᘩᙕ ‫؜‬ୣࣰሠࣰᙕ ޺ၚ໪໪ఱ፡፡ࣰࣰሠÙᙕ ޺ୣ‫ڬ‬ఱᄹࣰࡂᙕ ‫ڬ‬፡ᙕ ࣰ‫޺ڬ‬ୣᙕ ෹ࣰᐋࣰ෹ᙕ ‫ݯ‬ᒥᙕ ፡ୣࣰᙕ Րఱརఱሠ፡ࣰᄹᙕ ၚਰᙕ ӂར፡ࣰᄹఱၚᄹᙕ ၚᄹᙕ ୣఱሠᙕ ᄹࣰეᄹࣰሠࣳར፡‫ڬ‬፡ఱᐋࣰÙᙕ ‫ݯ‬ᄹఱར૥ᙕ ፡ၚ૥ࣰ፡ୣࣰᄹᙕ ၚਰਰఱ޺ఱ‫ڬ‬෹ሠᙕ ਰᄹၚ໪ᙕ ፡ୣࣰᙕ ໪ఱརఱሠ፡ᄹఱࣰሠᙕ ၚਰᙕ ӂར፡ࣰᄹఱၚᄹᙕ žఱར޺෹ᎍࡂఱར૥ᙕ ፡ୣࣰᙕ დၚ෹ఱ޺ࣰ¸Ùᙕ Դ‫ڬ‬རࡂሠᙕ ‫ڬ‬རࡂᙕ ‫ࣰכ‬፡፡෹ࣰ໪ࣰར፡Ùᙕ ‫ڬ‬རࡂᙕ σ૥ᄹఱ޺ᎍ෺፡ᎍᄹࣰᙕ ‫ڬ‬རࡂᙕ ѣၚᄹࣰሠ፡ᄹᒥÙᙕ ‫ڬ‬ሠᙕ ᑋࣰӔ෹ᙕ ‫ڬ‬ሠᙕ ᄹࣰდᄹࣰሠࣰར፡‫ڬ‬፡ఱᐋࣰሠᙕ ਰᄹၚ໪ᙕ ፡ୣࣰᙕ ᓱࣰ໪ࣰ޺ୣ‫ڬ‬ᙕ žఱར޺෹ᎍࡂఱར૥ᙕ ሠ፡ᎍࡂࣰར዁ᙕ ე‫ڬ‬ᄹ፡ఱ޺ఱე‫ڬ‬ར዁ሠ¸ᙕ ‫ڬ‬རࡂᙕ ፡ୣࣰᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬፡ఱၚརሠűᙕ ؉ୣᎍሠᙕ ፡ୣࣰᙕ ෹ࣰ‫ࡂڬ‬ᙕ ᄹၚ෹ࣰᙕ ၚਰᙕ ፡ୣࣰᙕ Րఱརఱሠ፡ᄹᒥᙕ ၚਰᙕ Դ‫ڬ‬རࡂሠᙕ ‫ڬ‬རࡂᙕ ‫ࣰכ‬፡፡෹ࣰ໪ࣰར፡ᙕ ఱሠᙕ ໪ᎍ޺ୣᙕ ᄹࣰࡂᎌ޺ࣰࡂŵᙕ ѣၚᄹᙕ ፡ୣࣰᙕ ਰᎌ፡ᎌᄹࣰᙕ ፡ୣఱሠᙕ ໪ఱརఱሠ፡ᄹᒥᙕ ᑋఱ෹෹ᙕ ‫ࣰݯ‬ᙕ ၚ޺޺ᎍეఱࣰࡂᙕ დᄹఱར޺ఱე‫ڬ‬෹෹ᒥᙕ ఱརᙕ ᄹࣰᙕ૥ ఱሠᙕ፡ ࣰᙕᄹ ఱར૥ᙕ ‫ڬ‬རࡂᙕ ‫ڬ‬ሠሠఱሠ፡ఱར૥ᙕ ఱརᙕ ‫ࡂڬ‬ᐋఱሠఱར૥ᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར፡ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬፡ఱၚརሠÙᙕ ఱརᙕ ፡ᄹ‫ڬ‬ఱརఱར૥ᙕ རࣰᑋᙕ ეࣰᄹሠၚརརࣰ෹ᙕ ਰၚᄹᙕ ෹ၚ޺‫ڬ‬෹ᙕ ᑋၚᄹඬÙᙕ ‫ڬ‬རࡂᙕ ఱརᙕ ሠࣰጆ፡෹ࣰ໪ࣰར፡ᙕ დᄹၚඊࣰ޺፡ሠᙕ დ෹‫ڬ‬རརࣰࡂᙕ ໪ၚሠ፡෹ᒥᙕ ਰၚᄹᙕ ෹ၚᑋ෹‫ڬ‬རࡂᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ሠ͖ȍᘩᙕ ӂརࡂࣰࣰࡂᙕ ፡ୣࣰᙕ ໪ఱརఱሠ፡ᄹᒥgሠᙕ རࣰᑋᙕ ར‫ڬ‬໪ࣳᙕ ၚ໪ఱ፡ሠᙕ ፡ୣࣰᙕ დୣᄹ‫ڬ‬ሠࣰᙕ ෺‫ڬ‬རࡂᙕ ᄹࣰਰၚᄹ໪  Ùᙕ ‫ ڬ‬ᄹࣰਰ෺ࣰग፡ఱၚརᙕ ၚਰᙕ ፡ୣࣰᙕ ᐋఱࣰᑋᙕ ፡ୣ‫ڬ‬፡ᙕ རၚᑍᙕ ፡ୣࣳᙕ ᄹᎌᄹ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰਰၚᄹ໪ᙕ ఱሠᙕ ޺ၚ໪დ෹ࣰ፡ࣰࡂűᙕ ӂརᙕ ਰ‫޺ڬ‬፡Ùᙕ ሠၚ໪ࣰᙕ ૥ၚᐋࣱᄹར໪ࣰར፡ᙕ ၚਰਰఱ޺ఱ‫ڬ‬෺ሠᙕ རၚᑋᙕ ਰ‫ڬ‬ᐋၚᄹᙕ ‫ݯڬ‬ሠၚᄹდ፡ఱၚརᙕ ၚਰᙕ ፡ୣࣰᙕ ໪ఱརఱሠ፡ᄹᒥgሠᙕ ᄹࣰ໪‫ڬ‬ఱརఱར૥ᙕ ਰᎍར޺፡ఱၚརሠᙕ ‫ݯ‬ᒥᙕ ፡ୣࣰᙕ Րఱརఱሠ዁ᄹᒥᙕ ၚਰᙕ σ૥ᄹఱ޺ᎍ෹፡ᎍᄹࣰᙕ‫ڬ‬རࡂᙕѣၚᄹࣰሠ፡ᄹᒥŵᙕ {)ɕ &ɕW  ɕ σ፡ᙕ፡ୣࣰᙕ ࣰརࡂᙕၚਰᙕ፡ୣࣰᙕਰఱᄹሠ፡ᙕᒥࣰ‫ڬ‬ᄹᙕ ၚਰᙕл፡ୣఱၚეఱ‫ڬ‬gሠᙕ ‫ڬ‬໪‫ݯ‬ఱ፡ఱၚᎍሠᙕ ᄹᎍᄹ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰਰၚᄹ໪Ùᙕ ፡ୣࣰᙕ ၚᎍ፡෹ၚၚඬᙕ ఱሠᙕ ᎌར޺ࣰᄹ፡‫ڬ‬సརŵᙕ ؉ୣࣰᙕ ეᄹࣰሠࣰར፡ᙕ ໪ఱ෹ఱ፡‫ڬ‬ᄹᒥᙕ ᄹࣰ૥ఱ໪ࣰᙕ ఱሠᙕ ਰ‫ڬ‬ᄹᙕ ਰᄹၚ໪ᙕ ሠࣰ޺ᎍᄹࣰŵᙕ Хఱሠगၚར፡ࣰར፡ᙕ ఱሠᙕ ᑋఱࡂࣰᔜ ሠეᄹࣰ‫ࡂڬ‬ᙕ ఱརᙕ ‫ڬ‬ҵᙕ ෹ࣰᐋࣰ෹ሠᙕ ၚਰᙕ ሠၚ޺సࣰ፡ᒥÙᙕ ሠეၚᄹ‫ࡁڬ‬ఱ޺ᙕ ၚᎍ፡‫ݯ‬ᄹࣰ‫ڬ‬ඬሠᙕ ၚਰᙕ ᐋఱၚ෹ࣰར޺ࣰᙕ ၚ޺޺ᎍᄹᙕ ఱརᙕ ሠࣰᐋࣰᄹ‫ڬ‬෹ᙕ ეᄹၚᐋఱར޺ࣰሠÙᙕ ፡ୣࣰᙕ ሠࣰ޺ࣰሠሠఱၚརఱሠ፡ᙕ ᑋ‫ڬ‬ᄹᙕ ఱརᙕ лᄹఱ፡ᄹࣰ‫ڬ‬ᙕ ޺ၚར፡ఱརᎍࣰሠᙕ ᎍར‫ڬݯڬ‬፡ࣰࡂÙᙕ ᐋ‫ڬ‬ᄹఱၚᎍሠᙕ ૥ၚᐋࣰᄹར໪ࣰར፡ᙕ ၚਰਰఱ޺స‫ڬ‬෹ቚᙕ ‫ڬ‬རࡂᙕ ၚ፡ୣࣰᄹቚᙕ ĸ ఱར޺෹ᎍࡂఱར૥Ùᙕ ၚ޺޺‫ڬ‬ሠఱၚར‫ڬ‬ҵᒥÙᙕ ໪ࣰ໪‫ࣰݯ‬ᄹሠᙕ ၚਰᙕ ፡ୣࣰᙕ ᄹᎍ෹ఱར૥ᙕ ໪ఱ෹ఱ፡‫ڬ‬ᄹᒥᙕ ૥ᄹၚᎌეᙕ ఱ፡ሠࣰ෹ਰᙕ ĸ ‫ڬ‬ᄹࣰᙕ ‫ڬ‬ᄹᄹࣰሠ፡ࣰࡂÙᙕ ‫ڬ‬རࡂᙕ ၚ፡ୣࣰᄹሠᙕ ޺ၚར፡ఱརᎍࣰᙕ ፡ၚᙕ ፡‫ڬ‬ඬࣰᙕ ᄹࣰਰᎍ૥ࣰᙕ ‫ݯڬ‬ᄹၚ‫ࡂڬ‬ųᙕ ࣰ֟ᄹୣ‫ڬ‬ᄦሠᙕ ୣ‫ڬ‬෹ਰᙕ ፡ୣࣳᙕ ᓱࣰ໪ࣰ޺ୣ‫ڬ‬ᙕ დ‫ڬ‬ᄹ፡ఱ޺ఱდ‫ڬ‬ར፡ሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ෹ࣰਰ፡ᙕ ፡ୣࣰఱᄹᙕ ეၚሠ፡ሠÙᙕ ‫ڬ‬རࡂᙕ ፡ୣၚሠࣰᙕ ᑋୣၚᙕ ᄹࣰ໪‫ڬ‬ఱརᙕ ఱར޺ᄹࣰ‫ڬ‬ቚఱར૥෹ᒥᙕ ‫ڬ‬ᄹࣰᙕ ࣰྭ૥‫ڬ‬૥ࣰࡂᙕ ఱརᙕࡁࣰ໪ၚརሠ፡ᄹ‫ڬ‬፡ఱၚརሠᙕ ‫ڬ‬૥‫ڬ‬ఱརሠ፡ᙕ ፡ୣࣰᙕ ໪ఱ෺ఱ዁‫ڬ‬ᄹᒥᙕ ᄹࣰ૥స໪ࣰÙᙕ ఱརᙕ ‫ڬ‬૥ఱ዁‫ڬ‬዁ఱར૥ᙕ ਰၚᄹᙕ დࣰၚდ෹ࣰቚᙕ ૥ၚᐋࣰᄹར໪ࣰར፡  Ùᙕ ‫ڳ‬རࡂᙕ ఱརᙕ ᎍᄹ૥ఱར૥ᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར፡ᙕ ‫ڬ‬ሠሠၚगఱ‫ڬ‬፡ఱၚརሠᙕ ፡ၚᙕ ਰၚᄹ໪ᙕ ፡ୣࣰఱᄹᙕ ၚᑋརᙕ ໪ఱ෹ఱ፡స‫ڬ‬ϸɚᘩᙕ ӂརᙕ ‫ࡂࡂڬ‬ఱ፡ఱၚརᙕ ፡ၚᙕ ፡ୣࣰሠࣰᙕ ეᄹࣰሠሠᎌᄹࣰሠᙕ ਰᄹၚ໪ᙕ ፡ୣࣰᙕ ෹ࣰਰ፡Ùᙕ ໪ࣰ໪‫ࣰݯ‬ᄹሠᙕ ၚਰᙕ ਰၚᄹ໪ࣰᄹᙕ ᄹᎍᄹ‫ڬ‬෹ᙕ ࣰ෹స፡ࣰሠᙕ ፡ၚ૥ࣰ፡ୣࣰᄹᙕ ᑋఱ፡ୣᙕ ໪‫ڬ‬རᒥᙕ ఱརᙕ ፡ୣࣰᙕ ࡂఱሠ‫ڬ‬ਰਰࣰ޺፡ࣰࡂᙕ ᎌᄹ‫ڬݯ‬རᙕ ໪ఱࡂࡂ෹ࣰᙕ ࡇ‫ڬ‬ሠሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ፡ୣࣰᙕ ეၚ፡ࣰར፡ఱ‫ڬ‬෹ᙕ ਰၚᄹᙕ ‫ڬ‬ᙕ ᄹࣰ‫޺ڬ‬፡ఱၚར‫ڬ‬ᄹᒥᙕ ໪ၚᐋࣰ໪ࣰར፡ᙕ ‫ڬ‬૥‫ڬ‬ఱརሠ፡ᙕ ፡ୣࣰᙕ ׂࣰᐋၚ෹ᎌ፡ఱၚརᙕ ఱ፡ሠࣰ෹ਰűᙕ ׂࣰ‫ݯ‬ఱᄹ፡ୣᙕ ၚਰᙕ ‫ڬ‬རᒥ፡ୣఱར૥ᙕ ሠఱ໪ఱ෹‫ڬ‬ᄹᙕ ፡ၚᙕ ፡ୣࣰᙕ ‫ڬ‬ར޺ఱࣰརᙕ ᄹः૥ఱ໪ࣰᙕ རၚᑋᙕ ሠࣰࣰ໪ሠᙕ ୣఱ૥ୣ෹ᒥᙕ ᎍར෹ఱඬࣰ෹ᒥÙᙕ ‫ݯ‬ᎍ፡ᙕ ᄹࣰ‫޺ڬ‬፡ఱၚརᙕ गၚᎍ෺ࡂᙕ ‫ݯ‬ᄹఱར૥ᙕ ‫ڬ‬ᙕ૥ၚᐋࣰᄹར໪ࣰར፡ᙕᑋࣰҵᙕ፡ၚᙕ፡ୣࣰᙕᄹఱ૥ୣ፡ᙕၚਰᙕ፡ୣࣰᙕ૥ᄹၚᎌდᙕརၚᑋᙕఱརᙕ ეၚᑋࣰᄹſᙕ ٝఱ፡ୢᙕ ᄻࣰ૥‫ڬ‬ᄹࡂᙕ ፡ၚᙕ ᄹᎌᄹ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰਰၚᄹ໪ᙕ ఱརᙕ л፡ୣఱၚᄦస‫ڬ‬Ùᙕ ఱ໪ეၚᄹ፡‫ڬ‬ར፡ᙕ ፡ࣰརሠఱၚརሠᙕ ፡ၚࡂ‫ڬ‬ᒥᙕ ࣰᒈఱሠ዁ᙕ ‫ࣰݯ‬፡ᑍࣰࣰརᙕ ፡ୣࣰᙕ ፡ᑋసརᙕ ૥ၚ‫ڬ‬෹ቚᙕ ၚਰᙕ ࡂࣰगࣰར፡ᄹ‫ڬ‬෹ఱᓱ‫ڬ‬፡ఱၚརᙕ ၚਰᙕ ეၚᑋࣰᄹᙕ ፡ၚᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར፡ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬፡ఱၚརሠᙕ ‫ڬ‬རࡂᙕ ࣰ૥‫ڬ‬෹ఱ፡‫ڬ‬ᄹఱ‫ڬ‬རఱሠ໪Ùᙕ ‫ڬ‬རࡂᙕ ਰၚᄹᙕ ፡ୣࣰᙕ ෹‫ڬ‬፡፡ࣰᄹᙕ ૥ၚ‫ڬ‬෹ᙕ ‫ࣰݯ‬፡ᑋࣰࣰརᙕ ፡ୣࣰᙕ ఱརఱ፡ఱ‫ڬ‬෹ᙕ ‫ڬ‬ఱ໪ᙕ ၚਰᙕ ᄹࣰࡂఱሠ፡ᄹఱ‫ݯ‬ᎍ፡ఱၚརᙕ ၚਰᙕ ෹‫ڬ‬རࡂᙕ ‫ڬ‬རࡂᙕ ፡ୣࣰᙕ ໪ၚᄹࣰᙕ ᄹࣰ޺ࣰར፡ᙕ ၚ‫ݯ‬ඈࣰ޺፡ఱᐋࣰᙕ ၚਰᙕ ޺ၚ෹෹ࣰ޺፡ఱᐋࣰᙕ ‫ڬ‬૥ᄹఱ޺ᎍ෹፡ᎌᄹ‫ڬ‬෹ᙕ ‫޺ڬ‬፡ఱᐋఱ፡ᒥŵᙕ ӂརᙕ ਰ‫޺ڬ‬፡ᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར፡ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬፡సၚརሠᙕ ፡ၚࡂ‫ڬ‬ᒥᙕ ୣ‫ڬ‬ᐋࣰᙕ ፡ୣᄹࣰࣰᙕ ޺ୣၚఱ޺ࣰሠ ͸ᙕ ፡ୣࣰᒥᙕ ໪‫ڬ‬ᒥᙕ ਰၚᄹ໪ᙕ ޺ၚıၚდࣰᄹ‫ڬ‬፡ఱᐋࣰሠᙕ ਰၚᄹᙕ ޺ၚҵࣳ޺፡ఱᐋࣳᙕ ‫ڳ‬ਏ፡ఱᐋఱ፡ᒦ δᙕ ፡ୢࣰᒦᙕ ໪‫ڬ‬ᒥᙕ ᄹࣰࡂఱሠ፡ᄹఱ‫ݯ‬ᎌ፡ࣰᙕ ෹‫ڳ‬རࡂᙕ ਰၚᄹᙕ ఱརࡂఱᐋఱࡂᎌ‫ڬ‬෹ᙕ žਰ‫ڬ‬໪ఱ෹ᒥ¸ᙕ ޺ᎌ෹፡ఱᐋ‫ڬ‬፡ఱၚར Ϊᙕ ၚᄹᙕ ፡ୣࣰᒦᙕ໪‫ڬ‬ᒦᙕቚఱ໪დ෹ᒥᙕდᄹࣰਰࣰᄹᙕ ፡ୣࣰᙕ ሠ፡‫ڬ‬፡ᎌሠᙕ ᄯᎌၚᙕఱརᙕᑍୣఱगୣÙᙕ ‫ݯڬ‬ሠࣰར፡ᙕᄹࣰࡂఱሠ፡ᄹఱ‫ݯ‬ᎍ፡ఱၚརÙᙕ ఱརࡂఱᐋఱࡂᎍ‫ڬ‬෹ᙕ RDଵ 3(ଵ %BÕÕB(ଵ 3B? ÕB(jଵ N1ଵ 6Ⱥଵ R  ଵ #ଵ %ଵ 3B? ÕB(ଵ Bଵ 3B"ÕMଵ KBଵ 1ଵ Qઌ?Õ1 (ଵ BKଵ ଵ ėi 0ଵ %1BÕ*jଵ 3B? ÕB(ଵ wB,ଵ $ R ଵ BKଵ – $+jଵ wÕଵ y5ଵ @4ଵ ԕଵ qBLଵ 2Dଵ ‫*[؂‬ଵ 6aଵ $+ ଵ G1ଵ ė ࢸ(ଵ %1BÕ૏ଵ Õଵ (ଵ B0B Bଵ ?Õଵ BÕ*ଵ KBଵ )1Õଵ 1ଵ N1Õ (ଵ BKଵ 1ଵ ǔBMଵ Õଵ 1ଵ CÕ0Õଵ BKଵ ğ(Mଵ (Mଵ # ( Lଵ ıÕÕ(ଵ ଵ Õ(ÕƖଵ 1(Õ?ଵ K(ÕB(ଵ ?Õ(ଵ Bଵ Õ(ଵ (Mଵ B1*ଵ ଵ ?Bଵ KB ଵ B(ଵ ଵ ?Õ"?*ଵ B(B Bଵ ÕLଵ R2ଵ %?Bଵ 1ଵ 0ଵ Õ?ÕB(ଵ 1BÕ5ଵ â0ଵ MK0ଵ ¾M đଵ )Õ1Õ(ଵ (ଵ BÕÕB(ˏଵ 3(ଵ %BÕÕB(ଵ 3B͵ÕB(jଵ %Lଵ 4ଵ ¬6aଵ 1ଵ ¾Mଵ ଵ Bଵ Ɩଵ Bଵ ÕƖଵ (Mଵ MK(ଵ )Bіଵ B(?*ଵ â BMÕ(ଵ Bଵ ଵ MÕÕB(ଵ BKଵ 1ଵ B"(·( à Lଵ kMìଵ ଵ %Lଵ ଵ ¬4 Lଵ %ଵ 0ଵ 1ଵ M (Mଵ Õଵ KBଵ ଵ B"( (ଵ Bଵ B"ÕMଵ 1ଵ ਘMଵ )Õଵ )B(,ଵ ' https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb ୢၚ෹ࡂఱར૥ሠᙕ ᐋ‫ڬ‬ᄹᒦᙕ ఱརᙕ ሠఱᓯࣰᙕ ᎌდᙕ ዁ၚᙕ ዁ୢࣰᙕ ࡂࣰᙕ ਱‫޺ڬ‬዁ၚᙕ ዁ࣰརᙕ ୢࣰ޺዁‫ڬ‬ᄹࣰᙕ ໪‫ڬ‬ᒈఱ໪ᎌ໪űᙕ ٝୢࣰᄹࣰᙕ ໪ࣰ໪‫ࣰݯ‬ᄹሠᙕ ၚ਱ᙕ ዁ୢࣰᙕ ዁ᄹ‫ࡂڬ‬ఱ዁ఱၚར‫ڬ‬෹ᙕ ᄹᎌᄹ‫ڬ‬෹ᙕ ࣰ෹ఱ዁ࣰሠᙕ ૥‫ڬ‬ఱརᙕ ޺ၚར዁ᄹၚ෹ᙕ ၚ਱ᙕ ዁ୢࣰᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬዁ఱၚརÜᙕ ዁ୢࣰᙕ ዁ୢఱᄹࡂᙕ ޺ୢၚఱ޺ࣰᙕ ሠࣰࣰ໪ሠᙕ ዁ୢࣰᙕ ෹ఱඬࣰ෹ᒦᙕ ၚརࣰŶᙕ ٝୢࣰ዁ୢࣰᄹᙕ ዁ୢࣰᙕ ޺ࣰར዁ᄹ‫ڬ‬෹ᙕ ૥ၚᐋࣰᄹར໪ࣰར዁ᙕ ᑋఱ෹෹ᙕ ᑋఱሠୢᙕ ዁ၚᙕ დࣰᄹ໪ఱ዁ᙕ ዁ୢఱሠÜᙕ ‫ڬ‬ሠᙕᑋࣰӉ෹ᙕ‫ڬ‬ሠᙕ዁ୢࣰᙕ޺ၚሠ዁ሠᙕၚ਱ᙕ‫ڬ‬዁዁ࣰ໪დ዁ఱར૥ᙕ዁ၚᙕდᄹࣰᐋࣰར዁ᙕఱ዁Ùᙕᄹࣰ໪‫ڬ‬ఱརᙕ዁ၚᙕ‫ࣰݯ‬ᙕሠࣰࣰརŵᙕ ؉ၚᙕ ࡁ‫ڬ‬዁ࣰᙕ ዁ୢࣰᙕ л዁ୢఱၚდఱ‫ڬ‬རᙕ ᄹᎌᄹ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰ਱ၚᄹ໪ሠᙕ ୢ‫ڬ‬ᐋࣰᙕ ሠᎌ޺޺ࣰࣰࡂࣰࡂᙕ ఱརᙕ ዁ᑋၚᙕ ᑋ‫ڬ‬ᒦሠűᙕ ѣఱᄹሠ዁Ùᙕ ዁ୢࣰᙕ დၚᑋࣰᄹᙕ ၚ਱ᙕ ዁ୢࣰᙕ ዁ఱརᒦᙕ ࣰ෹ఱ዁ࣰᙕ ᑋୢఱ޺ୢᙕ ޺ၚར዁ᄹၚ෹෹ࣰࡂᙕ ዁ୢࣰᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰሠၚᎌᄹ޺ࣰሠᙕ ၚ਱ᙕ ໪ၚሠ዁ᙕ ၚ਱ᙕ ዁ୢࣰᙕ ሠၚᎌ዁ୢÜᙕ ‫ڬ‬རࡂᙕ ᑋୢఱ޺ୢᙕ ૥ࣰརࣰᙕᄹ ‫ڬ‬෹෹ᒦᙕ ᑋ‫ڬ‬ሠᙕ ޺ၚར዁ࣰར዁ᙕ ዁ၚᙕ ෹ࣰ዁ᙕ ዁ୢࣰᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᄹᒦᙕ ሠ዁‫ڬ‬૥ར‫ڬ‬዁ࣰᙕ ఱརᙕ ໪ఱሠࣰᄹ‫ݯڬ‬෹ࣰᙕ ޺ၚརࡂఱᔦ ዁ఱၚརሠÜᙕ ୢ‫ڬ‬ሠᙕ ‫ࣰࣰݯ‬རᙕ ‫ݯ‬ᄹၚඬࣰརᙕ ਱ၚᄹᙕ ૥ၚၚࡂŲᙕ ‫޺ࣰכ‬ၚརࡁÜᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰ਱ၚᄹ໪ᙕ ‫ࡂڬ‬ᐋఱሠࣰᄹሠᙕ ‫ڬ‬རࡂᙕ ᓱࣰ໪ࣰ޺ୢ‫ڬ‬ᙕ ୢ‫ڬ‬ᐋਐᙕ ఱརᙕ ໪‫ڬ‬རᒦᙕ ‫ڬ‬ᄹࣰ‫ڬ‬ሠᙕ ၚ਱ᙕ ዁ୢࣰᙕ ޺ၚᎌར዁ᄹᒦᙕ ሠᎌ޺޺ࣰࣰࡂࣰࡂᙕ ఱརᙕ ໪ၚ‫ݯ‬ఱ෹ఱᓱఱར૥ᙕ ዁ୢࣰᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ሠᙕ ዁ၚᙕ ‫ࣰݯ‬૥ఱརᙕ ዁ୢᄹၚᎌ૥ୢᙕდࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬዁ఱၚརሠᙕ ዁ၚᙕ ‫ڬ‬዁዁‫޺ڬ‬ඬᙕ ዁ୢࣰఱᄹᙕၚᑋརᙕ ࡂࣰᐋࣰ෹ၚდ໪ࣰར዁ᙕდᄹၚ‫ݯ‬෹ࣰ໪ሠᙕ ၚརᙕ ‫ڬ‬ᙕ ෹ၚ޺‫ڬ‬෹Ùᙕ ‫ڬ‬ᎌ዁ၚརၚ໪ၚᎌሠᙕ‫ڬݯ‬ሠఱሠűᙕ؉ୢఱሠᙕఱሠᙕརၚᙕ໪ࣰ‫ڬ‬རᙕ‫޺ڬ‬ୢఱࣰᐋࣰ໪ࣰར዁Üᙕდ‫ڬ‬ᄹ዁ఱ޺ᎌ෹‫ڬ‬ᄹ෹ᒦᙕᑋୢࣰརᙕఱ዁ᙕఱሠᙕᄹࣰ໪ᙕࣰ ໪ᙕ‫ࣰ ݯ‬ᄹࣰࡂᙕ ዁ୢ‫ڬ‬዁ᙕ རࣰᐋࣰᄹᙕ ‫ࣰݯ‬਱ၚᄹࣰᙕ ୢ‫ڬ‬ሠᙕ ‫ڬ‬ᙕ დၚ෹ఱ዁ఱ޺‫ڬ‬෹ᙕ დ‫ڬ‬ᄹ዁ᒦᙕ ၚᄹᙕ ‫ ڬ‬ར‫ڬ‬዁ఱၚར‫ڬ‬෹ᙕ ૥ᄹ‫ڬ‬ሠሠįᄹၚၚ዁ሠᙕ ໪ၚᐋࣰ໪ࣰར዁ᙕ ਱ၚᄹᙕ ᄹࣰ਱ၚᄹ໪ᙕࣰᒈఱሠ዁ࣰࡂᙕఱརᙕл዁ୢఱၚდఱ‫ڬ‬Ŷᙕ փརᙕ ዁ୢࣰᙕ ၚ዁ୢࣰᄹᙕ ୢ‫ڬ‬རࡂÜᙕ ዁ୢࣰᙕ ሠఱ૥རఱ਱ఱ޺‫ڬ‬ར޺ࣰᙕ ၚ਱ᙕ ዁ୢࣰᙕ ᄹᎌᄹ‫ڬ‬෹ᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰ਱ၚᄹ໪ሠᙕ ਱ၚᄹᙕ ໪ᎌ޺ୢᙕ ၚ਱ᙕ ዁ୢࣰᙕ རၚᄹ዁ୢᙕ ᄹࣰ໪‫ڬ‬ఱརሠᙕ ᐋࣰᄹᒦᙕ ໪ᎌ޺ୢᙕ ఱརᙕ ࡂၚᎌ‫ݯ‬዁űᙕ ؉ୢࣰᄹࣰᙕ ᄹᎌᄹ‫ڬ‬෹ᙕ ࣰ෹ఱ዁ࣰሠᙕ ‫ڬ‬ᄹࣰᙕ ໪ၚᄹࣰᙕ ޺෹ၚሠࣰ෹ᒦᙕ ዁ఱࣰࡂᙕ ዁ၚᙕ ዁ᄹ‫ࡂڬ‬ఱ዁ఱၚརᙕ‫ ڬ‬෹ᙕ ෹ၚ޺‫ڬ‬෹ᙕ ሠၚ޺ఱ‫ڬ‬෹ᙕ ሠᒦሠ዁ࣰ໪ሠᙕ ዁ୢ‫ڬ‬རᙕ ఱརᙕ ዁ୢࣰᙕ ሠၚᎌ዁ୢÜᙕ ࡂఱሠ዁ᄹఱ‫ݯ‬ᎌ዁ఱၚརᙕ ၚ਱ᙕ ෹‫ڬ‬རࡁᙕ ‫ڬ‬རࡂᙕ ዁ୢࣰᙕ ࣰ෹ఱ໪ఱར‫ڬ‬዁ఱၚརᙕ ၚ਱ᙕ ‫ݯڬ‬ሠࣰར዁ࣰࣰᙕ ෹‫ڬ‬རࡂၚᑋརࣰᄹሠୢఱთᙕ ఱሠᙕ རၚ዁ᙕ རࣰ‫ڬ‬ᄹ෹ᒦᙕ ‫ڬ‬ሠᙕ རࣰࣰࡂࣰࡂᙕ ‫ڬ‬ሠᙕ ఱརᙕ ዁ୢࣰᙕ ሠၚᎌ዁ୢÙᙕ ‫ڬ‬རࡂᙕ დࣰརࣰ዁ᄹ‫ڬ‬዁ఱၚརᙕ ‫ݯ‬ᒦᙕ ‫ڬ‬རᒦᙕ დᄹၚ૥ᄹ‫ڬ‬໪ᙕ ఱརఱ዁ఱ‫ڬ‬዁ࣰࡂᙕ ఱརᙕ σࡁࡂఱሠᙕ σ‫ڬݯڬݯ‬ᙕ ఱሠᙕ ໪ၚᄹࣰᙕ ࡂఱ਱਱ఱ޺ᎌ෹዁űᙕ ؉ୢࣰᙕ ၚდ዁ఱၚརᙕ ၚ਱ᙕ ዁ᄹࣰ‫ڬ‬዁ఱར૥ᙕརၚᄹ዁ୢࣰᄹརᙕ ዁ࣰརᎌᄹࣰᙕ ሠᒦሠ዁ࣰ໪ሠᙕ ‫ڬ‬ሠᙕ ዁ୢࣰ໪ሠࣰ෹ᐋࣰሠᙕ ዁ୢࣰᙕ ‫ڬݯ‬ሠఱሠᙕ ਱ၚᄹᙕ л዁ୢఱၚდఱ‫ڬ‬ར ᙕ ሠၚ޺ఱ‫ڬ‬෹ఱሠ໪ᙕ ୢ‫ڬ‬ሠᙕ ‫ࣰࣰݯ‬རᙕ ᄹࣰඈࣰ޺዁ࣰࡂᙕ ఱརᙕ ਱‫ڬ‬ᐋၚᄹÜᙕ ఱརᙕ ዁ୢࣰᙕ ࣰ֟‫ڬ‬ሠ‫ڬ‬ར዁ᙕ σሠሠၚ޺ఱ‫ڬ‬዁ఱၚརሠᙕ ֟ᄹၚ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၚརÙᙕ ၚ਱ᙕ ఱࡂࣰ‫ڬ‬ሠᙕ ࡂᄹ‫ڬ‬ᑋརᙕ ਱ᄹၚ໪ᙕ ሠ޺ఱࣰར዁ఱ਱ఱ޺ ᙕ ሠၚ޺ఱ‫ڬ‬෹ఱሠ໪Ŷᙕ ؉ၚᙕ ఱ໪დ෹ࣰ໪ࣰར዁ᙕ ሠᎌ޺ୢᙕ ఱࡂࣰ‫ڬ‬ሠᙕ ໪‫ڬ‬ᒦᙕ ‫ࣰݯ‬ᙕ ఱར޺ᄹࣰ‫ڬ‬ሠᔦ ఱར૥෹ᒦᙕ ࡂఱ਱਱ఱ޺ᎌ෹዁ᙕ ‫ڬ‬ሠᙕ ዁ୢࣰᙕ ᓱࣰ໪ࣰ޺ୢ‫ڬ‬ᙕ ዁ᎌᄹརሠᙕ ‫ڬ‬૥‫ڬ‬ఱརሠ዁ᙕ ዁ୢࣰᙕ ໪ఱ෹ఱ዁‫ڬ‬ᄹᒦᙕ ᄹࣰ૥ఱ໪ࣰᙕ ‫ڬ‬རࡂᙕ м዁ୢఱၚდఱ‫ڬ‬iሠᙕ ෹ࣰ਱዁ᙕ਱ၚᄹ໪ሠᙕఱ዁ሠࣰ෹਱ᙕఱར዁ၚᙕ዁ᑋၚᙕୢၚሠ዁ఱ෹ࣰᙕ૥ᄹၚᎌდሠűᙕ ɝȆʈᙕ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb  ɕ «7ɕ Zɕ ɕ ]  ɕ Zɕ @ ] ɕ ɕ ɕ&¯(( ɕ ɕ ·/€ɕ ϴᒥᙕׂ‫ݎ‬Ճѱᙕ +@-K)f ӂརᙕ ໪‫ڬ‬རᒥᙕ ԰ХЎሠᙕ ĸ ར‫ڬ‬໪ࣰ෹ᒥᙕ ఱརᙕ σሠఱ‫ڬ‬ᙕ ‫ڬ‬རࡂᙕ ԰‫ڬ‬዁ఱརᙕ σ໪ࣰᄹఱ޺‫ڬ‬ᙕ ĸ ‫ڬ‬૥ᄹ‫ڬ‬ᄹఱ‫ڬ‬རᙕ ᄹࣰਰၚᄹ໪ሠᙕ ‫ڬ‬ᄹࣰᙕ ޻ၚརሠఱࡂࣰᄹࣰࡂᙕ ‫ڬ‬ሠᙕ ၚརࣰᙕ ၚਰᙕ ዁ୣࣰᙕ རࣰ޻ࣰሠሠ‫ڬ‬ᄹᒥᙕ დᄹࣰᄹࣰᄯᎍఱሠఱ዁ࣰሠᙕ ਰၚᄹᙕ ‫ڬ‬རᙕ ၚᐋࣰᄹ‫ڬ‬෹෹ᙕ ሠၚ޺ఱ‫ڬ‬෹ᙕ ࡂࣰᐋࣰ෹ၚდ໪ࣰར዁ᙕ ఱརᙕ ᑋୣఱ޺ୣᙕ ዁ୣࣰᙕ ෹ၚᑋࣰᄹᙕ ޺෹‫ڬ‬ሠሠࣰሠᙕ ‫ڬ‬෹ሠၚᙕ დ‫ڬ‬ᄹ዁ఱ޺ఱდ‫ڬ‬዁ࣰŵᙕ ҔၚᑋࣰᐋࣰᄹÙᙕ ᄹࣰ෹‫ڬ‬዁ఱᐋࣰ෹ᒥᙕ ਰࣰᑋᙕ ޺ၚᎍར዁ᄹఱࣰሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ޺‫ڬ‬ᄹᄹఱࣰࡂᙕ ၚᎍ዁ᙕ ࣰਰਰࣰ޻዁ఱᐋࣰᙕ ‫ڬ‬૥ᄹ‫ڬ‬ᄹఱ‫ڬ‬རᙕ ᄹࣰਰၚᄹ໪ሠŵᙕ ؉ୣఱሠᙕ ޺‫ڬ‬རརၚ዁ᙕ ‫ࣰݯ‬ᙕ ࣰᒈდง‫ڬ‬ఱརࣰࡂᙕ ሠၚงࣰงᒥᙕ ‫ݯ‬ᒥᙕ ዁ୣࣰᙕ ࡂၚ໫ఱཀྵ‫ڬ‬዁ఱར૥ᙕეၚ෹ఱ዁ఱ޺‫ڬ‬෹ᙕఱརਰงᎍࣰར޻ࣰᙕ ၚਰᙕ ዁ୣࣰᙕ ෹‫ڬ‬རࡂ෹ၚᄹࡂሠÙᙕ ᑋୣఱ޺ୣÙᙕ ໪ၚᄹࣰᙕ ၚਰ዁ࣰརᙕ ዁ୣ‫ڬ‬རᙕ ཀྵၚ዁Ùᙕ ఱሠᙕ ཀྵၚᙕ งၛར૥ࣰᄹᙕࣰᒈఱሠ዁‫ڬ‬ར዁ƶᙕ ҔࣱᄹࣰÙᙕ ఱ዁ᙕఱሠᙕ ໪ᎍ޻ୣᙕ໪ၚᄹࣰᙕ ዁ୣࣰᙕ ‫ڬ‬዁዁ఱ዁ᎍࡂࣰᙕ ၚਰᙕ዁ୣࣰᙕᎍᄹ‫ڬݯ‬རᙕሠ዁ᄹ‫ڬ‬዁‫ڬ‬ᙕ ᑋୣఱ޺ୣᙕ დง‫ڬ‬ᒥሠᙕ ‫ڬ‬ᙕ ࡂࣰ޺ఱሠఱᐋࣰᙕ ᄹၚงࣰƅᙕ ϴᎍ዁Ùᙕ ఱརᙕ ૥ࣰརࣰᄻ‫ڬ‬งÙᙕ ዁ୣࣰఱᄹᙕ ఱར዁ࣰᄹࣰሠ዁ᙕ ਰၚ޺ᎍሠࣰࡂᙕ დᄹఱ໪‫ڬ‬ᄹఱ෹ᒥᙕ ၚརᙕ ዁ୣࣰᙕ ఱརਰᄹ‫ڬ‬ᔜ ሠ዁ᄹᎍ޻዁ᎍᄹ‫ڬ‬งᙕ ‫ڬ‬རࡂᙕ ఱརࡂᎍሠ዁ᄹఱ‫ڬ‬෹ᙕ ࡂࣰᐋࣰ෹ၚდ໪ࣰར዁ᙕ ၚਰᙕ ዁ୣࣰᙕ ᎍᄹ‫ڬݯ‬རᙕ ‫ڬ‬ᄹࣰ‫ڬ‬Ùᙕ ዁ୣࣰᙕ ᄹᎍᄹ‫ڬ‬෹ᙕ ၚརࣰᙕ ‫ࣰݯ‬ఱར૥ᙕ རࣰ૥෹ࣰ޺዁ࣰࡂƶᙕ ؉ୣࣰᙕ ‫ڬ‬૥૥ᄹ‫ڬ‬ᐋ‫ڬ‬዁ఱၚརᙕ ၚਰᙕ ዁ୣࣰᙕ ‫ڬ‬૥ᄹ‫ڬ‬ᄹఱ‫ڬ‬རᙕ ޺ᄹఱሠఱሠÙᙕ ᑋୣఱ޺ୣᙕ རၚᑋᙕ ‫ڬ‬෹ሠၚᙕ ዁ၚၚඬᙕ ᎍརఱᐋࣰᄹሠ‫ڬ‬෹ᙕ ࡂఱ໫ࣱརሠౝၚརሠÙᙕ ਰఱᄹሠ዁ᙕ ၚ‫ݯ‬෹ఱ૥ࣰࡂᙕ ዁ୣࣰᙕ ᎍᄹ‫ڬݯ‬རᙕ ࡂၚ໪ఱར‫ڬ‬዁ࣰࡂ¸ᙕ ૥ၚᐋࣰᄹར໪ࣰར዁ሠᙕ ዁ၚᙕ ఱར዁ࣰརሠఱਰᒥᙕ ዁ୣࣰఱᄹᙕ ࡄࣰᐋࣰงၚდ໪ࣰཀྵ዁ᙕࣱਰਰၚᄹ዁ሠᙕఱརᙕ዁ୣࣰᙕᄹᎍᄹ‫ڬ‬෹ᙕ‫ڬ‬ᄹࣰ‫ڬ‬ᙕ‫ڬ‬ሠᙕᑋࣰ෹งŵᙕ؉ୣࣰሠࣰᙕࣰਰਰၚᄹ዁ሠßᙕୣၚᑋࣰᐋࣰᄹÙᙕᑋࣰᄹࣰᙕࣰᒈ዁ࣰརࡂࣰࡂᙕ ໫ၚሠጱงᒥᙕ዁ၚᙕ዁ࣰ޺ୣརၚ޺ᄹ‫ڬ‬዁ఱ޺ᙕ໪ࣰ‫ڬ‬ሠᎍᄹࣱሠᙕၛਰᙕდᄹၚࡂᎍ޺዁ఱၚརᙕࡂࣰᐋࣰ෹ၚდ໪ࣰར዁Ųᙕ ؉ୣࣰᙕ ‫ڬ‬རརၚᎍར޺ࣰ໪ࣱར዁ᙕ ‫ڬ‬རࡂᙕ ၚਰ዁ࣳརᙕ ၚརงᒥᙕ ఱར޺ၚརሠࣰᄯᎍࣰར዁¸ᙕ ఱ໪ეືࣰ໪ࣰར዁‫ڬ‬዁ఱၚརᙕ ၚਰᙕ ‫ڬ‬૥ᄹ‫ڬ‬ᄹఱ‫ڬ‬རᙕ ᄹࣰਰၚᄹ໪ሠᙕ ޻‫ڬ‬ཀྵᙕ ‫ࣰݯ‬ᙕ ໪ၚሠ዁งᒥᙕ ࣰᒈდง‫ڬ‬ఱརࣰࡂᙕ ၚᎍ዁ᙕ ၚਰᙕ ዁ୣᄹࣰࣰᙕ ሠി዁ᎍ‫ڬ‬዁ఱၚརሠᙕ ఱརᙕ ዁ୣࣰᙕ დၚงఱ዁ఱ޺‫ڬ‬෹ᙕ დᄹၚ޺ࣰሠሠÙᙕ ᑋୣࣰརᙕ ዁ୣࣰᙕ დᄹఱ໪‫ڬ‬ᄹఱ෹ᒥᙕ ᎍᄹ‫ڬݯ‬ར¸ᙕ ࣰงఱ዁ࣰሠᙕ ዁ᄹᒥᙕ ዁ၛᙕ ࣰᒈ዁ࣰརࡂᙕ ዁ୣࣰఱᄹᙕ ᄹᎍᄹ‫ڬ‬෹¸ᙕ ෹ࣰ૥ఱ዁ఱ໪‫ڬ‬዁ఱၚརᙕ ‫ڬݯ‬ሠఱሠŵᙕ ؉ୣࣰᄹࣰ‫ݯ‬ᒥÙᙕ ఱ዁ᙕ ޺‫ڬ‬རᙕ ‫ࣰݯ‬ᙕ ‫ڬ‬ᙕ ᄯᎍࣰሠ዁ఱၚརᙕ ၚਰᙕ ၚდდၚሠఱ዁ఱၚརᙕ ૥ᄹၚᎍდሠᙕ ᑋୣఱ޺ୣᙕ ዁ᄹᒥᙕ ዁ၚᙕ ࣰᒈდ‫ڬ‬རࡂᙕ ዁ୣࣰఱᄹᙕ งࣱ૥ఱ዁ఱ໫‫޻ڬ‬ᒥᙕ ‫ݯ‬ᒥᙕ ዁‫ڬ‬ᙕඬ ఱར૥ᙕ ᎍდᙕ ዁ୣࣰᙕ ᄯᎍࣰሠ዁ఱၚརᙕ ၚਰᙕ ‫ڬ‬૥ᄹ‫ڬ‬ᄹస‫ڬ‬རᙕ ᄹࣰਰၚᄹ໪ሠᙕ ‫ڬ‬ሠᙕ ዁ୣࣰసᄹᙕ ዁ୣࣰ໪ࣰŵᙕ ϴᒥᙕ ૥‫ڬ‬ఱརఱཀྵ૥ᙕდၚᑋࣰᄹÙᙕ ዁ୣࣰᒥᙕ޺‫ڬ‬ཀྵᙕ዁ᄹᒥᙕ዁ၚᙕ෹ࣰ૥ఱ዁ఱ໪‫ڬ‬዁ࣰᙕ዁ୣࣰఱᄹᙕ‫ڬ‬ᎍ዁ୣၚᄹఱ዁ᒥᙕ ‫ݯ‬ᒥᙕ ࣰਰਰࣰ޺዁ఱར૥ᙕ ᄹࣰਰၚᄹ໪ሠᙕ ‫ڬ‬རࡂຸᙕ ၚᄹᙕ ᑋୣၚᙕ ‫ڬ‬෹ሠၚᙕ ዁ᄹᒥᙕ ዁ၛᙕ ᑋఱ዁ୣࡂᄹ‫ڬ‬ᑋᙕ ዁ୣࣰᙕ ࣰ޺ၚརၚ໪ೝ޺ᙕ ‫ڬݯ‬ሠఱሠᙕ ၚਰᙕ ዁ୣࣰᙕ ୣఱ዁ୣࣰᄹ዁ၚᙕ ᄹᎍ෹సར૥ᙕ ࣰ෹ఱ዁ࣰሠŵᙕ ѣఱར‫ڬ‬งงᒥßᙕ ‫ڬ‬૥ᄹ‫ڬ‬ᄹఱ‫ڬ‬རᙕ ᄹࣳਰၚᄹ໪ሠᙕ ޺‫ڬ‬རᙕ ‫ڬ‬෹ሠၚᙕ ‫ࣰݯ‬ᙕ ࣰਰਰࣰ޺዁ࣰࡂᙕ ‫ݯ‬ᒥᙕ ૥ၚᐋࣰᄹར໪ࣰར዁ሠᙕ ᑋୣఱ޺ୣᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ࣰࣰݯ‬རᙕ ఱརᙕ ეၚᑋࣰᄹᙕ ਰၚᄹᙕ งၚར૥Ùᙕ ఱਰᙕ დᄹࣰሠሠᎍᄹࣰᙕ ఱሠᙕ დᎍ዁ᙕ ၚརᙕ ዁ୣࣰ໪ŵᙕ ؉ୣఱሠᙕ ޺‫ڬ‬རᙕ ၚᄹఱ૥ఱར‫ڬ‬዁ࣰᙕ ਰᄹၚ໪ᙕ ‫ڬ‬རᙕ ၚდდၚሠఱ዁ఱၚརᙕ ૥ᄹၛᎍდÙᙕ‫ڬ‬ᙕდࣰ‫ڬ‬ሠ‫ڬ‬ར዁ሠhᙕ໪ၚᐋࣰ໪ࣰར዁ᙕၚᄹᙕਰᄹၚ໪ᙕ‫޺ڬ‬዁ၚᄹሠᙕਰᄹၚ໪ᙕ዁ୣࣰᙕఱར዁ࣰᄹར‫ڬ‬዁ఱၚར‫ڬ‬෹ᙕሠᒥሠ዁ࣰ໪ŵᙕ À ɕ·Zɕɕ ɕ] ; ɕɀ (  IJɕ&ɕWɕÔIɕ ϴᒥᙕ +GG/KE@f Ўűᙕ Х Q@@-@&f ӂརᙕ዁ୣఱሠᙕᄹࣰᐋఱࣰᑋᙕၚਰᙕ዁ୣࣰᙕ ਰఱᄹሠ዁ᙕ ᒥࣰ‫ڬ‬ᄹᙕ ၚਰᙕᄹᎍᄹ‫ڬ‬෹ᙕ ง‫ڬ‬རࡂᙕ ᄹࣰਰၚᄹ໪ᙕ ఱརᙕሠၚ޺ఱ‫ڬ‬෹ఱሠ዁ᙕл዁ୣఱၚდఱ‫ڬ‬Ùᙕ ዁ୣࣰᙕ ‫ڬ‬Ᏺ዁ୣၚᄹᙕ ࡂࣰ‫ڬ‬෹ሠᙕ ᑋఱ዁ୣᙕ ዁ᑋၚᙕ ໪‫ڬ‬ඈၚᄹᙕ ෹ࣰ૥ఱሠง‫ڬ‬዁ఱᐋࣰᙕ ᄹࣰਰၚᄹ໪ሠŵᙕ ӂརఱ዁ఱ‫ڬ‬ง෹ᒥᙕ ዁ୣࣰᙕ ૥ၚᐋࣰᄹར໪ࣰར዁ᙕ ᑋఖఱ޺ୣᙕ ၚᐋࣰᄹᔜ ዁ୣᄹࣰᑋᙕ Ҕ‫ڬ‬ఱงࣰᙕ ‫ࣰכ‬ง෹‫ڬ‬ሠሠఱࣰᙕ ‫ࡂڬ‬ၚდ዁ࣰࡂᙕ ‫ڬ‬ᙕ ׂᎍᄹ‫ڬ‬งᙕ ԰‫ڬ‬ཀྵࡂሠᙕ ֟ᄹၚ޺ง‫ڬ‬ላ‫ݏ‬዁ఱၚརÙᙕ ᑋୣఱ޺ୣᙕ ᑋ‫ڬ‬ሠᙕ ‫ڬݯ‬ሠࣰࡂᙕ ᎍეၚརᙕ ዁ୣࣰᙕ ޺෹‫ڬ‬ሠሠఱ޺‫ڬ‬෹ᙕ རၚ዁ఱၚརᙕ ၛਰᙕ ง‫ڬ‬རࡂᙕ ዁ၚᙕ ዁ୣࣰᙕ ዁ఱӍ෺ࣰᄹ  ŵᙕ Ўᎍ෹዁ఱᐋ‫ڬ‬዁ၚᄹሠᙕ ᑋࣰᄹࣰᙕ ޻ၚརਰఱᄹ໪ࣰࡂᙕ ఱརᙕ རၚརᔜ ዁ᄻ‫ڬ‬ཀྵሠਰࣱᄹ‫ݯڬ‬งࣱᙕ ეၛሠሠࣰሠሠၛᄹᒥᙕ ᄹఱ૥ୣ዁ሠ ᙕ ၚᐋࣰᄻᙕ ዁ୣࣰᙕ ง‫ڬ‬རࡂᙕ ᎍརࡂࣰᄹᙕ ޺ᎍง዁ఱᐋ‫ڬ‬዁ఱၚརÙᙕ ‫ڬ‬རࡂᙕ დᄹၚᐋఱሠఱၚརᙕ ᑋ‫ڬ‬ሠᙕ ໪‫ࣰࡂڬ‬ᙕ ਰၚᄹᙕ ᄹࣰࡂఱሠ዁ᄹఱ‫ݯ‬ᎍ዁ఱၚརᙕ ၚਰᙕ ෹‫ڬ‬རࡂᙕ ‫ݯ‬ᒥᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬዁ఱၚརሠᙕ సརᙕ ၚᄹࡂࣰᄹᙕ ዁ၚᙕ ૥ఱᐋࣰᙕ ޺ᎍง዁ఱᐋ‫ڬ‬዁ၚᄹሠᙕ დ‫ڮ‬ᄹ޺ࣰงሠᙕ ‫ڬ‬დდᄹၚᒈఱ໪‫ڬ‬዁ࣰ෹ᒥᙕ ࣰᄯᎍ‫ڬ‬෹ᙕఱརᙕሠఱᓯࣰŵᙕ ؉ୣࣰሠࣰᙕᆏࣰਰၚᄹ໪ሠᙕᑋࣰᄹࣰᙕ໪ၚᄹࣰᙕ ሠᎍ޻޻ࣰሠሠਰᎍงᙕ ఱརᙕ ሠၚᎍ዁ୣࣱᄹརᙕ ዁ୣ‫ڬ‬རᙕ ఱརᙕ ཀྵၛᄹ዁ୣࣰᄹརᙕ л዁ୣఱၚდఱ‫ڬ‬Ùᙕ ਰၚᄹᙕ ఱ዁ᙕ ᑋ‫ڬ‬ሠᙕ ዁ୣࣰᙕ ሠၚᎍ዁ୣᙕ ᑋୣఱ޺ୣᙕ ୣ‫ࡂڬ‬ᙕ ඬརၚᑋརᙕ ᑋఱࡂࣰሠეᄹࣰ‫ࡂڬ‬ᙕ ‫ڬ‬૥ᄹఱ޺ᎍง዁ᎍᄹ‫ڬ‬งᙕ ዁ࣱར‫ڬ‬ར޻ᒥᙕ ᑋఱ዁ୣᙕ ୣࣰ‫ڬ‬ᐋᒥᙕ ‫ݯ‬ᎍᄹࡂࣰརሠᙕ დง‫ࡂࣰ޺ڬ‬ᙕ ᎍდၚརᙕ ዁ୣࣰᙕ ዁ࣰར‫ڬ‬ར዁Ųᙕ лᐋࣰརᙕ ఱརᙕ ዁ୣࣰᙕ ሠၚᎍ዁ୣÙᙕ ୣၚᑋࣰᐋࣰᄹÙᙕ งఱ዁࡬ࣰᙕ ᄻࣰࡂఱሠ዁ᄹఱ‫ݯ‬ᎍ዁ఱၚརᙕ ၚਰᙕ ง‫ڬ‬རࡂᙕ ਰᄹၚ໪ᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ዁ၚᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ዁ၚၚඬᙕ ეง‫ࣰ޺ڬ‬ƶᙕ ӂརᙕ ‫ڬ‬ᙕ ሠࣰ޺ၛརࡂᙕ ᄹࣰਰၛᄹ໪Ùᙕ ዁ୣࣰᙕ ࣰ֟‫ڬ‬ሠ‫ڬ‬ར዁ᙕσሠሠၚ޻ఱ‫ڬ‬዁ఱၚརሠᙕ ֟ᄹၚ޺෹‫ڬ‬ላ‫ڬ‬዁ఱၚརÙᙕ ᄹࣰࡂఱሠ዁ᄹఱ‫ݯ‬ᎍ዁ఱၚརᙕ ၚਰᙕ ง‫ڬ‬རࡂᙕ ఱሠᙕ ᄹࣰდง‫ࡂࣰ޺ڬ‬ᙕ ‫ڬ‬ሠᙕ ዁ୣࣰᙕ ໪‫ڬ‬ඈၚᄹᙕ ૥ၚ‫ڬ‬งᙕ ‫ݯ‬ᒥᙕ ዁ୣࣰᙕ ࡂࣰᐋࣰ෹ၚდ໪ࣰར዁ᙕ ၚਰᙕ ‫ڬ‬ᙕ ሠၚ޺ఱ‫ڬ‬෹ఱሠ዁ᙕ ‫ڬ‬૥ᄹఱ޺ᎍ෹዁ᎍᄹࣰᙕ ఱརᙕ ᑋୣఱ޻ୣᙕ ዁ୣࣰᙕ დࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၚ޺ఱ‫ڬ‬዁ఱၚརᙕ ఱሠᙕ ၚਰᙕ ޺ᄹఱ዁ఱ޻‫ڬ‬งᙕ ఱ໪დၚᄹ዁‫ڬ‬ར޺ࣰŵᙕ ؉ୣࣰᙕ ‫ڬ‬ᎍ዁ୣၚᄹᙕ ޺ၚར޺งᎍࡂࣰሠᙕ ዁ୣ‫ڬ‬፩ᙕ ‫ڬ‬዁ᙕ ዁ୣࣰᙕ ࣰཀྵࡂᙕ ၚਰᙕ л዁ୣఱၚდఱ‫ڬ‬hሠᙕ ਰఱᄹሠ዁ᙕ ᒥࣰ‫ڬ‬ᄹᙕ ၚਰᙕ ᄹᎍᄹ‫ڬ‬งᙕ ෹‫ڬ‬རࡂᙕ ᄹࣰਰၚᄹ໪Ùᙕ ዁ୣࣰᙕ ਰᎍ዁ᎍᄹࣰᙕ ᑋ‫ڬ‬ሠᙕ ᐋࣰᄹᒥᙕ 6Ȁ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - https://www.nomos-elibrary.de/agb ᎏར޺ࣰᄺ዁‫ڬ‬ఱརŶᙕ ؉ୣࣰᙕ ‫ڬݯ‬෹‫ڬ‬ར޺ࣰᙕ ‫ࣰݯ‬዁ᑋࣰࣰརᙕ ࡂࣰ޺ࣰར዁ᄺ‫ڬ‬෹ఱᓯ‫ڬ‬዁ఱၛརᙕ ၛਰᙕ ეၛᑋࣰᄺᙕ ዁ၛᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ‫ڬ‬ሠሠၛ޺ร‫ڬ‬዁ร֊རሠᙕ ᑋୣఱ޺ୣᙕ ໪ఱ૥ୣ዁ᙕᑋࣰӍ෹ᙕ ეᄺࣰሠࣰᄺᐋࣰᙕ ዁ୣࣰᙕ ሠ዁‫ڬ‬዁ᎏሠᙕ ᄯᎏၛᙕ ‫ڬ‬རࡂᙕ ࣰ૥‫ڬ‬෺ఱ዁‫ڬ‬ᄺఱ‫ڬ‬རᙕ ໪ࣰ‫ڬ‬ሠᎏᄺࣰሠᙕ ࣰརਰၛᄺ޺ࣰࡂᙕ ‫ݯ‬ᒥᙕ ዁ୣरᙕ ޺ࣰར዁ᄺ‫ڬ‬෹ᙕ ૥ၛᐋࣰᄺར໪ࣰར዁ᙕ ᄺࣰ໪‫ڬ‬ఱརࣰࡂᙕ ᎏརࡂࣰ዁ࣰᄺ໪ఱརࣰࡂÙᙕ ‫ڬ‬ሠᙕ ࡂఱࡂᙕ ዁ୣ‫ڬ‬዁ᙕ ‫ࣰݯ‬዁ᑋࣰࣰརᙕ ࣰ૥‫ڬ‬สహ዁‫ڬ‬ᄺఱ‫ڬ‬རఱሠ໪ᙕ ‫ݯ‬ᒥᙕ ᄻࣰࡂహሠ዁ᄺఱ‫ݯ‬ᎏ዁ఱၛརᙕၛਰᙕ෹‫ڬ‬རࡂᙕ‫ڬ‬རࡂᙕ‫ݯ‬ᒥᙕ޺ၛ෺෺ࣰ޺዁హᐋࣰᙕ‫ڬ‬૥ᄺఱ޺ᎏ෺዁ᎏᄺ‫ڬ‬෺ᙕ‫޺ڬ‬዁ఱᐋహ዁ᒥűᙕ Z=mUOz \m 'mHolO -HH†s=\om =mM .toM †H \o m \m ZO Ut=t\=m 2OHqt H@†}NM E‹ ZO B ~œ~ɕ.Ot†‡\=m*=mM 1ORotl ϴᒪᙕ = [(N(-:f =-@5@ Gf ؉ୣࣰᙕ ‫ڬ‬རརၛᎏར޺ࣰ໫ࣰར዁ᙕ ၛਰᙕ ዁ୣࣰᙕ ‫ࣰه‬෼‫ڬ‬ሠ޺ၛňୌၛᐋࣰᄺར໫ࣰར዁gሠᙕ ෺‫ڬ‬རࡂᙕ ᄺࣰਰၛᄺ໫ᙕ ෺‫ڬ‬ᑋᙕ ²կၛűᙕ ȉ ̡̡ ȉ ́Êᙕ ၛརᙕ ԁᎏརࣰᙕ ɛʮÙᙕ Ȇ ͤ́ͤÙᙕ ໪‫ڬ‬ᄺඬሠᙕ ዁ୣࣰᙕ ‫ࣰݯ‬૥ఱརརఱར૥ᙕ ၛਰᙕ ‫ڬ‬ᙕ རࣰᑋᙕ ე୥‫ڬ‬ሠࣰᙕ హརᙕ ዁ୣࣰᙕ ࣰ֟ᄺᎏᐋహ‫ڬ‬རᙕ ส‫ڬ‬རࡂᙕ ᄺरੁၛᄺབྷᙕ ეᄺၛ޺ࣰሠሠűᙕυ޺޺ၛᄺࡂఱར૥ᙕ዁ၛᙕ዁ୣࣰᙕ‫ڬݯ‬ሠహ޺ᙕ෺ࣰ૥ఱሠ෺‫ڬ‬዁ఱၛརÙᙕ዁ୣࣰᙕ‫ڬ‬૥ᄺ‫ڬ‬ᄺఱ‫ڬ‬རᙕᄺࣰਰၛᄺ໫ᙕహሠᙕ‫ڬ‬རᙕహར዁ࣰ૥ᄺ‫ڬ‬෺ᙕვᄺၛ޽ࣰሠሠᙕ ‫ڬ‬རࡂᙕ ‫ڬ‬རᙕ ఱརሠ዁ᄺᎏ໪ࣰར዁ᙕ ਰၛᄺᙕ ዁ୣࣰᙕ ዁ᄺ‫ڬ‬རሠਰၛᄺ໫‫ڬ‬዁ఱၛརᙕ ‫ڬ‬རࡂᙕ ᄺࣰၛᄺఱࣰར዁‫ڬ‬዁ఱၛརᙕ ၛਰᙕ ዁ୣࣰᙕ ‫ڬ‬૥ᄺ‫ڬ‬ᄺఱ‫ڬ‬རᙕ ሠ዁ᄺᎏ޺዁ᎏᄺࣰűᙕ ӂརᙕ ዁ୣఱሠᙕ ᑋ‫ڬ‬ᒥÙᙕ ఱ዁ᙕ ఱར዁ࣰརࡂሠᙕ ዁ၛᙕ ఱར዁ࣰ૥ᄺ‫ڬ‬዁ࣰᙕ ዁୥ࣰᙕ ໪‫ڬ‬ᄺ૥హར‫ڬ‬෺ᙕ ૥ᄺၛᏳვሠᙕ ၛਰᙕ ጖୥रᙕ ᄺᎏᄺ‫ڬ‬สᙕ ეၛეᎏ෹‫ڬ‬዁ఱၛརᙕ ዁ၛᙕ ዁ୣࣰᙕ ར‫ڬ‬዁ఱၛར‫ڬ‬෹ᙕ ࡂࣰᐋࣰ෺ၛე໫ࣰར዁űᙕ υ዁ᙕ ዁୥ࣰᙕ ሠ‫ڬ‬໪ࣰᙕ ጖ఱ໪ࣰᙕ ዁ୣࣰᙕ ෺‫ڬ‬རࡂᙕ ᄺࣰਰၛᄺ໫ᙕ హሠᙕ ጖୥ࣰᙕ ޺ᄺᎏ޺ఱ‫ڬ‬෹ᙕ ਰ‫޺ڬ‬዁ၛᄺᙕ ఱརᙕ ၛᄺࡂࣰᄺᙕ ዁ၛᙕ ეᄺၛ໪ၛ዁ࣰᙕ ‫ڬ‬૥ᄺఱ޺ᎏ෺዁ᎏᄺ‫ۏ‬෹ᙕ ࡂࣰᐋࣰ෺ၛე໪ࣰར዁ᙕ ‫ڬ‬རࡂᙕ ዁ၛᙕ ޽୥‫ڬ‬རརࣰสᙕ ਰఱར‫ڬ‬ར޺ఱ‫ڬ‬෺ᙕ ᄺࣰሠሠၛᎏᄺ޺ࣰሠᙕ ዁ၛᙕ ࣰሠ዁ఱ໪ᎏ෺‫ڬ‬዁ࣰᙕ ዁୥ࣰᙕ ఱརࡂᎏሠ዁ᄺఱ‫ڬ‬෺ఱᓯ‫ڬ‬዁హၛརűᙕ ӂརᙕ ዁ୣࣰᙕ Ȇ ͤ́ͤᙕ ᄺࣰਰၛᄺ໫ᙕ ෺‫ڬ‬ᑌᙕ ጖୥ࣰᙕ ໪‫ڬ‬ᒈహ໪ᎏ໪ᙕ ሠఱᓯࣰᙕ ‫ڬ‬෺෺ၛᑋࣰࡂᙕ ਰၛᄺᙕ ეᄺహᐋ‫ڬ‬዁ࣰᙕ ส‫ڬ‬རࡂୣၛ෺ࡂఱར૥ሠᙕ ୣ‫ڬ‬ሠᙕ ‫ࣰࣰݯ‬རᙕ ᄺࣰࡂᎏ޽ࣰࡂÙᙕ ਰၛᄺᙕ ࣰᒈ‫ڬ‬໫ეึࣰᙕ ఱརᙕ ዁ୣࣰᙕ ޺ၛ‫ڬ‬ሠ዁‫ڬ‬෹ᙕ ᓯၛརࣰᙕ ዁ၛᙕ Ȇ ˕ ȁ ᙕ ୣ‫ڬ‬ᙕ ၛਰᙕ ఱᄺᄺఱ૥‫ڬ‬዁ࣰࡂᙕ ޺ᄺၛე෺‫ڬ‬རࡂᙕ ሠఱར޺ࣰᙕ ȉ ̡ͤ˕Úᙕ ˕ǯᙕ ୥‫¸ڬ‬Úᙕ ‫ڬ‬૥ᄺ‫ڬ‬ᄺఱ‫ݐ‬རᙕ ఱརࡂᎏሠ዁ᄺఱ‫ڬ‬෹ᙕ ޺ၛ໪ე෺ࣰᒈࣰሠᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ࣰࣰݯ‬རᙕ ሠᎏ‫ݯ‬໪ఱ዁዁ࣰࡂᙕ ዁ၛᙕ ዁ୣࣰᙕ ᄺࣰਰၛᄺ໪Ùᙕ ‫ڬ‬རࡂᙕ ‫ڬ‬ሠሠၛ޽ఱ‫ڬ‬጖ఱᐋࣰᙕ रรɁ዁ࣰᄺᔜ ეᄺఱሠࣰሠ ᙕ ޺ୣ‫ڬ‬ᄺ‫޺ڬ‬዁ࣰᄺఱᓯࣰࡂᙕ ‫ݯ‬ᒥᙕ ආၛఱར዁ᙕ ၛᑋརࣰᄺሠୣఱეᙕ ‫ڬ‬རࡂᙕ ሠࣰ෺ਰį໪ηར‫ڬ‬૥ࣰ໫ࣰར዁ᙕ ୣ‫ڬ‬ᐋࣰᙕ ‫ࣰࣰݯ‬རᙕ హ໫ეสࣰᔝ ໪ࣰར዁ࣰࡂᙕ ‫ڬ‬ሠᙕ ‫ڬ‬ᙕ ޺ࣰར዁ᄺ‫ڬ‬෹ᙕ ࣰ෹ࣰ໪ࣰར዁ᙕ ၛਰᙕ዁ୣࣰᙕརࣰᑋᙕ ሠ዁ᄺᎏ޺዁ᎏᄺࣰűᙕ υਰ዁ࣰᄺᙕ ໪ၛᄺࣰᙕ ዁ୣ‫ڬ‬རᙕ ̡ᙕ ᒥࣰ‫ڬ‬ᄺሠᙕ ၛਰᙕ ෹‫ڬ‬རࡂᙕ ᄺࣰਰၛᄺ໪Ùᙕ ዁ୣࣰᙕ ఱ෺෹ᎏሠఱၛརሠᙕ ‫ݯڬ‬ᙕၛ ᎏ዁ᙕ ዁୥ࣰᙕ ૥ᄺࣰ‫ڬ‬዁ᙕ ޺ၛᐋࣰᄺ‫ڬ‬૥ࣰᙕ ၛਰᙕ ዁ୣࣰᙕ ᄺࣰਰၛᄺ໪ᙕ ໪ࣰሠᎏᄺࣰᙕ ‫ڬ‬ᄺࣰᙕ ૥ၛီरÙᙕ ‫ڬ‬རࡂᙕ ᑋࣳᙕ ޺‫ڬ‬རᙕ ਰఱརࡂᙕ ໪ၛᄺࣰᙕ ዁ୣ‫ڬ‬རᙕ ၛརࣰᙕ ‫ڬ‬ᎏ዁ୣၛᄺఱᓯࣰࡂᙕ ᐋၛఱ޺ࣰᙕ ሠ዁‫ڬ‬዁ఱར૥ᙕ ዁୥‫ڬ‬዁ᙕ ዁ୣࣰᙕ ૥ᄺࣰ‫ڬ‬዁ᙕ ໫‫ڬ‬ሠሠᙕ ၛਰᙕ ვၛၛᄺᙕ ਰ‫ڬ‬ᄺ໪ࣰᄺሠᙕ‫ڬ‬རࡂᙕᄺᎏᄺ‫ڬ‬෹ᙕᑋၛᄺඬࣰᄺሠᙕ‫ڬ‬ᄺࣰᙕ዁ୣࣰᙕ෹ၛሠࣰᄺሠᙕఱརᙕ዁ୣࣰᙕȆ ͤ́ͤᙕ෺‫ڬ‬རࡂᙕᄺࣰਰၛᄺ໪űᙕ ؉ୣࣰᙕ ‫ڬ‬ᄺ዁ఱࡇࣰᙕ ࡂࣰ‫ڬ‬෹ሠᙕᑋఱ዁ୣᙕሠၛ໪ࣰᙕ‫ڬ‬ሠეࣰ޺዁ሠᙕ ၛਰᙕ዁ୣࣰᙕఱརਰ෹ᎏࣰར޽ࣰᙕၛਰᙕ዁ୣࣰᙕ෹‫ڬ‬རࡂᙕ ᄺࣰਰၛᄺ໪ᙕ ၛརᙕ዁ୣࣰᙕ ෹‫ڬ‬རࡂᙕ ዁ࣰརᎏᄺࣳᙕე‫ڬ‬዁዁ࣰᄺརሠÙᙕ ၛརᙕ ዁ୣࣰᙕᄺᎏᄺ‫ڬ‬෹ᙕఱར޺ၛ໪ࣰᙕ ‫ڬ‬རࡂᙕ ၛརᙕ ၛ޺޺ᎏე‫ڬ‬዁ఱၛརÙᙕ ‫ڬ‬ሠᙕᑋࣰӍ෺ᙕ ‫ڬ‬እᙕ ၛརᙕ ዁୥ࣰᙕ ࡂࣰᐋࣰູၛვᔝ ໪ࣰར዁ᙕ ၛਰᙕეᄺၛࡂᎏ޺዁ఱၛརűᙕ ҔၛᑋࣰᐋࣰᄺÙᙕ ዁ୣࣰᙕ ሠ዁‫ڬ‬዁హሠ዁ఱ޺‫ڬ‬෹ᙕ ఱརਰၛᄺ໪‫ڬ‬዁హၛརᙕ ၛརᙕ ዁୥ࣰᙕ ޺୥‫ڬ‬ར૥ࣰሠᙕ ၛ޽޺ᎏᄺࣰࡂᙕ ሠఱར޺ࣰᙕ Ȇ ͤ́ͤᙕ ఱརᙕ ዁ୣࣰᙕ ‫ڬ‬૥ᄺ‫ڬ‬ᄺఱ‫ڬ‬རᙕ ሠࣰ޺዁ၛᄺᙕ ఱሠᙕ ᐋࣰᄺᒥᙕ ეၛၛᄺŶᙕ ؉ୣࣰᄺࣰਰၛᄺࣰÚᙕ ዁ୣࣰᙕ ࡂఱਰਰࣰᄺࣰར዁ᙕ ვᄺၛ‫ݯ‬෹ࣰ໫ሠᙕ ޺‫ڬ‬རᙕ ၛར෹ᒥᙕ ‫ࣰݯ‬ᙕ ዁ᄺࣰ‫ڬ‬዁ࣰࡂᙕ ‫ڬ‬෹ၛར૥ᙕ ᐋࣰᄺᒥᙕ ‫ݯ‬ᄺၛ‫ࡂڬ‬ᙕ ෺ఱརࣰሠűᙕ ؉ୣࣰᙕ ሠၛᎏᄺ޺ࣰሠᙕ ၛਰᙕ ࡂ‫ڬ‬዁‫ڬ‬ᙕ ‫ڬ‬ᄺࣰᙕ ዁୥रᙕ ࣰᒈఱሯድീར୍ᙕ ၛਰਰఱ޺ఱ‫ڬ‬෹ᙕ ᄺࣰეၛᄺ዁ሠÙᙕ ሠၛ໪ࣰᙕ ‫ࣰࡂڬ޺ڬ‬໪ఱ޺ᙕ ᄺࣰሠࣰ‫ڬ‬ᄺ޺ୣᙕ ޺‫ڬ‬ᄺᄺఱࣰࡂᙕ ၛᎏ዁ᙕ ၛརᙕ ዁ୣࣰᙕ ሠᎏ‫ݯ‬ආࣰ޺዁ᙕ ‫ڬ‬རࡂᙕ ዁ୣࣰᙕ హར዁ࣰᄺᔦ ᐋఱࣰᑋሠᙕࡂၛརࣰᙕ‫ݯ‬ᒥᙕ໪ᒥሠࣰ෹ਰᙕఱརᙕԴఱ໪‫ڬ‬ᙕ‫ڬ‬རࡂᙕఱརᙕ዁ୣࣰᙕ޺ၛᎏར዁ᄺᒥᙕሠహࡂࣰΐᙕ ٘ར዁ఱ෹ᙕ ԁᎏརࣰᙕ ʆǯÙᙕ Ȇ ̡ͤ́Ùᙕ ᑋఱ዁ୣᙕ ዁ୣࣰᙕ ࣰᒈეᄺၛეఱ‫ڬ‬዁ఱၛརᙕ ၛਰᙕ ‫ݯڬ‬ၛᎏ዁ᙕ ̡Úͅᙕ Րహ෺෺ఱၛརᙕ ୥‫ڬ‬ᙕ ‫ڬ‬རࡂᙕ ȉ ȉ ᙕȉ ȉ ǯᙕ ეᄺၛეࣰᄺ዁ఱࣰሠᙕ ዁ୣࣰᙕ ૥ၛᐋࣰᄺར໪ࣰར዁ᙕ ୣ‫ڬ‬ሠᙕ ਰᎏ෺ਰఱ෹෺ࣰࡂᙕ ̡ɛᙕ AƼ ᄺࣰሠეűᙕ ̡́ᙕ —ƨ ၛਰᙕ ዁ୣࣰᙕ ᄺࣰਰၛᄺ໪ᙕ ૥ၛ‫ڬ‬෺űᙕ ؐ୥ࣰᙕ ᄺࣰࡂఱሠ዁ᄺఱ‫ݯ‬ᎏ዁ఱၛརᙕ ᑋ‫ڬ‬ሠᙕ ޺‫ڬ‬ᄺᄺఱࣰࡂᙕ ၛᎏ዁ᙕ ໪ၛᄺࣰᙕ ሠสၛᑋสᒥűᙕ ؎ୣࣰᙕ ეᄺఱၛᄺఱ዁ᒥᙕ ၛਰᙕ  ‫ڬ‬ሠሠၛ޽ఱ‫ڬ‬዁ఱᐋࣰᙕ रု጖रᇭᔝ ეᄺఱሠࣰሠ ᙕ ఱརᙕ ዁ୣࣰᙕ ᄺࣰࡂఱሠ዁ᄺఱ‫ݯ‬ᎏ዁ఱၛརᙕ ეᄺၛ޺ࣰሠሠᙕ ఱሠᙕ ᐋࣰᄺᒥᙕ ࡇࣰ‫ڬ‬ᄺűᙕ υ૥ᄺఱ޺ᎏ෹዁ᎏᄺ‫ڬ‬สᙕ ვᄺၛࡂᎏ޽጖ఱၛརᙕ ޺ၛᙕၛ ეࣰᄺ‫ڬ‬዁ఱᑅࣰሠᙕ ‫ڬ‬རࡂᙕ ዁ஙࣰᙕ ᄯᎏ‫ڬ‬ሠఱį޺ၛၛეࣰᄺ‫ڬ‬዁ఱᐋࣰᙕ ਰၛᄺ໪ᙕ ඬརၛᑋརᙕ ‫ڬ‬ሠᙕ ‫׬‬υӂ‫׬‬ᙕ ‫ڬ‬ᄺࣰᙕ ዁୥ࣰᙕ ૥ᄺࣰ‫ڬ‬዁ࣰሠ዁ᙕ ‫ࣰݯ‬རࣰਰఱ޺ఱ‫ڬ‬ᄺఱࣰሠᙕ ၛਰᙕ ዁ୣࣰᙕ ᄺࣰਰၛᄺ໪Ùᙕ ୣ‫ڬ‬ᐋఱར૥ᙕ ᄺࣰ޽ࣰఱᐋࣰࡂᙕ ̡ȁᙕAƼ ၛਰᙕ ዁ୣࣰᙕ ᄺࣰࡂఱሠ጖ᄺహ‫ݯ‬ᎏ጖रࡂᙕ ส‫ڬ‬རࡂſᙕ ‫؞‬୥ࣰᙕ ᄺࣰਰၛᄺ໪ᙕ ୣ‫ڬ‬ሠᙕ ዁ᄺ‫ڬ‬རሠਰၛᄺ໪ࣰࡂᙕ ࡂᄺ‫ڬ‬ሠ዁ఱ޺‫ڬ‬ส෺ᒥᙕ ዁ୣࣰᙕ ෺‫ڬ‬རࡂᙕ ეᄺၛეࣰᄺ዁ᒥᙕ ე‫ڬ‬዁዁ࣰᄺརሠÚᙕ ‫ݯ‬ᒥᙕ ࣰ෺హ໫ఱར‫ڬ‬጖హར૥ᙕ ዁୥ࣰᙕ ეᄺၛეࣰᄺ዁ᒥᙕၛਰᙕ዁ୣࣰᙕ‫ڬ‬૥ᄺఱ޺ᎏ෹዁ᎏᄺ‫ڬ‬෺ᙕ޺ၛ໫ე‫ڬ‬རఱࣰሠÙᙕᄺࣰࡂᎏ޺హར૥ᙕ‫ڬ‬෹෹ᙕ዁ᒥეࣰሠᙕ ၛਰᙕᄺࣰ෺‫ڬ‬዁ఱၛརሠᙕ‫ڬݯ‬ሠࣰࡂᙕၛརᙕᄺࣰར዁ᙕ ‫ڬ‬རࡂᙕ ࣰར෹‫ڬ‬ᄺ૥ఱར૥ᙕ ሠᎏ‫ݯ‬ሠ዁‫ڬ‬ར዁ఱ‫ڬ‬෹෺ᒥᙕ ዁ୣࣰᙕ ‫ڬ‬ᄺࣰ‫ڬ‬ᙕ ‫ڬ‬རࡂᙕ ዁ୣࣰᙕ ఱ໫ვၛᄺ዁‫ڬ‬ར޽ࣰᙕ ၛਰᙕ ޺ၛၛვࣰᄺ‫ڬ‬጖ఱᐋࣰᙕ ਰၛᄺ໫ሠᙕ ‫ڬ‬རࡂᙕ ეࣰ‫ڬ‬ሠ‫ڬ‬ར዁ᙕ ޺ၛ໪໪ᎏརఱ዁ఱࣰሠűᙕ ؉ୣࣳᙕ ෹‫ڬ‬རࡂᙕ ᄺࣰࡂఱሠ዁ᄺఱ‫ݯ‬ᎏ዁ఱၛརᙕ ఱሠᙕ རၛ዁ᙕ ࡂࣰሠహ૥རࣰࡂᙕ ዁ၛᙕ ᄺࣰࡂᎏ޽ࣰᙕ ጖ୣࣼᙕ ሠహᓲࣰᙕ ၛਰᙕ ዁ୣࣳᙕ ᐋࣰᄺᒥᙕ ෹‫ڬ‬ᄺ૥ࣰᙕ ୣၛ෹ࡂఱར૥ሠűᙕ փརᙕ ዁ୣࣰᙕ ޺ၛར዁ᄺ‫ڬ‬ᄺᒥÙᙕ རၛᑋᙕ ఱਰᙕ ዁ୣࣰᙕ ᄺࣰࡂహሠ዁ᄺఱ‫ݯ‬ᎏ዁హၛူᙕ ეᄺၛᙕେ ᄺ‫ڬ‬໫ᙕ ఱሠᙕ རࣰ‫ڬ‬ᄺᙕ ዁ၛᙕ ޺ၛ໪ე෹ࣰ዁ࣰࡂÙᙕ ਰࣰᑋࣰᄺᙕ ෹‫ڬ‬ᄺ૥ࣰᙕ ეᄺၛࡂᎏ޺዁ఱၛརᙕ ᎏརఱ዁ሠᙕ ᑋఱ෹สᙕ ޺ၛར዁ᄺၛ෹ᙕ ‫ڬ‬ᙕ ส‫ڬ‬ᄺ૥ࣰᄺᙕ ሠ୥‫ڬ‬ᄺࣰᙕ ၛਰᙕ ዁୥ࣰᙕ ޺ၛᎏར዁ᄺᒥgሠᙕ ਰ‫ڬ‬ᄺ໪෹‫ڬ‬རࡂűᙕ ϴᎏ዁ᙕఱརᙕ ዁ୣࣰᙕ ሠ໪ᙕ‫ ڬ‬෺෺ᙕ ሠఱᓯࣰᙕ ეᄺၛࡂᎏ޽዁ఱᐋࣰᙕ ᎏརఱ጖ሠᙕ ዁୥ࣰᙕ རᎏ໫‫ࣰݯ‬ᄺᙕ ၛਰᙕ ვᄺၛვࣰᄺ዁ᒥᙕ B+µɕ https://doi.org/10.5771/0506-7286-1977-2-203, am 13.07.2024, 14:41:05 Open Access – - 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Estimating cumulative incidence of SARS-CoV-2 with imperfect serological tests: exploiting cutoff-free approaches
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ETH Library Estimating the cumulative incidence of SARS CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches Judith A. BoumanID1*, Julien RiouID2, Sebastian BonhoefferID1, Roland R. RegoesID1* 1 Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland, 2 Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland Judith A. BoumanID1*, Julien RiouID2, Sebastian BonhoefferID1, Roland R. RegoesID1* 1 Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland, 2 Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland Judith A. BoumanID1*, Julien RiouID2, Sebastian BonhoefferID1, Roland R. RegoesID1* 1 Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland, 2 Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland * judith.bouman@env.ethz.ch (JB); roland.regoes@env.ethz.ch (RRR) * judith.bouman@env.ethz.ch (JB); roland.regoes@env.ethz.ch (RRR) a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Bouman JA, Riou J, Bonhoeffer S, Regoes RR (2021) Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches. PLoS Comput Biol 17(2): e1008728. https://doi. org/10.1371/journal.pcbi.1008728 Editor: James Lloyd-Smith, University of California, Los Angeles, UNITED STATES Received: May 18, 2020 Accepted: January 20, 2021 Published: February 26, 2021 Editor: James Lloyd-Smith, University of California, Los Angeles, UNITED STATES Received: May 18, 2020 Accepted: January 20, 2021 Published: February 26, 2021 Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pcbi.1008728 Copyright: © 2021 Bouman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Large-scale serological testing in the population is essential to determine the true extent of the current SARS-CoV-2 pandemic. Serological tests measure antibody responses against pathogens and use predefined cutoff levels that dichotomize the quantitative test measures into sero-positives and negatives and use this as a proxy for past infection. With the imperfect assays that are currently available to test for past SARS-CoV-2 infection, the fraction of sero- positive individuals in serosurveys is a biased estimator of the cumulative incidence and is usually corrected to account for the sensitivity and specificity. Here we use an inference method—referred to as mixture-model approach—for the estimation of the cumulative inci- dence that does not require to define cutoffs by integrating the quantitative test measures directly into the statistical inference procedure. We confirm that the mixture model outper- forms the methods based on cutoffs, leading to less bias and error in estimates of the cumula- tive incidence. We illustrate how the mixture model can be used to optimize the design of serosurveys with imperfect serological tests. We also provide guidance on the number of con- trol and case sera that are required to quantify the test’s ambiguity sufficiently to enable the reliable estimation of the cumulative incidence. Lastly, we show how this approach can be used to estimate the cumulative incidence of classes of infections with an unknown distribu- tion of quantitative test measures. This is a very promising application of the mixture-model approach that could identify the elusive fraction of asymptomatic SARS-CoV-2 infections. An R-package implementing the inference methods used in this paper is provided. Our study advocates using serological tests without cutoffs, especially if they are used to determine parameters characterizing populations rather than individuals. This approach circumvents some of the shortcomings of cutoff-based methods at exactly the low cumulative incidence levels and test accuracies that we are currently facing in SARS-CoV-2 serosurveys. Author(s): Bouman, Judith A.; Riou, Julien; Bonhoeffer, Sebastian ; Regoes, Roland R. This page was generated automatically upon download from the ETH Zurich Research Collection. For more information, please consult the Terms of use. Introduction Past SARS-CoV-2 infection can be detected with serological tests, which classify individuals as sero-positive when their antibody level exceeds a predefined cutoff-value. Such serological tests are imperfect; currently available tests have high specificity but relatively low sensitivity [1–7]. Thus, they can give rise to false positive and false negative results. Such incorrect test outcomes are particularly problematic when the serological tests are used to determine the immune status of individuals. To estimate the cumulative incidence in a population, however, the accurate determination of the serological status of each individual is not required, as it is possible to correct for the sensitivity and specificity of the serological test. It is well known that the proportion of positive tests in a serosurvey is a biased estimator of cumulative incidence. Tests with a high specificity and low sensitivity, for example, underesti- mate the cumulative incidence because the low sensitivity leads to a high frequency of false negatives. Post-hoc corrections of the binomial estimator have been developed and refined over the past decades [8–10], and have been applied to SARS-CoV-2 serosurveys [11]. More specifically, Rogan and Gladen describe a post-hoc correction that essentially subtracts the expected number of false positives and adds the expected number of false negatives to the binomial estimator [8]. However, this Rogan-Gladen estimator works well only for high cumulative incidence and relatively high test specificity [8]. Additionally, the uncertainty in the sensitivity and specificity is not taken into account by the Rogan-Gladen estimator of the cumulative incidence. An estimator that considers the uncertainty in the sensitivity and specificity is, in this study, referred to as the Bayesian framework. In this framework, the uncertainty in the sensitivity and specificity is taken into account by using the number and test outcomes of control and case sera used for test validation in the estimation of the cumulative incidence [12–16]. (Basically, sensitivity and specificity, as well as their uncertainty, are estimated as the Binomial probabili- ties of detecting true positives and negatives, respectively.) Similar to the Rogan-Gladen esti- mator, this framework dichotomizes the data using a predefined cutoff by assigning a positive or negative test result for each individual in the cohort. Thus the Bayesian framework is also cutoff-based. In this study, we use an alternative approach to estimate cumulative incidence that does not rely on a predefined cutoff. This is a PLOS Computational Biology Methods paper. This is a PLOS Computational Biology Methods paper. Author summary As other pathogens, SARS-CoV-2 elicits antibody responses in infected people that can be detected in their blood serum as early as a week after the infection until long after Data Availability Statement: All R-code files are available from the gitlab database here: https:// gitlab.ethz.ch/jbouman/pist. 1 / 19 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 PLOS COMPUTATIONAL BIOLOGY PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Funding: RRR gratefully acknowledges funding from the ETH Zurich and the Botnar Research Centre for Child Health (grant number 2020-FS- 354). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. recovery. The presence of SARS-CoV-2 specific antibodies can therefore be used as a marker of past infection, and the prevalence of seropositive people, i.e. people with spe- cific antibodies, is a key measure to determine the extent of the SARS-CoV-2 pandemic. The serological tests, however, are usually not perfect, yielding false positive and false negative results. Here we exploit an approach that refrains from classifying people as sero- positive or negative, but rather compares the antibody level of an individual to that of con- firmed cases and controls. This approach leads to more reliable estimates of cumulative incidence, especially for the low prevalence and low test accuracies that we face during the current SARS-CoV-2 pandemic. We also show how this approach can be extended to infer the presence of specific types of cases that have not been used for validating the test, such as people that underwent a mild or asymptomatic infection. Competing interests: The authors have declared that no competing interests exist. Competing interests: The authors have declared that no competing interests exist. Introduction This approach has been developed to study the cumulative inci- dence of infections with various pathogens and is referred to as mixture model [17–23]. Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 2 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Throughout this study, we will also refer to this method as mixture model method. Rather than relying on dichotomized serological test data and correcting for the test’s sensitivity and speci- ficity, this method uses the quantitative test measures together with data on the distribution of these measures in controls and confirmed cases. Serological tests differ in the quantitative test measures they yield. Some measure optical densities, other neutralization titers (NT50). The mixture-model approach can be applied to all these measures irrespective of the type of assay that is used, as long as the measures of the serosurvey and test validation data have the same units. If there is significant variation in measures between laboratories, as suggested by Benda- vid et al. [11], measurements should be standardized or performed in the same laboratory. Using simulated serosurveys, we investigated the statistical properties of mixture-model estimators of cumulative incidence, and compare them to cutoff-based estimators. Further, we conducted power analyses to determine the required size of a serosurvey for serological tests with varying accuracies. We also studied how the statistical power of the mixture model esti- mator is affected by the number of control and case sera used for the validation of the serologi- cal assay. This sheds light on the under-explored relationship between the effort put into test validation on the one hand, and the serosurvey on the other. Last, we addressed an issue that can only be studied with the mixture model approach: the detection of a discrepancy between the serological observations in the epidemiological surveys and the quantitative test measures collected during the validation phase of the serological assay. There is evidence that individuals who underwent an asymptomatic or mild infection have lower antibody levels than those who had a severe infection [4, 24, 25]. A past asymptom- atic or mild infection is therefore detected with a lower sensitivity than a severe infection for most serological assays [4, 24]. This results in a biased estimate of the cumulative incidence with the cutoff-based methods if the serological assay is not validated with a representative sample of cases. Introduction The mixture model approach, however, can detect such a discrepancy, correct for it, and even estimate the relative incidence of the category of samples that was excluded from the validation data. Thus, the mixture-model approach has the potential to map the diversity of disease profiles, and could shed light on the yet-to-be-determined frequency of asymptomatic infections with SARS-CoV-2. Mixture-model estimator outperforms cutoff-based methods Name in this study Cutoff- based Used cutoff Method of incorporating sensitivity and specificity Estimated parameters Ref Uncorrected cutoff-based methods yes High specificity None Cumulative incidence yes Max Youden None Cumulative incidence Rogan-Gladen corrected cutoff- based methods yes High specificity Post-hoc Rogan-Gladen correction Cumulative incidence [8] yes Max Youden Post-hoc Rogan-Gladen correction Cumulative incidence Cutoff-based methods in a Bayesian framework yes High specificity Simultaneous, Bayesian estimation of cumulative incidence, sensitivity and specificity Cumulative incidence, sensitivity and specificity [12, 14– 16] yes Max Youden Simultaneous, Bayesian estimation of cumulative incidence, sensitivity and specificity Cumulative incidence, sensitivity and specificity Mixture model no - Mixture model for the estimation of cumulative incidence Cumulative incidence [17–23] https://doi.org/10.1371/journal.pcbi.1008728.t001 Table 1. Overview of methods for the estimation of cumulative incidence. rview of methods for the estimation of cumulative incidence. S2 Fig illustrates the well-known fact that the observed fraction of positive serological tests is a biased estimator of the cumulative incidence. For both cutoffs we consider, the maximum Youden and the high specificity cutoffs, the bias is substantial, increases for test of lower accu- racy, and, depending on the cutoff, can lead to over- of underestimation of the cumulative incidence. The results of the analyses that take the sensitivity and specificity of the serological test into account are shown in Fig 1. We find that the Rogan-Gladen correction [8] (see Methods) results in unbiased estimations of the cumulative incidence (see Fig 1A). Note that for low cumulative incidence levels or low test accuracy, the corrected point estimate of the prevalence can become negative. This is due to the fact that the number of observed seropositives—being a realization of a stochastic process—can be smaller than the expected number of false posi- tives. For the same reason, the Rogan-Gladen correction gives rise to more variable estimates compared to the mixture model for low cumulative incidence levels and low test accuracies (see Fig 1B). In contrast, the mixture-model estimator does not inflate the variation of point- estimates and does not result in negative estimates for any true cumulative incidence level or test accuracy. The Bayesian framework results in slightly overestimated cumulative incidences for low incidence levels and low test accuracy. This is likely due to the flat priors that have been used. Fig 1B shows that the 95% credible intervals obtained by the Bayesian framework are larger than the 95% confidence intervals of the mixture-model estimator. Mixture-model estimator outperforms cutoff-based methods Thus, the mixture model also outperforms the Bayesian framework. Mixture-model estimator outperforms cutoff-based methods To compare the mixture model to the cutoff-based methods, we simulated serosurveys con- ducted with serological tests of varying accuracies. As a proxy for the accuracy, we selected the area under the ROC-curve (AUC-ROC) and varied it from 0.8 to 1. This range is consistent with the AUC-ROC values of most currently available SARS-CoV-2 antibody tests [4, 7, 26]. (The sensitivity and specificity corresponding to the standard cutoffs across the range of AUC-ROC values that we consider here, are given in S1 Fig) An overview of the cutoff-based methods can be found in Table 1. In the simulated serosurveys, we assumed cumulative incidences of 1%, 4% and 8% and enrolled 10, 000 virtual individuals and used 5, 000 control and case sera for test validation. We then derived estimates of the cumulative incidence with the cutoff-based methods and the mixture-model approach, and repeated this 50 times for each test accuracy. We calculated 95% confidence intervals for the uncorrected and Rogan-Gladen corrected cutoff-based methods and the mixture model using a bootstrap procedure. A function for calculating these intervals is provided in the R-package. The uncertainty in the estimates from the Bayesian framework are determined based on the 95% credible interval. 3 / 19 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Table 1. Overview of methods for the estimation of cumulative incidence. Name in this study Cutoff- based Used cutoff Method of incorporating sensitivity and specificity Estimated parameters Ref Uncorrected cutoff-based methods yes High specificity None Cumulative incidence yes Max Youden None Cumulative incidence Rogan-Gladen corrected cutoff- based methods yes High specificity Post-hoc Rogan-Gladen correction Cumulative incidence [8] yes Max Youden Post-hoc Rogan-Gladen correction Cumulative incidence Cutoff-based methods in a Bayesian framework yes High specificity Simultaneous, Bayesian estimation of cumulative incidence, sensitivity and specificity Cumulative incidence, sensitivity and specificity [12, 14– 16] yes Max Youden Simultaneous, Bayesian estimation of cumulative incidence, sensitivity and specificity Cumulative incidence, sensitivity and specificity Mixture model no - Mixture model for the estimation of cumulative incidence Cumulative incidence [17–23] S2 Fig illustrates the well-known fact that the observed fraction of positive serological tests is a biased estimator of the cumulative incidence. Mixture-model estimator outperforms cutoff-based methods For both cutoffs we consider, the maximum Youden and the high specificity cutoffs, the bias is substantial, increases for test of lower accu- racy, and, depending on the cutoff, can lead to over- of underestimation of the cumulative incidence. The results of the analyses that take the sensitivity and specificity of the serological test into account are shown in Fig 1. We find that the Rogan-Gladen correction [8] (see Methods) results in unbiased estimations of the cumulative incidence (see Fig 1A). Note that for low cumulative incidence levels or low test accuracy, the corrected point estimate of the prevalence can become negative. This is due to the fact that the number of observed seropositives—being a realization of a stochastic process—can be smaller than the expected number of false posi- tives. For the same reason, the Rogan-Gladen correction gives rise to more variable estimates compared to the mixture model for low cumulative incidence levels and low test accuracies (see Fig 1B). In contrast, the mixture-model estimator does not inflate the variation of point- estimates and does not result in negative estimates for any true cumulative incidence level or test accuracy. The Bayesian framework results in slightly overestimated cumulative incidences for low incidence levels and low test accuracy. This is likely due to the flat priors that have been used. Fig 1B shows that the 95% credible intervals obtained by the Bayesian framework are larger than the 95% confidence intervals of the mixture-model estimator. Thus, the mixture model also outperforms the Bayesian framework. Mixture model leads to more reliable estimates of the temporal trends in cumulative incidence In the ongoing SARS-CoV-2 pandemic, the cumulative incidence is still increasing, and an estimation of its temporal trend is an urgent public health objective. To assess how well the dif- ferent methods can estimate temporal trends in cumulative incidence, we simulated serosur- veys during an ongoing epidemic. In particular, we assumed that the cumulative incidence increases from 1.5% to 15%. W f d th t th t d t ff b d th d b th d ti t th t l Table 1. Overview of methods for the estimation of cumulative incidence. Mixture model leads to more reliable estimates of the temporal trends in cumulative incidence In the ongoing SARS-CoV-2 pandemic, the cumulative incidence is still increasing, and an estimation of its temporal trend is an urgent public health objective. To assess how well the dif- ferent methods can estimate temporal trends in cumulative incidence, we simulated serosur- veys during an ongoing epidemic. In particular, we assumed that the cumulative incidence increases from 1.5% to 15%. We found that the uncorrected cutoff-based methods both underestimate the temporal trend in the cumulative incidence (Fig 2). The Rogan-Gladen estimator removes the bias in the estimate, but introduces a large variation in the point-estimates of the temporal trend. This is similar for the cutoff-based methods within the Bayesian framework. The estimate for the 4 / 19 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Fig 1. Point-estimates of cumulative incidence using the cutoff-based methods and the mixture model. Each violin represents 50 in silico serosurveys conducted with cohorts of 10, 000 virtual individuals and the points represent the median values. (A) Point-estimates of the cumulative incidence. The dashed line indicates the true cumulative incidence we assumed in the simulations. Please note that the scale of the y-axis differs between the sub-figures. (B) Size of the 95% uncertainty intervals. For the Rogan-Gladen and mixture-model estimates, the uncertainty intervals are the 95% confidence intervals, which we calculated with the bootstrap method (see Methods). For the Bayesian estimators, the uncertainty interval are the 95% credible intervals. Fig 1. Point-estimates of cumulative incidence using the cutoff-based methods and the mixture model. Each violin represents 50 in silico serosurveys conducted with cohorts of 10, 000 virtual individuals and the points represent the median values. (A) Point-estimates of the cumulative incidence. The dashed line indicates the true cumulative incidence we assumed in the simulations. Please note that the scale of the y-axis differs between the sub-figures. (B) Size of the 95% uncertainty intervals. For the Rogan-Gladen and mixture-model estimates, the uncertainty intervals are the 95% confidence intervals, which we calculated with the bootstrap method (see Methods). For the Bayesian estimators, the uncertainty interval are the 95% credible intervals. Fig 1. Point-estimates of cumulative incidence using the cutoff-based methods and the mixture model. Each violin represents 50 in silico serosurveys conducted with cohorts of 10, 000 virtual individuals and the points represent the median values. (A) Point-estimates of the cumulative incidence. https://doi.org/10.1371/journal.pcbi.1008728.g001 Mixture model leads to more reliable estimates of the temporal trends in cumulative incidence The dashed line indicates the true cumulative incidence we assumed in the simulations. Please note that the scale of the y-axis differs between the sub-figures. (B) Size of the 95% uncertainty intervals. For the Rogan-Gladen and mixture-model estimates, the uncertainty intervals are the 95% confidence intervals, which we calculated with the bootstrap method (see Methods). For the Bayesian estimators, the uncertainty interval are the 95% credible intervals. PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 5 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 ONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Fig 2. Estimated fold increases in cumulative incidence for the cutoff-based methods and the mixture model. In the simulated serosurveys, we assumed the cumulative incidence to increase from 1.5% to 15%, resulting in a true fold increase of 10 (dashed line). The violins show the distribution of 50 in silico serosurveys for both cumulative incidence levels conducted with cohorts of 10, 000 individuals and a test with an AUC-ROC value of 0.975. The dots indicate the median value. Fig 2. Estimated fold increases in cumulative incidence for the cutoff-based methods and the mixture model. In the simulated serosurveys, we assumed the cumulative incidence to increase from 1.5% to 15%, resulting in a true fold increase of 10 (dashed line). The violins show the distribution of 50 in silico serosurveys for both cumulative incidence levels conducted with cohorts of 10, 000 individuals and a test with an AUC-ROC value of 0.975. The dots indicate the median value. https://doi.org/10.1371/journal.pcbi.1008728.g002 https://doi.org/10.1371/journal.pcbi.1008728.g002 temporal trend can even be negative for the reason mentioned above. In contrast, the mixture model leads to more reliable point-estimates of the temporal trend without inflating their variation. temporal trend can even be negative for the reason mentioned above. In contrast, the mixture model leads to more reliable point-estimates of the temporal trend without inflating their variation. Low specificity/sensitivity can be compensated by enrolling more participants into the serosurvey (A) Statistical power versus the number of individuals in the serosurvey for varying levels of test accuracy (AUC-ROC). The power is calculated as the fraction of simulated serosurveys that resulted in a cumulative incidence estimate that is within 25% of the true cumulative incidence and for which the true cumulative incidence level lies within 2 standard deviations of the estimated value. Each point in the graph represents the result of 3, 000 in silico serosurveys. (B) The minimal number of virtual individuals necessary to obtain a statistical power of 0.9 over a range of AUC-ROC values. https://doi org/10 1371/journal pcbi 1008728 g003 https://doi.org/10.1371/journal.pcbi.1008728.g003 if the estimate of the cumulative incidence was sufficiently close to the true cumulative inci- dence (see Methods). The statistical power is defined as the fraction of successful in silico serosurveys. We find that a lower accuracy of the serological test can be compensated by higher sample sizes (Fig 3A), but only if the accuracy is not too low. For example, to achieve a statistical power of 0.9, 1, 000 individuals need to be enrolled into the serosurvey for a high-accuracy test (AUC-ROC = 0.975). In contrast, for a lower accuracy test (AUC-ROC = 0.9) 3, 000 are required (Fig 3B). However, for a test accuracy lower than 0.9 enrolling even up to 10, 000 individuals does not increase the power of the test above 0.9. Low specificity/sensitivity can be compensated by enrolling more participants into the serosurvey To understand how the test accuracy and the number of individuals enrolled in the serosurvey affect the statistical power of serosurveys analyzed with the mixture-model approach, we simu- lated serosurveys with tests characterized by varying AUC-ROC values and different numbers of individuals enrolled, and evaluated their success. A serosurvey was defined to be successful 6 / 19 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Fig 3. Statistical power of the mixture model. In all simulations, the number of control and case data is fixed to 5, 000 each and the true cumulative incidence level is 8%. (A) Statistical power versus the number of individuals in the serosurvey for varying levels of test accuracy (AUC-ROC). The power is calculated as the fraction of simulated serosurveys that resulted in a cumulative incidence estimate that is within 25% of the true cumulative incidence and fo which the true cumulative incidence level lies within 2 standard deviations of the estimated value. Each point in the graph represents the result of 3, 000 in silico serosurveys. (B) The minimal number of virtual individuals necessary to obtain a statistical power of 0.9 over a range of AUC-ROC values. https://doi.org/10.1371/journal.pcbi.1008728.g003 Fig 3. Statistical power of the mixture model. In all simulations, the number of control and case data is fixed to Fig 3. Statistical power of the mixture model. In all simulations, the number of control and case data is fixed to 5, 000 each and the true cumulative incidence level is 8%. (A) Statistical power versus the number of individuals in the serosurvey for varying levels of test accuracy (AUC-ROC). The power is calculated as the fraction of simulated serosurveys that resulted in a cumulative incidence estimate that is within 25% of the true cumulative incidence and for which the true cumulative incidence level lies within 2 standard deviations of the estimated value. Each point in the graph represents the result of 3, 000 in silico serosurveys. (B) The minimal number of virtual individuals necessary to obtain a statistical power of 0.9 over a range of AUC-ROC values. Fig 3. Statistical power of the mixture model. In all simulations, the number of control and case data is fixed to 5, 000 each and the true cumulative incidence level is 8%. Detecting discrepancies between test validation and serosurvey data The reliance of the mixture model on quantitative test data, allows us to investigate inconsisten- cies between the populations used for validating the test on the one hand, and the population recruited into the serosurvey on the other. For example, assume that the serological test has been validated only with sera from individuals who underwent a severe infection, in addition to sera from controls (see Fig 5A). If these severe cases used in the validation set are a good repre- sentation of the infections in the population, we would expect our serosurvey data to look like Fig 5C. However, if other types of infections are very prevalent, such as mild or asymptomatic infections, that are characterized by distributions of antibody levels very different from severe infections (see Fig 5B), the resulting serosurvey data would look like those shown in Fig 5D. We have extended the mixture model such that it can detect from the serosurvey data whether there exists an additional distribution of cases that was not included in the validation data. We set up a simulation assuming three distributions of test measures. These distributions can be thought of as corresponding to severe and asymptomatic cases and controls, but could also describe classes of infections that differ by a factor other than disease severity. We further assume that the total cumulative incidence in the population is 8%, of which 20% were asymp- tomatic infections, consistent with the current estimate [27]. We then simulate a serosurvey with 10, 000 individuals that results in quantitative test measures randomly drawn from these three distribution according to their cumulative incidences. First, we show that ignoring a missing class of case sera leads to an underestimation bias in the estimated cumulative incidence by analysing the simulated serosurvey data assuming a mixture model based on quantitative test measure of only severe cases and controls (see Fig 6A). This misspecified mixture model, however, is valuable as a null model against which a more complex likelihood can be tested. Fig 6A compares the misspecifation scenario to the scenario where both asymptomatic and severe infections have been included into the distribu- tion of the case sera of the validation data. Secondly, we fit the three-distribution likelihood to estimate the cumulative incidences of asymptomatic and severe cases, and the mean of the test measure distribution of asymptomatic cases. The number of control and case sera used for validation of serological tests impacts the reliability of the cumulative incidence estimate The mixture-model estimator relies directly on the quantitative test measures and their distri- bution for control and case sera. Therefore, the reliability of the method is expected to depend on the precision with which these distributions have been determined, which depends on the number of control and case sera used in test validation. Here, we asses how the number of control and case sera influences the variation of the estimated cumulative incidences and the power of the serosurvey (see Methods). In our simulations, the confidence interval of the estimated cumulative incidence decreases with the number of control and case sera used for the validation of the test (Fig 4C). As a result, the statistical power increases for higher numbers of control and case sera (Fig 4D). Addition- ally, we find that, with increasing test accuracy, the number of control and case sera required 7 / 19 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 to obtain a statistical power of 0.9 decreases. For a true prevalence of 8% and 10, 000 individu- als in the serosurvey, as used in Fig 4D, and a AUC-ROC value of 0.9, 2, 500 control and case sera samples are needed to obtain a statistical power of 0.9 (Fig 4D). However, for a AUC-ROC value of 0.975, sampling 750 cases and controls would be sufficient. A low number of control and case sera for the validation of the test can be compensated by a higher number of individuals in the serosurvey (Fig 4E). The relation between the number of control and case sera and the minimal number of individuals in the serosurvey depends on the accuracy of the serological assay. Detecting discrepancies between test validation and serosurvey data This analysis—without knowledge of the third distribution—succeeds in estimating the total cumulative incidence without bias (Fig 6B). It also yields estimates for the cumulative incidences for asymptomatic and severe cases separately (Fig 6B). The identifiability of the individual cumulative incidences depends strongly on how distinct the test measure distribu- tions of asymptomatic and severe cases and the controls are. In practice, one can test for the existence of a missing case distribution by applying a likelihood ratio test on the extended model and the standard mixture model. Discussion In this study, we evaluate the performance of a mixture-model approach in estimating the cumulative incidence of a population. Throughout this paper, we refrained from referring to 8 / 19 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Fig 4. Effect of varying the number of control and case sera used to calibrate the serological test. (A) An example of the true distribution (solid lines) of the control (grey) and case (orange) sera, the data simulated from those distributions (histograms) and the inferred densities (dashed lines) used in the inference of the cumulative incidence. Here, 150 control and case sera have been simulated and the AUC-ROC value of the test is equal to 0.975. (B) Point estimates of cumulative incidence for various numbers of control and case sera used to calibrate the serological test and three AUC-ROC values. Each violin shows the distribution of the estimated cumulative incidence of 50 in silico serosurveys conducted with cohorts of 10, 000 virtual individuals. The red line shows NAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Fig 4. Effect of varying the number of control and case sera used to calibrate the serological test. (A) An example of the true distribution (solid lines) of the control (grey) and case (orange) sera, the data simulated from those distributions (histograms) and the inferred densities (dashed lines) used in the inference of the cumulative incidence. Here, 150 control and case sera have been simulated and the AUC-ROC value of the test is equal to 0.975. (B) Point estimates of cumulative incidence for various numbers of control and case sera used to calibrate the serological test and three AUC-ROC values. Each violin shows the distribution of the estimated cumulative incidence of 50 in silico serosurveys conducted with cohorts of 10, 000 virtual individuals. The red line shows PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 9 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 the true cumulative incidence we assumed in the simulated serosurveys (8%). (C) Size of the 95% confidence intervals of the estimated cumulative incidences. Discussion (D) Statistical power versus the number of control and case sera used in the validation data for varying levels of test accuracy (AUC-ROC). Each point in the graph represents the result of 3, 000 in silico serosurveys. (E) The minimal number of virtual individuals necessary to obtain a statistical power of 0.9 over a range of number of control and case sera in the validation data. the true cumulative incidence we assumed in the simulated serosurveys (8%). (C) Size of the 95% confidence intervals of the estimated cumulative incidences. (D) Statistical power versus the number of control and case sera used in the validation data for varying levels of test accuracy (AUC-ROC). Each point in the graph represents the result of 3, 000 in silico serosurveys. (E) The minimal number of virtual individuals necessary to obtain a statistical power of 0.9 over a range of number of control and case sera in the validation data. https://doi.org/10.1371/journal.pcbi.1008728.g004 https://doi.org/10.1371/journal.pcbi.1008728.g004 sero-prevalence for two reasons. First, sero-prevalence is the frequency of sero-positive indi- viduals in a population and hence inherently coupled to cutoffs. Focusing on the distribution of antibody levels without dichotomizing into sero-positives and -negatives makes it more challenging to determine sero-prevalence. Second, serological tests are usually validated against pre-pandemic sera and sera from individuals with confirmed infection, and not against sera that do or do not contain pathogen-specific antibodies. As a consequence of this choice of positive and negative controls, false positives are individuals that have specific antibodies despite not having been infected, and not individuals for which the test wrongly shows they harbor specific antibodies while they actually do not. Correcting for false positives and nega- tives by both cutoff-based and mixture model methods therefore results in an estimate of cumulative incidence rather than of sero-prevalence. This distinction between sero-prevalence and cumulative incidence is common in epidemiological studies (see for example a metastudy on the cumulative incidence of the 2009 influenza pandemic by Van Kerkhove et al [28]). sero-prevalence for two reasons. First, sero-prevalence is the frequency of sero-positive indi- viduals in a population and hence inherently coupled to cutoffs. Focusing on the distribution of antibody levels without dichotomizing into sero-positives and -negatives makes it more challenging to determine sero-prevalence. Second, serological tests are usually validated against pre-pandemic sera and sera from individuals with confirmed infection, and not against sera that do or do not contain pathogen-specific antibodies. Discussion As a consequence of this choice of positive and negative controls, false positives are individuals that have specific antibodies despite not having been infected, and not individuals for which the test wrongly shows they harbor specific antibodies while they actually do not. Correcting for false positives and nega- tives by both cutoff-based and mixture model methods therefore results in an estimate of cumulative incidence rather than of sero-prevalence. This distinction between sero-prevalence and cumulative incidence is common in epidemiological studies (see for example a metastudy on the cumulative incidence of the 2009 influenza pandemic by Van Kerkhove et al [28]). The mixture-model approach uses the quantitative serological test measurements before they have been dichotomized, i.e. categorized as “positive” or “negative” with a cutoff. We con- firm that cutoff-based estimators that do not correct for the sensitivity and specificity of the serological test can lead to strong biases in the estimate of cumulative incidence and its time trends, especially for situations of low cumulative incidence [8]. Even though the commonly The mixture-model approach uses the quantitative serological test measurements before they have been dichotomized, i.e. categorized as “positive” or “negative” with a cutoff. We con- firm that cutoff-based estimators that do not correct for the sensitivity and specificity of the serological test can lead to strong biases in the estimate of cumulative incidence and its time trends, especially for situations of low cumulative incidence [8]. Even though the commonly Fig 5. Conceptual figure on how a discrepancy between the test validation and serosurvey data can be detected. (A) Histograms of simulated validation data from controls and severe cases. (B) Histograms of simulated validation data from controls and severe and asymptomatic cases. (C) Histogram of simulated serosurvey data when all infections in a population are severe. (D) Histogram of simulated serosurvey data when one third of all cases is asymptomatic and two thirds severe. https://doi.org/10.1371/journal.pcbi.1008728.g005 Fig 5. Conceptual figure on how a discrepancy between the test validation and serosurvey data can be detected. (A) Histograms of simulated validation data from controls and severe cases. (B) Histograms of simulated validation data from controls and severe and asymptomatic cases. (C) Histogram of simulated serosurvey data when all infections in a population are severe. (D) Histogram of simulated serosurvey data when one third of all cases is asymptomatic and two thirds severe. Discussion https://doi.org/10.1371/journal.pcbi.1008728.g006 used Rogan-Gladen correction and the Bayesian framework that accommodates the sensitivity and specificity alleviate the biases, the estimates of the cumulative incidence have generally wider confidence or high probability intervals than the mixture-model estimates. This is espe- cially pronounced for low levels of cumulative incidence and low test accuracies, and should therefore be of value specifically for SARS-CoV-2 serosurveys early in the pandemic. p y y y p Paired with the simulation of serosurveys, the mixture model can provide guidance on the design of serosurveys. It reveals how the test’s accuracy, the number of individuals in the sero- survey, and the number of control and case sera affect in the statistical power of the serosurvey. First, we found that a low test accuracy can, up to a level, be compensated by higher sample sizes in the serosurvey. Specifically, a compensation is possible for AUC-ROC values higher than 0.9, but even for these relatively accurate tests the increase in required sample size can be large. Thus, serosurveys need to employ tests of sufficiently high accuracy to be feasible, and increasing a tests accuracy pays off in terms of smaller serosurveys. Secondly, we showed how the number of control and case sera used in the validation of the test influence the statistical power of a serosurvey. Please note that the increasing the number of case and control sera in test validation do not make the test more accurate, but provide more exact estimates of the test’s accuracy. For example, to obtain a statistical power of 0.9 for a serosurvey performed at a true cumulative incidence level of 8% and a test accuracy of AUC-ROC = 0.975, 3, 000 individ- uals need to be enrolled if the test has been validated on 750 control and case serum samples. If the number of control and case sera used for test validation is equal to 2, 500 each, only 1, 000 individuals would have to be enrolled in the serosurvey for the same statistical power. It is therefore worthwhile to carefully weigh the benefits of more thorough test validation against that of expanding the serosurvey. The fact that the number of serum samples used to deter- mine the accuracy of a serological test affects the feasibility and statistical power of serosurveys is an argument for a collaborative scientific effort to establish large, standardized, open valida- tion data sets for SARS-CoV-2 serological tests. Discussion https://doi.org/10.1371/journal.pcbi.1008728.g005 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 10 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Fig 6. Estimates of the cumulative incidence in a population where individuals have been uninfected, as well as symptomatically and severely infected. The x-axes represent the AUC-ROC value between the asymptomatic and severe case distribution. The AUC-ROC value between the control and the severe case distributions is 1. Each violin represents the result of 50 simulated serosurveys with 10, 000 individuals per serosurvey. The true total cumulative incidence of severe and asymptomatic infections is 10%, of which 20% are asymptomatic. (A) Cyan violins show Fig 6. Estimates of the cumulative incidence in a population where individuals have been uninfected, as well as symptomatically and severely infected. The x-axes represent the AUC-ROC value between the asymptomatic and severe case distribution. The AUC-ROC value between the control and the severe case distributions is 1. Each violin represents the result of 50 simulated serosurveys with 10, 000 individuals per serosurvey. The true total cumulative incidence of severe and asymptomatic infections is 10%, of which 20% are asymptomatic. (A) Cyan violins show Fig 6. Estimates of the cumulative incidence in a population where individuals have been uninfected, as well as symptomatically and severely infected. The x-axes represent the AUC-ROC value between the asymptomatic and severe case distribution. The AUC-ROC value between the control and the severe case distributions is 1. Each violin represents the result of 50 simulated serosurveys with 10, 000 individuals per serosurvey. The true total cumulative incidence of severe and asymptomatic infections is 10%, of which 20% are asymptomatic. (A) Cyan violins show PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 11 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 estimates of the total cumulative incidence based on an inferred case distribution containing only severe case sera, whereas purple violins show estimates where the case distribution is containing both asymptomatic and severe case sera. (B) The estimated cumulative incidence of the mild (light purple) and the severe (dark purple) cases, where the case sera distribution is only based on severe cases, but the likelihood equation also estimates the shape of the asympotomatic cases and their relative prevalence. Discussion The mixture-model approach as well as the cutoff-based methods rely on representative data from cases. Representative means this cohort should contain individuals who have under- gone severe, mild and asymptomatic infections, and the proportions of the infections with dif- ferent severities should recapitulate the proportions in the population. We have illustrated that an over-representation of severe cases compared to asymptomatic cases in the validation of the serological test leads to underestimation of the cumulative incidence. Thus, it is preferable to include cases detected by contact tracing rather than by more biased detection channels, such as hospitalisation. Unlike the cutoff-based methods, however, the mixture-model approach allows us to infer the presence of cases that were not used for the validation of the test. To this end, the likelihood of the mixture model is extended by an unknown distribution of test measures. In addition to being able to identify a discrepancy of test validation versus serosurvey data, this extended like- lihood also allows for the estimation of the cumulative incidence of the subpopulation with the unknown distribution (Fig 6B). This is crucial for a reliable estimation of the true extent of the current SARS-CoV-2 pandemic. The mixture model can be easily extended to include more than two types of cases. We recommend to always use a mixture model with an additional unknown distribution and to test its fit with a likelihood-ratio test against a null model that PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 12 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 includes all known case distributions. This guards against strong biases arising from neglecting a large fraction with distinct test measure distributions. However, the biological interpretation of an additional distribution is complex. In addition to the severity of infection, many alterna- tive factors could influence the antibody response levels. Most notably, antibody levels have been found to drop over time [29] which can introduce heterogeneities in test measure distri- butions over time. The mixture-model approach is applicable over a broad range of serological tests and accepts any common type of quantitative test measures of specific antibody levels, such as opti- cal densities or “arbitrary units” in ELISAs or neutralization titers that inhibit viral replication to any degree specified (e.g NT50 or NT90) in neutralization assays. It is not essential that these measures are linearly correlated with the level of antibodies. Discussion It is important, however, that the isotype, units and scales are the same as those for the test measure distributions of con- trol and case sera. While the mixture-model approach has been developed to increase the reli- ability of cumulative incidence estimates especially for tests with low accuracy, it of course also works for perfect tests. Similar to the cutoff-based methods, it has been shown that the mixture model can be easily extended by categorical or continuous covariates of the cumulative incidence, such as sex or age [17–23]. Also temporal changes in cumulative incidence—as predicted, for example, by epidemiological models—can be incorporated into this framework. The mixture model pro- vides a more natural approach to integrating multiple test measures, such as IgA and IgG lev- els. In cutoff-based methods, in contrast, including multiple measures may require complex cutoff functions that depend on these multiple measures and will complicate the determina- tion of sensitivity and specificity. This work as well as other similar studies that investigate the effect of test accuracy on estimating cumulative incidence highlight the necessity of integrating the development of serological tests with the design of the serosurveys, in which they will be applied [30]. This is especially relevant during the current SARS-CoV-2 pandemic as the serological tests are devel- oped at the same time as the serosurveys are being conducted. The likelihood of the mixture model The likelihood of the mixture model The mixture model approach to inference relies directly on the quantitative measures obtained from serological tests [18–21]. It estimates the cumulative incidence (π) by maximizing the likelihood of observing the quantitative test measures in the serosurvey data, given the distri- bution of known case and control sera (see Fig 7A). The likelihood for the data is shown in Eq 1. Eq 1. llðUÞ ¼ X i¼n i¼1 log  pðsi ¼ 1jpÞ pðUijsi ¼ 1Þ þ pðsi ¼ 0jpÞ pðUijsi ¼ 0Þ  ð1Þ ð1Þ Here, U is a vector with the quantitative test measures of all n tests, σ is a binary vector of length n with their underlying true serological status (1 for infected and 0 for not infected). The probabilities p(Ui|σi = 1) and p(Ui|σi = 0) capture the distributions of quantitative test measures of control and case sera, and p(σi = 1|π) and p(σi = 0|π) denote the probability of sampling individuals who have been truly infected or not. The distributions of the quantita- tive test measures of control and case sera are derived from the observations of known cases and controls. The units of U can be anything that is commonly used in serological tests, such PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 13 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 Fig 7. Conceptual diagram of the distribution of the quantitative test measures for control and case sera. (A) Hypothetical probability density of quantitative test measures of control sera and three possible case sera distributions. (B) ROC-curves corresponding to the distribution of quantitative test measures of the control sera and each of the possible distributions for the case sera. (C) Visualization of the ‘maximal Youden’ and ‘high specificity’ cutoffs. (D) Visualization of the ‘maximal Youden’ and ‘high specificity’ cutoffs in the ROC curves. https://doi.org/10.1371/journal.pcbi.1008728.g007 Fig 7. Conceptual diagram of the distribution of the quantitative test measures for control and case sera. (A) Hypothetical probability density of quantitative test measures of control sera and three possible case sera distributions. (B) ROC-curves corresponding to the distribution of quantitative test measures of the control sera and each of the possible distributions for the case sera. (C) Visualization of the ‘maximal Youden’ and ‘high specificity’ cutoffs. (D) Visualization of the ‘maximal Youden’ and ‘high specificity’ cutoffs in the ROC curves. Cutoff-based methods For the cutoff-based methods, the quantitative test measures are dichotomized into seroposi- tives and negatives using a cutoff. There are many ways to estimate a cutoff value for a test [31, 32]. One strategy is to set the cutoff such that the test is highly specific (99%) (see Fig 7C). This is equivalent to minimizing the number of false positives. This will go at the cost of the sensi- tivity and will lead to more false negatives. This method is referred to as the ‘high specificity’ method throughout this study. Another method that is often used to determine the cutoff is to maximize the Youden index (Youden index = sensitivity + specificity −1 [33]) (see Fig 7C). Graphically, this is equivalent to maximizing the distance between the diagonal and the receiver-operator characteristic (ROC) curve (see Fig 7D). This method is referred to as the ‘max Youden’ method throughout this study. To estimate the cumulative incidence in the data with a cut-off based method, the binomial cumulative incidence estimate q is corrected for the sensitivity and specificity of the test. The standard correction is described by Rogan and Gladen [8]: p ¼ q þ s 1 r þ s 1 : ð2Þ ð2Þ Here, r is the sensitivity and s the specificity of the test, and π is the corrected estimator of cumulative incidence. Effectively, this correction adds the expected number of false negative and subtracts the expected number of false positives from the number of observed positives. The correction works best when the expected number of false positives is smaller than the observed number of positives. We apply this correction to the maximal Youden and the high specificity method and refer to it as the ad-hoc correction. An alternative way to account for the sensitivity and specificity of the serological test is by using a Bayesian approach which simultaneously estimates the cumulative incidence and the sensitivity and specificity of the serological test [12–14, 16, 30]. This is done based on the sero- survey data and the test validation data. Eq 3 provides the joint posterior distribution of these three parameters, as given in Larremore et al. [30]. The likelihood of the mixture model https://doi.org/10.1371/journal.pcbi.1008728.g007 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 14 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 as optical densities obtained from ELISAs or neutralization titers obtained in neutralization assays. Cutoff-based methods Here, X represents the serosurvey data, V the validation data, n+ the number of positive tests in the serosurvey data, Nfields the number of individuals in the serosurvey, Nneg the number of control sera, Npos the number of case sera, tp the number of true positives in the cases sera and tn the number of true negatives in the con- trol sera. We apply this method using the cut-offs calculated with the maximal Youden and the high specificity method. Prðp; s; rjX; VÞ /  ð1 s þ pðr þ s 1ÞÞ nþðs pðr þ s 1ÞÞ Nfieldsnþ  stnð1 sÞ Nnegtnrtpð1 rÞ Npostp: ð3Þ ð3Þ Simulations We simulate serosurveys by assuming given cumulative incidences and distributions of the quantitative test measures for control and case sera. For each virtual individual enrolled in these in silico serosurveys, we conduct a Bernoulli trial with the probability of success set to the chosen cumulative incidence. In a second step, we simulate the serological test of each PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 15 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 individual. To this end, we draw a random quantitative test measure from the distribution of either case or control sera—depending on whether the individual is truly seropositive or not. individual. To this end, we draw a random quantitative test measure from the distribution of either case or control sera—depending on whether the individual is truly seropositive or not. Besides the serosurvey, we also simulate data of known control and case sera. Unless oth- erwise specified we simulated 5, 000 control as well as case sera. For each of these 5, 000 con- trol and case sera we randomly drew a value from the assumed distribution. We assume the distribution of quantitative test measures for the control sera to be Γ-distributed with a shape and scale parameter of 1, which results in a mean of 1, and the distribution for case sera to be Γ-distributed with varying shape parameters and a scale parameter of 1. The scale parameter of the distribution for case sera determines the amount of overlap between the quantitative test measure of cases with controls, and thus modifies test accuracy as measured by AUC-ROC (Fig 7). Besides the serosurvey, we also simulate data of known control and case sera. Unless oth- erwise specified we simulated 5, 000 control as well as case sera. For each of these 5, 000 con- trol and case sera we randomly drew a value from the assumed distribution. We assume the distribution of quantitative test measures for the control sera to be Γ-distributed with a shape and scale parameter of 1, which results in a mean of 1, and the distribution for case sera to be Γ-distributed with varying shape parameters and a scale parameter of 1. The scale parameter of the distribution for case sera determines the amount of overlap between the quantitative test measure of cases with controls, and thus modifies test accuracy as measured by AUC-ROC (Fig 7). Simulations The simulated validation data are used to perform the estimation of the cumulative inci- dence with the methods described above. For the mixture model, we fitted a density distribu- tion through the control and case sera data with the function ‘density’ in R [34]. For the Rogen-Gladen correction, we use the simulated control and case sera to calculate the sensitiv- ity and specificity of the test. For the Bayesian method, we use the simulated control and case sera to include also the uncertainty in the sensitivity and specificity of the test in the cumulative incidence estimate. Power analysis To estimate the statistical power of a serosurvey, we conducted 3, 000 serosurveys for each given test accuracy and sample size. The power is determined as the proportion of simulations for which the cumulative incidence is estimated successfully. We define an estimate to be suc- cessful when it deviates less than 25% from the true cumulative incidence and the true cumula- tive incidence is within 2 standard deviations of the estimate. Confidence interval We suggest a two-step bootstrap procedure to calculate a confidence interval for the estimated cumulative incidence inferred with the mixture model and the ad-hoc corrected cutoff-based methods. First, we re-sample the test measures of control and case sera, and use the re-sampled dataset to obtain a new fitted density distribution for both the control and case sera. Second, we re-sample the test measures of the serosurvey, and, using the new density distributions of the test measures for the control and case sera, obtain bootstrap estimates of the cumulative incidence. This procedure makes sure that the uncertainties arising from the lack of test accuracy as well as the lack of precision in the test measure distributions are appropriately accounted for in the estimation of the cumulative incidence. An R-function that performs this procedure is included in the supplementary R-package. In the results, we compare the mixture model to a Bayesian implementation of the cutoff based methods that includes uncertainty in the sensitivity and specificity [15, 16]. These meth- ods provide credible intervals instead of confidence intervals. Implementation The likelihood function for estimating cumulative incidence as well as the simulations were implemented in the R language for statistical computing [34]. The Bayesian correction is implemented with the ‘Rstan’ package in R [35, 36]. An R-package containing the code can be found here: https://gitlab.ethz.ch/jbouman/pist. Supporting information S1 Fig. Sensitivity and specificity corresponding to the cutoff-based methods across the range of AUC-ROC values we consider in this study. (TIF) S2 Fig. Performance of the uncorrected cutoff-based methods. (A) Estimated cumulative incidence for three levels of true cumulative incidence. (B) Half of the 95% confidence inter- vals estimated based on the bootstrap method for both uncorrected cutoff-based methods. (TIF) Acknowledgments We are thankful to Claudia Igler, Christian Althaus, Sarah Kadelka and Michiel van Boven for discussions and comments on the manuscript. We are thankful to Claudia Igler, Christian Althaus, Sarah Kadelka and Michiel van Boven for discussions and comments on the manuscript. Incorporating distinct distributions for asymptomatic and severe case sera Eq 4 represents a likelihood that allows for the possibility that there are various types of case sera with distinguishable distributions (See Fig 5B) [23]. For the sake of simplicity, we assume that there are two types of case sera: those from individuals who underwent a severe infection (severe cases) and those from individuals who underwent an asymptomatic infection Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 16 / 19 PLOS COMPUTATIONAL BIOLOGY Cutoff-free approaches for the estimation of the cumulative incidence of SARS-CoV-2 (asymptomatic cases). (asymptomatic cases). asymptomatic cases). llðUÞ ¼ X i¼n i¼1 log  pðsi ¼ 2jpS; pAÞ pðUijsi ¼ 2Þ þ pðsi ¼ 1jpAÞ pðUijsi ¼ 1Þþ pðsi ¼ 0jpS; pAÞÞ pðUijsi ¼ 0Þ  ð4Þ llðUÞ ¼ X i¼n i¼1 log  pðsi ¼ 2jpS; pAÞ pðUijsi ¼ 2Þ þ pðsi ¼ 1jpAÞ pðUijsi ¼ 1Þþ ð4Þ pðsi ¼ 0jpS; pAÞÞ pðUijsi ¼ 0Þ  Compared to Eq 1, σi is now a categorical value that represents whether an individuals is sero- negative (0), seropositive due to an asymptomatic infection (1) or seropositive due to a severe infection (2). πA is the cumulative incidence of asymptomatic infections and πS the cumulative incidence of severe infections. This likelihood is formally equivalent to the one presented in van Boven et al [23], without the age-structure. We used the extended likelihood to estimate the total cumulative incidence, the cumulative incidence of asymptomatic cases and the shape parameter of the distribution of quantitative test measures of the asymptomatic case sera. The identifiability and confidence of the estimates of these three parameters depends on the amount of overlap between the distribution of the asymptomatic and severe case sera and the overlap between those and the control sera. In our simulations, we hold the area under the ROC-curve between the control and severe case sera constant, at a level of 1, while we vary the area under the ROC curve between the asymptomatic and severe case sera. We set the mean of the distribution of asymptomatic cases always to a lower value than that of the severe cases (see Fig 5B). Both these means are larger than 1, which is the mean of the distribution of test mea- sures for control sera. We use a scale parameter of 1 for both distributions. References 1. Johns Hopkins Center for Health Security. Global Progress on COVID-19 Serology-Based Testing Johns Hopkins Center for Health Security. 2020 Apr 13. 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Stan: A probabilistic pro- gramming language Journal of statistical software. 2017; 76. https://doi.org/10.18637/jss.v076.i01 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1008728 February 26, 2021 19 / 19
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Assessing the physical violence component of the Revised Conflict Tactics Scales when used in heterosexual couples: an item response theory analysis
Cadernos de Saúde Pública
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Correspondence M. E. Reichenheim Instituto de Medicina Social, Universidade do Estado do Rio de Janeiro. Rua São Francisco Xavier 524, 7o andar, Rio de Janeiro, RJ 20559-900, Brasil. michael@ims.uerj.br 1 Instituto de Medicina Social, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brasil. 2 Fundação Cesgranrio, Rio de Janeiro, Brasil. 53 ARTIGO ARTICLE 53 ARTIGO ARTICLE 53 ARTIGO ARTICLE Assessing the physical violence component of the Revised Confl ict Tactics Scales when used in heterosexual couples: an item response theory analysis Avaliando o componente de violência física da Revised Confl ict Tactics Scales quando usado em casais heterossexuais: uma análise via teoria de resposta ao item Michael E. Reichenheim 1 Ruben Klein 2 Claudia Leite Moraes 1 Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Abstract Although there are psychometric evaluations of the Revised Conflict Tactics Scales (CTS2) when applied to heterosexual relationships, none has used item response theory (IRT). To address this gap, the present paper assesses the instrument’s physical violence subscale. The CTS2 was ap- plied to 764 women who also responded for their partners. Single dimensionality assump- tion was corroborated. A 2-parameter logistic IRT model was used for estimating location and discriminating power of each item. Differential item functioning and item information pattern along the violence continuum were assessed. Gender differences were detected in 3 out of 12 items. Item coverage of the latent trait spectrum indicated little information at the lower ends, while plenty in the middle and upper ranges. Still, depending on gender, some item overlaps and regions with gaps could be detected. Despite some unresolved problems, the analysis shows that the items form a theoretically coherent in- formation set across the continuum. Provided the user is aware of possible drawbacks, using the physical violence subscale of the CTS2 in heterosexual couples is still a sensible option. The increase in family violence has generated a growing body of research on the development of measurement tools, including the class of instru- ments known as Conflict Tactics Scales 1,2,3,4,5,6,7. These are based on ‘conflict theory’ and aim to identify strategies used by individuals to solve disagreements and impasses 8,9. The first instru- ment in the series (CTS1) was proposed in the late 1970s and sought to address any kind of violent relationship 10. Despite its encouraging evaluations over the years and successful use in at least 20 countries 3,11,12,13,14,15, a more re- fined instrument was subsequently developed for dealing exclusively with intimate partner vio- lence. The Revised Conflict Tactics Scales (CTS2) was presented in 1996 and consists of 39 items forming five scales, namely negotiation (6 items), psychological aggression (8 items), physical vio- lence (12 items), sexual coercion (7 items), and injury (6 items) 13. The CTS2 has been studied since its release. Results show acceptable reliability, validity, and a factor structure in tune with the underlying the- ory 13,16,17,18,19. However, when focusing on inti- mate partner violence in heterosexual couples, such psychometric evaluations have exclusively used classical test theory 20. In order to address this gap, the aim of the present paper is to pro- vide a more in-depth item analysis than is pos- sible with traditional psychometric procedures. Domestic Violence; Questionnaires; Reliability and Validity Statistical analysis p g g As a first development of this more detailed scrutiny of the CTS2 applied to heterosexual couples, the present article focuses solely on the physical violence subscale. Three main issues are examined: (1) gender differences, assessing whether the items display similar properties re- gardless of the perpetrator (the woman versus her male partner); (2) the ability of items to differ- entiate between individuals/couples possessing different levels of the violence trait, both in terms of their location along the construct continuum and their discriminating capacity; and (3) the ex- tent to which items provide useful and reliable in- formation about intimate partner violence along the violence continuum, which implies search- ing for possible item gaps or redundancies along the spectrum. An important assumption under- lying the appropriateness of the item response theory models used here is also addressed, i.e., to replicate previous studies indicating that the scale on physical violence is effectively measur- ing a single dimension 24. However, unlike pre- vious studies, full information factor analysis is employed to deal with the dichotomous nature of test items 25. As a first step, one-factor and two-factor full in- formation factor analyses 25 were conducted to determine the extent to which a single latent de- pendence factor accounted for a common vari- ance among items. The solution used tetrachoric matrices and was implemented in TESTFACT 29. Differential item functioning was evaluated to address how the items behaved between genders 24. The method used here follows Thissen et al. 30. The procedure uses a 1-parameter logistic (1PL) item response theory model and aims to detect interactions between gender and the item loca- tion parameters (bi). These indicate at what level of the latent variable an item is able to differen- tiate between a positive and negative response, and equals the latent score (θs) at which half the respondents answer positively to the item. The 1PL model predicting the probability of endorse- ment for person on item is defined as Differential item functioning was evaluated to address how the items behaved between genders 24. The method used here follows Thissen et al. 30. Abstract Domestic Violence; Questionnaires; Reliability and Validity Reichenheim ME et al. 54 54 Because item response theory techniques offer more insight than those of classical test theory, more refined issues may be addressed such as examining the properties of individual items in order improve the scale’s efficiency and reliability in mapping the full continuum of intimate part- ner violence 20,21. Although there are two other studies about the Conflict Tactics Scales using item response theory, one evaluates an adapted edition of the CTS2 to measure physical violence in the context of male same-sex relationships 22, while the other relates exclusively to the CTS1 23. Moreover, little is known about the relative con- tribution and efficiency of the CTS2 constituent items in capturing the range of violence severity according to specific subgroups of interest. This issue also deserves attention since it is desirable for a scale to be group-independent in order to have breadth and general expediency. From an empirical perspective, insofar as possible the role played by each component item should be in- variant with respect to age, gender, and so on. 764 couples. The physical violence subscale is part of a formally adapted Portuguese version of the CTS2 27,28. Items refer to the respondent (woman) and by proxy in relation to her male partner or ex-partner. The recall period covers 6 to 9 months, depending on gestational age. Item contents are presented in the first table of the Re- sults section. Complete wordings can be found in Straus et al. 13. Readers are referred to Moraes et al. 27 for the complete Portuguese version. The study was formally approved by the Re- search Ethics Committee of the Rio de Janeiro Municipal Health Department in conformance to the principles embodied in the Declaration of Helsinki. Participation in the study followed free informed consent. Confidentiality of infor- mation was guaranteed. All the women received orientation on where to seek help if they felt it was necessary. Statistical analysis p P(Xis = 1 | θs , bi) = 1 (1) 1 + {exp (bi – θs)} P(Xis = 1 | θs , bi) = P(Xis = 1 | θs , bi) = 1 (1 (1) Recognizing that the present analysis takes women’s responses as “reference” and regards partners as the “focus” group 31, the procedure involves calculating d = bi(p) – bi(w), d = b*i(p) – bi(p) and ∆i = b*i(p) – bi(w), where bi(w) and bi(p) are the means of all location estimates for women and partners, respectively; b*i(p) are the individual ad- justed estimates regarding the second group; and ∆i are the differential item functioning estimates obtained by subtracting the effectively estimated parameters for women from the adjusted b*i(p) values. Standard normal test statistics were used to assess the significance of ∆i. Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Reichenheim ME et al. 54 Methods Generally, the dif- ference between the -2log(likelihood)s associ- ated with each model is given by G2diff = G2(1PL) – G2(2PL), which is distributed as a chi-square with df = df(1PL) – df(2PL). Since in the present data G2diff = 5386.070 – 5333.460 = 52.61 and df = 14, p = 0.0001. Acknowledging three items with differential item functioning, the main item response theory estimates are shown in Table 3. Standard errors are relatively small for both types of estimates, even for item 11 that had relatively few subjects endorsing it and the least satisfactory fit (last column). All but item 11 and item 1 for partners present discriminations (ai) above 2.0. The root mean square-fit statistic was used to explore item fit 24,32. This statistic is given by 2 2 1 RMS( ) ( ) / N i si s z z N = = , where zsi is the standard- ized residual defined as ( ) ( ) [ ] si si i s si z x p V x q = and, in turn, xsi is the observed status of subject s on item i (either 0 or 1). The variance of xsi is V[xsi] = pi(θs) (1 – pi(θs)), pi(θs) being the model-derived conditional probability of a subject s endorsing an item i calculated from the parameters esti- mated in Equation 2. Values of 2 RMS( ) iz outside the range of -2 to +2 may indicate that the overall item fit is questionable. The “steepness” of each item may be better examined in Figure 1, which shows the ICC ob- tained from the fitted estimates. In addition, the curves convey the item coverage of the latent trait spectrum, indicating that there is very little, if any, information below θs = – 1. This is expected since the mean of θs is approximately zero and there are not many positive responses to the items. The third main goal, namely to examine the amount of item information along the violence continuum, was addressed through the test in- formation 24. Methods The present study is subsidiary to a hospital- based case-control study exploring the relation- ship between violence within families of pregnant women and premature childbirth. Further details of the study population and field procedures may be found in Reichenheim & Moraes 26. The effec- tive sample used in the present analysis includes Once the items involving differential item functioning were uncovered, a 2-parameter lo- Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 AN ITEM RESPONSE THEORY ANALYSIS OF THE CTS2 55 55 total variance is accounted for by the first factor, whereas the second “explains” less than 7%. An even more striking pattern is found for partners. gistic (2PL) model was considered for the main item response theory analysis. The 2PL model is given by g y P(Xis = 1 | θs , bi) = 1 (2) 1 + {exp (ai (bi – θs))} The differential item functioning results are in Table 2. Three items present differential func- tioning (i-1, i-8, and i-9) as judged from the sta- tistical significance of the ∆i estimates. Note that negative values emerge when the adjusted loca- tion estimates for the “focus” group (b*i(p)) are lower than those for the “reference” group (b*i(w)), a situation following a lower endorsement fre- quency in the latter. Thus, from a psychometric standpoint, a negative value indicates that a given act captures a higher level of the trait (violence) when perpetrated by women. Concentrating on the statistically significant differential item func- tioning items, this is the case for beating up (i-8) and grabbing the other (i-9). Conversely, throwing something that may hurt (i-1) is less common in men than in women, which entails a higher θs when carried out by the former. { p ( i ( i s))} where bi and θs are defined in equation (1) and ai represents item discrimination. Larger values of ai correspond to steeper item characteristic curves (ICC), indicating that an item is discriminating increasingly well between levels of the construct. Items with differential item functioning include separate bi and ai estimates for each gender group, while those not involving differential item functioning are common to both. The choice of a 2PL model was based on a formal comparison with the 1PL model using a likelihood ratio test of statistical significance 30. Methods In a 2PL model, this is given by 1 ( ) ( ) I s s i TI I q q = = , which is a function of the in- formation curve for item i at trait level θs, i.e., ( ) 2 ( ) ( ) 1 ( ) s i i s i s I a P P q q q = . Note that, since TI (θs) = 1/(SE(θs))2 24, this is also an indicator of the in- strument’s precision at θs. A similar picture is expressed by the location estimates presented in Table 3 (second column) extending from b3 = 1.060 to b11 = 3.503, and more markedly, by the gender specific information functions (curves) shown in Figure 2. Notice that information peaks at θs = 1.6 for women and θs = 1.7 for partners. The item response theory analysis was carried out in BILOG-MG 31. Item response curves shown in Figures 1 and 2 were obtained in Stata 8.2 33. Figure 2 also displays the positioning of items along the violence continuum, where item over- laps and regions with gaps may be best inspect- ed. Irrespective of gender, there is some sparse- ness at the upper spectrum between i-6 and i-11, which adds to the previously alluded absence of information taking place at the lower ends. Con- versely, items 5, 7, and 12 tend to cluster in a very narrow region, precisely where information is most abundant. Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Results Table 1 provides the factor structure of the sub- scale. Irrespective of perpetrator, the full infor- mation factor analysis indicates that almost all loadings are above 0.6 in model A and in the first factor of the two-factor B model. Focusing on the woman as perpetrator, nearly two-thirds of the Besides those “common” aspects, some fea- tures also emerge as a consequence of differential item functioning. Focusing on the three items, b1 and b8 are much farther apart than b9, the first Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Reichenheim ME et al. 56 Table 1 (type of perpetrator) and sorted by appearance in the original form. Women Partners Model A Model B Model A Model B Item * f1 f1 f2 f1 f1 f2 i-1: Threw something that could hurt (7/8) 0.746 0.745 0.193 0.744 0.743 0.143 i-2: Twisted arm or hair (9/10) 0.619 0.619 0.167 0.846 0.845 0.084 i-3: Pushed or shoved (17/18) 0.819 0.832 0.361 0.863 0.864 0.176 i-4: Used a knife or gun (21/22) 0.725 0.727 –0.182 0.854 0.865 –0.365 i-5: Punched/Hit with something (27/28) 0.796 0.792 0.033 0.946 0.945 0.064 i-6: Choked the other (33/34) 0.890 0.890 –0.173 0.941 0.939 –0.014 i-7: Slammed against the wall (37/38) 0.833 0.829 0.034 0.814 0.817 0.204 i-8: Beat up the other (43/44) 0.826 0.832 0.279 0.940 0.937 0.012 i-9: Grabbed the other (45/46) 0.639 0.637 –0.105 0.809 0.807 –0.035 i-10: Slapped the other (53/54) 0.850 0.846 0.012 0.908 0.905 0.018 i-11: Burned or scalded on purpose (61/62) 0.569 0.604 –0.637 0.637 0.660 –0.502 i-12: Kicked the other (73/74) 0.790 0.789 –0.136 0.893 0.892 0.117 Eigenvalue 7.013 7.068 0.773 8.749 8.782 0.505 Percent of variance 59.9 61.8 6.4 74.1 76.6 4.1 * O d i f ll th i th E li h diti f th CTS2 i hi h it h i l i l d l l d th f th th Table 2 Table 2 Differential item functioning estimates (∆i). Items sorted by appearance in the original form. Differential item functioning estimates (∆i). Items sorted by appearance in the original form. Results Item ∆i * z ** p value i-1: Threw something that could hurt 0.727 (0.220) 3.305 0.001 i-2: Twisted arm or hair -0.462 (0.256) 1.805 0.071 i-3: Pushed or shoved 0.146 (0.102) 1.431 0.152 i-4: Used a knife or gun 0.270 (0.383) 0.705 0.481 i-5: Punched/Hit with something 0.012 (0.140) 0.086 0.932 i-6: Choked the other -0.108 (0.363) 0.297 0.766 i-7: Slammed against the wall -0.145 (0.163) 0.890 0.374 i-8: Beat up the other -0.644 (0.226) 2.850 0.004 i-9: Grabbed the other -0.290 (0.116) 2.500 0.012 i-10: Slapped the other -0.076 (0.104) 0.731 0.465 i-11: Burned or scalded on purpose 0.614 (0.713) 0.861 0.389 i-12: Kicked the other -0.042 (0.171) 0.246 0.806 * In brackets: standard errors (s.e. (∆i) ); ** z = |∆i / s.e. (∆i)| between i-12 and i-2, and another between the latter and i-4. between i-12 and i-2, and another between the latter and i-4. two estimates clearly occupying different areas of the spectrum according to gender. Further gaps or overlaps are thus especially discernible among women. In contrast to the distribution among partners (men), i-1 and i-9 tend to occupy the same area forming a new cluster along with i-10; i-8 now clutters the already crowded region filled in by i-4 and i-6; while two gaps are left open, one two estimates clearly occupying different areas of the spectrum according to gender. Further gaps or overlaps are thus especially discernible among women. In contrast to the distribution among partners (men), i-1 and i-9 tend to occupy the same area forming a new cluster along with i-10; i-8 now clutters the already crowded region filled in by i-4 and i-6; while two gaps are left open, one Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 * Ordering follows the appearance in the English edition of the CTS2 in which items on physical violence are randomly placed among those of the other subscales and items pertaining to respondents and partners as perpetrators receive consecutive numbers 13. The original numbering system is provided in brackets pearance in the English edition of the CTS2 in which items on physical violence are randomly placed among those of the other ning to respondents and partners as perpetrators receive consecutive numbers 13. The original numbering system is provided Discussion Note that this result is central to what follows, since a single dimensionality of a scale being scrutinized is essential to render item response theory interpretable 24. residual confounding if included in a model as a confounder 39,40. Further research could identify items to fill this gap. Note that this result is central to what follows, since a single dimensionality of a scale being scrutinized is essential to render item response theory interpretable 24. Several gaps and item overlaps also occur along the continuum where information is avail- able. Besides, the item distribution pattern is somewhat distorted by differential item function- ing, especially for women. While not markedly in- fluencing the information curves (Figure 2), some redundancies are still found. One may thus argue whether certain items might need refinement or replacement or should even be withdrawn alto- gether. Of course, precisely which items is a mat- ter for debate and future investigations. All item slopes were reasonably large, indi- cating that the items discriminate well between levels of the construct. Most ICC tend to cover about one unit interval of the qs (violence con- tinuum). This is indicative that the majority of subjects endorsing a given item are quite similar in their underlying latent-trait. The same trend has been found in other studies on the CTS using item response theory 22,23. Between partners, the effect of differential item functioning is more on the ordering of items than on distribution along the continuum. While there is a fairly even spread, an apparent incon- sistency vis-à-vis the theoretically expected item build-up may be spotted, which, incidentally, is preserved among women. Anticipated at the lower end, item 1 (threw something that could hurt) now occupies the middle range of the spec- trum. The same “misplacement” was found by Regan et al. 22 studying same-sex male partners. One may conjecture that, although representing a more “trivial” act for women, the item has an- other meaning for men, tending to be performed mostly by those “bearing” higher violence levels in this group. Another idea to explore is that the act is culturally “feminine” in essence and is sim- ply less used by men (whether violent or not). This is also true for the mapping of items along the violence continuum 22,23, which, with- out further qualification, seems to be quite rea- sonable. Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Discussion The present study supports a single-factor solution for the physical abuse scale of the CTS2. Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 AN ITEM RESPONSE THEORY ANALYSIS OF THE CTS2 57 Table 3 Table 3 2-parameter logistic (2PL) model estimates, including separate bi and ai for three items presenting gender differentials (DIF). Sorted by increasing intensity of violence (bi). Item * bi ** ai ** 2 RMS( ) iz *** i-3: Pushed or shoved 1.060 (0.038) 3.012 (0.182) 0.574 i-9: Grabbed the other (P) 1.133 (0.085) 2.184 (0.193) 0.589 i-9: Grabbed the other (W) 1.325 (0.058) 2.692 (0.246) 0.697 i-1: Threw something that could hurt (W) 1.409 (0.069) 2.360 (0.223) 0.735 i-10: Slapped the other 1.429 (0.039) 3.847 (0.354) 0.471 i-5: Punched/Hit with something 1.686 (0.059) 3.236 (0.310) 0.516 i-7: Slammed against the wall 1.821 (0.066) 3.695 (0.400) 0.426 i-12: Kicked the other 1.857 (0.079) 2.513 (0.224) 0.629 i-8: Beat up partner (P) 2.018 (0.109) 3.246 (0.488) 0.346 i-2: Twisted arm or hair 2.204 (0.119) 2.032 (0.196) 0.710 i-1: Threw something that could hurt (P) 2.366 (0.206) 1.722 (0.224) 0.703 i-4: Used a knife or gun 2.567 (0.161) 2.273 (0.285) 0.576 i-8: Beat up the other (W) 2.592 (0.211) 3.500 (0.797) 0.313 i-6: Choked the other 2.759 (0.190) 2.965 (0.532) 0.445 i-11: Burned or scalded on purpose 3.503 (0.409) 1.968 (0.384) 0.923 * Items with DIF identifi ed according to perpetrator. In brackets: W – women; P – partners (men); ** In brackets: standard errors; *** Item root mean square fi t statistic. 2-parameter logistic (2PL) model estimates, including separate bi and ai for three items presenting gender differentials (DIF). Sorted by increasing intensity of violence (bi). Even if this finding agrees with several previous reports 16,17,18,22,23,28,34,35,36, it has the strength of being based on a full information factor analysis. Even if this finding agrees with several previous reports 16,17,18,22,23,28,34,35,36, it has the strength of being based on a full information factor analysis. Even if this finding agrees with several previous reports 16,17,18,22,23,28,34,35,36, it has the strength of being based on a full information factor analysis. Note that this result is central to what follows, since a single dimensionality of a scale being scrutinized is essential to render item response theory interpretable 24. Even if this finding agrees with several previous reports 16,17,18,22,23,28,34,35,36, it has the strength of being based on a full information factor analysis. Discussion Still, a few points require some thought, since this mapping does not happen along the entire range, given that information on violence is confined exclusively to the upper half of the spectrum. As a result, moderately violent sub- jects may go unnoticed in practice. Failure to detect violence-positive individuals can have public health consequences if incipient cases that could escalate in the future are missed. In addition, from an epidemiological research per- spective, misclassifying couples as “negatives” could lead to the attenuation of risk measures if the variable is the target exposure 37,38 or to Reichenheim ME et al. 58 Figure 1 Common item characteristic curves (ICC) for items without differential item functioning (DIF) (a); Common item characteristic curves (ICC) for items without differential item functioning (DIF) (a); Common item characteristic curves (ICC) for items without differential item functioning (DIF) (a); -1 0 1 2 3 4 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1 (b) Proportion endorsement Violence continuum -1 0 1 2 3 4 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1 (a) Proportion endorsement Violence continuum -1 0 1 2 3 4 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1 (c) Proportion endorsement Violence continuum -1 0 1 2 3 4 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1 (d) Proportion endorsement Violence continuum 3 10 5 7 12 2 4 6 11 1 (women) 1 (partners) 8 (women) 8 (partners) 9 (women) 9 (partners) -1 0 1 2 3 4 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1 (a) Proportion endorsement Violence continuum 3 10 5 7 12 2 4 6 11 -1 0 1 2 3 4 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1 (b) Proportion endorsement Violence continuum 1 (women) 1 (partners) Violence continuum Violence continuum -1 0 1 2 3 4 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1 (d) Proportion endorsement Violence continuum 9 (women) 9 (partners) -1 0 1 2 3 4 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1 (c) Proportion endorsement Violence continuum 8 (women) 8 (partners) (d) (c) Violence continuum At any rate, according to the present study the component items are definitely not gender-invari- ant. Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Discussion While acknowledging that the acts allegedly perpetrated by partners were obtained by proxy responses and that spousal consensus on the CTS scales may not always be optimal 41,42,43,44, the very presence of differential item functioning can raise concern. Depending on gender, the same enactment may indicate different levels of vio- lence, whether factual or related to a given item idiosyncrasy. Regardless, the ramification is that an item may not be grasping the same intensity of violence. This is particularly important if the use of raw scores is foreseen in practice because a given count may not actually correspond to iden- tical levels of the construct being tapped. From a psychometric perspective, such a discrepancy detracts from the scale’s “universality”, which recognizably is a quite desirable (if not essential) property of any measurement tool. Several issues are worth considering when as- sessing the present findings. First, one can con- tend that the results emerge in a different cul- tural milieu than that of the instrument’s original development (USA), thus potentially limiting the generalizations. However, as indicated in the methods section, the CTS2 version employed here underwent a careful cross-cultural adapta- tion 27,28 based on strict procedural guidelines 45,46. Even so, given the instrument’s widespread use, it would be interesting to have more studies using item response theory models replicated on the scales of the original CTS2 in English, as well as on other versions besides Portuguese. AN ITEM RESPONSE THEORY ANALYSIS OF THE CTS2 59 59 Figure 2 Positioning of items along the violence continuum and information region by gender (type of perpetrator). Women Partners qs qs -1 0 4 5 1 2 3 -1 0 4 5 1 2 3 grabbed (i-9) pushed and shoveed (i-3) threw something (i-1) beat up (i-8) grabbed (i-9) threw something (i-1) beat up (i-8) burned or scalded (i-11) choked (i-6) used a knife or gun (i-4) twisted arm or hair (i-2) kicked (i-12) slapped (i-10) punched/hit (i-5) slammed against the wall (i-7) Partners Another important point when generalizing the findings is that the present study was restrict- ed to pregnancy. This not only implies a shorter recall period than the usual 12 months, but may also be portraying an atypical situation. Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Resumo Ainda que existam avaliações psicométricas da Re- vised Conflict Tactics Scales (CTS2) quando aplicada a casais heterossexuais, nenhuma usou o método de Teo- ria de Resposta ao Item (TRI). Preenchendo essa lacu- na, este estudo examina a subescala de violência física do instrumento. A CTS2 foi aplicada a 764 mulheres que também respondiam pelos seus companheiros. A assunção de unidimensionalidade foi corroborada. Utilizou-se um modelo logístico de 2 parâmetros para estimar a localização e capacidade discriminante dos itens. Avaliou-se o funcionamento diferencial destes, bem como padrão de informação ao longo do con- tínuo de violência. Detectou-se diferenciais de gênero em três dos 12 itens. A cobertura dos itens relativa ao espectro do traço latente indicou pouca informação nos segmentos inferiores, mas plena no centro e nos superiores. Todavia, dependentes de gênero, algumas superposições e lacunas puderam ser detectadas. A despeito de alguns problemas detectados, mostrou-se que os itens formam um conjunto coerente ao longo do contínuo. Desde que o usuário esteja ciente dos pos- síveis problemas, usar a subescala de violência física da CTS2 em casais heterossexuais continua sendo uma opção sensata. M. E. Reichenheim participated in all phases of the study (fundraising/administration; theoretical develo- pment; field work, data processing, and analysis; and drafting the paper as first author). R. Klein was invol- ved in designing the paper’s theoretical and statistical framework, as well as collaborating in the analysis and final versions. C. L. Moraes participated in the fundrai- sing/administration, fieldwork, data processing, and drafting of the paper. Discussion Although this still has to be confirmed, one can envisage certain events (items) happening more often out- side of pregnancy, and as a consequence, item response theory results showing better coverage of the instrument along the violence continuum. It should be born in mind that bi is also a func- tion of the endorsement proportion, the more frequent the item, the lower the respective es- timate 24. Again, the research program on the CTS2 would gain from further studies using item response theory models applied to data from a general heterosexual population, which thus far has surprisingly never been done. In addition to the suggestions made so far, an interesting development would be to conduct a more refined evaluation of the CTS2 using item responses coded into more than two categories. Noting that each level bears its own discriminat- ing power and position in ordered-response item Reichenheim ME et al. 60 response theory models 47, identifying those with good psychometric properties could help reduce the total number of component items and ulti- mately improve the instrument’s operational ca- pability. Readers should be reminded that if used in its current full edition (78 items), application of the CTS2 in one sitting is tiresome for all con- cerned, even if responses are limited to dichoto- mous answers. the physical abuse subscale and effectively serve as a useful complement rather than merely “one more” tool in the early detection of intimate part- ner violence. Despite the limitations noted above and some still untapped questions, the item response the- ory analysis reported here shows that the CTS2 items on physical violence define a one-dimen- sional trait and form a theoretically coherent information set across the continuum, at least where there is actual coverage. Provided the user is aware of some possible gender discrepancies and that not all empirically negative cases are necessarily void of violence, use of the physical violence CTS2 subscale in heterosexual relation- ships is still a sensible option. As emphasized previously, this study is the first in a series aiming to explore the component scales of the CTS2 applied to heterosexual cou- ples using item response theory methods. Thus, further studies are needed to examine the other subscales, particularly psychological aggression. A more in-depth scrutiny of this subscale might shed light on the violence spectrum missed by Contributors Violência Doméstica; Questionários; Confiabilidade e Validade Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Reichenheim ME et al. 0 References 1. Kashani JH, Daniel AE, Dandoy AC, Holcomb WR. Family violence: impact on children. J Am Acad Child Adolesc Psychiatry 1992; 31:181-9. 20. Nunnally JCJ, Bernstein I. Psychometric theory. New York: McGraw-Hill; 1995. 21. Wilson M. Constructing measures. An item re- sponse modeling approach. Mahwah: Lawrence Erlbaum Associates; 2005. 2. Heise L, Pitanguy J, Germain A. Violence against women: the hidden health burden. Washington DC: The World Bank; 1994. 22. Regan KV, Bartholomew K, Oram D, Landolt MA. Measuring physical violence in male same-sex relationships: an item response theory analysis of the Conflict Tactics Scales. J Interpers Viol 2002; 17:235-52. 3. Straus MA, Gelles RJ. Physical violence in Ameri- can families: risk factors and adaptations to vio- lence in 8145 families. New Brunswick: Transac- tion Publisher; 1995. 4. Gelles RJ. Intimate violence in families. London: Sage Publications; 1997. 23. Schafer J. Measuring spousal violence with the Conflict Tactics Scale. Notes on reliability and va- lidity issues. J Interpers Viol 1996; 11:572-85. 5. Carlson BE. Children exposed to intimate part- ner violence: research findings and implications for intervention. Trauma Violence Abuse 2000; 1: 321-42. 24. Embretson SE, Reise SP. Item response theory for psychologists. Mahwah: Lawrence Erlbaum Asso- ciates; 2000. 6. Krug EG, Dahlberg LL, Mercy JA, Zwi AB, Lozano R. World report on violence and health. Geneva: World Health Organization; 2002. 25. Bock RD, Gibbons RD, Muraki E. Full-information factor analysis. Appl Psychol Meas 1988; 12:261-80. 26. Reichenheim ME, Moraes CL. A comparison between the abuse assessment screen and the Re- vised Conflict Tactics Scales for measuring physi- cal violence during pregnancy. J Epidemiol Com- munity Health 2004; 58:253-7. 7. Waters H, Hyder A, Rajkotia Y, Basu S, Rehwinkel JA, Butchart A. The economic dimensions of inter- personal violence. Geneva: Department of Injuries and Violence Prevention, World Health Organiza- tion; 2004. 27. Moraes CL, Hasselmann MH, Reichenheim ME. Adaptação transcultural para o português do instrumento “Revised Conflict Tactics Scales (CTS2)” utilizado para identificar a violência entre casais. Cad Saúde Pública 2002; 18:163-75. 8. Simmel G. Conflict and the web of group affilia- tions. New York: The Free Press; 1955. 9. Adams BN. Coercion and consensus theories: so- me unresolved issues. Am J Sociol 1965; 71:714-6. 10. Straus MA. Measuring intra-familiar conflict and violence: the conflict tactics (CT) scales. J Marriage Fam 1979; 41:75-88. 28. Moraes CL, Reichenheim ME. References Cross-cultural mea- surement equivalence of the Revised Conflict Tac- tics Scales (CTS2) Portuguese version used to iden- tify violence within couples. Cad Saúde Pública 2002; 18:783-96. 11. Archer J. Assessment of the reliability of the con- flict tactics scales: a meta-analytic review. J Inter- pers Viol 1999; 14:1263-89. 29. Wilson D, Wood R, Gibbons RD. TESTFACT: test scoring, item statistics, and item factor analysis. Mooresville: Scientific Software; 1984. 12. Straus M. Handbook for the Conflict Tactics Scales (CTS). Durham: Family Research Laboratory, Uni- versity of New Hampshire; 2000. 30. Thissen D, Steinberg L, Wainer H. Detection of DIF using the parameters of item response models. In: Holland PW, Wainer H, editors. Differential item functioning. Hillsdale: Lawrence Erlbaum Associ- ates; 1993. p. 67-113. 13. Straus MA, Hamby SL, Boney-McCoy S, Sugarman DB. The revised Conflict Tactics Scales (CTS2): de- velopment and preliminary psychometric data. J Fam Issues 1996; 17:283-316. 31. Zimowski MF, Muraki E, Mislevy R, Bock RD. BI- LOG-MG for Windows 3.0. Lincolnwood: Scientific Software International; 2002. 14. Barnett OW, Miller-Perrin CL, Perrin R. Family vio- lence across the lifespan: an introduction. London: Sage Publications; 1997. 15. Hasselmann MH, Reichenheim ME. Adaptação transcultural da versão em português da Conflict Tactics Scales Form R (CTS-1), usada para aferir violência no casal: equivalências semântica e de mensuração. Cad Saúde Pública 2003; 19:1083-93. 32. Masters GN, Wright BD. The essential process in family of measurement models. Psychometrika 1984; 49:529-44. 33. StataCorp. Stata Statistical Software/SE, Release 8.2. College Station: Stata Corporation; 2004. 16. Newton RR, Connely CD, Landsverk JA. An exami- nation of measurement characteristics and facto- rial validity of the Revised Conflict Tactics Scale. Educ Psychol Meas 2001; 61:317-35. 34. Barling J, O’Leary KD, Jouriles EM, Vivian D, Mace- wen KE. Factor similarity of the Conflict Tactics Scales across samples, spouses, and sites: Issues and implications. J Fam Viol 1987; 2:37-54. 17. Lucente SW, Fals-Stewart W, Richards HJ, Goscha J. Factor structure and reliability of the Revised Conflict Tactics Scales for incarcerated female sub- stance abusers. J Fam Viol 2001; 16:437-50. 35. Moffitt TE, Caspi A, Krueger RF, Magdol L, Margo- lin G, Silva PA, et al. Do partners agree about abuse in their relationship? A psychometric evaluation of interpartner agreement. Psychol Assess 1997; 9:47-56. 18. Jones NT, Ji P, Beck M, Beck N. The reliability and validity of the revised conflict tactics scale (CTS2) in a female incarcerated population. Acknowledgements This project received funding from the Conselho Na- cional de Desenvolvimento Científico e Tecnológi- co (CNPq), grant 663073/9987 (PRONEX Project) and the Fundação Carlos Chagas Filho de Amparo à Pes- quisa do Estado do Rio de Janeiro (FAPERJ), grants E-26/171.223/98 and E-26/150.893/99. M.E.R. is partia- lly funded by CNPq, grant 300234/94-5. Violência Doméstica; Questionários; Confiabilidade e Validade Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 AN ITEM RESPONSE THEORY ANALYSIS OF THE CTS2 61 References Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 References J Fam Issues 2002; 23:441-57. 36. Cascadi M, Avery-Leaf S, O’Leary KD, Slep AMS. Factor structure and convergent validity of the Conflict Tactics Scale in high school students. Psy- chol Assess 1999; 11:546-55. 19. Straus MA. Cross-cultural reliability and validity of the Revised Conflict Tactics Scales: a study of university student dating couples in 17 nations. Cross-Cult Res 2004; 38:407-32. 37. Wacholder S. When measurement errors correlate with truth: surprising effects of nondifferential misclassification. Epidemiology 1995; 6:157-61. Cad. Saúde Pública, Rio de Janeiro, 23(1):53-62, jan, 2007 Reichenheim ME et al. 2 62 38. Dosemeci M, Wacholder S, Lubin JH. Does non- differential misclassification always bias a true ef- fect toward the null value? Am J Epidemiol 1990; 132:746-8. 44. O’Leary KD, Arias I. Assessing agreement of re- ports of spousal abuse. In: Hotaling GT, Finkelhorn D, Kirkpatrick JT, Straus MA, editors. Family abuse and its consequences: new directions in research. Newbury Park: Sage Publications; 1989. p. 218-27. 39. Greenland S, Robins JM. Confounding and mis- classification. Am J Epidemiol 1985; 122:495-506. 45. Herdman M, Fox-Rushby J, Badia X. A model of equivalence in the cultural adaptation of HRQoL instruments: the universalist approach. Qual Life Res 1998; 7:323-35. 40. Blettner M, Sauerbrei W. Influence of model-build- ing strategies on the results of a case-control study. Stat Med 1993; 12:1325-38. 46. Behling O, Law KS. Translating questionnaires and other research instrument: problems and solu- tions. Thousand Oaks: Sage Publications; 2000. 41. Browning J, Dutton D. Assessment of wife assault with the Conflict Tactics Scale: using couple data to quantify the differential reporting effect. J Mar- riage Fam 1986; 48:375-9. 47. van der Linden WJ, Hambleton RK. Handbook of modern item response theory. New York: Springer; 1996. 42. Edleson JL, Brygger MP. Gender differences in re- porting of battering incidences. J Appl Fam Child Stud 1986; 35:377-82. Submitted on 02/Mar/2005 Final version resubmitted on 28/Sep/2005 Approved on 07/Nov/2005 Submitted on 02/Mar/2005 Final version resubmitted on 28/Sep/2005 Approved on 07/Nov/2005 43. Jouriles EN, O’Leary KD. Interspousal reliability of reports of marital violence. J Consult Clin Psychol 1985; 53:419-21.
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Propuesta metodológica para la gestión de la sostenibilidad empresarial mediante el Balance Scorecard
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1 PROPUESTA METODOLOGICA PARA LA GESTION DE LA SOSTENIBILIDAD EMPRESARIAL MEDIANTE EL BALANCED SCORECARD Ricardo Chalmeta∗, Sergio Palomero, Grupo Integración y Re-Ingeniería de sistemas Universitat Jaume I, Campus Riu Sec s/n, 12071 Castellón, Spain Abstract: Cada vez mas las organizaciones tienden a tener en cuenta en sus diferentes modelos de gestión los conceptos de sostenibilidad económica, social y medioambiental. Si bien es cierto que desde el momento en que se detectó esta necesidad se han realizado diferentes aportaciones teóricas tendentes a orientar a las organizaciones en las actuaciones que deberían seguir para ello, el desarrollo de herramientas para su implementación apenas ha evolucionado, detectándose una importante carencia en esta área. Ante esta circunstancia, el objetivo de este paper es dar respuesta a la cuestión que se plantean muchas organizaciones preocupadas por los temas de sostenibilidad: ¿Cómo pueden integrar en sus modelos de gestión los conceptos sociales y medioambientales?. En este sentido y dada la falta de definición de un marco metodológico práctico que permita a las diferentes organizaciones poder implementar en su gestión diaria éstos conceptos, en este artículo se pretende enriquecer una de las herramientas más conocidas y utilizadas en el entorno empresarial como es el Balanced scoredcard (BSC), mediante la utilización de la metodología del caso aplicada a diversas organizaciones con el fin de obtener lo que se podría denominar un Sustainable Balanced Scorecard (SBSC), cuadro de mando en el que estén implícitos los conceptos considerados en la denominada sostenibilidad empresarial. 1.- Introducción El turbulento entorno en el cual está inmersa la sociedad actual caracterizada por la globalización de los mercados y por una necesaria reconsideración del denominado “estado del bienestar”, obliga a las organizaciones a revisar profundamente algunos paradigmas que hasta ahora se consideraban perfectamente asumidos para su correcto funcionamiento. En este sentido, los cambios en las exigencias de los clientes, que en la actualidad consideran como un valor más el respeto del entorno medioambiental, o la necesidad de superar la crisis de confianza generada por las actuaciones éticamente incorrectas de algunas organizaciones, hacen necesario que desde el mundo empresarial se consideren aspectos que tal como indica Lantos (2001)1, deben ir más allá del clásico modelo económico de maximización de los beneficios para sus accionistas. Como consecuencia, se están proponiendo nuevos modelos de gestión socioeconómicos (Freeman, 19842; Carrol, 19793) en los que además de los aspectos de rentabilidad económica, se consideran en la gestión diaria de las organizaciones nuevas dimensiones de trabajo como son el impacto medioambiental y social de la organización. Este concepto se ha venido a denominar indistintamente sostenibilidad empresarial o Responsabilidad Social Corporativa (RSC) y puede definirse como “la ∗ Corresponding author: Ricardo Chalmeta, Universitat Jaume I, Av. de Vicent Sos Baynat, s/n. 12071 Castelló de la Plana. Spain, Tel:+34.964.728329, Fax: +34964728435, rchalmet@uji.es 2 integración voluntaria de las preocupaciones sociales y medioambientales en las operaciones comerciales de las empresas y en sus relaciones con sus stakeholders. De forma amplia es definida como un concepto con arreglo al cual las empresas deciden voluntariamente contribuir al logro de una sociedad mejor y un medio ambiente más limpio” (CEC, 2001)4. Realmente, el concepto de sostenibilidad empresarial o RSC no es nuevo. De hecho durante más de 30 años, tal como indicó Friedman (1970)5, academics and practitioners han debatido para determinar en qué medida las empresas tienen una responsabilidad para mejorar su desempeño ambiental y social, y los costes y beneficios que suponen estas actuaciones, concluyendo que existe cierta complementariedad entre los objetivos económicos y los sociales y medioambientales (Collins et al. 2007)6. No obstante, la consideración definitiva del concepto RSC en la estrategia empresarial se ha producido en la última década, experimentando un interés creciente por parte de las organizaciones. Desde esta perspectiva, la gestión de la sostenibilidad se puede considerar como una actividad estratégica que puede reportar importantes beneficios a la organización. Así, Simpson y Kohers (2002)7 defienden que la integración de la RSC mejora el rendimiento de la empresa, lo cual desencadena un incremento de las ventas debido a una mayor fidelización de los clientes Maignan (2001)8, con la consiguiente mejora de la imagen de la empresa Smith (2003)9. Sin embargo, la integración de la RSC en los modelos de gestión organizacionales es en muchas ocasiones más superficial que efectiva (Figge et al., 2002)10, limitándose a responder a presiones externas para incorporar sistemas de gestión medioambiental pero sin incluir todos los aspectos que implica la RSC (Deegan, 2002)11. Una de las causas fundamentales de esta falta de integración es el desconocimiento por parte de las empresas de cómo abordarla desde un enfoque holístico y de falta de herramientas de soporte (Figge et al. (2001a12, 2001b13). Si bien no existe ninguna herramienta metodológica unánimemente aceptada desarrollada para ayudar a las organizaciones en la implementación y control de los diferentes conceptos de la RSC, una de las más adecuadas para integrar los conceptos de sostenibilidad con la gestión de la empresa es el Balanced Scorecard (BSC) desarrollado por Kaplan y Norton en 199614. El BSC provee de “a framework that translates strategy into action” organizado en torno a cuatro perspectivas (Financiera, Clientes, Procesos y Formación). En la formulación del BSC, los objetivos e indicadores de rendimiento de todas las perspectivas se deducen de unos objetivos estratégicos a largo plazo en un proceso top-down. Esta estructura jerárquica del BSC garantiza que todas las actividades de negocio estén alineadas con la implementación de la estrategia de negocio. Esta característica del BSC, unida a su relativa sencillez a la hora de gestionar los intangibles de la empresa, se puede utilizar también para la gestión de los conceptos de sostenibilidad (Figge et al. 2002). Adicionalmente, tal como indican Epstein y Roy (2001)15, para implementar las estrategias de sostenibilidad, los managers necesitan conocer perfectamente las decisiones a considerar para mejorar el performance así como sus consecuencias. Esto requiere un cuidadoso análisis de los indicadores del rendimiento (key drivers performance), de su cuantificación y de su grado de alineamiento con los objetivos, y para ello la herramienta adecuada sigue siendo el BSC. En este sentido, existen pocos trabajos de investigación realizados sobre el uso del BSC en la implementación de las dimensiones de sostenibilidad en la gestión estratégica de las organizaciones. Las principales propuestas realizadas referentes al 3 uso del BSC para la gestión de la sostenibilidad se pueden resumir en los siguientes planteamientos: 1. Integración de los conceptos sociales y medioambientales en las perspectivas clásicas del BSC (Epstein, 199616; Jhonson, 199817; Deegen, 200118; Figee et al., 2002). En este planteamiento se propone incorporar objetivos que integren alguna componente de ámbito social o medioambiental en cada una de las cuatro perspectivas clásicas del BSC. 2. Incorporación en la Perspectiva de Cliente (Jhonson, 1998)19. Este planteamiento incorpora los conceptos sociales y medioambientales a través de la perspectiva de cliente pasando a denominarla “Clientes y stakeholders externos” incluyendo objetivos de carácter interno y externo y definiendo la denominada Línea estratégica transversal a las cuatro perspectivas existentes. 3. Definición de una nueva perspectiva (Figee et al., 2001a, 2001b). Se plantea la incorporación de una nueva perspectiva independiente que recoja los objetivos relacionados con las dimensiones de sostenibilidad. Este planteamiento únicamente se deberá abordar si los aspectos sociales o medioambientales son considerados críticos para la organización. 4. Definición de un nuevo BSC que considere únicamente las dimensiones de sostenibilidad (Kaplan y Norton, 200120; Figee et al., 2002). Este planteamiento depende del nivel estratégico de las dimensiones social y medioambiental, siendo considerado por algunos autores como una extensión de las alternativas 1 y 3. Sin embargo, existen pocos ejemplos prácticos de cómo implementar una adecuada gestión de la sostenibilidad usando el BSC. En este sentido, comprender como individual companies have gone about adopting BSC comos soporte para la gestión de la sostenibilidad is important. The lessons learned from this understanding should be useful in promoting the adoption of sustanability by managers around the world. Con el objeto de facilitar a las empresas la gestión de la RSC apoyándose en un SBSC (Sustainable Balanced Scorecard), en este paper se realiza un estudio exploratorio sobre las experiencias obtenidas por 16 organizaciones a las que se les propone agregar a sus planteamientos estratégicos las dimensiones de sostenibilidad ecológica y social y gestionarlos mediante el BSC. Los resultados obtenidos permiten identificar aspectos claves en el proceso metodológico de utilización del Sustainable Balanced Scorecard (SBSC) como una herramienta para integrar la RSC en la gestión de la empresa. Como metodología de investigación se utiliza la metodología cualitativa del estudio del caso Yin (1994)21 . El artículo se estructura del siguiente modo. En la sección primera se ha presentado el marco conceptual de referencia y las principales líneas de investigación existentes para la implementación de los conceptos de sostenibilidad sobre un BSC clásico. En la sección dos se muestra el planteamiento metodológico seguido para realizar el trabajo de investigación. En la sección tres se presentan los resultados obtenidos del estudio realizado sobre diversas organizaciones con el objetivo de obtener un marco metodológico para implementar un Cuadro de Mando Sostenible (SBSC). Por último, la sección cuarta muestra las conclusiones y discusión de los resultados. 2.- Metodología de investigación 4 La metodología de investigación seguida en este trabajo para definir un marco metodológico que permita la gestión de la sostenibilidad soportada por el BSC, se basa en el estudio del caso aplicado a 16 organizaciones. La selección de los casos se ha realizado buscando una representación equilibrada de las diferentes características de las empresas como tamaño de las organizaciones, pertenencia al sector público o privado, sector industrial o de servicios, con acreditaciones de calidad o sin ellas, etc. El objetivo es conseguir que los resultados del estudio consigan la denominada “saturación” de la teoría, permitiendo la replicabilidad y la extensión a otros casos individuales (Eisenhardt, 1991)22 y por lo tanto, tratando de ofrecer, como indican Denzin y Lincoln (1994)23, una mayor oportunidad de aprendizaje. Dentro de la metodología de investigación basada en el estudio del caso, en este trabajo se ha seguido el planteamiento metodológico propuesto por Orlikowski (1993)24. Inicialmente se parte de un marco metodológico teórico (en este trabajo es la teoría clásica del BSC) que a partir de un proceso iterativo de análisis y recogida de datos (la implementación del BSC para la gestión de la sostenibilidad en cada organización), permite obtener un resultado final (el enriquecimiento de la teoría inicial del BSC logrando una metodología para la implementación de un SBSC). El plan de trabajo seguido se organiza en siete etapas y se basa en el análisis inductivo de datos cualitativos (Yin, 1994: 102), adaptado a los planteamientos de Walsham (1995) para el enriquecimiento de una teoría existente: 1. Definición de Propósitos, objetivos y preguntas de la investigación. 2. Definición del contexto conceptual, perspectivas. Revisión de la literatura. Modelo Teórico Propuesto. 3. Identificación de las unidades de análisis. Selección de Casos. 4. Definición de Métodos y Recursos de la investigación. 5. Trabajo de campo. Toma de datos, triangulación y clasificación de la información. 6. Planteamiento de la Metodología mejorada. 7. Verificación del rigor y calidad del estudio. A continuación se muestran los resultados obtenidos en cada etapa. 3.- Diseño Metodológico del Estudio del Caso. 3.1.- Definición de Propósitos, objetivos y preguntas de la investigación. Tal como ya se planteó al principio de este trabajo, el objetivo es dar respuesta a la cuestión que se plantean muchas organizaciones preocupadas por los temas de sostenibilidad: ¿Cómo pueden integrar en sus modelos de gestión los conceptos sociales y medioambientales?. O dicho de otra forma: ¿Qué herramientas están a la disposición del mundo empresarial para realizar esta implementación?. Lamentablemente, a día de hoy, la respuesta a esta pregunta es que apenas existe un marco metodológico real y practico que sirva como herramienta de trabajo para que las organizaciones puedan integrar en su gestión conceptos como la RSC. 5 El objetivo de este trabajo es brindar al entorno empresarial una herramienta que sirva de guía para poder realizar esta implementación de una forma estructurada en base al BSC. 3.2.- Definición del contexto Conceptual, perspectivas. Revisión de la literatura y propuestas. Modelo Teórico Propuesto. En esta etapa, inicialmente, the literature related to this line of research was reviewed and the results of different research projects related with the gestión de la sostenibilidad, especialmente apoyandose en el BSC were analyzed. In that way, clear vision and better understanding about the topic was obtained. Posteriormente se definió el marco teórico que se aplicaría a las diferentes empresas con el objetivo de enriquecerlo. El marco teórico se basa en el balanced scorecard de Kaplan y Norton. El objetivo es definir un conjunto de indicadores que organizados en diferentes perspectivas permitan medir el resultado de las decisiones tomadas para alcanzar unos objetivos previos. Para obtener el balanced scorecard se deben seguir una serie de fases (figura 1). Inicialmente, en la fase 1 se deberá definir el alcance del proyecto y la estructura organizativa de dirección y control de la cual deberán formar parte los especialistas de las diferentes áreas sobre las que se implementará el proyecto. Las principales tareas a realizar en esta etapa previa serán las siguientes: • • • • • Creación de equipos para el desarrollo del proyecto BSC. Realización de seminarios de formación para la elaboración e implantación del proyecto. Elaboración y comunicación del Plan del Proyecto. Establecimiento de los mecanismos de control de calidad. Elaboración del plan para el cambio. 6 FASE 1 Planificación del Proyecto Alcance, Equipos y Plan del Proyecto FASE 2 Definición del marco empresarial Misión, Visión, Valores y Estrategias. CSF Diseño del Cuadro de Mando Estratégico FASE 3 Definición de Objetivos, Metas y Mapa Estratégico Diseño del Sistema de Indicadores estratégicos Definición de Perspectivas FASE 4 Diseño y Mejora de Procesos AS-IS Æ TO-BE Plan de Mejora de Procesos FASE 5 Despliegue del Sistema de indicadores A nivel operativo por las unidades de negocio Establecer relaciones causa-efecto FASE 6 Validación del BSC Comportamiento de Indicadores Auditoría de Indicadores Implantación del BSC BSC Estratégico BSC Táctico FASE 7 Recursos Humanos „ „ „ BSC Operacional Formar equipos lideres Impulsar la implantación del BSC Toma de decisiones Tecnología de la Información Control y Seguimiento del BSC FASE 8 Reajuste de indicadores Figura 1. Marco teorico para el desarrollo de un BSC. Una vez definida la estructura y responsabilidades del proyecto, se deberá analizar y definir su misión, visión, valores, estrategia organizacional y el entorno de la empresa, su situación interna, cultura y estructura organizacional, identificando los factores críticos para el éxito de la empresa y consolidando los equipos formados en la fase previa (Fase 2). A continuación, en la Fase 3, se deberá estructurar el cuadro de mando a nivel estratégico, definiendo los objetivos estratégicos, metas y el mapa estratégico, y diseñando a continuación el sistema de indicadores que permita su control en cada una de las perspectivas básicas de trabajo que pueden ser, por ejemplo, las definidas por Kaplan y Norton (1996) (financiera, de clientes, de procesos y de formación). En la Fase 4 se deberá abordar mediante el análisis de la situación de partida (AS-IS) el re-diseño y mejora de procesos de negocio claves para llegar a la situación deseada (TO-BE). En la Fase siguiente (Fase 5) se deberá realizar el despliegue del conjunto de objetivos e indicadores para las diferentes unidades de negocio, departamentos o procesos, y estableciendo las relaciones causa-efecto. El BSC obtenido deberá ser validado por los managers (Fase 6). A continuación, en la Fase 7 se implementará el BSC en la organización utilizando dos pilares básicos: el 7 Sistema Informático de soporte al BSC, integrado con los sistemas de información de la empresa; y el entrenamiento y aprendizaje de los Recursos Humanos para comprender el BSC diseñado. Una vez implementado el BSC, éste ofrecerá la información adecuada para valorar el grado de cumplimiento los objetivos establecidos. En la última fase (Fase 8), se deberá diseñar un conjunto de políticas y procedimientos que permitirán el control y seguimiento del BSC. Para ello, de forma periódica, según los ciclos de medición establecidos en cada nivel, se deberá verificar y evaluar la correcta implantación del BSC, monitoreando el sistema en tiempo real mediante los indicadores obtenidos y llevando a cabo los ajustes y mejoras pertinentes mediante la preparación de un plan de reevaluación periódica del proyecto. 3.3.- Identificación de las unidades de análisis. Selección de Casos. Tomando este marco teorico como punto de partida del estudio y siguiendo los planteamientos realizados por Walsham (1995) sobre la generalización de una teoría desde una investigación interpretativa de los casos de estudio mediante una visión de enriquecimiento (“Rich insight”), se va a aplicar dicho marco teorico a 16 organizaciones proponiendoles integrar las dimensiones de sostenibilidad en sus diferentes modelos de gestión utilizando el BSC. Del análisis interpretativo de los diferentes casos se pretende obtener una metodología que sirva de herramienta de trabajo para las organizaciones que quieran integrar la RSC en sus modelos de gestión utilizando el BSC. El trabajo de investigación se llevó a cabo durante 18 meses, siendo la primera tarea realizada la selección de las organizaciones a las que se les tenía que aplicar la metodología del caso. Para ello se realizó una primera selección en las 120 empresas con las que nuestro grupo de investigación ha colaborado, de las que se preseleccionaron 43 empresas que podían ofrecer un mayor potencial de información válida para el propósito de la investigación. Entre las 43 organizaciones preseleccionadas se encontraban empresas de muy diferentes tamaños y actividad. El muestreo teórico sobre el que se realizó la selección se hizo tomando como base fundamental la predisposición de colaboración en la investigación y la capacidad potencial de generar el necesario enriquecimiento de la teoría de base. Adicionalmente, el grupo de investigación realizó una segunda selección de las diferentes organizaciones candidatas al estudio buscando además, el equilibrio entre los diferentes sectores de actividad (públicas o privadas, industriales o de servicios), número de trabajadores, normas de calidad implementadas, etc. con el fin de trabajar sobre una muestra representativa que abarcara al máximo el abanico de la actividad empresarial. Fruto de esta segunda selección de empresas se decidió trabajar con 16 organizaciones que cumplían todos los requisitos exigidos por el planteamiento de esta investigación. En la tabla 1 se muestra un resumen de las principales características de las empresas seleccionadas para el estudio del caso: Organiz . Sector Tipo Actividad Central o Delegación Nº de Delegaciones Nº de Trabajadores 1 Construcción Privada Viviendas Central No 60 2 Energético Pública M.P. Nucleares Central No 596 3 Mecánico Privada Tratamiento Superficies Delegación ‐ > 100 4 Construcción Pública Infraestruct. Central 52 14525 Certificado s de Calidad No ISO 14001 ISO 9001 ISO 14001 ISO 9001 OHSAS 18001 ISO 14001 8 Infraestruct. Ferroviarias 5 Sanitario 6 Servicios 7 8 Servicios Servicios Privada Subcontr. Publica Privada Subcontr. Publica ONG Privada 9 Sanitario Privada 10 Servicios Privada 11 Servicios ONG 12 Servicios Privada 13 Alimentación Privada 14 Construcción Privada 15 Servicios 16 Sanitario ISO 9001 GRI A+ Atención Primaria Central 34 1014 Atención al cliente Delegación ‐ 150 Central Central No 5 12 1100 Central 20 3558 Inmobiliaria Central 14 45 Serv. sociales Telecomunicac iones Derivados lácteos Delegación 10 68 Delegación 170 1500 Serv. sociales Hostelería Atención medica Modelo EFQM No No GRI 3 ISO 14001 ISO 9001 ISO 14001 ISO 9001 No ISO 14001 ISO 14001 ISO 9001 ISO 14001 ISO 9002 OHSAS Delegación 5 2180 Vivienda Unifamiliares Central 7 263 Privada Organiz. Eventos Central No 15 No Publica Atención Primaria Central 248 34006 ISO 14001 ISO 9001 OHSAS 18001 Tabla 1. Características de las empresas participantes en el estudio Tal como recomienda Yin (1989:29), se seleccionó la utilización de múltiples fuentes de datos y por tanto el cumplimiento del principio de triangulación para garantizar la replicabilidad teórica de la investigación. Esto permitió verificar si los datos obtenidos a través de la aplicación a diferentes empresas guardaban relación entre sí, es decir, si desde los diferentes modelos de gestión de los casos analizados se observaba la convergencia de los efectos explorados hacia el objetivo de la investigación. Siguiendo el principio de triangulación, en este estudio se siguió el criterio de introducir en la Metodología BSC inicial aquellas propuestas coincidentes realizadas al menos por cuatro de las organizaciones participantes. 3.4.- Definición de Métodos y Recursos de la investigación. Tras la selección de las 16 organizaciones se preparó e inició el estudio de campo. Hay que indicar que las características de las diferentes organizaciones eran ya conocidas por el Grupo de Investigación IRIS. Es decir, se conocía su organización, sus instalaciones, sus productos y servicios, sus recursos tecnológicos tales como páginas web y además se disponía ya de evidencia documental de las mismas. Este conocimiento previo de las organizaciones seleccionadas permitió tomar un óptimo punto de partida de la investigación ya que se pudo reducir mucho las tareas de recogida de información y análisis que se deben realizar en un trabajo de campo. Independientemente de las consideraciones anteriores, para dar inicio a este trabajo de investigación, se realizaron entrevistas de presentación en cada una de las organizaciones, indicando las fases de la Metodología BSC a utilizar, los aspectos a trabajar sobre la RSC en cada una de ellas y el objetivo último del proyecto. La duración de cada una de estas reuniones fue de 120 minutos, realizándose en base a un protocolo de entrevistas semiestructuradas. Posteriormente se realizaron entrevistas de 60 minutos de duración con los responsables correspondientes de las áreas de RSC (cuando los había) o con los diferentes equipos directivos cuando las dimensiones de sostenibilidad o no estaban implementadas o no correspondían a un área determinada. Todas las entrevistas fueron grabadas en vídeo y transcritas para su posterior análisis detallado. 9 Para realizar todas las tareas de investigación se estructuraron grupos de trabajo mixtos formados por miembros del Grupo de Investigación IRIS y por componentes representativos de cada una de las organizaciones participantes. Su misión fue la toma de datos, el análisis de los mismos y su triangulación y análisis de resultados para otorgar validez a los mismos. Su trabajo se extendió a lo largo de las diferentes fases de implementación del método del caso, desde el planteamiento del mismo hasta la elaboración de las conclusiones, habiendo empleado para ello un total de 18 meses. 3.5.- Trabajo de campo. Toma de datos, triangulación y clasificación de la información. Una vez presentados los objetivos de esta investigación se realizó la correspondiente toma de datos consistente en obtener los resultados de la aplicación de la teoría de BSC para gestionar la sostenibilidad en cada una de las empresas. A continuación se estructuraron los datos que consistían en las diferentes propuestas de mejora realizadas sobre la teoria de BSC para gestionar la sostenibilidad. Como resultado se obtuvo una metodología BSC enriquecida por las diferentes aportaciones para implementar los conceptos de sostenibilidad. 3.6.- Planteamiento de la Metodología BSC mejorada. A continuación se presentan las principales mejoras aportadas por las diferentes organizaciones, estructuradas en base a las fases mostradas en la figura 1. FASE 0. PRELIMINAR: Como punto de partida para implementar los conceptos de sostenibilidad, se constató que las empresas participantes en esta investigación consideraban necesaria la implementación de una fase previa al inicio de la aplicación de la metodología de partida consistente en las tareas siguientes: FASE 0: Fase Previa Actividades de la metodología BSC NUEVA FASE (No propuesta en la metodología BSC Tradicional) Cambios y mejoras propuestos • • • • Adopción de un compromiso sostenible, claro y explícito por parte de la Dirección de la organización como agente social responsable. Identificación de los grupos de interés claves para la empresa. Comunicación: información y consultas previas con los grupos de interés identificados e indicando cómo va a afectar a la organización. Realización de estudios de Benchmarking. Tabla 2. Fase previa identificada en la investigación. Si bien algunos de los aspectos considerados en esta nueva fase, ya estaban indicados en la primera fase de la metodología BSC, los grupos de trabajo consideraron interesante que como paso previo al inicio propiamente dicho de la metodología, se identificasen explícitamente algunos aspectos tan importantes como el compromiso formal de la Dirección, la identificación e inicio de consultas con los que serán los principales stakeholders y la viabilidad del proyecto. FASE 1. Planificación del Proyecto. 10 Las principales mejoras propuestas en esta fase fueron las siguientes: Actividades de la metodología BSC Cambios y mejoras propuestos • • Creación de equipos para el desarrollo del proyecto. • • • • Alcance del proyecto. • • • Plan del proyecto. • • Crear Plan de Comunicación del proyecto. • • Creación de los Equipos de Proyecto incluyendo a los principales grupos de interés. Creación de un equipo de sostenibilidad y RSC e integración en el equipo de proyecto. Selección y sensibilización en temas de sostenibilidad y responsabilidad social de los equipos multidisciplinares. Designación de un responsable claro de cada equipo y de sus responsabilidades. Definición del plan de reuniones de seguimiento. Definición del ámbito del proyecto: áreas en donde se va a implantar, procesos a tratar, plazo temporal, estimación inicial de indicadores incluidos en el BSC. Determinación de los grupos de interés afectados por el desarrollo del proyecto, tanto directos como indirectos. Toma en consideración en el alcance del proyecto de aspectos sociales y medioambientales. Temporización el proyecto y concreción clara de los objetivos, las metas y lo criterios socialmente responsables. Redacción de un plan de proyecto conforme a la gestión orientada a procesos. Trasmisión del plan de comunicación para dar a conocer el proyecto desde el equipo directivo, resaltando su sensibilización en temas de sostenibilidad. Conseguir (a través de la difusión del proyecto de la organización entre todos los stakeholders) una percepción positiva de la organización, tanto de su público interno como externo. El plan deberá hacer hincapié en que la adopción de medidas de RSC influye de modo positivo en la organización e incidirá en que es un factor que contribuye a aumentar su competitividad. Tabla 3. FASE 1. Planificación del Proyecto Como principales mejoras propuestas en esta fase se pueden destacar la formación e integración de los expertos en RSC en los diferentes equipos de proyecto, la determinación del alcance del proyecto que se deberá extender hasta la consideración de aspectos sociales y medioambientales, y la definición de un plan de comunicación que consiga que todos sus destinatarios consideren los temas referentes a sostenibilidad como un beneficio para todos Los grupos de interés y como una oportunidad única para incrementar la competitividad. FASE 2. Diseño de Marco Empresarial. Actividades de la metodología BSC Cambios y mejoras propuestos 11 • • Misión, visión, valores, estrategia organizacional. • • • • Análisis interno y externo de la empresa. Matriz DAFO. • • • Identificación de los factores críticos para el éxito. • Los elementos integrantes de la Cultura Organizativa (Visión, Misión y Valores), recogerán de forma expresa aspectos relacionados con la RSC, fundamentados en la ética empresarial, de forma que el conjunto de valores éticos sea una importante herramienta para la toma de decisiones acorde con las metas y objetivos estratégicos. En esta fase se deberán definir objetivos identificados con el aspecto ambiental y social de la organización, yendo más allá de los tradicionales objetivos económicos. La visión y los valores deberán incorporar aspectos sociales y medioambientales, para que se pueda definir una estrategia de RSC. Fomentar conceptos de sostenibilidad en los Valores (actuación) y Visión (futuro). Concepto de Alineación, relacionada con la visión, que debe ser buena, realista y común para todos y que tenga en cuenta la propuesta de valor que se da al cliente. Se debe realizar un análisis de riesgos a partir del conocimiento de los stakeholders relevantes, sus impactos y sus expectativas. La estrategia de la organización estará apoyada en unos valores y se dirigirá hacia una visión que incluya aspectos sociales y ambientales, dando valor a las personas. Incluir en las debilidades y amenazas el Impacto Ambiental así como sus consecuencias. Se buscará la máxima integración y compatibilidad de los sistemas de gestión responsable existentes o en implantación: Modelos de calidad y excelencia empresarial (ISO 9000, EFQM), CSR Framework for EFQM, ISO 14001, SGE21, Pacto Mundial, Memorias GRI, OHSAS 18001, ... Sostenibilidad en el Medio y Largo Plazo Tabla 4. FASE 2. Diseño del Marco Empresarial. En esta Fase, en el análisis interno y externo a la organización, se deberán tener muy presentes todos los condicionantes que pudieran incidir sobre la sostenibilidad. Por otro lado, en la formalización de la Misión, la Visión y los Valores, debe existir una clara orientación hacia los conceptos fundamentales de la RSC. En cuanto a la definición de la estrategia organizacional, si bien el clásico BSC se centra casi exclusivamente en objetivos financieros, con esta nueva perspectiva del BSC (SBSC), la consideración de los aspectos sociales y medioambientales como objetivos estratégicos deberá primar sobre los clásicos objetivos económicos. De esta forma, se deberán identificar los factores críticos de éxito que estén relacionados con compromisos socialmente responsables. FASE 3: Diseño de Cuadro de Mando Estratégico Como resultado de la implementación de los conceptos de sostenibilidad en el diseño del BSC, en esta fase se obtuvieron las principales diferencias respecto a la metodología inicial ya que, si bien en las fases anteriores se fue siguiendo el esquema clásico propuesto con la inclusión de los diferentes aspectos relacionados con la sostenibilidad, en el desarrollo del cuadro de mando estratégico las diferentes organizaciones, al evidenciar la necesidad de considerar nuevas perspectivas contrastaron la validez de las diferentes propuestas metodológicas apuntadas por Kaplan y Norton (1997) e identificadas por Figge et al. (2002). Tomando como alternativas de actuación a las empresas las diferentes propuestas metodológicas, las propuestas de mejora recibidas fueron las siguientes: 12 Actividades de la metodología BSC Cambios y mejoras propuestos • • Perspectiva Financiera: • Perspectiva de Clientes: • • • Perspectiva de Procesos Internos: a)Procesos orientados al cliente b) Procesos de soporte • Se buscará la innovación permanente para la mejora de los procesos de soporte, bajo las cuatro dimensiones de gestión del cambio: innovación en el proceso, innovación en el producto, innovación tecnológica e innovación en la cultura de la organización. Ampliar el alcance de esta perspectiva (Formación) al ámbito genérico definido en los CMI: Formación y Desarrollo de las personas. Se trata de considerar a los integrantes de la organización ante todo como personas, superando el viejo esquema de “recursos humanos” para la producción. NUEVA PERSPECTIVA • La selección e implantación de las tecnologías se realizará siempre considerando sus impactos sociales, laborales y medioambientales. • Incluir los aspectos de diversidad e igualdad en el empleo, conciliación laboral, prácticas sociales, códigos éticos, promociones, carrera profesional, colaboraciones con asociaciones, administraciones públicas, filantropía, patrocinios inserción discapacitados, etc. • Se deberán incluir criterios medioambientales que tengan relevancia en los procesos de la organización y puedan influir en el entorno medioambiental. • Realización de encuestas con el fin de saber que alcance tiene la introducción de nuevas actuaciones (causa-efecto). Realización de análisis experimentales de la percepción de la gestión. Perspectiva de Tecnologías: Perspectiva Social / Laboral: Perspectiva Medioambiental: Realizar el mapa causaefecto. Se buscará la eficacia y eficiencia de los procesos orientados a los clientes, orientados a conseguir su máxima satisfacción La función de Compras, Contratación y Aprovisionamiento está actualmente muy poco desarrollada. Es recomendable profundizar en este aspecto. Procesos de RSC: • Evaluación y certificación de proveedores. • Gestión ética de la cadena de valor (ej. Auditorías de centros productivos) La función de Producción debería desarrollarse más en función del sector, la actividad de la organización y su tamaño. Procesos de RSC: - Marketing Responsable de Producto. Perspectiva de Formación: NUEVA PERSPECTIVA Se incluirán aspectos de RSC en la planificación del ciclo de vida de cada producto o servicio, desde su concepción y diseño hasta su puesta en el mercado, incluyendo el servicio post-venta y la recogida final del producto al final de su vida útil si procede. Se valorará la posibilidad de utilizar, adaptar o crear productos o servicios para aplicaciones sociales fuera del core del negocio. • • NUEVA PERSPECTIVA Se valorará la posibilidad de considerar criterios de inversión ética (ISR) en la gestión financiera de la organización. Se incorporarán criterios éticos en la gestión de tesorería, especialmente en la planificación de pagos a proveedores y contratas, y gestión de cobros a clientes. En caso necesario, se buscarán soluciones negociadas con proveedores, contratas y clientes para gestionar los flujos de tesorería de la forma más adecuada y eficiente. • Tabla 5. FASE 3. Diseño del Cuadro de Mando Estratégico. 13 Como puede observarse en la tabla anterior, las diez y seis organizaciones consideraron oportuno incrementar el número de perspectivas de análisis. Así, además de las perspectivas ya consideradas (Financiera, Clientes, Procesos, Tecnológica y Formación), para poder implementar en el BSC los requisitos de sostenibilidad se implementaron dos nuevas perspectivas Social/Laboral y Medioambiental con el objetivo, por un lado, de servir en beneficio del bienestar social y desarrollo cultural, y por otro lado, aumentar el compromiso de la organización en temas medioambientales. La consideración de estas dos nuevas perspectivas por parte de las empresas viene a corroborar la validez de los argumentos expuestos en el artículo de Figge et al. (2002) y la constatación de que, a nivel práctico, las organizaciones optaron, al menos en nuestro caso, por el aumento del número de perspectivas. Es posible que esta elección sea consecuencia de la consideración de los conceptos de sostenibilidad en todas las fases de la metodología propuesta. Como complemento al incremento de perspectivas de trabajo, las organizaciones de mayor entidad participantes en el estudio plantearon como interesante la posibilidad de incluir baterías de indicadores de RSC conocidos como pueden ser los del GRI o aplicar principios como los del Pacto Mundial. Una vez definidos los nuevos objetivos e indicadores se considera muy conveniente su comparación con los de las organizaciones similares que estén desarrollando las denominadas “best practices”. FASE 4: Diseño y Mejora de Procesos Actividades de la metodología BSC Cambios y mejoras propuestos • Análisis de los procesos. Modelo AS-IS. • • • Re-diseño de proceso. Modelo TO-BE. • • Determinar los procesos clave para el éxito. Plan de mejora de procesos. • Investigación de los procesos actuales, en los departamentos más críticos. Gestión, análisis y rediseño de los procesos conforme a estándares reconocidos: ISO 9001, ISO/TS 16949, ISO 14001, Reglamento EMAS y OHSAS 18001 o similares. La obtención de certificaciones en estas normas facilitaría la tarea de la gestión de indicadores. Análisis del impacto social y ambiental. Una vez detectadas las deficiencias, colaboración con la alta dirección de todos los stakeholders y del Equipo de Proyecto para plantear las mejoras oportunas. Implicación de todos los stakeholders implicados y los diferentes niveles de la organización. Sobre todo los que producen mejoras económicas, sociales y medioambientales. Los fundamentales en el negocio de la empresa, los que contribuyen a que exista. • Marcas hitos y controles de los avances estableciendo reuniones de control con los representantes de los diferentes grupos de interés. • Determinar claramente los objetivos y las metas. Tabla 6. FASE 4. Diseño y Mejora de procesos. El diseño y mejora de procesos deberá buscar la máxima eficiencia de los diferentes procesos de la organización circunscritos a las diferentes normativas de calidad ISO 9000, pero considera de aplicación necesaria su extensión a dos nuevas series de normas: 14 Como referencia a la nueva perspectiva social y laboral y buscando unos estándares que permitan mejorar las condiciones de trabajo, se deberán considerar las recomendaciones definidas en las series de normas OHSAS1 18000 como definición de estándares internacionales relacionados con la gestión de seguridad y salud ocupacional. Haciendo referencia a la nueva perspectiva medioambiental, serán de referencia las normas ISO 14000 como sistema de gestión medioambiental para asegurar el control y cumplimiento de gran número de requisitos legales relacionados con temas ambientales. El cambio fundamental incluido en esta fase es que además de considerar en los procesos de mejora continua los clásicos estándares identificados en la serie de normas ISO 9000, con la implementación de las nuevas normas se consigue incluir en los procesos de trabajo y en los requisitos de calidad los requerimientos definidos en las dos nuevas perspectivas. Una ventaja adicional al implementar estas nuevas normas es que la organización se compromete a su cumplimiento ya que al ser periódicamente auditables, requerirán su atención en las tareas del día a día. FASE 5: Despliegue del Cuadro de Mando por las unidades de negocio Actividades de la metodología BSC Cambios y mejoras propuestos Indicación de objetivos a cada stakeholder Control de los objetivos por tipología (económicos, sociales, medioambientales) Establecer indicadores de RSC: gestión de residuos, optimización del nivel de existencias, consumo energético, consumo de otros recursos limitados... • • Definición de indicadores a nivel operacional. • Realizar mapa causaefecto. • • Comprobar periódicamente los índices alcanzados o no, y analizarlos. Justificar la relación causa efecto. Tabla 7. FASE 5‐ Despliegue del Cuadro de Mando. Esta fase no presenta ningún cambio sustancial respecto de la presentada en la metodología inicial, salvo la consideración de los conceptos de RSC. FASE 6: Validación del Cuadro de Mando Actividades de la metodología BSC Análisis de comportamiento de indicadores de periodos anteriores con el BSC actual. 1 Cambios y mejoras propuestos • Ver comportamiento de indicadores correspondientes a periodos anteriores. Contrastar con indicadores de otras organizaciones (best practices) Serie OHSAS 18000, Occupational health and safety management systems – specification. (Directrices sobre Sistemas de Gestión de la Seguridad y Salud en el Trabajo). 15 • Auditoria de Indicadores • • Verificar la validez de los indicadores correspondientes a las nuevas perspectivas. Realizar estimaciones subjetivas. Los indicadores deben ser significativos para cada uno de sus nuevos objetivos y alcanzar a todos los stakeholders Deben ser relevantes, fiables, cuantificables y comparables en el tiempo. Tabla 8. FASE 6‐ Validación del Cuadro de Mando. Los cambios introducidos en esta fase se refieren a la validación de los indicadores detectados en las nuevas perspectivas consideradas. Esta verificación se deberá basar tanto en la validez de cumplimiento de los criterios definidos para su selección, como en su validez como apoyo en la toma de decisiones. Para comenzar a actuar sobre los indicadores de las nuevas perspectivas se deberán realizar estimaciones subjetivas de los mismos, estimaciones que se pueden cuantificar analizando indicadores similares de empresas del sector que destaquen por su modelo de gestión. Otro aspecto importante al realizar la auditoría de los nuevos indicadores es verificar si cubren todo el ámbito de stakeholders y si su implementación ayuda para poder realizar una mejor gestión de objetivos. FASE 7: Implementación del Cuadro de Mando Actividades de la metodología BSC Cambios y mejoras propuestos • Diseñar, implementar/parametrizar el software de BI. SISTEMA INFORMÁTICO • • Integrar la aplicación con los ERP y otros sistemas. • Seminarios de capacitación a los RRHH en el uso e interpretación del SI. Será preferible la homogeneidad de los ERP parametrizables, a las aplicaciones a medida. Implicar a todos los stakeholders en el nuevo sistema. • A realizar conjuntamente con personal interno y externo de la organización, lo cual evitará rechazos iniciales por parte de los usuarios finales. • Importante dar cobertura a los usuarios finales, durante las primeras pruebas e inicio del nuevo sistema informático. Implicación del departamento de RRHH, con la nueva gestión de la organización. “Plan de Gestión del Cambio”. Prueba del sistema. RRHH Optar por el software lo mas estándar posible siempre que considere aspectos de sostenibilidad. Implementar y parametrizar el software en todas las perspectivas. • Tabla 9. FASE 7‐ Implementación del Cuadro de Mando. Las principales mejoras detectadas por las diferentes organizaciones están en la línea de extender la metodología inicial hacia la consideración de todos los factores de sostenibilidad. En este sentido, la selección del sistema informático debe tener como premisa principal que soporte los diferentes procesos de negocio relacionados 16 con las nuevas perspectivas social/laboral y medioambiental. Por otro lado, en el área de recursos humanos se deberá elaborar e implantar el denominado “Plan de Gestión del Cambio” para poder crear una nueva cultura corporativa con un nuevo enfoque en los valores de la sostenibilidad. FASE 8: Control y Seguimiento Actividades de la metodología BSC Cambios y mejoras propuestos • • Preparación del plan de reevaluación periódica del proyecto. • • • • • • Monitoreo de la marcha del BSC. • • Necesariamente a realizar por personal externo, no involucrado en la organización. Auditorías ISO, OHSAS, etc. Control por parte de la empresa de la auditoría externa y acciones proactivas de aprendizaje de mejoras. Seguimiento y control del Cuadro de Mando Integral comunicando apropiadamente a los diferentes grupos de interés los resultados económicos, sociales y ambientales alcanzados. Evaluación periódica para identificar posibles actuaciones de mejora futuras. Toma de acciones en función del punto anterior: con elaboración de un Plan de Mejora. Reuniones periódicas con el Consejo de administración para valorar la aportación de los indicadores al cumplimiento de los objetivos estratégicos, y éstos a la sostenibilidad de la empresa. Medición de la satisfacción de los grupos de interés. Validación de la cadena de contactos de la empresa con los diferentes grupos de interés. Informar a los departamentos de la evolución de las nuevas estrategias de gestión. Elaboración y difusión del Triple Informe indicando el impacto de los resultados en cada uno de los aspectos: económico, social y medioambiental. Sería recomendable seguir las pautas marcadas para la elaboración de informes de RSC por organismos como el GRI. Tabla 10. FASE 8‐ Control y Seguimiento. En esta fase de la metodología se plantea que la reevaluación periódica del nuevo cuadro de mando se apoye en las diferentes metodologías de auditoría existentes para las nuevas perspectivas definidas. Así, si la auditoría de procesos se realizaba anteriormente mediante los estándares de la ISO 9000, la cumplimentación o no de los compromisos adquiridos en las nuevas perspectivas social y medioambiental se puede ir reevaluando periódicamente mediante los mecanismos previstos en las series de normas ISO 14000 y OHSAS respectivamente. Por otro lado el monitoreo de la marcha de nuevo BSC deberá considerar la consecución de objetivos relacionados con la sostenibilidad y la comunicación de los resultados a todos los stakeholders. 3.7.- Verificación del rigor y calidad del estudio Antes de finalizar la aplicación del estudio del caso en el enriquecimiento de la clásica teoría clásica de BSC se ha querido contrastar su validez y grado de confianza en los resultados obtenidos. Para ello, de entre los diferentes modelos existentes en la literatura de gestión, se ha seleccionado el modelo desarrollado por Yin (1998)25, basado en la verificación de cuatro pruebas para garantizar la confiabilidad y consistencia de investigaciones basadas en el estudio del caso. Estas pruebas 17 propuestas por Yin son las siguientes: la validez constructiva, interna, externa y la prueba de confiabilidad. En el desarrollo de esta investigación se ha ido contrastando el cumplimiento de cada una de estas pruebas ya que los trabajos se han llevado a cabo siguiendo escrupulosamente las fases definidas por la Propuesta de Diseño Metodológico del Estudio del Caso y mediante la triangulación tanto teórica como metodológica y de datos. Por otro lado, se ha realizado la comparación crítica sistemática entre las proposiciones estructuradas del modelo teórico de referencia y las obtenidas de las fuentes de evidencia a las que se aplicó la lógica replicante (estudios de casos múltiples) para la consecución de generalización analítica. Con estas premisas de actuación se puede concluir la validez y calidad del estudio realizado. 4.- Conclusiones. El planteamiento fundamental de este trabajo ha sido ofrecer al entorno empresarial una herramienta que les permitiera implementar los conceptos de sostenibilidad en su gestión del día a día y dando respuesta a la pregunta fundamental de la investigación: ¿Cómo pueden integrar en sus modelos de gestión los conceptos sociales y medioambientales?. Dado que las fuentes de datos han sido organizaciones reales y que la metodología para el desarrollo de la investigación se ha basado en el estudio del caso en 16 organizaciones de diferentes sectores y tamaños, fue fundamental la definición de un marco de trabajo que asegurara la validez del estudio. Para ello, como se ha podido contrastar durante todo este estudio, se ha trabajado dentro de una estructura que asegurara la validez del análisis de los casos, siguiendo cada una de sus fases y validando finalmente el rigor y calidad de la investigación. Como conclusión fundamental del presente estudio se puede indicar que partiendo de la Metodología clásica BSC, ampliamente contrastada en el entorno empresarial real y tomándola como estructura inicial de apoyo para la implementación de los conceptos de sostenibilidad en las organizaciones participantes en la investigación, se ha conseguido al menos una primera aproximación para la obtención de una herramienta de apoyo a la implementación de BSC considerando conceptos de sostenibilidad (SBSC, Sustainable Business Scorecard). Esta primera aproximación se puede considerar como el inicio de futuros trabajos de investigación que, siguiendo las pautas de rigor consideradas, pudieran contrastar su validez tanto en el entorno académico como en el empresarial (academics and practitioners) complementando en el primer caso la metodología propuesta mediante nuevas aportaciones teóricas que mejoraran los planteamientos de este estudio o analizando en el segundo caso un mayor número de organizaciones y sectores industriales que permitieran la validación del modelo propuesto para los mismos. References 1 Lantos, G.P. (2001), “The boundaries of strategic corporate social responsibility”, Journal of Consumer Marketing, 18(7), 595-630. 2 Freeman, R.E. (1984), “Strategic Management: A Stakeholder Approach”, Pitman Publishing Inc., Boston. 18 3 Carroll, A.B. (1979), “A three Dimensional Conceptual Model of Corporate Performance”, Academy of Management Review, 4(4), 497-505. 4 Commission of the European Communities (2001), Brussels COM(2001) 366. 5 Friedman, M. (1970). The social responsability of Business is to increase its profits. The New York Magazine, 13 September 1970. 6 Collins, E., Lawrence, S., Pavlovich, K. and Ryan, C. (2007). Business networks and the uptake of sustainability practices: the case of New Zealand. Journal of Cleaner Production. 15, 729-740. 7 Simpson, W.G. and T. Kohers (2002), “The Link between Corporate Social and Financial Performance Evidence from the Banking Industry”, Journal of Business Ethics, 35(2), 97109. 8 Maignan, I. (2001), “Consumers perceptions of Corporate Social Responsibilities: A Cross-Cultural Comparison”, Journal of Business Ethics, 30(1), 57-72. 9 Smith, N.C. (2003), “Corporate Social Responsibility: Whether or How?”, California Management Review, 45(4), 52-76. 10 Figee, F., Hahn T, Schaltegger S, Wagner M. (2002). The sustainability balanced scorecard – linking sustainability management to business strategy. Business Strategy and the Environment. 11, 269-284. 11 Deegan C, (2002), “The legitimising effect of social and environmental disclosures - a theoretical foundation”, Accounting, Auditing & Accountability Journal, Vol. 15 (3), pp. 281-311. 12 Figge F, Hahn T, Schaltegger S, Wagner M. (2001a). Sustainability Balanced Scorecard. Wertorientiertes Nachhaltigkeitsmanagement mit der Balanced Scorecard. Center for Sustainability Management: Lüneburg. 13 Figge F, Hahn T, Schaltegger S, Wagner M. (2001b). The Sustainability Balanced Scorecard – a tool for value- oriented sustainability management in strategy focused organisations. Conference Proceedings of the 2001 Eco-Management and Auditing Conference. ERP Environment: Shipley; 83–90. 14 Kaplan, R.S. and Norton, D.P. (1996) Translating strategy into action – the Balanced Scorecard. Harvard Business School Press, Boston. 15 Epstein M.J. and Roy MJ. (2001). Sustainability in Action: Identifying and Measuring the Key Performance Drivers. Long Range Planning 34, 585-604. 16 Epstein M.J. (1996). Measuring Corporate Environmental Performance: Best Practices for Costing and Managing an Effective Environmental Strategy. Irwin: Chicago, IL. 17 Johnson, S. D. (1998), Identification and Selection of Environmental Performance Indicators: Application of the Balanced Scorecard Approach, Corporate Environmental Strategy, vol. 5 (4), 35-41. 18 Deegen T. (2001). Ansatzpunkte zur Integration von Umweltaspekten in die ’Balanced Scorecard’. Center for Sustainability Management: Lüneburg. 19 Jhonson, S.D. (1998). Identification and Selection of Environmental Performance Indicators: Application of the Balanced Scorecard Approach. Corporate Environmental Strategy. 5 (4), 35-41. 20 Kaplan R, Norton D. (2001). The Strategy-Focused Organization: how Balanced Scorecard Companies Thrive in the New Business Environment. Harvard Business School Press: Boston, MA. 21 Yin, R.K. (1994). Case Study Research – Design and Methods, Applied Social Research Methods. Vol. 5, 2nd ed., Newbury Park, CA, Sage. 22 Eisenhardt, K.M. (1991). “Better stories and better constructs: the case for rigor and comparative logic”, Academy of Management Review, 16 (3), 620-7. 23 Denzin, N.K. y Y.S. Lincoln (1994), “Handbook of Qualitative Research”, Sage Publications, Thousand Oaks. 19 24 Orlikowski W.J. (1993) CASE tools as organizational change: investigating incremental and radical changes in systems development. MIS Quarterly 17(3), 309-340. 25 Yin, R.K. (1998). The Abridged Version of Case Study Research. Bickman, L. and Rog, D. J. (eds.): Handbook of Applied Social Research Methods, Sage Publications, Thousand Oaks, pp. 229-259.
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Microstructure and Mechanical Properties of Joints Depending on the Process Used
Materials
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13,101
Article Microstructure and Mechanical Properties of Joints Depending on the Process Used anisz 1,2 , Tomasz Machniewicz 3 , Sławomir Parzych 1, Grzegorz Je˙z 2, Leonid Dvorkin 4 k Hebda 1,* Dawid Stanisz 1,2 , Tomasz Machniewicz 3 , Sławomir Parzych 1, Grzegorz Je˙z 2, Leonid and Marek Hebda 1,* Dawid Stanisz 1,2 , Tomasz Machniewicz 3 , Sławomir Parzych 1, Grzegorz Je˙z 2, Leonid Dvorkin 4 and Marek Hebda 1,* 1 Faculty of Materials Engineering and Physics, Cracow University of Technology, Warszawska 24, y g g y y gy 31-155 Kraków, Poland; d.stanisz@wisniowski.pl (D.S.); slawomir.parzych@pk.edu.pl (S.P.) , ; p ( ); p y p p ( ) 2 Wi´sniowski Sp. z o.o. S.K.A., Wielogłowy 153, 33-311 Wielogłowy, Poland; g.jez@wisniowski.pl 4 Department of Building Materials Technology and Material Science, The National University of Water and Environmental Engineering, 11 Soborna St., 33028 Rivne, Ukraine; dvorkin.leonid@gmail.com * Correspondence: marek.hebda@pk.edu.pl; Tel.: +48-126283423 * Correspondence: marek.hebda@pk.edu.pl; Tel.: +48-126283423 Abstract: Today, numerous design solutions require joining thin-walled sheets or profiles as the traditional methods of welding with a consumable electrode in gas shielding, most often used in production processes, do not work well. The reason for this is that a large amount of heat is supplied to the joint, causing numerous welding deformations, defects, and incompatibilities. Moreover, the visual aspect of the connections made more and more often plays an equally crucial role. Therefore, it is important to look for solutions and compare different joining processes in order to achieve production criteria. The paper compares the properties of a 1.5 mm thick steel sheet joined by the manual and robotic MAG 135 and 138 welding process, manual and robotic laser welding, CMT welding with the use of solid or flux-cored wire, and butt welding. The macro- and microstructure, as well as the microhardness distribution of individual regions of the joints, were analyzed depending on the type of joining technology used. Furthermore, the mechanical properties of individual zones of joints were investigated with the use of a digital image correlation system. On the basis of the obtained test results, it was found that the joints made by the processes of manual laser welding and butt welding were characterized by a very regular weld shape, the smallest joint width, and greater grain refinement compared to other analyzed processes. Citation: Stanisz, D.; Machniewicz, T.; Parzych, S.; Je˙z, G.; Dvorkin, L.; Hebda, M. Microstructure and Mechanical Properties of Joints Depending on the Process Used. Materials 2022, 15, 5171. https:// doi.org/10.3390/ma15155171 Keywords: arc welding MIG/MAG; laser welding; Cold Metal Transfer; joining thin-walled steel materials; robotic welding; butt welding Keywords: arc welding MIG/MAG; laser welding; Cold Metal Transfer; joining thin-walled steel materials; robotic welding; butt welding Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Article Microstructure and Mechanical Properties of Joints Depending on the Process Used Moreover, this method was characterized by the narrowest zone of hardness increase, only 3 mm, compared to, e.g., a joint made in the process of robotic welding CMT, for which this zone was more than twice as wide. Furthermore, the heat- affected zone for the joints made in this way, in relation to the welds produced by the MAG 135/138 method, was, respectively, 2 and 2.7 times smaller. materials materials 1. Introduction Furthermore, the present trend observed is focused on solutions for the privacy of use, which can be obtained by reducing the translucency of fillings, for example, in fence systems. However, the use of classic components would result in a significant increase in the weight of the product, which, in turn, would necessitate the use of special fittings and more powerful drives. Therefore, it is necessary to reduce the cross-sections of the profiles used and the thickness of the sheets in order to minimize the weight of the product, as well as the operating and assembly costs. However, the aesthetics of individual products depends not only on the welding method used, but also on the process parameters, experience and knowledge of employees, the use of additional technological procedures, and even the sequence of connections. Another method of joining materials that is more often used in the industry is the laser welding process, with or without additional material. However, it should be noticed that due to the specific heat source, which is the laser beam, the welding process itself and the metallurgical processes taking place during welding are significantly different from the processes taking place in arc welding methods. As a consequence, the properties of welded joints will be different from those obtained when using conventional technologies [12–14]. One of the latest solutions in the field of laser welding is the dynamically developing devices for manual welding in recent years, which use a beam of laser radiation generated by sources with a power of 1kW to 2kW [5,15,16]. However, at the moment there is a lack of precise information regarding the safety of employees in the workplace equipped with this type of equipment. yp q p The processes of joining thin-walled steel materials can also be carried out using vari- ous resistance welding technologies [17,18]. This method is characterized by low operating costs and no need to use additional materials. As a result, welding does not cause signifi- cant changes in the chemical composition and metallurgical properties, while maintaining the mechanical properties. Additional advantages of the resistance welding processes are the speed of making connections, simplicity of the course, and the possibility of remote control. 1. Introduction Joining elements with a consumable electrode in arc welding Metal Inert Gas (MIG) or a consumable electrode in active gas Metal Active Gas (MAG) are leading methods in production processes. These methods enable high welding performance, easy inspection of the arc weld, the possibility of careful observation of the weld pool, the possibility of combining a wide range of materials, obtaining good mechanical properties of connections, and ease of mechanization and robotization of the welding process [1–4]. However, the traditional methods of MIG/MAG welding of steel materials with a thickness of less than 3 mm cause many technological problems. These are mainly related to the introduction of a large amount of heat to the welded joint, which can cause numerous welding deformations and distortions. Moreover, they can also lead to the formation of numerous welding spatters, Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). https://www.mdpi.com/journal/materials Materials 2022, 15, 5171. https://doi.org/10.3390/ma15155171 Materials 2022, 15, 5171 2 of 17 thus lowering the aesthetics of manufactured products and increasing the laboriousness of finish machining of the detail after welding [5]. Today, more and more often in various industries, e.g., automotive, household appli- ances, or fencing systems, there is a necessity of making permanent joints of thin-walled steel elements, either without or with various coatings. Due to the above, in order to eliminate the previously described issues that arise when welding thin-walled elements, new variants of MIG/MAG welding have been developed, such as Cold Metal Transfer (CMT), Cold Arc, or Surface Tension Transfer (STT) [6–8]. In comparison to classic methods, the low-energy welding process MIG/MAG lends itself to welding defects reduction, a significant reduction in the amount of welding spatters, reduction in the amount of total energy implemented to the joint during welding, and reduction in harmful pollutants emission and thereby the improvement of the working conditions. As a result, they shorten the time and labor consumption of the production process and reduce cost-consuming technological procedures [9–11]. In addition, currently, the quality, precision, and aesthetics of welded joint designing are becoming more and more relevant for customers, which are essential, for example, during fence system production, door joinery, or the broadly understood furniture industry. 1. Introduction However, it should be remembered that when welding thin-walled elements, there are great difficulties with ensuring dimensional tolerances of the structures made, which are related to the need to select an appropriate technological allowance and the upset speed of the joined elements. The appropriate selection of process parameters, such as current intensity and welding pressure force, enables the minimization of welding deformations and deformations [19,20]. In addition, welding allows you to connect two elements with a large variation in the thickness of the materials to be joined, which is very difficult or sometimes even impossible to achieve based on the MIG/MAG arc welding processes. The literature contains only residual information presenting a comparison of the properties of inseparable connections of thin-walled steel elements made with the use of Materials 2022, 15, 5171 3 of 17 various bonding methods. Therefore, the article presents the results of research on the strength properties and metallographic structures of joints made by the following methods: MAG (135 and 138), CMT (using solid or flux-cored wire), laser welding, and butt welding. In addition, the results of manual and robotic welding (for the MAG and laser welding methods) were compared. In addition, the article also presents the possibilities of using the digital image correlation (DIC) system to analyze the strength properties of joints and joint zones depending on the method used. 2. Materials and Methods The welding process was analyzed for cold-rolled low-carbon steel 1.0330 (DC01), 1.5 mm thick and chemical composition according to EN10130/EN10139 C ≤0.12, Mn ≤ 0.60, P ≤0.045 and S ≤0.045. The strength parameters of the base material were determined in the static tensile test. These parameters reached the following values: Rm = 317 MPa and R0.2 = 228 MPa. Table 1 presents a list of the analyzed welding methods along with the process parameters used. The samples were prepared and made in accordance with the guidelines of PN-EN ISO 15614-1 and PN-EN ISO 15614-11. Table 1. Methods of welding thin-walled steel elements with the applied process parameters. The methods of welding Process parameters Welding current (A) Welding voltage (V) Wire feed speed (m/min) Time of welding (sec) Speed of welding (cm/min) Heat input (kJ/cm) MIG/MAG MAG 135 manual 120 18.1 7.1 47.0 44.7 2.33 MAG 138 manual 70 17.0 7.1 35.0 60.0 0.95 MAG 135 robotic 167 17.0 5.1 33.2 63.3 2.15 MAG 138 robotic 144 15.8 3.8 33.3 63.1 1.73 CMT solid wire 195 16.1 6.2 15.0 140.0 1.07 CMT flux-cored wire 160 13.3 4.0 34.0 61.8 1.65 Laser welding Laser beam power (W) Oscillation (mm) Wire feed speed (m/min) Time of welding (sec) Speed of welding (cm/min) Heat input (kJ/cm) Laser robotic without additional material 1800 0.6 - 12.0 150 0.43 Laser manual with additional material 1050 1.5 0.65 27.7 65 0.58 Welding Welding current (kA) - - - Butt welding displace (mm) Heat input (kJ) Resistance upset butt welding 5.8 - - - 4 6.728 Samples welded manually using the MAG 135 and MAG 138 methods were made at a stationary welding station using the inverter MIG/MAG Powertec i320c Advanced welding device (Lincoln Electric Bester, Bielawa, Poland). The MAG 135 process was carried out with the use of an electrode in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.0 mm. In the MAG 138 process, an electrode in the form of an EN ISO 17632-A-T 46 4 M M 2 H5 metallic core with a diameter of 1.2 mm was used. The shielding gas for both processes was a mixture of 92% Ar 8% CO2 according to PN-EN ISO 14175-M20-ArC-8, with a constant shielding gas flow rate 12 l/min. 2. Materials and Methods In the MAG 138 process, an electrode in the form of an EN ISO 17632-A-T 46 4 M M 2 H5 metallic core with a diameter of 1.2 mm was used. The shielding gas for both processes was a mixture of 92% Ar 8% CO2 according to PN-EN ISO 14175-M20-ArC-8, with a constant shielding gas flow rate 12 l/min. The samples made using the MAG 135/138 and CMT robotic processes were prepared on a welding station equipped with a Kawasaki RA006L (Kawasaki Robotics, Lakeview Drive, Wixom, MI, USA) an industrial robot and Fronius TPS 400i MIG/MAG welding sources (Fronius International GmbH, Wels, Austria). The MAG 135 robotic process was carried out using an electrode in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.2 mm, and in the MAG 138 process, an electrode in the form of a wrapped wire with a metallic core was used EN ISO 17632-A-T 46 4 M M 2 H5 with a diameter of 1.2 mm. For the CMT process, electrodes in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.2 mm and a cored wire with a metallic core EN Samples welded manually using the MAG 135 and MAG 138 methods were made at a stationary welding station using the inverter MIG/MAG Powertec i320c Advanced welding device (Lincoln Electric Bester, Bielawa, Poland). The MAG 135 process was carried out with the use of an electrode in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.0 mm. In the MAG 138 process, an electrode in the form of an EN ISO 17632-A-T 46 4 M M 2 H5 metallic core with a diameter of 1.2 mm was used. The shielding gas for both processes was a mixture of 92% Ar 8% CO2 according to PN-EN ISO 14175-M20-ArC-8, with a constant shielding gas flow rate 12 l/min. Th l d i h MAG 135/138 d CMT b i d g g The samples made using the MAG 135/138 and CMT robotic processes were prepared on a welding station equipped with a Kawasaki RA006L (Kawasaki Robotics, Lakeview Drive, Wixom, MI, USA) an industrial robot and Fronius TPS 400i MIG/MAG welding sources (Fronius International GmbH, Wels, Austria). 2. Materials and Methods The samples made using the MAG 135/138 and CMT robotic processes were prepared on a welding station equipped with a Kawasaki RA006L (Kawasaki Robotics, Lakeview Drive, Wixom, MI, USA) an industrial robot and Fronius TPS 400i MIG/MAG welding sources (Fronius International GmbH, Wels, Austria). The MAG 135 robotic process was carried out using an electrode in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.2 mm, and in the MAG 138 process, an electrode in the form of a wrapped wire with a metallic core was used EN ISO 17632-A-T 46 4 M M 2 H5 with a diameter of 1 2 mm For the CMT process electrodes in the form of a solid wire EN ISO Table 1. Methods of welding thin-walled steel elements with the applied process parameters. The methods of welding Process parameters Welding current (A) Welding voltage (V) Wire feed speed (m/min) Time of welding (sec) Speed of welding (cm/min) Heat input (kJ/cm) MIG/MAG MAG 135 manual 120 18.1 7.1 47.0 44.7 2.33 MAG 138 manual 70 17.0 7.1 35.0 60.0 0.95 MAG 135 robotic 167 17.0 5.1 33.2 63.3 2.15 MAG 138 robotic 144 15.8 3.8 33.3 63.1 1.73 CMT solid wire 195 16.1 6.2 15.0 140.0 1.07 CMT flux-cored wire 160 13.3 4.0 34.0 61.8 1.65 Laser welding Laser beam power (W) Oscillation (mm) Wire feed speed (m/min) Time of welding (sec) Speed of welding (cm/min) Heat input (kJ/cm) Laser robotic without additional material 1800 0.6 - 12.0 150 0.43 Laser manual with additional material 1050 1.5 0.65 27.7 65 0.58 Welding Welding current (kA) - - - Butt welding displace (mm) Heat input (kJ) Resistance upset butt welding 5.8 - - - 4 6.728 Table 1. Methods of welding thin-walled steel elements with the applied process parameters. Samples welded manually using the MAG 135 and MAG 138 methods were made at a stationary welding station using the inverter MIG/MAG Powertec i320c Advanced welding device (Lincoln Electric Bester, Bielawa, Poland). The MAG 135 process was carried out with the use of an electrode in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.0 mm. 2. Materials and Methods The MAG 135 robotic process was carried out using an electrode in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.2 mm, and in the MAG 138 process, an electrode in the form of a wrapped wire with a metallic core was used EN ISO 17632-A-T 46 4 M M 2 H5 with a diameter of 1.2 mm. For the CMT process, electrodes in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.2 mm and a cored wire with a metallic core EN Materials 2022, 15, 5171 4 of 17 as car ISO 17632-A: T 42 4 ZMn M M21 1 H5 were used. For all robotic processes, the shielding gas was 92% Ar 8% CO2 according to PN-EN ISO 14175-M20-ArC-8, with a constant shielding gas flow rate 14 l/min. process was carried out without a gas shield. On the other h consumables were made in the process of manual laser weld device by IPG Photonics (Oxford MA USA) The manual Laser welding was performed in the research laboratory of IPG Photonics in Gliwice. The laser welding process without additional material was carried out on a robotic station equipped with an ABB industrial robot and a laser source with a power of 6 kW. The process was carried out without a gas shield. On the other hand, samples with welding consumables were made in the process of manual laser welding using the LightWeld XC device by IPG Photonics (Oxford, MA, USA) The manual laser welding process was carried out with the use of an electrode in the form of a solid wire EN ISO 14341-A: G 38 3 C1 3Si1 with a diameter of 1.0 mm, in a welding gas shield with nitrogen N50, with a constant flow rate of the shielding gas 25 l/min. device by IPG Photonics (Oxford, MA, USA) The manual carried out with the use of an electrode in the form of a solid 3 C1 3Si1 with a diameter of 1.0 mm, in a welding gas shield constant flow rate of the shielding gas 25 l/min. The process of resistance butt welding was carried out circuit welding machine (ASPA, Wrocław, Poland). 2. Materials and Methods A photo of specimens prepared for the static tensile test with the use of a digital image correlation system (DIC). Figure 2. A photo of specimens prepared for the static tensile test with the use of a digital image correlation system (DIC). Figure 2. A photo of specimens prepared for the static tensile test with the use of a digita correlation system (DIC). The deformation analysis of the area of welded joints was performed us D t D i I t 4D ( i 4 7 0 495) [21] di it l i l ti t o of specimens prepared for the static tensile test with the use of a digital image m (DIC). Figure 2. A photo of specimens prepared for the static tensile test with the use of a digital image correlation system (DIC). The deformation analysis of the area of welded joints was performed us D t D i I t 4D ( i 4 7 0 495) [21] di it l i l ti t mation analysis of the area of welded joints was performed using the cs Istra 4D (version 4.7.0.495) [21] digital image correlation system (DIC). o cameras with a resolution of 5 Mpx placed opposite to each other was ously recording the image of both flat surfaces of the tested sample (Figure ting, stochastic speckles of an average physical size of 0.3 mm were e surface of the samples by spraying black and white paint. In combination tion of the cameras and the zoom of the lens, this corresponded to the spot sizes of 3–5 pixels [22,23]. The speed of the image acquisition was 2 ombination with the speed of the test, corresponded to one frame for the sample by 1.7 µm. The analysis of the deformation fields was carried out The deformation analysis of the area of welded joints was performed using the Dantec Dynamics Istra 4D (version 4.7.0.495) [21] digital image correlation system (DIC). A sys- tem of two cameras with a resolution of 5 Mpx placed opposite to each other was used, simultaneously recording the image of both flat surfaces of the tested sample (Figure 3). Prior to testing, stochastic speckles of an average physical size of 0.3 mm were produced on the surface of the samples by spraying black and white paint. 2. Materials and Methods Static tensile tests of the manufactured joints were carri The process of resistance butt welding was carried out using the ZDZ7 butt-short- circuit welding machine (ASPA, Wrocław, Poland). Static tensile tests of the manufactured joints were carrie geometry shown in Figures 1 and 2, using an MTS 81 Static tensile tests of the manufactured joints were carried out on samples with the geometry shown in Figures 1 and 2, using an MTS 810 machine (MTS Systems Corporation, Eden Prairie, MN, USA) equipped with a digital image correlation (DIC) system. Tensile tests were carried out with a displacement rate of 2 mm/min, until destruction. geometry shown in Figures 1 and 2, using an MTS 81 Corporation, MN, USA) equipped with a digital image corre tests were carried out with a displacement rate of 2 mm/min, Figure 1. The geometry of samples for the static tensile test of thin-w various methods. Designation of areas used for analysis using the di (DIC): 0 - a center of the welded joint, BM - based material, 1÷13 - a from the weld axis upwards, and 1'÷13 '- an area of the analyzed sam Figure 1. The geometry of samples for the static tensile test of thin-walled steel elements bonded by various methods. Designation of areas used for analysis using the digital image correlation system (DIC): 0—a center of the welded joint, BM—based material, 1÷13—an area of the analyzed sample from the weld axis upwards, and 1'÷13'—an area of the analyzed sample from the axis weld down (Unit: mm). Figure 1. The geometry of samples for the static tensile test of thin-w various methods. Designation of areas used for analysis using the d DIC): 0 - a center of the welded joint, BM - based material, 1÷13 - a rom the weld axis upwards and 1'÷13 ' an area of the analyzed sam Figure 1. The geometry of samples for the static tensile test of thin-walled steel elements bonded by various methods. Designation of areas used for analysis using the digital image correlation system (DIC): 0—a center of the welded joint, BM—based material, 1÷13—an area of the analyzed sample from the weld axis upwards, and 1'÷13'—an area of the analyzed sample from the axis weld down (Unit: mm). Materials 2022, 15, 5171 Materials 2022, 15, x FOR 5 of 17 Figure 2. 2. Materials and Methods In combination with the resolution of the cameras and the zoom of the lens, this corresponded to the recommended spot sizes of 3–5 pixels [22,23]. The speed of the image acquisition was 2 Hz, which, in combination with the speed of the test, corresponded to one frame for the extension of the sample by 1.7 µm. The analysis of the deformation fields was carried out with the use of the Istra 4D [21] program, with the face size of 17 pxs and the mesh spacing of 13 pxs [21,22]. A system of two cameras with a resolution of 5 Mpx placed opposite to each oth used, simultaneously recording the image of both flat surfaces of the tested sample 3). Prior to testing, stochastic speckles of an average physical size of 0.3 mm produced on the surface of the samples by spraying black and white paint. In comb with the resolution of the cameras and the zoom of the lens, this corresponded recommended spot sizes of 3–5 pixels [22,23]. The speed of the image acquisitio Hz, which, in combination with the speed of the test, corresponded to one frame extension of the sample by 1.7 µm. The analysis of the deformation fields was car with the use of the Istra 4D [21] program, with the face size of 17 pxs and the mesh of 13 pxs [21,22]. the Istra 4D [21] program, with the face size of 17 pxs and the mesh spacing . or static tensile tests with simultaneous analysis of sample deformation based on l ti t (DIC) i lt l di th i f b th fl t f Figure 3. Stand for static tensile tests with simultaneous analysis of sample deformation b the digital image correlation system (DIC), simultaneously recording the image of both flat of the tested sample. Figure 3. Stand for static tensile tests with simultaneous analysis of sample deformation based on the digital image correlation system (DIC), simultaneously recording the image of both flat surfaces of the tested sample. r static tensile tests with simultaneous analysis of sample deformation based on Figure 3. Stand for static tensile tests with simultaneous analysis of sample deformation the digital image correlation system (DIC), simultaneously recording the image of both fla of the tested sample. Figure 3. 3. Results and discussion 3. Results and discussion Figure 5 shows representative microstructures of the tested joints. Regardless of the method of joining thin-walled steel elements, characteristic weld zones were observed in each case: weld metal (WM), heat effect zone (HAZ), and base material (BM) [24,25]. The made connections were free from welding imperfections and structural defects, e.g., ma- terial discontinuities. It was found that the shape of the welds obtained after welding with MIG/MAG methods has a characteristic appearance resembling the so-called "mush- rooms". Moreover, the joints made with metallic core wires were characterized by a more regular weld profile, which, consequently, resulted in much smaller deformations in the joined sheets Figure 5 shows representative microstructures of the tested joints. Regardless of the method of joining thin-walled steel elements, characteristic weld zones were observed in each case: weld metal (WM), heat effect zone (HAZ), and base material (BM) [24,25]. The made connections were free from welding imperfections and structural defects, e.g., ma- terial discontinuities. It was found that the shape of the welds obtained after welding with MIG/MAG methods has a characteristic appearance resembling the so-called “mush- rooms”. Moreover, the joints made with metallic core wires were characterized by a more regular weld profile, which, consequently, resulted in much smaller deformations in the joined sheets. joined sheets. The smallest width of the weld and heat-affected zone (HAZ) was obtained in the process of robotic laser welding without the addition of material. Compared to traditional MAG 135/138 welding methods, they were more than three times smaller. Moreover, the processes of manual laser welding and butt welding were characterized by smaller areas of joints compared to the MAG 135/138 method, by 2 and 2.7 times, respectively. This property is of great importance in the context of minimizing the longitudinal deformation of the welded elements, which results from the occurrence of longitudinal shrinkage. It is related to the reduction in the volume of the weld in relation to other methods and the reduction in the ratio of the surface area of the joined elements to the cross-sectional area of the welds obtained. The direction of contraction of the joint follows the direction of its axis. As a result of thermo-mechanical changes in the weld and in the heat-affected zone, the contraction force is distributed over the entire cross-section of the element. The plane of this section is perpendicular to the axis of the welds. 3. Results and discussion 3. Results and discussion The greater the ratio of the cross- sectional area of the element to the cross-sectional area of the welds in a given plane, the lower the longitudinal shrinkage. The force of contraction is distributed over a larger area and thus the longitudinal elastic deformation of the element will be smaller [26 27] j The smallest width of the weld and heat-affected zone (HAZ) was obtained in the process of robotic laser welding without the addition of material. Compared to traditional MAG 135/138 welding methods, they were more than three times smaller. Moreover, the processes of manual laser welding and butt welding were characterized by smaller areas of joints compared to the MAG 135/138 method, by 2 and 2.7 times, respectively. This property is of great importance in the context of minimizing the longitudinal deformation of the welded elements, which results from the occurrence of longitudinal shrinkage. It is related to the reduction in the volume of the weld in relation to other methods and the reduction in the ratio of the surface area of the joined elements to the cross-sectional area of the welds obtained. The direction of contraction of the joint follows the direction of its axis. As a result of thermo-mechanical changes in the weld and in the heat-affected zone, the contraction force is distributed over the entire cross-section of the element. The plane of this section is perpendicular to the axis of the welds. The greater the ratio of the cross-sectional area of the element to the cross-sectional area of the welds in a given plane, the lower the longitudinal shrinkage. The force of contraction is distributed over a larger area and thus the longitudinal elastic deformation of the element will be smaller [26,27]. and thus the longitudinal elastic deformation of the element will be smaller [26,27]. It was also observed that the application of these processes allows us to obtain a very regular profile of the joint, which in turn translates into negligible deformation of the joined elements. It is an important parameter in the case of bonding thin-walled elements i d t i i i ldi d f ti f th t ti [26 27] It was also observed that the application of these processes allows us to obtain a very regular profile of the joint, which in turn translates into negligible deformation of the joined elements. 2. Materials and Methods Stand for static tensile tests with simultaneous analysis of sample deformation based on the digital image correlation system (DIC), simultaneously recording the image of both flat surfaces of the tested sample. r static tensile tests with simultaneous analysis of sample deformation based on l I l l d h f b h fl f Figure 3. Stand for static tensile tests with simultaneous analysis of sample deformation the digital image correlation system (DIC), simultaneously recording the image of both flat of the tested sample. Figure 3. Stand for static tensile tests with simultaneous analysis of sample deformation based on the digital image correlation system (DIC), simultaneously recording the image of both flat surfaces of the tested sample. correlation system (DIC), simultaneously recording the image of both flat surfaces ple. sections of the welded joints were subjected to the microscopic analysis 7000, Osaka, Japan) and microhardness measurements using the Vickers The cross-sections of the welded joints were subjected to the microscopic a (Keyence VHX-7000, Osaka, Japan) and microhardness measurements using the HV 0.5 kg (49.1N) method (TUKON 2500 by Willson Instruments, Flums, Switz The microhardness was analyzed along three parallel lines (Figure 4). The cross-sections of the welded joints were subjected to the microscopic analysis (Keyence VHX-7000, Osaka, Japan) and microhardness measurements using the Vickers HV 0.5 kg (49.1 N) method (TUKON 2500 by Willson Instruments, Flums, Switzerland). The microhardness was analyzed along three parallel lines (Figure 4). Materials 2022, 15, 5171 6 of 17 Figure 4. Representative diagram of the microhardness measurement locations: in the sample axis - green line, at a distance of 0.25 mm from the sample axis - yellow lines. Figure 4. Representative diagram of the microhardness measurement locations: in the sample axis—green line, at a distance of 0.25 mm from the sample axis—yellow lines. Figure 4. Representative diagram of the microhardness measurement locations: in the sample axis - green line, at a distance of 0.25 mm from the sample axis - yellow lines. Figure 4. Representative diagram of the microhardness measurement locations: in the sample axis—green line, at a distance of 0.25 mm from the sample axis—yellow lines. Measurements were started in the unaffected base material, covered the weld zone, and ended again in the unaffected base material. The first measurement was made in the axis of the joined sheets, and the next ones were symmetrically distant from the axis by 0.25 mm. 2. Materials and Methods Measurements were carried out in 0.5 mm intervals. Measurements were started in the unaffected base material, covered the weld zone, and ended again in the unaffected base material. The first measurement was made in the axis of the joined sheets, and the next ones were symmetrically distant from the axis by 0.25 mm. Measurements were carried out in 0.5 mm intervals. 3. Results and discussion 3. Results and discussion It is an important parameter in the case of bonding thin-walled elements in order to minimize welding deformations of the construction [26,27]. in order to minimize welding deformations of the construction [26,27]. The macroscopic analysis of the structures showed that the joints made by classical welding and laser welding were characterized by a weld face width of 2.5–3.6 mm, which was about 50% of the width of joints made using semi-automatic methods. Moreover, it was observed that for the CMT process (Figure 5e,f), the fusion width was much smaller compared to the other joints. Furthermore, the joint made by manual laser welding with the use of filler material was of similar width to the joint made by butt welding (Figure. 5g) The macroscopic analysis of the structures showed that the joints made by classical welding and laser welding were characterized by a weld face width of 2.5–3.6 mm, which was about 50% of the width of joints made using semi-automatic methods. Moreover, it was observed that for the CMT process (Figure 5e,f), the fusion width was much smaller compared to the other joints. Furthermore, the joint made by manual laser welding with the use of filler material was of similar width to the joint made by butt welding (Figure 5g) or robotic laser welding (Figure 5h). Materials 2022, 15, 5171 7 of 17 R REVIEW 7 o Figure 5. Representative macrostructures of cross-sections of joints depending on the bonding p cess used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG138, CMT solid wire, (f) CMT flux cored wire, (g) butt welding, (h) robotic laser, (i) manual laser w solid wire. Figure 6 shows the representative microstructure of the welds depending on bonding processes. Depending on the process used, acicular ferrite (AF), polygonal ferr (PF), boundary ferrite (GBF) and Widmanstatten ferrite (WF) [26,28] can be observed Figure 5. Representative macrostructures of cross-sections of joints depending on the bonding proce used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG138, (e) CM solid wire, (f) CMT flux cored wire, (g) butt welding, (h) robotic laser, (i) manual laser with solid wir Figure 6 shows the representative microstructure of the welds depending on th bonding processes. Depending on the process used, acicular ferrite (AF), polygonal ferri (PF), boundary ferrite (GBF) and Widmanstatten ferrite (WF) [26,28] can be observed in th microstructures Figure 5. 3. Results and discussion 3. Results and discussion In the case of welds made with the use of flux-cored wires and a robotic station, a high content of AF, GBF was noticed (Figure 6c,d). The CMT samples (Figure 6e,f) had a smaller size of the primary austenite grain and amount of PF compared to manual MAG 135 and MAG 138 (Figure 6a,b). Moreover, more AF ferrite was found for the CMT method (Figure 6e,f). In the case of using the welding and laser welding processes (with and without filer material), no GBF was observed but only AF and PF (Figure 6h–j). Additionally, the smallest grain was visible in these samples. p Analyzing the microstructure of the welds in Figure 6e,f it can be concluded that both welds contain Widmanstatten ferrite (FW, nucleating at the boundaries of the former austenite grain). This means that in both cases the thermodynamic conditions for the formation of this microstructure were met. Estimating the amount of this ferrite based on the observation of the microstructure, it can be assumed that in the weld in Figure 6e (made with a solid wire) there is slightly more FW ferrite than in the weld made with a flux-cored wire (Figure 6f). When analyzing the documentation of the manufacturers of binders (used in the experiment) regarding the chemical composition of welds after MAG processes, it can be noticed that the weld made with flux-cored wire contains more manganese by as much as 1/3 (1.52% by weight) compared to solid wire (0.94% wt). Since manganese promotes the formation of FW ferrite, a slightly higher amount of this ferrite in the weld with a lower manganese content may suggest that other factors had a greater influence on the formation of this phase. In this case, the cooling speed can be considered, which was probably lower for a joint made with a flux-cored wire (Figure 6f). This may be indicated by the width of the heat affected zone and the zones of increased hardness, which are much larger for this joint than for a joint made with a solid wire (Figure 6e), as shown in Figure 7. The differences in the kinetics of FW formation are also indicated by its morphology. The ferrite in the weld from Figure 6e has a greater share of the needle zone in relation to the FW nucleation area. 3. Results and discussion 3. Results and discussion Representative macrostructures of cross-sections of joints depending on the bonding pro- cess used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG138, (e) CMT solid wire, (f) CMT flux cored wire, (g) butt welding, (h) robotic laser, (i) manual laser with solid wire. Figure 5. Representative macrostructures of cross-sections of joints depending on the bonding process used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG138, (e) CMT solid wire, (f) CMT flux cored wire, (g) butt welding, (h) robotic laser, (i) manual laser with solid wire. Figure 6 shows the representative microstructure of the welds depending on the bonding processes. Depending on the process used, acicular ferrite (AF), polygonal ferrite (PF), boundary ferrite (GBF) and Widmanstatten ferrite (WF) [26,28] can be observed in the microstructures Figure 6 shows the representative microstructure of the welds depending on the bonding processes. Depending on the process used, acicular ferrite (AF), polygonal ferrite (PF), boundary ferrite (GBF) and Widmanstatten ferrite (WF) [26,28] can be observed in the microstructures. Materials 2022, 15, 5171 8 of 17 EVIEW Figure 6. Representative microstructures of cross-sections of joints depending on the bond cess used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MA CMT solid wire, (f) CMT flux cored wire, (g) butt welding, (h) robotic laser, (i) manual l solid wire. Figure 6. Representative microstructures of cross-sections of joints depending on the bon used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG1 solid wire, (f) CMT flux cored wire, (g) butt welding, (h) robotic laser, (i) manual laser wit Figure 6. Representative microstructures of cross-sections of joints depending on the bonding pro- cess used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG138, (e) CMT solid wire, (f) CMT flux cored wire, (g) butt welding, (h) robotic laser, (i) manual laser with solid wire. Figure 6. Representative microstructures of cross-sections of joints depending on the bonding process used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG138, (e) CMT solid wire, (f) CMT flux cored wire, (g) butt welding, (h) robotic laser, (i) manual laser with solid wire. Materials 2022, 15, 5171 9 of 17 9 of 17 The largest size of the primary grain of austenite and GBF, PF, WF occurs in the sample welded by the manual method 135 and 138 (Figure 6a,b). 3. Results and discussion 3. Results and discussion Distribution of the microhardness of the joints depending on the bonding process used: ual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG138, (e) CMT solid CMT flux-cored wire, (g) butt welding, (h) robotic laser, (i) manual laser with solid wire, e average value of the microhardness of the base material. Figure 7. Distribution of the microhardness of the joints depending on the bonding process used: (a) manual MAG135, (b) manual MAG138, (c) robotic MAG135, (d) robotic MAG138, (e) CMT solid wire, (f) CMT flux-cored wire, (g) butt welding, (h) robotic laser, (i) manual laser with solid wire, AV - the average value of the microhardness of the base material. general, it was observed that the shape of the microhardness distribution on the ection of the joints was similar, regardless of the bonding method used. The meas- fferences in microhardness were a consequence of the joining process used: man- MT, laser, and solid and flux-cored wire. Moreover, for the MAG 135 and 138 pro- in which the additional material was used, the difference in the recorded micro- ss values was caused by the different content of Si and Mn, which influenced the n hardening resulting in the increase in microhardness [28–30]. ery similar widths of zones with increased hardness were also observed for joints n the arc welding processes (MIG/MAG and CMT), with simultaneous different ss values between joints made with additional material in the form of solid wire, nts made with the addition of flux-cored wire. The hardness values of the welds ividual processes ranging from 10 to 20 (HV). The exceptions were samples made CMT process, for which the maximum hardness values are the same, while for solid h l i il h h d f h b i l h f Thi h Very similar widths of zones with increased hardness were also observed for joints made in the arc welding processes (MIG/MAG and CMT), with simultaneous different hardness values between joints made with additional material in the form of solid wire, and joints made with the addition of flux-cored wire. The hardness values of the welds for individual processes ranging from 10 to 20 (HV). The exceptions were samples made in the CMT process, for which the maximum hardness values are the same, while for solid wire they reach values similar to the hardness of the base material much faster. 3. Results and discussion 3. Results and discussion On the other hand, the needles of the FW shown in Figure 6f are less exposed, which suggests a greater tendency for longer growth with a stable transformation front and destabilization only at the final stage, when the needles were formed. Referring also to the remaining part of the microstructure, i.e., the space inside the former austenite grain, it can be seen that the microstructure in the weld obtained with the use of a flux-core wire (Figure 6f) is finer, where acicular ferrite is probably present. It should be remembered that with a carbon content of approx. 0.1% by weight (according to catalog data), carbon also has its share in the microstructure, in which it will mainly be deposited together with coniferous ferrite inside the former austenite grain. However, based on studies using only a light microscope, its role in morphology has not yet been determined. It can only be assumed that due to the probable presence of coniferous ferrite in these areas, the microstructure will be bainitic [26–30]. The above-described changes in the microstructure are reflected in the results of microhardness measurements on the cross-section of the joints presented in Figure 7. It was observed that regardless of the method used, all the registered microhardness profiles within the welded joints made have a characteristic shape of a symmetrical normal distribution, typical for steel welded joints. The highest values of microhardness were always recorded in the central zone of FZ of the weld [24,25]. This effect was independent of the side from which the analyses were carried out (face, ridge) [31–33]. In general, it was observed that the shape of the microhardness distribution on the cross-section of the joints was similar, regardless of the bonding method used. The mea- sured differences in microhardness were a consequence of the joining process used: manual, CMT, laser, and solid and flux-cored wire. Moreover, for the MAG 135 and 138 processes, in which the additional material was used, the difference in the recorded microhardness values was caused by the different content of Si and Mn, which influenced the solution hardening resulting in the increase in microhardness [28–30]. 10 of 17 Materials 2022, 15, 5171 i b f h h d f h d d h b d d Figure 7. Distribution of the microhardness of the joints depending on the bonding process used: 7. 3. Results and discussion 3. Results and discussion This phenomenon is due to the fact that the synergic line for the CMT process has been developed by Fronius dedicated to solid wires. The CMT method in combination with metal cored wires is characterized by a lack of stability in the process parameters and the inability to achieve a welding speed similar to solid wires. The conducted tests show that it would be necessary to develop a special synergic line dedicated to flux-cored wires, without which, for the welded joints made, there is a wide zone of increased microhardness and a diversified microstructure. ey reach values similar to the hardness of the base material much faster. This phe- on is due to the fact that the synergic line for the CMT process has been developed nius dedicated to solid wires. The CMT method in combination with metal cored s characterized by a lack of stability in the process parameters and the inability to e a welding speed similar to solid wires. The conducted tests show that it would be ary to develop a special synergic line dedicated to flux-cored wires, without which, welded joints made, there is a wide zone of increased microhardness and a diver- microstructure. mong all the analyzed processes, the widest zone of hardness increase was noted oint made in the process of resistance butt welding, for which the maximum values bl t th h d l bt i d i th f ldi ith fl Among all the analyzed processes, the widest zone of hardness increase was noted for the joint made in the process of resistance butt welding, for which the maximum values were comparable to the hardness values obtained in the process of welding with flux-cored wires. This phenomenon may result from the course of the resistance butt welding process, in which the joined elements are heated at the same time over their entire contact surface. In addition, the length of the electrode attachment zone is responsible for the width of the material heating zone, which depends on the type of materials to be joined. The welding area is heated to plasticize. When the metal in the welding zone reaches the required temperature, it undergoes characteristic swelling under the influence of the pressure force, and the contacting surfaces join. 3. Results and discussion 3. Results and discussion The welding current is automatically switched off even Materials 2022, 15, 5171 11 of 17 11 of 17 before the upsetting process is completed while maintaining the pressure force. The applied pressure force introduces significant stresses in the welded joint, limiting the grain growth. This process course in combination with the uniform and gradual cooling of the joint under ambient conditions may have an impact on the width of the heat-affected zone and the zone of increased hardness. The stability of the process may also be demonstrated by the correctly columnar arrangement of grains and the fine-grained structure obtained, consisting mainly of acicular ferrite and polygonal ferrite. g y p yg On the other hand, the narrowest zones of hardness increase were obtained for joints made in the laser welding processes, which is associated with the use of the high energy density of the laser beam. The comparison of the robotic and manual laser welding processes made it possible to show a large difference between the obtained results of the maximum weld hardness, amounting to about 50 (HV) more in the robotic process. Moreover, it was observed that for the samples made in the process of manual laser welding with the additional material, the smallest changes in hardness in the area of the entire weld were obtained. The reduced hardness of the heat-affected zone, in relation to the other considered variants, may be associated with more far-reaching processes of microstructure renewal with regard to the reduction in the dislocation density. In iron-based alloys, especially in low-carbon steels, this process is generally accomplished by achieving the thermodynamic conditions of transformation into austenite and another transformation into a ferrite-based structure [28,29]. It should be noted, however, that the discussed variant of welding (manual laser) involves the use of high energy density in a less stable way (manual process control). Large temperature gradients accompanying heating by the laser beam, combined with the variability of the amount of energy at a given point of the joint, can cause a very rapid temperature increase and subsequent rapid cooling [34]. 3. Results and discussion 3. Results and discussion Bearing in mind that the acceleration of the rate of temperature changes also causes a change in the temperature at which the phase changes take place, it is also possible to consider the variant that there is no typical kinetics of changes in the HAZ, and it is possible not to obtain a regular austenite grain at the HAZ showing low hardness [28–30,34]. In addition, the analyzed material is cold-rolled steel, and therefore contains a high density of dislocation, which allows us to analyze the possibility of healing or even recrystallization processes in a more classic approach. Of course, it should be noted that high-strain recrystallization leads to grain refinement, and, thus, material strengthening, and requires thermodynamic conditions for nucleation and new grain growth, which may be difficult to achieve with rapidly changing processes [26–30]. Verification of the indicated hypotheses is possible through more detailed microstructure studies, especially with the use of transmission electron microscopy (TEM), which is planned at the next stages of the research. The analysis of the microstructure at such a level will provide answers regarding the mechanisms of material strengthening or the lack of them. The digital image correlation system (DIC) was used to assess the differences in mechanical properties occurring during static tensile tests for individual areas of each of the analyzed joints. This enabled the determination of tensile curves for individual sections of welded joints in planes transverse to the axis of the samples under tension. Figure 8 shows an exemplary representative image of the sample at individual stages of its analysis using the Istra 4D software. Moreover, Figures 9–11 show the curves determined by the DIC system for robotic and manual samples, respectively. The values of axial deformation for a given location within the scope of the weld were determined along the same lines indicated on both surfaces of the samples (i.e., on both sides of it) in the same cross-sections distant by 1 mm. In order to take into account the possible secondary bending effect, the deformations in the section under consideration were calculated as the average of the values determined on both sides of the sample [31]. 12 of 17 e averag 12 of 17 Materials 2022, 15, 5171 Materials 2022 15 x FOR (a) (b) (c) Figure 8. 3. Results and discussion 3. Results and discussion Phases of sample image analysis with the use of Istra 4D software: (a) image of th with specks, (b) image of the sample with the deformation field, (c) image of the sample deformation field, including lines defining the cross-section planes in which the tension cur determined. Figure 8. Phases of sample image analysis with the use of Istra 4D software: (a) image of the sample with specks, (b) image of the sample with the deformation field, (c) image of the sample with the deformation field, including lines defining the cross-section planes in which the tension curves were determined. the deformations in the section under consideration were calculated as the average of the values determined on both sides of the sample [31]. (a) (b) (c) Figure 8. Phases of sample image analysis with the use of Istra 4D software: (a) image of the sample with specks, (b) image of the sample with the deformation field, (c) image of the sample with the deformation field, including lines defining the cross-section planes in which the tension curves were determined. (b) section under consid oth sides of the samp (b) (c) were calculated as th (c) (a) values determin (a) (c) (b) (a) a) Figure 8. Phases of sample image analysis with the use of Istra 4D software: (a) image of th with specks, (b) image of the sample with the deformation field, (c) image of the sample deformation field, including lines defining the cross-section planes in which the tension cur determined. Figure 8. Phases of sample image analysis with the use of Istra 4D software: (a) image of the sample with specks, (b) image of the sample with the deformation field, (c) image of the sample with the deformation field, including lines defining the cross-section planes in which the tension curves were determined. Figure 8. Phases of sample image analysis with the use of Istra 4D software: (a) image of the sample with specks, (b) image of the sample with the deformation field, (c) image of the sample with the deformation field, including lines defining the cross-section planes in which the tension curves were determined. Figure 9. The curves of the static tensile test determined on the basis of the DIC method for j i t d i b ti ldi d MAG 135 MAG 138 bl l Figure 9. 3. Results and discussion 3. Results and discussion The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: red - MAG 135; orange - MAG 138; blue - laser welding without additional material; black - base material. Figure 9. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: red—MAG 135; orange—MAG 138; blue—laser welding without additional material; black—base material. Figure 9 The curves of the static tensile test determined on the basis of the DIC method for Figure 9. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: red - MAG 135; orange - MAG 138; blue - laser welding without additional material; black - base material. Figure 9. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: red—MAG 135; orange—MAG 138; blue—laser welding without additional material; black—base material. Materials 2022, 15, 5171 13 of 17 13 of 17 Figure 10. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: brown - CMT solid wire; violet - CMT flux-cored wire; blue - laser welding without additional material; black - base material. Figure 10. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: brown—CMT solid wire; violet—CMT flux-cored wire; blue—laser welding without additional material; black—base material. Figure 10. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: brown - CMT solid wire; violet - CMT flux-cored wire; blue - laser welding without additional material; black - base material. Figure 10. The curves of the static tensile test determined on the basis of the DIC method for welded oints made in robotic welding processes: brown - CMT solid wire; violet - CMT flux-cored wire; blue - laser welding without additional material; black - base material. Figure 10. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: brown—CMT solid wire; violet—CMT flux-cored wire; blue—laser welding without additional material; black—base material. 3. Results and discussion 3. Results and discussion Figure 10. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in robotic welding processes: brown - CMT solid wire; violet - CMT flux-cored wire; blue - laser welding without additional material; black - base material. Figure 11. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in manual welding processes: red - MAG 135; purple - MAG 138; blue – manual laser welding with additional material; black - base material. It is well known that the yielding and strain hardening behavior is determined by Figure 11. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in manual welding processes: red - MAG 135; purple - MAG 138; blue – manual laser welding with additional material; black - base material. It is well known that the yielding and strain hardening behavior is determined by Figure 11. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in manual welding processes: red—MAG 135; purple—MAG 138; blue—manual laser welding with additional material; black—base material. Figure 11. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in manual welding processes: red - MAG 135; purple - MAG 138; blue – manual laser welding with additional material; black - base material. Figure 11. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in manual welding processes: red - MAG 135; purple - MAG 138; blue – manual laser welding with additional material; black - base material. Figure 11. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in manual welding processes: red—MAG 135; purple—MAG 138; blue—manual laser welding with additional material; black—base material. Figure 11. The curves of the static tensile test determined on the basis of the DIC method for welded oints made in manual welding processes: red - MAG 135; purple - MAG 138; blue – manual laser welding with additional material; black - base material. Figure 11. 3. Results and discussion 3. Results and discussion The effect of the yield stress de- ng, visible in Figures 9–11, qualitatively corresponds very well with the microhard- hanges presented in Figure 7. On the basis of the obtained results, the relationship between the microhardness values and the conventional yield point Re0.2 was determined, depending on the method of producing welded joints. The R0.2/HVA ratio for the base material was 1.75. The obtained results are presented in Figure 12. On their basis, it is possible to indirectly determine the local values of the mechanical parameters of the joint. n the basis of the obtained results, the relationship between the microhardness val- d the conventional yield point Re0.2 was determined, depending on the method of cing welded joints. The R0,2/HVA ratio for the base material was 1.75. The obtained s are presented in Figure 12. On their basis, it is possible to indirectly determine the alues of the mechanical parameters of the joint. Figure 12. The relationship between the microhardness values and the conventional yield strength Re0.2 depending on the joining method used. Figure 12. The relationship between the microhardness values and the conventional yield strength Re0.2 depending on the joining method used. 12. The relationship between the microhardness values and the conventional yield strength pending on the joining method used. Figure 12. The relationship between the microhardness values and the conventional yield strength Re0.2 depending on the joining method used. ased on the data presented in Figure 6, it can be concluded that the microhardness material (HVA) decreased with increasing distance from the weld axis. This phe- non was accompanied by an increase in the strength parameters represented by the point R0.2 (Figures 9-11). However, due to the different bonding techniques contem- herein, including the different types of welding wire used, the R0.2/HVA ratios de- ned for the different welds and different connection zones have varied over a fairly range. As shown in Figure 12, which includes the results of all measurements in the R0.2/HVA ratio ranged from 1.1 to 2.4, which could be described by a Gaussian with a mean value 1.7 and a standard deviation 0.26. The relatively large range of es in this ratio does not allow us to conclude the mechanical characteristics of the ial only on the basis of the microhardness. Determining such a relationship would o be limited to only one joining technique [26,31]. 3. Results and discussion 3. Results and discussion The curves of the static tensile test determined on the basis of the DIC method for welded joints made in manual welding processes: red - MAG 135; purple - MAG 138; blue – manual laser welding with additional material; black - base material. Figure 11. The curves of the static tensile test determined on the basis of the DIC method for welded joints made in manual welding processes: red—MAG 135; purple—MAG 138; blue—manual laser welding with additional material; black—base material. Materials 2022, 15, 5171 14 of 17 It is well known that the yielding and strain hardening behavior is determined by hardness distribution across the weld joints. Figures 9–11 demonstrate the consistent trends of the increase in plastic strains in the cross-sections of the welded specimens with increasing the distance from the weld center, which indicates a decrease in the yield stress for subsequent zones. This type of trend is characteristic of fusion joints [35]. The changes in the yield point were in each of the considered welding techniques symmetrical around the weld center line, which is qualitatively different compared, for example, to friction stir welds [31,36]. All the welded specimens ruptured in the cross sections away from the fusion zone, as shown in Figure 8c For the material from weld center sections, the 0.2% proof stress (R0.2) was not reached before specimen fracture, which indicates that it was higher than the ultimate tensile strength of the base material. The effect of the yield stress decreasing, visible in Figures 9–11, qualitatively corresponds very well with the microhardness changes presented in Figure 7. 14 of 17 of the increase in plastic strains in the cross-sections of the welded specimens with sing the distance from the weld center, which indicates a decrease in the yield stress bsequent zones. This type of trend is characteristic of fusion joints [35]. The changes yield point were in each of the considered welding techniques symmetrical around ld center line, which is qualitatively different compared, for example, to friction stir [31,36]. All the welded specimens ruptured in the cross sections away from the fu- one, as shown in Figure 8c For the material from weld center sections, the 0,2% proof (R0.2) was not reached before specimen fracture, which indicates that it was higher he ultimate tensile strength of the base material. 3. Results and discussion 3. Results and discussion Based on the data presented in Figure 6, it can be concluded that the microhardness of the material (HVA) decreased with increasing distance from the weld axis. This phe- nomenon was accompanied by an increase in the strength parameters represented by the yield point R0.2 (Figures 9–11). However, due to the different bonding techniques contem- plated herein, including the different types of welding wire used, the R0.2/HVA ratios determined for the different welds and different connection zones have varied over a fairly wide range. As shown in Figure 12, which includes the results of all measurements in total, the R0.2/HVA ratio ranged from 1.1 to 2.4, which could be described by a Gaussian curve, with a mean value 1.7 and a standard deviation 0.26. The relatively large range of changes in this ratio does not allow us to conclude the mechanical characteristics of the material only on the basis of the microhardness. Determining such a relationship would have to be limited to only one joining technique [26,31]. Materials 2022, 15, 5171 15 of 17 15 of 17 4. Conclusions On the basis of the obtained results of various steel joining methods, it was found that the narrowest zone of hardness growth, approximately 3 mm, was obtained for joints made by laser welding. This process was characterized by high dynamics and high energy density concentrated in a small area of connected materials. Therefore, there was also no growth of microstructure grains, which is a standard phenomenon observed for other joining processes, introducing large amounts of thermal energy to the joints. On the other hand, the widest zone of hardness increase, about 7 mm, was recorded for a joint made in the CMT robotic welding process. Moreover, this method, regardless of the type of wire used, solid or flux-cored, gave the highest microhardness values. It was found that the manual laser welding and butt-welding processes were characterized by smaller areas of joints compared to the MAG 135/138 method. Furthermore, the heat-affected zone for the joints made in this way, in relation to the welds produced by the MAG 135/138 method, was, respectively, 2 and 2.7 times smaller. Joints made by butt welding and laser welding processes were characterized by a weld face in the range of 2.5–3.6 mm, which was about 50% of the width of welds made using robotic methods. In addition, the butt welding processes and, in particular, manual laser welding, were characterized by a uniform distribution of stresses in the welded joint, which, in turn, resulted in minimizing the deformation of the joined elements. This parameter is particularly important in the case of joining thin- walled structures and indicates great potential for using these processes as an alternative to conventional welding processes used in the industry. Author Contributions: Conceptualization, D.S., S.P. and M.H.; Data curation, G.J. and L.D.; Formal analysis, D.S., T.M., S.P. and M.H.; Funding acquisition, S.P. and M.H.; Investigation, D.S., T.M., G.J., S.P. and M.H.; Methodology, D.S., T.M., S.P., L.D. and M.H.; Resources, M.H.; Supervision, S.P. and M.H.; Visualization, D.S., T.M. and M.H.; Writing—original draft, D.S., T.M., S.P. and M.H.; Writing—review and editing, D.S. and M.H. All authors have read and agreed to the published version of the manuscript. Author Contributions: Conceptualization, D.S., S.P. and M.H.; Data curation, G.J. and L.D.; Formal analysis, D.S., T.M., S.P. and M.H.; Funding acquisition, S.P. and M.H.; Investigation, D.S., T.M., G.J., S.P. and M.H.; Methodology, D.S., T.M., S.P., L.D. and M.H.; Resources, M.H.; Supervision, S.P. and M.H.; Visualization, D.S., T.M. 4. Conclusions and M.H.; Writing—original draft, D.S., T.M., S.P. and M.H.; Writing—review and editing, D.S. and M.H. All authors have read and agreed to the published version of the manuscript. Funding: This work has been financed by the Polish National Agency for Academic Exchange under the International Academic Partnership Program within the framework of the grant: E-mobility and sustainable materials and technologies EMMAT (PPI/APM/2018/1/00027). The presented research was also supported by Ministry Education and Science DWD/4/25/2020 (IMat SD/15/2020). Institutional Review Board Statement: Not applicable. Institutional Review Board Statement: Not applicable. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. Informed Consent Statement: Not applicable. Informed Consent Statement: Not applicable. Informed Consent Statement: Not applicable. Data Availability Statement: Not applicable. Data Availability Statement: Not applicable. Data Availability Statement: Not applicable. Conflicts of Interest: The authors declare no conflict of interest. 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Predicting chemotherapy response using a variational autoencoder approach
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© The Author(s), 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the mate- rial. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​ creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​mmons.​org/​publi​ cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Qi Wei1* and Stephen A. Ramsey2 Qi Wei1* and Stephen A. Ramsey2 *Correspondence: weiq@oregonstate.edu 1 School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA Full list of author information is available at the end of the article *Correspondence: weiq@oregonstate.edu 1 School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA Full list of author information is available at the end of the article Abstract Background:  Multiple studies have shown the utility of transcriptome-wide RNA-seq profiles as features for machine learning-based prediction of response to chemother- apy in cancer. While tumor transcriptome profiles are publicly available for thousands of tumors for many cancer types, a relatively modest number of tumor profiles are clini- cally annotated for response to chemotherapy. The paucity of labeled examples and the high dimension of the feature data limit performance for predicting therapeutic response using fully-supervised classification methods. Recently, multiple studies have established the utility of a deep neural network approach, the variational autoencoder (VAE), for generating meaningful latent features from original data. Here, we report the first study of a semi-supervised approach using VAE-encoded tumor transcriptome features and regularized gradient boosted decision trees (XGBoost) to predict chemo- therapy drug response for five cancer types: colon, pancreatic, bladder, breast, and sarcoma. Results:  We found: (1) VAE-encoding of the tumor transcriptome preserves the cancer type identity of the tumor, suggesting preservation of biologically relevant information; and (2) as a feature-set for supervised classification to predict response-to- chemotherapy, the unsupervised VAE encoding of the tumor’s gene expression profile leads to better area under the receiver operating characteristic curve and area under the precision-recall curve classification performance than the original gene expression profile or the PCA principal components or the ICA components of the gene expres- sion profile, in four out of five cancer types that we tested. Conclusions:  Given high-dimensional “omics” data, the VAE is a powerful tool for obtaining a nonlinear low-dimensional embedding; it yields features that retain biological patterns that distinguish between different types of cancer and that enable more accurate tumor transcriptome-based prediction of response to chemotherapy than would be possible using the original data or their principal components. Keywords:  Variational auto-encoder, Transcriptome, TCGA​, Chemotherapy drug response classification, Cancer, Colon adenocarcinomas, Pancreatic adenocarcinoma, Bladder carcinoma, Sarcoma, Breast invasive carcinoma Open Access Predicting chemotherapy response using a variational autoencoder approach Qi Wei1* and Stephen A. Ramsey2 Wei and Ramsey BMC Bioinformatics (2021) 22:453 https://doi.org/10.1186/s12859-021-04339-6 Wei and Ramsey BMC Bioinformatics (2021) 22:453 https://doi.org/10.1186/s12859-021-04339-6 Introduction Background Although chemotherapy is a mainstay of treatment for aggressive cancers, many agents have serious side effects [1]. Whether or not chemotherapy will provide a net benefit to a patient depends in large part on whether the malignancy responds to the treatment. Chemotherapy is often administered in cycles [2], leading to multiple opportunities where treatment appropriateness may be (re-)assessed [3]. Currently, the medical cost-benefit of chemotherapy (versus a non-pharmaceutical approach) is assessed in light of patient health status, expected therapeutic tolerance, and tumor pathological classification [4, 5]. For many cancer types, there is a broad spectrum of cases where the decision of whether or not to undergo chemotherapy is difficult [6–8]. The development of a quantitative model that could predict—based on a spe- cific tumor’s molecular profile—whether or not the tumor will respond to chemother- apy would have significant clinical utility. Moreover, an advance in machine-learning methods for the response-to-chemotherapy prediction problem [9, 10] would have potential benefits for other prediction problems in medicine. i Tumorigenesis is driven by alterations in the somatic genome and epigenome in cancer cells [11]; however, the somatic genetic or epigenetic determinants of response to chemotherapy also affect gene expression. Studies of various cancer types have demonstrated that tumor gene expression biomarkers correlate with the probability that a tumor will respond to chemotherapy, for example, a five-protein signature in breast cancer [12], a 13-gene signature in rectal cancer [13, 14], a 63-gene signature in liver cancer [15], and a support vector machine (SVM)-based model to predict survival time in breast cancer based on a 19-gene signature [16]. The findings from such “omics” studies suggest that RNA sequencing (RNA-seq)-based transcriptome measurements of tumor samples labeled for clinical response can be used to train machine-learning classifiers for predicting response to chemotherapy. However, the accuracy of models that can be learned by fully supervised approaches is limited by the small number of available clinically labeled training cases, given that tumor tran- scriptome data are high-variance and high-dimensional. For typical cancers, most available tumor transcriptomes are not labeled for chem- otherapeutic response; the ratio of such unlabeled to labeled tumor datasets in the Cancer Genome Atlas (TCGA; [17]) is in the range of 10–20, depending on the cancer type. Unlabeled data are a substantial resource that could—in the context of a semi- supervised approach—reveal multivariate patterns that could ultimately improve pre- dictive accuracy. Page 2 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Previous applications of VAE in cancer Multiple studies [20–23] have demonstrated the power of the variational autoen- coder (VAE; [24, 25])—an unsupervised nonlinear data embedding model in which two deep neural networks are oppositely connected through a low-dimensional, probabilistic latent space—for finding useful features in high-dimensional data. In the context of cancer, VAEs have been variously used to (1) model gene expression and capture biological features using the TCGA Pan-cancer Project RNA-seq dataset [26, 27]; (2) find encodings that can be used to predict gene inactivation [28]; and (3) obtain an encoding for predicting chemotherapy resistance [29]. Way and Greene [28] explored VAE architectures for predicting gene inactivation in a pan-cancer dataset and reported biological insights obtained from the latent-space embeddings. George and Lio [29] used a VAE-based, unsupervised approach to encode tumor transcrip- tomes to obtain latent-space features associated with chemotherapy response. Dincer et al. [30] used a semi-supervised, VAE-lasso approach to predict drug sensitivity of cancer cells in vitro. In contrast to previous efforts to model cancer cell line drug sen- sitivity in vitro [30–33], in this work we focused on predicting therapeutic response in vivo, across five different cancer types (colon adenocarcinoma, pancreatic adeno- carcinoma, bladder carcinoma, sarcoma, and breast invasive carcinoma). Specifically, we tested the hypothesis that a tumor transcriptome VAE would be useful for predict- ing response-to-chemotherapy in vivo, across multiple cancer types. Introduction Background Semi-supervised approaches that fuse unsupervised data reduction methods for low-dimensional embedding with supervised methods (such as deci- sion trees) for prediction have proved beneficial in problems where large unlabeled datasets are available; for example, a principal components analysis (PCA)-XGBoost method has been previously used in finance [18], and an independent component analysis (ICA)-based method has been used to classify electroencephalographic sig- nals [19]. Page 3 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Research objectivesi We first asked to what extent VAE-encoding tumor transcriptomes would preserve characteristics that are associated with distinct cancer types. To that end, we trained a pan-cancer transcriptome VAE and used it to encode over 11k tumor transcriptomes from 33 cancer types. By comparing two-dimensional embeddings of the original tumor transcriptomes with embeddings of the VAE-encoded transcriptomes, we found (“VAE encoding preserves cancer type features” section) that the VAE preserves the clustering of tumors of the same cancer type. Next, we selected five cancer types based on suffi- ciency of clinical data and trained six VAE models (three architectures and two different loss functions) to encode clinically-unlabeled transcriptomes of the five cancer types. Using TCGA clinical data, we assigned a label “responded” or “progressive” to tumors where the response to chemotherapy information was available (“Obtaining a labeled tumor transcriptome dataset” section). We then used the VAE-encoded transcriptomes for the clinically-labeled tumors as feature data for predicting response to chemotherapy using gradient boosted decision trees (XGBoost; [34]), which we found to be superior to kernel SVM. Using this “semi-supervised VAE-XGBoost” approach, we investigated (“L1 loss is better than L2 loss and cross-entropy loss for this application” section) which loss function type is best for this VAE application. In the main part of this work, we focused (“Chemotherapy response classification results” section) on the question of whether and to what extent the semi-supervised VAE-XGBoost (our new method, Fig. 1) approach would improve performance for transcriptome-based prediction of response to chemotherapy, versus a fully-super- vised approach or versus alternative semi-supervised approaches using PCA or ICA Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 4 of 22 Gene Expression Data (Original Input, )x Reconstructed Gene Expression Data ( Output, ) ˜x Encoder Network Eq. 2 mean vector ( )̂θ Variance vector ( ) σ ̂θ Sampled latent vector ( )z Decoder Network g ̂ ϕ Add labeled input ( )y Latent vector + Label as input (z, y) XGBoost Classifier Eq. 12 & Eq. 13 Probability of predicated Label P(˜y|z) Reparameterize Sampling Eq. 5 & Eq.6 Fig. 1  Overview of the VAE-XGBoost method that we used for predicting tumor response to chemotherapy in vivo for five different cancer types. For each tumor t, the encoder’s input vector xt contains the levels of the top 20% of genes by intertumoral gene expression variance. Each network has multiple fully connected dense layers (“VAE model architectures” section). Research objectivesi The sampled encoding Z|xt = zt is passed to the decoding neural network (decoder), whose architecture is identical to (with inversion) that of the encoder network. The sampled latent-space vector zt is passed to XGBoost for supervised classification to predict response to chemotherapy (training label y , prediction y) transcriptome encodings. We further investigated the relative importance of these approaches through the lens of XGBoost feature importance (“PCA & VAE feature importance scores, for COAD” section). We carried out these analyses using a com- prehensive, five-cancer set of labeled tumor transcriptomes and obtained unbiased classification performance measurements using cross-validation. Research objectivesi The encoder outputs two vectors of configurable latent variable dimension h ≪m : a vector of means µ and a vector of standard deviations σ that parameterize the multivariate normal latent-space vector Z|xt (“Variational autoencoder (VAE)” section). The sampled encoding Z|xt = zt is passed to the decoding neural network (decoder), whose architecture is identical to (with inversion) that of the encoder network. The sampled latent-space vector zt is passed to XGBoost for supervised classification to predict response to chemotherapy (training label y , prediction y) Gene Expression Data (Original Input, )x Reconstructed Gene Expression Data ( Output, ) ˜x Encoder Network Eq. 2 mean vector ( )̂θ Variance vector ( ) σ ̂θ Sampled latent vector ( )z Decoder Network g ̂ ϕ Add labeled input ( )y Latent vector + Label as input (z, y) XGBoost Classifier Eq. 12 & Eq. 13 Probability of predicated Label P(˜y|z) Reparameterize Sampling Eq. 5 & Eq.6 Fig. 1  Overview of the VAE-XGBoost method that we used for predicting tumor response to chemotherapy in vivo for five different cancer types. For each tumor t, the encoder’s input vector xt contains the levels of the top 20% of genes by intertumoral gene expression variance. Each network has multiple fully connected dense layers (“VAE model architectures” section). The encoder outputs two vectors of configurable latent variable dimension h ≪m : a vector of means µ and a vector of standard deviations σ that parameterize the multivariate normal latent-space vector Z|xt (“Variational autoencoder (VAE)” section). The sampled encoding Z|xt = zt is passed to the decoding neural network (decoder), whose architecture is identical to (with inversion) that of the encoder network. The sampled latent-space vector zt is passed to XGBoost for supervised classification to predict response to chemotherapy (training label y , prediction y) Fig. 1  Overview of the VAE-XGBoost method that we used for predicting tumor response to chemotherapy in vivo for five different cancer types. For each tumor t, the encoder’s input vector xt contains the levels of the top 20% of genes by intertumoral gene expression variance. Each network has multiple fully connected dense layers (“VAE model architectures” section). The encoder outputs two vectors of configurable latent variable dimension h ≪m : a vector of means µ and a vector of standard deviations σ that parameterize the multivariate normal latent-space vector Z|xt (“Variational autoencoder (VAE)” section). VAE encoding preserves cancer type features Given reports [35, 36] that unsupervised embeddings can be used to visualize the grouping of cancer types based on high-dimensional molecular tumor data, using unsupervised methods, we investigated the extent to which VAE encod- ing of tumor transcriptomes preserves data-space features that determine can- cer type-specific groupings. In order to do so, we obtained RNA-seq transcriptome data from the TCGA data portal for 11,057  tumors labeled for 33  different cancer types (Figs. 2, Additional file 1: S2, S3). As a baseline visualization, we generated a two-dimensional embedding of the 11,057 tumor samples by applying t-distributed stochastic neighbor embedding (t-SNE) to the expression levels of the the top-20% highest-variance genes (threshold selected as described in “Gene expression data” section), yielding 33 clusters (Fig. 2A). Next, we trained a VAE (“Variational autoen- coder (VAE), VAE model architectures” sections) with a deep architecture (VAE-1) to encode the expression levels of the highest-variance genes in each of 11,057 tumors into an equivalent number of points in a 50-dimensional latent space. An unsuper- vised t-SNE visualization (Fig. 2B) of the VAE-encoded tumor transcriptome data was remarkably similar in structure to the t-SNE visualization of the 13,584-dimensional original dataset (Additional file 1: Fig. S1). Additionally, we compared the clustering of the original transcriptome data with VAE-reconstructed transcriptome data by Page 5 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Fig. 2  Two-dimensional embedding of the 11,057 tumor transcriptomes based on t-SNE. Each mark represents a transcriptome, with color representing the cancer type. A Original gene expression data of the top-20% highest-variance genes. B VAE compressed gene expression data. VAE encoding preserves cancer type features Red rectangles denote the five cancer types selected for chemotherapy response classification Page 6 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Table 1  Numbers of tumor samples that have clinical information available regarding response-to- chemotherapy, for each cancer type (n.b., the total number of labeled tumor samples exceeds the total number of patients because some patients had multiple tumors) Table 1  Numbers of tumor samples that have clinical information available regarding response-to- chemotherapy, for each cancer type (n.b., the total number of labeled tumor samples exceeds the total number of patients because some patients had multiple tumors) Table 1  Numbers of tumor samples that have clinical information available regarding response-to- chemotherapy, for each cancer type (n.b., the total number of labeled tumor samples exceeds the total number of patients because some patients had multiple tumors) Each cancer type’s TCGA abbreviation is shown in parentheses Cancer type Total number of samples (labeled and unlabeled) Number of labeled samples Proportion of labeled samples Class balance ratio (responding/ progressive) Breast invasive carcinoma (BRCA) 1217 394 0.324 8.61 Colon adenocarcinomas (COAD) 512 117 0.229 1.72 Bladder carcinoma (BLCA) 430 115 0.267 0.95 Pancreatic adenocarci- noma (PAAD) 182 115 0.632 0.77 Sarcoma (SARC) 265 65 0.245 0.82 Sum 2606 806 Uniform manifold approximation and projection (UMAP), and found similar results (Additional file 1: Figs. S2, S3). These analyses indicated that the VAE encoding pre- serves data-space features that distinguish individual cancer types. Obtaining a labeled tumor transcriptome dataset Having demonstrated that the VAE can efficiently encode tumor transcriptomes while preserving features that distinguish different cancer types, and to set the stage for implementing a semi-supervised approach for predicting response to chemotherapy, we obtained a five-cancer-type tumor transcriptome dataset with a significant subset of the tumors labeled as to whether or not the patient responded to chemotherapy, as described below. We obtained transcriptomes of 2,606 tumors across five cancer types [colon adenocarcinoma (COAD), pancreatic adenocarcinoma (PAAD), bladder carci- noma (BLCA), sarcoma (SARC), and breast invasive carcinoma (BRCA); Table 1]. We selected the five cancer types based on availability of a sufficient amount of labeled data in TCGA and for 806 of the tumor transcriptomes, we generated binary labels corre- sponding to “responded” or “progressive”. The ratio of responding tumors to progressive disease tumors (i.e., the class balance ratio) ranged from a low of 0.77 for pancreatic cancer to a high of 8.61 for breast cancer. L1 loss is better than L2 loss and cross‑entropy loss for this application Having obtained 2,606 transcriptomes of tumors of five cancer types (with 806 of the tumors labeled by response), we next sought to determine which type of VAE recon- struction loss function—L1, L2, or binary cross entropy—would yield transcriptome encodings that are most amenable to accurate XGBoost-based prediction chemotherapy response. On the 2,606 tumor transcriptomes, we trained three sets of cancer type-spe- cific VAEs (“VAE model architectures” section) using L1 loss, L2 loss, and binary cross- entropy loss respectively. We used the L1, L2, and binary cross-entropy VAEs to encode the 806 labeled tumor transcriptomes (the top 20% most variable genes in each cancer type, merged across the five cancers, for a total of 13,584 genes) spanning the five can- cer types, yielding (for each cancer type) three feature matrices: one based on L1 loss, Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 7 of 22 0.56 0.57 0.58 0.59 0.60 0.61 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 0.70 L1_loss L2_loss BinaryCrossEntropy_loss AUROC Fig. 3  Predicting chemotherapy response using VAE-XGBoost models with different types of reconstruction loss for the VAE training. Marks represent AUROC values averaged over five different types of cancer, grouped by VAE loss function type. Squares, within-group sample mean; bars, 95% confidence intervals (c.i.) Fig. 3  Predicting chemotherapy response using VAE-XGBoost models with different types of reconstruction loss for the VAE training. Marks represent AUROC values averaged over five different types of cancer, grouped by VAE loss function type. Squares, within-group sample mean; bars, 95% confidence intervals (c.i.) one based on L2 loss, and a third one based on binary cross-entropy loss. We separately evaluated the three feature matrices for XGBoost prediction of the binary response-to- chemotherapy class label. By test-set area under the receiver operating characteristic (AUROC), averaged across the five cancers, we found (Fig. 3) that the features that were generated by the L1 VAEs led to 6.2% better ( p < 10−9 , Welch’s t-test) classification per- formance than the features generated by the L2 VAEs, 11.7% better ( p < 10−9 , Welch’s t-test) classification performance than the features generated by the binary cross- entropy VAEs and thus, for all subsequent analyses, we used VAEs trained with L1 loss. Chemotherapy response classification results Having selected L1 reconstruction loss for training VAEs to encode tumor transcrip- tomes for predicting response-to-chemotherapy, we developed a semi-supervised approach based on VAE encoding of the tumor transcriptome, for predicting chemo- therapy response. In brief, our approach consisted of three steps: 1. Training a VAE to encode clinically unlabeled tumor transcriptomes (for the top 20% most variable genes) for a single cancer type, into a low-dimensional space (“VAE model architectures” section). 2. Using that VAE to obtain latent-space encodings for the tumor transcriptomes that are labeled for a relevant clinical endpoint (in this work, response to chemotherapy). are labeled for a relevant clinical endpoint (in this work, response to chemotherapy). 3. Training and testing a supervised classifier for predicting chemotherapy response. 3. Training and testing a supervised classifier for predicting chemotherapy response. Because some cancer types benefited from a deeper VAE network architecture than oth- ers for effective encoding, we used three different VAE architectures for learning fea- tures for predicting chemotherapy response in the context of three subsets of cancer types (VAE-1 for breast and pancreatic; VAE-2 for colon; and VAE-3 for bladder and sarcoma; Table 5). For each VAE architecture, our approach was to use all of the data Page 8 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Table 2  Comparison of chemotherapy response prediction performance for XGBoost models trained with VAE-derived features versus autoencoder (AE)-derived features, for three cancer types (BRCA, BLCA, and PAAD) The p values are for row-wise difference of means tests for the two columns under “AUROC” and for the two columns under “AUPRC”, respectively. For each cancer type (row), the highest mean AUROC performance is shown in boldface Cancer type Mean p (Welch’s t-test) AUROC AUPRC AUROC AUPRC VAE AE VAE AE VAE versus AE VAE versus AE BRCA​ 0.674 0.575 0.192 0.137 1.61 × 10−15 5.38 × 10−10 PAAD 0.738 0.660 0.764 0.695 3.46 × 10−10 6.72 × 10−7 BLCA 0.659 0.573 0.649 0.577 7.97 × 10−12 1.23 × 10−7 SARC​ 0.704 0.611 0.736 0.654 2.78 × 10−7 1.75 × 10−6 The p values are for row-wise difference of means tests for the two columns under “AUROC” and for the two columns under “AUPRC”, respectively. Chemotherapy response classification results For each cancer type (row), the highest mean AUROC performance is shown in boldface from the five-cancer set of 2,606 unlabeled tumors for VAE training, but for predicting chemotherapy response for a given cancer type, we used encodings from the VAE archi- tecture that corresponds to the cancer type (Table 5). To select the supervised classification algorithm for step (3) above, we used an empiri- cal approach, comparing the AUROC performance of XGBoost, kernel SVM, and k-nearest neighbors for predicting sarcoma response to chemotherapy with features based on VAE-3 encodings (semi-supervised) or expression levels of individual genes (fully-supervised). We found (Additional file 1: Fig. S4) XGBoost to be superior to ker- nel SVM and k-nearest neighbors (KNN), in both semi-supervised and fully supervised analyses, and thus we chose XGBoost as the classification algorithm for subsequent analyses. To address the primary question of to what extent a VAE-based, semi-supervised (VAE-XGBoost) approach could advance the state-of-the-art for transcriptome-based prediction of chemotherapy response, we sought to compare VAE-XGBoost’s perfor- mance to that of three alternative approaches: (1) a semi-supervised approach using a regular auto-encoder (AE) with the same architecture as the VAE; (2) a fully supervised approach directly using the transcriptome data; and (3)  a semi-supervised approach based on a traditional dimensional reduction technique (either principal component analysis, PCA; or independent component analysis, ICA). VAE‑XGBoost versus AE‑XGBoost This analysis was carried out across five cancers (BRCA, COAD, BLCA, PAAD, and SARC) The p values are for row-wise difference of means tests for the indicated pairs of sample groups (columns). For each cancer type (row), the highest mean AUPRC performance is shown in boldface AUPRC (mean) p (Welch’s t-test) Cancer type VAE Raw data PCA ICA VAE versus Raw data VAE versus PCA VAE versus ICA BRCA​ 0.192 0.157 0.145 0.150 4.21 × 10−6 7.42 × 10−10 5.01 × 10−8 PAAD 0.764 0.729 0.746 0.713 3.38 × 10−4 9.12 × 10−2 2.02 × 10−6 COAD 0.593 0.535 0.579 0.545 6.52 × 10−4 3.91 × 10−1 1.27 × 10−3 BLCA 0.649 0.623 0.587 0.654 4.30 × 10−2 1.60 × 10−7 6.13 × 10−1 SARC​ 0.736 0.713 0.714 0.729 6.15 × 10−2 1.61 × 10−1 5.96 × 10−1 The p values are for row-wise difference of means tests for the indicated pairs of sample groups (columns). For each cancer type (row), the highest mean AUPRC performance is shown in boldface The p values are for row-wise difference of means tests for the indicated pairs of sample groups (columns). For each cancer type (row), the highest mean AUPRC performance is shown in boldface sarcoma), with ( p < 10−9 , Welch’s t-test) classification performance. Thus, we used the VAE for neural network-based unsupervised embeddings, for subsequent analyses. VAE‑XGBoost versus AE‑XGBoost To address alternative approach  (1) (“traditional auto-encoder”), we compared the performance of VAE-XGBoost to that of a model consisting of a regular auto-encoder combined with XGBoost (“AE-XGBoost”; Table  2 and Additional file  1: Figs. S5–S6). For this four-cancer analysis, we used the VAE-1 architecture for BRCA and PAAD, which was the same network that we used in the t-SNE analysis and the VAE-3 architec- ture for BLCA and SARC (Table 5). We measured performance using test-set AUROC and AUPRC using five-fold cross-validation. We found  (Table  2) that VAE-XGBoost outperformed AE-XGBoost by an average AUROC increase of 14.5% and an average AUPRC increase of 16.3% over the four-cancer average (breast, pancreatic, bladder, and Page 9 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Table 3  Comparison of chemotherapy response prediction performance (AUROC) for XGBoost models trained with original transcriptome data (“Raw data”) or transcriptome data encoded with PCA, ICA, or VAE. This analysis was carried out across five cancers (BRCA, COAD, BLCA, PAAD, and SARC) Table 3  Comparison of chemotherapy response prediction performance (AUROC) for XGBoost models trained with original transcriptome data (“Raw data”) or transcriptome data encoded with PCA, ICA, or VAE. This analysis was carried out across five cancers (BRCA, COAD, BLCA, PAAD, and SARC) The p values are for row-wise difference of means tests for the indicated pairs of sample groups (columns). For each cancer type (row), the highest mean AUROC performance is shown in boldface Cancer type AUROC (mean) p (Welch’s t-test) VAE Raw data PCA ICA VAE versus Raw data VAE versus PCA VAE versus ICA BRCA​ 0.674 0.649 0.614 0.609 8.07 × 10−4 3.80 × 10−12 3.39 × 10−14 PAAD 0.738 0.694 0.710 0.685 6.99 × 10−6 5.04 × 10−3 2.41 × 10−6 COAD 0.707 0.674 0.726 0.689 1.19 × 10−3 2.81 × 10−2 5.65 × 10−2 BLCA 0.659 0.626 0.593 0.650 7.81 × 10−5 4.27 × 10−9 2.61 × 10−1 SARC​ 0.704 0.679 0.682 0.701 3.49 × 10−2 2.91 × 10−2 8.64 × 10−1 The p values are for row-wise difference of means tests for the indicated pairs of sample groups (columns). For each cancer type (row), the highest mean AUROC performance is shown in boldface Table 4  Comparison of chemotherapy response prediction performance (AUPRC) for XGBoost models trained with original transcriptome data (“Raw data”) or transcriptome data encoded with PCA, ICA, or VAE. VAE‑XGBoost versus PCA‑XGBoost and ICA‑XGBoost VAE‑XGBoost versus PCA‑XGBoost and ICA‑XGBoost To address alternative approach (3), we empirically compared VAE-XGBoost to mod- els in which PCA or ICA components were used as XGBoost features (i.e., “PCA- XGBoost” and “ICA-XGBoost”). We aimed to empirically study prediction performance of these models for each of the five cancer types separately, using the set of cancer type- specific labeled tumors (806 labeled tumors in all). For four out of five cancer types (bladder, breast, pancreatic, and sarcoma), in terms of AUROC the semi-supervised VAE-XGBoost method significantly outperformed the semi-supervised PCA-XGBoost method (Table 3 and Additional file 1: Fig. S7). Additionally, for three out of five cancer types (breast, colon, and pancreatic), the semi-supervised VAE-XGBoost method signifi- cantly outperformed the semi-supervised ICA-XGBoost method (Table 3 and Additional file 1: Fig. S7). The five-cancer average AUROC for VAE-XGBoost was 0.688, a perfor- mance gain of 6.3% over the five-cancer average AUROC for PCA-XGBoost (0.646), a gain of 6.5% over the ICA-XGBoost (0.645) and a gain of 4.5% over the fully-supervised model’s average (0.658). Notably, a single deep VAE architecture (VAE-1, which had a 50-dimensional latent space and six layers in the encoder) yielded latent-space encod- ings that outperformed semi-supervised PCA-XGBoost for two cancer types (breast and pancreatic); a single shallow VAE architecture (VAE-3, which had a 500-dimensional latent space and two layers in the encoder) yielded latent-space encodings that outper- formed semi-supervised PCA-XGBoost for two cancer types (bladder and sarcoma). For three out of five cancer types (breast, bladder, and pancreatic), in terms of AUPRC the semi-supervised VAE-XGBoost method significantly outperformed the semi- supervised PCA-XGBoost method (Additional file 1: Fig. S8 and Table 4). Additionally, for three out of five cancer types (breast, colon, and pancreatic), the semi-supervised VAE-XGBoost method significantly outperformed the semi-supervised ICA-XGBoost method (Additional file 1: Fig. S8 and Table 4). The five-cancer average AUPRC for VAE- XGBoost was 0.441, a performance gain of 9.1% over the five-cancer average AUPRC for PCA-XGBoost (0.403), a gain of 8.2% over the ICA-XGBoost (0.406), and a gain of 8.5% over the fully-supervised model’s average (0.405). VAE‑XGBoost versus fully‑supervised XGBoost To address alternative approach (2) (“fully supervised”), we empirically compared the performance of the VAE-XGBoost method to a fully supervised model in which we applied XGBoost directly to the tumor expression levels of the top 20% most variable genes (13,584 genes) as feature data. For five out of five cancer types (breast, colon, pan- creatic, bladder, and sarcoma), in terms of test-set AUROC, the VAE-XGBoost approach outperformed the fully-supervised XGBoost approach (Additional file  1: Fig. S7), by Welch’s t-test (Table 3). In terms of test-set AUPRC, for four out of five cancer types (breast, colon, pancreatic, and bladder), the VAE-XGBoost approach outperformed the fully-supervised approach of applying XGBoost directly to the expression levels of the tumors’ top 20% most variable genes (Additional file 1: Fig. S8), by Welch’s t-test (Table 4); for SARC, the semi-supervised VAE-XGBoost and fully-supervised models’ performances were statistically indistinguishable. Page 10 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 PCA & VAE feature importance scores, for COAD Bars separately ordered from highest to lowest (only top 20 most important features shown) Table 5  VAE architectures used for predicting chemotherapy response (h, latent space dimension; “layers”, # of layers used in the encoder/decoder) Name Cancer types h Layers VAE-1 BRCA, PAAD 50 Six VAE-2 COAD 400 Two VAE-3 BLCA, SARC​ 500 Two 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 0 200 400 600 Sum of importance Rank of features Group PCA VAE Fig. 4  Comparing the distributions of feature importance scores for the most informative features for PCA-XGBoost and VAE-XGBoost, for predicting response to chemotherapy in colon cancer (COAD). Bars indicate the sum (over 30 replications) of XGBoost feature importance scores. “Group” indicates the low-dimensional embedding method used (VAE or PCA). Bars separately ordered from highest to lowest (only top 20 most important features shown) Fig. 4  Comparing the distributions of feature importance scores for the most informative features for PCA-XGBoost and VAE-XGBoost, for predicting response to chemotherapy in colon cancer (COAD). Bars indicate the sum (over 30 replications) of XGBoost feature importance scores. “Group” indicates the low-dimensional embedding method used (VAE or PCA). Bars separately ordered from highest to lowest (only top 20 most important features shown) Table 5  VAE architectures used for predicting chemotherapy response (h, latent space dimension; “layers”, # of layers used in the encoder/decoder) Name Cancer types h Layers VAE-1 BRCA, PAAD 50 Six VAE-2 COAD 400 Two VAE-3 BLCA, SARC​ 500 Two Table 5  VAE architectures used for predicting chemotherapy response (h, latent space dimension; layers”, # of layers used in the encoder/decoder) PCA & VAE feature importance scores, for COAD Having established that the semi-supervised VAE-XGBoost outperforms the semi- supervised PCA-XGBoost approach for tumor transcriptome-based prediction of chem- otherapy response for four out of five cancer types, we sought to understand the basis for the higher performance of PCA-XGBoost over VAE-XGBoost on the fifth cancer type, colon adenocarcinoma (COAD). Specifically, we investigated whether the strong performance of PCA-XGBoost on COAD is attributable to differences in the distribu- tions of XGBoost feature importance scores of the PCA features versus VAE latent-space features. We found that the distribution of feature importance scores (as a function of rank) was more sharply peaked at lowest-ranked features in the VAE than in the PCA (Fig. 4), suggesting that the performance gain with PCA reflects a broader spectrum of informative features for that particular cancer type. Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 11 of 22 Discussion As far as we are aware, this work is the first report of a multi-cancer investigation of the potential for a VAE-based, semi-supervised approach for predicting in  vivo chemotherapy response from the tumor transcriptome. Across the five cancer types that we studied, the ratio of responding tumors to progressive disease tumors ranged from a low of 0.77 for pancreatic cancer to a high of 8.61 for breast cancer, reflect- ing a broad range of resistances to standard-of-care chemotherapy. Our results clearly demonstrate the utility of the VAE for compressing high-dimensional data to a con- tinuous, low-dimensional latent space while retaining features that are essential for distinguishing different cancer types and for predicting response to chemotherapy. Nevertheless, three limitations of this work bear noting. The first limitation concerns the type(s) of tumor “omics” data from which fea- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 0 200 400 600 Sum of importance Rank of features Group PCA VAE Fig. 4  Comparing the distributions of feature importance scores for the most informative features for PCA-XGBoost and VAE-XGBoost, for predicting response to chemotherapy in colon cancer (COAD). Bars indicate the sum (over 30 replications) of XGBoost feature importance scores. “Group” indicates the low-dimensional embedding method used (VAE or PCA). Discussion As far as we are aware, this work is the first report of a multi-cancer investigation of the potential for a VAE-based, semi-supervised approach for predicting in  vivo chemotherapy response from the tumor transcriptome. Across the five cancer types that we studied, the ratio of responding tumors to progressive disease tumors ranged from a low of 0.77 for pancreatic cancer to a high of 8.61 for breast cancer, reflect- ing a broad range of resistances to standard-of-care chemotherapy. Our results clearly demonstrate the utility of the VAE for compressing high-dimensional data to a con- tinuous, low-dimensional latent space while retaining features that are essential for distinguishing different cancer types and for predicting response to chemotherapy. Nevertheless, three limitations of this work bear noting. The first limitation concerns the type(s) of tumor “omics” data from which fea- tures are derived for the predictive model. While in this work we focused on tumor Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 12 of 22 transcriptome data which can be measured with high precision over a wide dynamic range of transcript abundances by RNA-seq, we note that TCGA datasets of tumor somatic mutations and copy number alteration events are also available [17]. Given the voluminous literature on the use of tumor somatic genomic data for precision cancer diagnosis [37–39], tumor DNA datasets are fertile ground for developing a semi-supervised, multi-omics model for predicting response to chemotherapy. Second, for decision tree-based response-to-chemotherapy prediction, the perfor- mance of VAE-encoded transcriptome features is somewhat sensitive to the type of nor- malization used for the gene expression levels (data not shown). We explored various published normalization methods for the RNA-seq data including standardization of log counts and using FPKM; we ultimately chose min-max-normalized log2 total-count- normalized counts for the gene expression levels to be used to derive features. However, there are additional transcript quantification methods [40] that could be explored in the context of finding optimal tumor transcriptome VAE encodings for precision oncology. A similar comment applies to the specific form of the reconstruction loss function: in our analysis, features from the VAE trained with L1 loss clearly (across five cancers) out- performed those from the VAE trained with L2 or cross-entropy loss, and thus, consist- ent with Way and Greene [28], we used L1 loss for the VAE that we used to address the main question of this work as well as the pan-cancer t-SNE analysis. Discussion The third limitation relates to the VAE architecture. While it is promising that a sin- gle deep VAE architecture (VAE-1, with a 50-dimensional latent space and six fully- connected layers) yielded features that outperformed PCA and the original RNA-seq feature data for two different cancer types (breast and pancreatic), for the other three cancer types, it was necessary to use shallower (two-layer) VAE architectures with big- ger latent space dimensions (400 and 500, respectively). Of the five cancer types that we studied, colon cancer and sarcoma had the lowest proportions of labeled samples (0.229 and 0.245 respectively; see Table 1). Our findings suggest that for some cancers, a deep, low-latent-dimension VAE architecture yields optimal features for predicting response, while for other cancers, a shallow, medium-sized-latent-dimension VAE architecture is more effective. Hu and Greene [41], based on a study employing single-cell transcrip- tome profiling, noted substantial performance differences with hyperparameter tuning on VAE architectures; they further noted that in terms of the robustness of performance with respect to hyperparameter variation, a base VAE with two layers was better than a deeper VAE architecture. Lakhmiri et al. [42] reported VAE architecture hyperparame- ter tuning as well as the training phase have a great impact on the overall precision of the network and its ability to generalize, and proposed -MADS, a hybrid derivative-free optimization algorithm for VAE fitting. More study with larger datasets will be required in order to determine whether a single VAE architecture could be successfully used for general-purpose tumor transcriptome feature extraction for precision oncology. While our results show promise for the VAE in the context of a semi-supervised approach for response-to-chemotherapy prediction, for colon cancer, the VAE-XGBoost method did not outperform PCA-XGBoost (though it did outperform the fully super- vised approach of XGBoost trained on the unencoded gene expression data). One pos- sible explanation for the colon cancer-specific superior performance of PCA features over VAE features for predicting response to chemotherapy may be due to the fact that Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 13 of 22 while (for COAD) feature importance for the VAE features is sharply peaked for the first few features and falls off fairly rapidly with feature rank, the PCA features have a signifi- cantly flatter distribution of relative feature importance (Fig. 4). Conclusions For four of the five cancer types that we studied, the semi-supervised VAE-XGBoost approach significantly outperformed a semi-supervised PCA-XGBoost approach for tumor transcriptome-based prediction of response to chemotherapy, reaching a top AUROC of 0.738 for pancreatic adenocarcinoma. For three of the five cancer types that we studied, the semi-supervised VAE-XGBoost approach significantly outperformed a semi-supervised ICA-XGBoost approach for tumor transcriptome-based prediction of response to chemotherapy. For BLCA and SARC, the semi-supervised VAE-XGBoost and ICA-XGBoost models’ performances were statistically indistinguishable. For five out of five cancer types, the semi-supervised VAE-XGBoost approach significantly out- performed a fully-supervised approach consisting of XGBoost applied to the expression levels of the top 20% most variably expressed genes. Given high-dimensional “omics” data, the VAE is a powerful tool for obtaining a nonlinear low-dimensional embed- ding; it yields features that retain biological patterns that distinguish between different types of cancer and that enable more accurate tumor transcriptome-based prediction of response to chemotherapy than would be possible using the original data or their princi- pal components. Discussion Follow-on studies with larger datasets will be required to delineate under what circumstances transcriptome VAE encodings will prove superior to linear principal components. Multiple groups have argued [43–45] that to improve current precision oncology models, significantly expanded training datasets are needed to overcome the challenges posed by tumor het- erogeneity, and that models must more broadly leverage somatic genetic and epigenetic information. We anticipate that the performance of VAE-XGBoost could improve sig- nificantly with more unlabeled and labeled tumor transcriptome data. Finally, we note a possible future extension of this work that will become feasible when larger train- ing datasets are available: because response to chemotherapy is drug-dependent, the XGBoost classifier can easily include and use the chemotherapy drug type used for the patient (Additional file 1: Table S1) as a categorical feature. Methods We carried out all data processing and machine-learning tasks on a Dell XPS 8700 work- station equipped with Nvidia Titan RTX GPU and running the Ubuntu GNU/Linux operating system version 16.04. All of the analysis code that we implemented was exe- cuted in Python version 3.5.5 except that we used R version 3.3.3 for statistical analysis of AUROC and AUPRC values (“Area Under ROC Curve (AUROC), Area Under the pre- cision-recall Curve (AUPRC)” sections), gene-level MAD calculations (“Gene expression data” section) and plotting (“Lower-dimensional embedding” section). We carried out all statistical tests using the R computing environment (version 3.3.3) and using the R soft- ware package stats version 3.4.4. Page 14 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Lower‑dimensional embedding We computed t-SNE embedding components of the tumors using the func- tion sklearn.manifold.TSNE from the python software package scikit- learn version 0.19.1 with parameters init = “pca′′ , perplexity = 20 , learning_rate = 300 , and n_iter = 400 . We computed UMAP embedding com- ponents using the function sklearn.manifold.umap.UMAP from the python soft- ware package scikit-learn version 0.19.1 with parameters n_neighbors = 50 , min_dist = 0.3 , and metric = “euclidean′′ . For plotting the embeddings, we used the R software package ggplot2 version 3.1.1. Gene expression data From the Xena data portal [46], we obtained TCGA Level  3 tumor RNA-seq tran- scriptome data of 33 cancer types (totaling 11, 057 tumors) and, for the response-to- chemotherapy prediction problem, five cancer types [colon adenocarcinomas (COAD), pancreatic adenocarcinoma (PAAD), bladder carcinoma (BLCA), sarcoma (SARC), and breast invasive carcinoma (BRCA)] totaling 2,606 tumors. We selected the five cancer types based on two criteria: (1) a sufficient number (at least 65) of paired tumor-tran- scriptome and clinical data samples available for the cancer type; and (2)  a sufficient number (at least 180) of tumor transcriptome samples available (regardless of the clin- ical data availability) for the cancer type. We obtained both the RNA-seq (gene-level) total-read-count-normalized log2(1 + C) read counts and normalized (fragments per kilobase of transcript per million mapped reads, FPKM [47]) expression data for for 60,483 human genes. To focus the machine-learning on the portion of the tumor tran- scriptome that had the most variation from tumor to tumor, we identified the top 20% most variable genes as measured by the median absolute deviation (MAD) across tumors, of gene expression in terms of FPKM (we used FPKM for this purpose in order to mitigate bias due to read length and tumor-specific depth of sequencing) based on our preliminary results for prediction of response-to-chemotherapy for SARC, for dif- ferent quantile thresholds of genes by variability of expression (Additional file 1: Fig. S4). For deriving feature-sets for XGBoost prediction directly based on transcript abun- dances or based on VAE- or PCA encoding, the 20% criterion applied to each of the five cancer types yielded a set of 13,584 genes. We computed MAD using the R package stats version 3.4.4 [48] with default parameters. After the variance-filtering step, we used the log2(1 + C) of total-count-normalized count values for the top-20% highest- variance genes (that were selected as described above) to obtain (or encode) feature val- ues. We compared the performance—in terms of minimizing the VAE reconstruction loss (see “Variational autoencoder (VAE)” section)—of different feature scaling methods (no scaling, min-max normalization, and standardization [49]) and selected min-max normalization as the method that we used to rescale gene-level count data for input into the VAE. Z|xt ∼N(µ(xt), diag(σ(xt))), (1) Z|xt ∼N(µ(xt), diag(σ(xt))), where diag(m) is a matrix whose diagonal elements are the elements of the vector m . This equation is the same as Eq. 1 in Zemouri et  al. [51]. The decoder is a function g : Rh →[0, 1]m that, for an outcome Z|xt = zt ∈Rh , maps (2) g : zt →g(zt) ≡xt; (2) g : zt →g(zt) ≡xt; the tilde on xt denotes that it is the decoded data for the tumor transcriptome xt . A good autoencoder should have low reconstruction error L, which is convenient to define in terms of the p-norm of the difference between the tumor transcriptome data xt and the reconstructed data xt , i.e., ||xt −xt|| p p , where || ||p denotes the p-norm. However, this definition of the reconstruction error is only deterministic in the context of a spe- cific outcome Z|xt = zt . Thus, it is conventional to define the reconstruction error as an expectation value over outcomes of Z|xt, the tilde on xt denotes that it is the decoded data for the tumor transcriptome xt . A good autoencoder should have low reconstruction error L, which is convenient to define in terms of the p-norm of the difference between the tumor transcriptome data xt and the reconstructed data xt , i.e., ||xt −xt|| p p , where || ||p denotes the p-norm. However, this definition of the reconstruction error is only deterministic in the context of a spe- cific outcome Z|xt = zt . Thus, it is conventional to define the reconstruction error as an expectation value over outcomes of Z|xt, (3) L|(X =xt) ≡E Z|xt=zt(||xt −g(zt)|| p p ), (3) L|(X =xt) ≡E Z|xt=zt(||xt −g(zt)|| p p ), where E represents an expectation value over a space of outcomes  . It should be noted the above representation of the reconstruction error is in terms of the outcome, zt , of a r.v. ( Z|xt ) whose distributional parameter functions µ and σ have hyperparameters (neu- ral network coefficients) that will be fitted. This equation is similar to Eq. 3 in Zemouri et al. [51]. Compared to the binary cross-entropy loss used in Eq. 3 in Zemouri et al. [51], our Eq. t follows from Eqs. 4 and 1 that Et is standard multivariate normal, Variational autoencoder (VAE) An autoencoder is a type of model that combines “encoder” and “decoder” neural net- works to learn a low-dimensional continuous data encoding from which the input signal can be approximately reconstructed [50]. A key advantage of an autoencoder is that it is Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 15 of 22 unsupervised, i.e., it can be trained without labeled examples. Unlike classical autoen- coders (e.g., sparse or denoising autoencoders), the variational autoencoder (VAE) is a generative probabilistic model which maps an input vector to a latent-space random var- iable (r.v.). Below, we mathematically define the VAE. i Let T denote the set of tumors for which the VAE is to be fit to the tumor transcrip- tomes (with n ≡|T| ) and let m denote the number of genes for which transcript abun- dances are used to represent the tumor transcriptome. After min-max transformation of the tumor transcriptome measurements (“Gene expression data” section), each tumor’s transcriptome is represented as a vector x ∈[0, 1]m . Let X denote the random variable representing the population distribution from which tumor transcriptomes are sampled, and let X ∈[0, 1]m×n represent the composite matrix of all sampled tumor transcriptomes). We aim to learn a VAE that will comprise an encoder and decoder, with the encoder consisting of mean and variance functions µ : [0, 1]m →Rh and σ : [0, 1]m →Rh + , respectively. Together, µ and σ map the tumor transcriptome vector xt to a h-dimensional r.v. Z|xt, (1) Z|xt ∼N(µ(xt), diag(σ(xt))), Z|xt ∼N(µ(xt), diag(σ(xt))), 3 used L1 loss instead (see findings from an empirical study in “L1 loss is better than L2 loss and cross-entropy loss for this application” section demonstrating the supe- riority of L1 over L2 or binary cross-entropy for the VAE reconstruction loss function). Because Eq. 3 is ill-suited to backpropagation, it is helpful to recast it in terms of a new random variable Et that depends on Z|xt by It follows from Eqs. 4 and 1 that Et is standard multivariate normal, (4) Et ≡(diag(σ(xt)))−1 2 (Zt|xt −µ(xt)). Et ≡(diag(σ(xt)))−1 2 (Zt|xt −µ(xt)). (4) Et ≡(diag(σ(xt)))−1 2 (Zt|xt −µ(xt)). (4) It follows from Eqs. 4 and 1 that Et is standard multivariate normal, It follows from Eqs. 4 and 1 that Et is standard multivariate normal, Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 16 of 22 (5) Et ∼N(0, I), Et ∼N(0, I), (5) where I is the h × h identity matrix, and thus, Et does not depend on µ , σ , or t. We there- fore drop the subscript t and simply denote the rescaled latent-space random variable as E . Solving Eq. 4 for Z|xt and applying it to Eq. 3, the reconstruction error L|(X =xt) can be represented by (6) L|(X =xt) = EE  xt −g  µ(xt) +  diag(σ(xt)) E   p p  , (6) which is amenable to backpropagation because the only r.v. in it is E , whose distribu- tional parameters do not depend on the neural network coefficients that we will be varying. In practice, rather than computing the multivariate integral over outcomes of E , L|(X =xt) is typically approximated by averaging over a limited number J of samples from E, (7) L|(X = xt) ≃  xt −g  µ(xt) +  diag(σ(xt)) ǫj   p p  j , (7) where ⟨⟩j denotes average over j ∈{1, . . . , J} and ǫj is sample j from E . Following Way and Greene [28], we used a number of samples that is equivalent to the dimension of the transcriptome, i.e., J = m . For the case of p = 2 (i.e., L2 norm), minimizing L|(X = xt) as defined above is equivalent to maximizing the expectation value of the log-likelihood log(P(g(Z) = xt | X = xt)) . 1  Note, functions µ and σ are just two different outputs of the encoding neural network, differing only at the final layer, and thus for simplicity of notation we represent them as having a common parameter vector θ. Z|xt ∼N(µ(xt), diag(σ(xt))), However, following Way and Greene  [28] and consistent with empirical evidence (“L1 loss is better than L2 loss and cross-entropy loss for this application” section), for our five-cancer study of the utility of a VAE-based approach for response-to-chemotherapy prediction, as well as for the pan-cancer t-SNE analysis (“VAE encoding preserves cancer type features” section), we chose to use L1 reconstruc- tion loss, i.e., p = 1 in Eq. 3. The reconstruction loss measures bias error, whose minimization must be balanced against the simultaneous goal of controlling variance error through regularization. In the VAE, regularization requires incentivizing (in the learning of µ , σ , and g ) the latent space distributions of Z|x to be close to standard multivariate normal. This is accom- plished by assigning a penalty based on the Kullback-Leibler divergence between the dis- tribution of Z|xt and the target distribution E , represented by DKL(P(Z|xt) || P(E)) . This regularization is analytically tractable [52], and for a given tumor t yields (Supplemen- tary Equation, Eq. S2) the following regularization function: (8) DKL  P(Zt|xt)  P(E)  = ||µ(xt)|| 2 2 + ||σ(xt)|| 2 2 −|| log(σ(xt))||1 −1, (8) where log(σ t) denotes an element-wise log and || ||1 is the L1 norm. where log(σ t) denotes an element-wise log and || ||1 is the L1 norm. Fitting the VAE to X requires selecting µ , σ , and g from their respective function spaces; in practice, we search over functions that can be represented using a neural net- work for µ and σ (parameterized by the vector θ)1 and a neural network for the function Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 17 of 22 g (parameterized by the vector φ ). Exploring the space of functions µθ , σ θ , and gφ corre- sponds to computationally searching for the vector pair (ˆθ, ˆφ) that together minimize the joint (over all tumors) sum of the tumor-specific reconstruction loss and the regulariza- tion penalty, g (parameterized by the vector φ ). Exploring the space of functions µθ , σ θ , and gφ corre- sponds to computationally searching for the vector pair (ˆθ, ˆφ) that together minimize the joint (over all tumors) sum of the tumor-specific reconstruction loss and the regulariza- tion penalty, (9) (θ, φ) = argmin (θ,φ)  t∈T  L|(X = xt) + DKL  P(Z|xt)  P(E)  . (9) Applying Eqs. Z|xt ∼N(µ(xt), diag(σ(xt))), 6, 7, and 8, and setting p = 1 as discussed above, we obtain the explicit formula for fitting a VAE to X, (10) (θ, φ) = argmin (θ,φ)  t∈T  1 J J j=1 xt −gφ  µθ(xt) +  diag(σ θ(xt)) ǫj  1  +||µθ(xt)|| 2 2 + ||σ θ(xt)|| 2 2 −|| log(σ θ(xt))||1 −1  . (10) We implemented Eq. 10 in Tensorflow version 1.4.1 with Keras version 2.1.3 as the model-level library. We solved Eq. 10 using the Adam optimization algorithm [53] (with batch normalization) from the python package keras-gpu version 2.1.3 with param- eters learning_rate = 2 × 10−3 , beta_1 = 0.9 , and beta_2 = 0.999 , to obtain (θ, φ) . Then, for each tumor t, we used a single sample Z|xt = zt from the distribution N(µθ(xt), diag(σ θ(xt))) as the final latent-space encoding of the tumor to be used for supervised learning (“Regularized gradient boosted decision trees (XGBoost)” section). VAE model architectures We trained six transcriptome-encoding VAEs based on three VAE architectures, the pan-cancer VAE architecture (for the 33-cancer unsupervised analysis, “VAE encoding preserves cancer type features” section) and three cancer type-specific VAE architec- tures for response-to-chemotherapy prediction (“Chemotherapy response classification results” section) (VAE-1 was used for two different cancer types, BRCA and PAAD, VAE-2 was used for COAD, and VAE-3 was used for two different cancer types, BLCA and SARC). For the pan-cancer, we used the VAE-1 model with a latent space dimen- sion h = 50 . For the cancer  type-specific VAE architectures, we again used the same number of fully-connected layers in the encoder as in the decoder (Table 5). Labeling tumors based on response to chemotherapy From Xena and cBioPortal [54, 55], we obtained and combined TCGA clini- cal data (where available) for the patients whose tumor transcriptomes we acquired (“Gene expression data” section). From Xena, we extracted the variables submitter_id.samples , therapy_type , and measure_of_response ; from cBioPortal, we extracted the variables Sample_ID , Disease.Free.Status , and Pharmaceutical.Therapy.Indicator . We co-analyzed the Xena- and cBio- Portal-obtained clinical data to label tumors “responded” ( y = 0 ) or ”progressive” ( y = 1 ), by assigning y = 0 when the clinical record had Complete response or partial response in the measure_of_response column of the clinical data Page 18 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Table 6  XGBoost classification algorithm hyperparameters and hyperparameter ranges used in grid-search tuning Table 6  XGBoost classification algorithm hyperparameters and hyperparameter ranges used in grid-search tuning Hyperparameter name Hyperparameter description Hyperparameter range n_estimators Number of trees to fit (1, 2, 3, . . . , 40) max_depth Maximum tree depth (1, 2, 3, . . . , 10) learning_rate Boosting learning rate (0.05, 0.1, 0.2, 0.4, 0.6, 0.8) min_child_weight Minimum sum of instance weight needed in a child (1, 2, 3, . . . , 10) subsample Sub-sample ratio of the training instance (0.1, 0.2, 0.3, . . . , 1.0) colsample_bytree Sub-sample ratio of columns when constructing each tree (0.1, 0.2, 0.3, . . . , 1.0) reg_alpha Coefficient of L1 regularization for the node weights (0, 1, 2, 3) reg_lambda Coefficient of L2 regularization for the node weights (1, 2, . . . , 100) Table 7  SVM classification algorithm hyperparameters and hyperparameter ranges used in grid- search tuning Hyperparameter name Hyperparameter description Hyperparameter range kernel Kernel type to be used (‘linear’, ‘poly’, ‘rbf’, ‘sigmoid’) C Regularization parameter (5, 6, 7, . . . , 50) degree Degree of the polynomial kernel function (‘poly’) (1, 2, 3, . . . , 20) from Xena, or with value DiseaseFree in the Disease.Free.Status column of the clinical data from cBioPortal while therapy type is recorded as Chemotherapy in both. We assigned y = 1 to tumors whose clinical records had values Radiographic progressive disease , Clinical progressive disease , or stable disease in the Xena clinical data column measure_of_response , or had value Recurred / progressed in the cBioPortal data column Disease.Free.Status while the therapy_type is recorded as Chemotherapy in both files. Labeling tumors based on response to chemotherapy This yielded 806 labeled tumors out of 2,606 total. A total of 39 different drugs were used to treat the 794 patients (Additional file 1: Table S1). Regularized gradient boosted decision trees (XGBoost) For predicting whether or not (based on its transcriptome-derived feature-set: raw, PCA, ICA, or VAE) a tumor would respond to chemotherapy, we used XGBoost [34], an efficient implementation of regularized gradient boosted decision trees. We used the classifier function XGBClassifier from the python software package xgboost version 0.80, with gamma=0. We tuned eight hyper-parameters (Table 6) by exhaus- tive grid-search with five-fold cross-validation, using model_selection.Grid- SearchCV from scikit-learn version 0.19.1. To obtain feature importance scores, we used get_score with importance_type = cover. Support vector machine (SVM) For predicting whether or not (based on its transcriptome-drived feature-set: raw or VAE) a tumor would respond to chemotherapy, we used SVM [56]. We used the clas- sifier function SVC from the python software package sklearn.svm, with gamma = “auto”. We tuned three hyper-parameters (Table  7) by exhaustive grid-search with five-fold cross-validation, using model_selection.GridSearchCV from scikit- learn version 0.19.1. Principal component analysis (PCA) and independent component analysis (ICA) For PCA, we used the function decomposition.PCA (with parameters svd_solver=“full′′) and n_components=0.9 (90% variance, yielding 387 com- ponents) from the python package scikit-learn version 0.19.1. For plotting, we used matplotlib version 2.1.2. For ICA, we used the function decomposition. Page 19 of 22 Wei and Ramsey BMC Bioinformatics (2021) 22:453 Table 8  KNN classification algorithm hyperparameters and hyperparameter ranges used in grid- search tuning Hyperparameter name Hyperparameter description Hyperparameter range n_neighbors Number of neighbors to use (1, 2, 3, . . . , 20) weights Weight function used in prediction (‘uniform’, ‘distance’) algorithm Algorithm used to compute the nearest neighbors (‘ball_tree’, ‘kd_tree’, ‘brute’, ‘auto’) leaf_size Leaf sized passed to BallTree or KDTree (1, 2, 3, . . . , 20) p Power parameter for the Minkowski metric (1, 2, 3, 4) Table 8  KNN classification algorithm hyperparameters and hyperparameter ranges used in grid- search tuning FastICA (with parameters n_components=387 (i.e., the same number of compo- nents as used in the PCA method) from the python package scikit-learn version 0.19.1. For plotting, we used matplotlib version 2.1.2. K‑nearest neighbors vote (KNN) For predicting whether or not (based on its transcriptome-drived feature-set: raw or VAE) a tumor would respond to chemotherapy, we used KNN [57], an implementation based on the k nearest neighbors of each query point. We used the classifier function neighbors.KNeighborsClassifier from the python software package scikit- learn. We tuned five hyper-parameters (Table  8) by exhaustive grid-search with five-fold cross-validation, using model_selection.GridSearchCV from scikit- learn version 0.19.1. Funding SAR acknowledges support from the Animal Cancer Foundation. Funding SAR acknowledges support from the Animal Cancer Foundation. SAR acknowledges support from the Animal Cancer Foundation. Area under the precision‑recall curve (AUPRC) For computing the AUPRC, we used the function metrics.precision_recall_ curve and metrics.auc from the python software package scikit-learn version 0.19.1. We logit-transformed AUPRC values before testing (using two-tailed Welch’s t-test). We carried out 30 replications of five-fold cross-validation; within each rep- lication, across the five folds, we obtained prediction scores for each tumor from the fold in which the tumor was in the test set, enabling us to compute an overall AUPRC within each replication. For each training data set, we have done 30 replications of five- fold cross-validation by altering the random seed used for assign split of data during cross-validation. We have conducted the same procedure for five different cancer types (BLCA, BRCA, COAD, PAAD, SARC) as shown in the panel names of Additional file 1: Figure S8. Area under ROC curve (AUROC) For computing the AUROC (i.e., sensitivity versus false positive error rate curve), we used the function metrics.roc_auc_score from the python software package scikit-learn version 0.19.1 with parameter average=“weighted”. We logit- transformed AUROC values before testing (using two-tailed Welch’s t-test). For the L1 versus L2 analysis (“L1 loss is better than L2 loss and cross-entropy loss for this applica- tion” section), we carried out 30 replications of five-fold cross-validation; within each replication, across the five folds, we obtained prediction scores for each tumor from the fold in which the tumor was in the test set, enabling us to compute an overall AUROC within each replication. For each training data set, we carried out 30 replications of five-fold cross-validation by altering the random seed used for assigning data to folds, during the cross-validation. We used the same procedure for five different cancer types (BLCA, BRCA, COAD, PAAD, SARC) as shown in the panel names of Additional file 1: Figure S7. Wei and Ramsey BMC Bioinformatics (2021) 22:453 Page 20 of 22 Availability of data and materials y Software code written for this project “VAE for chemotherapy drug response prediction” are freely available under an open-source license, platform independent, written in Python and R with CUDA and tensorflow installed, at the URL: https://​github.​com/​ATHED/​VAE_​for_​chemo​thera​py_​drug_​respo​nse_​predi​ction. Supplementary data are available at BMC Bioinformatics online. Supplementary Information The online version contains supplementary material available at https://​doi.​org/​10.​1186/​s12859-​021-​04339-6. Additional file 1. This supplementary file contains Supplementary Figures S1, S2, S3, S4, S5, S6, S7, and S8, as well as Table S1 and Supplementary Note C. Additional file 1. This supplementary file contains Supplementary Figures S1, S2, S3, S4, S5, S6, S7, and S8, as well as Table S1 and Supplementary Note C. Authors’ contributions Authors contributions Designed the study: SAR and QW; wrote the software: QW; carried out the computational analyses: QW; processed and analyzed the data: QW and SAR; wrote the article: SAR and QW. Both authors read and approved the final manuscript. Author details 1 Author details 1 School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA. 2 Department of Bio- medical Sciences, Oregon State University, Corvallis, OR, USA. Received: 30 April 2021 Accepted: 17 August 2021 Received: 30 April 2021 Accepted: 17 August 2021 Received: 30 April 2021 Accepted: 17 August 2021 Received: 30 April 2021 Accepted: 17 August 2021 References Independent component analysis and blind signal separation. Berlin: Springer; 2006. p. 214 21. 20. An J, Cho S. Variational autoencoder based anomaly detection using reconstruction probability. 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https://openalex.org/W3191934775
https://ojs.reformedjournals.co.za/stj/article/download/2235/3091
English
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Exploring Exodus themes in the book of Amos
Stellenbosch theological journal
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Stellenbosch Theological Journal 2021, Vol 7, No 1, 1–22 DOI: http://dx.doi.org/10.17570/stj.2021.v7n1.a08 Online ISSN 2226-2385 | Print ISSN 0028-2006 2021 © Pieter de Waal Neethling Trust Stellenbosch Theological Journal 2021, Vol 7, No 1, 1–22 DOI: http://dx.doi.org/10.17570/stj.2021.v7n1.a08 Online ISSN 2226-2385 | Print ISSN 0028-2006 2021 © Pieter de Waal Neethling Trust Keywords Exodus tradition; Egypt; Book of Amos; plague; Cush Abstract Tere is little doubt that the exodus event is regarded as a most important turning point for Israel’s understanding of itself. Te aim of this article is to investigate the occurrence of the Exodus tradition in the book of Amos. Once the occurrence of the exodus tradition has been determined the second aim is to establish the function of the exodus tradition in the book. Tis is done by providing the reader with cursory overview of the exodus event as it is told in Exodus 1–15, followed by a careful reading of the relevant texts taking the literary and historical dimensions of the texts in consideration. Te investigation came to mainly three results: the exodus tradition is utilized in the book of Amos as a motivation for the prophecies of doom directed to Israel. Secondly, the exodus tradition is in fact turned against Israel and thirdly, the exodus event is radically relativized as an event not unique to Israel alone. Exploring Exodus themes in the book of Amos SD (Fanie) Snyman University of the Free State Bloemfontein, South Africa snymansd@ufs.ac.za Introduction Tere is little doubt that the Exodus event as recorded in Exodus 1–15 is foundational in the Old Testament/Hebrew Bible. Books on the theology of the Old Testament/Hebrew Bible confrm the importance of the exodus in the Old Testament/Hebrew Bible and for Israel’s faith in YHWH. A quick survey of some books on Old Testament Teology confrm this consensus in scholarly circles: • Von Rad (1975:176) regards the deliverance from Egypt as “Israel’s original confession”. • Von Rad (1975:176) regards the deliverance from Egypt as “Israel’s original confession”. Snyman • STJ 2021, Vol 7, No 1, 1–22 2 • Zimmerli (1978:25) speaks of the Exodus event as a “fundamental confessional statement for the faith attested by the Old Testament”. • Zimmerli (1978:25) speaks of the Exodus event as a “fundamental confessional statement for the faith attested by the Old Testament”. • In many ways the narrative of Exodus 1–15 may be considered “the birth story of Israel as a people”, says Birch (1999:99). • For Rendtorf (2005:47) the Exodus “is the determinative event in Israel’s history, for all times to come”. Right at the beginning of the exodus narrative, for the frst time ever, the children of Israel are now called a people (Ex 1:9.) עַם בְ ּנֵי יִשְ ׂרָ אֵ ל •For Waltke (2007:390) the signal act of deliverance in the Old Testament is Israel’s exodus from Egypt. • Jeremias (2015:89) noted that for Israel the deliverance from Egypt that culminated in the events at the Reed Sea in Exodus 14–15 was nothing else but the “Grunderfahrung der Fürsorge Gottes für sein Volk”. Later experiences of God’s redemptive acts only serve as the confrmation of this frst experience. It would be hard to overstate the central importance of the Exodus experience for Israel’s understanding of itself and of its faith. Brueggemann (1997:179) stated that the Exodus became paradigmatic for Israel’s testimony about Yahweh and it became an interpretative lens to guide, inform and discipline Israel’s utterances about many aspects of its life. It is then no surprise that the exodus event reverberates through many parts of the Old Testament/Hebrew Bible. Von Rad (1975:176) stated in this regard that in the deliverance from Egypt Israel saw the guarantee for all the future, the absolute surety for YHWH’s will to save, something like a warrant to which faith could appeal in times of trial. A brief overview of the Exodus event as recorded in Exodus 1–15 Te Exodus continues the story of Joseph (Gen 37–50) who arrived in Egypt as a result of his brothers’ conspiracy to get rid of him. Te Israelites living in Egypt became a threat to a new pharaoh because they “were fruitful and multiplied greatly and became exceedingly numerous” (Ex 1:6). Te pharaoh decided to put them to forced labour in an efort to control their numbers. In another more extreme efort the pharaoh issued an order that every Israelite boy that is born should be thrown in the river Nile (Ex 1:22). YHWH heard and saw the terrible plight of his people (Ex 2:24–25) and decided to do something about this dire situation. He revealed himself to Moses as YHWH, the God of Abraham, Jacob and Isaac and commissioned Moses “to bring my people the Israelites out of Egypt” (Ex 3:10). Eventually Moses, with the assistance of his brother Aaron, confronted the king of Egypt in a series of meetings where the king together with his people had to sufer “signs and wonders” (Ex 7:3). Zimmerli (1978:22) remarked in this regard “that there is no other event in the entire history of Israel so surrounded by a plethora of miraculous interventions on the part of YHWH as the event of the deliverance from Egypt”. Te last wonder was the death of the Egyptian frstborn including the frstborn of the pharaoh himself. As a result of this he summoned Moses and Aaron to allow the people of Israel to go and worship YHWH (Ex 12:31) as they initially requested. Te tenth wonder is closely linked with the Passover festival celebrating the fact the fact that YHWH “passes over” the Israelites and did not strike down the frstborn of the Israelites due to the blood smeared unto the sides and tops of the doorframes of the houses where ate the lamb slaughtered (Ex 12). Te Exodus narrative culminated in the passing of the Israelites through the Reed Sea while the Egyptian military forces were defeated by YHWH who swept them into the sea so that no one of the entire army of Egypt survived (Ex 14:27–28). Tis saving event was summarized in a victory song in Exodus 15. Miriam, the sister of Moses and Aaron sang a song: “Sing to the Lord, for he is highly exalted. Te horse and its rider he cast into the sea” (Ex 15:21). Introduction Hofman (1989:169) noted that the Exodus is the most frequently mentioned event in the entire Old Testament. Te topic discussed in this contribution is to investigate the occurrence and function of the Exodus in the book of Amos. What is the function of the Exodus theme in the book of Amos? To answer this question, the main thrust of the Exodus narrative in Exodus 1–15 will frst be determined and briefy summarized. Following on that, the central question put in this paper will be answered via a careful reading of the relevant texts taking the literary and historical contexts of the texts in consideration. Snyman • STJ 2021, Vol 7, No 1, 1–22 3 A brief overview of the Exodus event as recorded in Exodus 1–15 God has led his people out of Egypt “and can derive from this the hope of helping, saving, and forgiving action in the future” (Rendtorf 2005 47) Snyman • STJ 2021, Vol 7, No 1, 1–22 4 2 English texts are quoted from the Revised Standard Version (1971). 1 Hebrew texts are quoted from Elliger, K & Rudolph, W 1984. Biblia Hebraica Stuttgartensia. Stuttgart: Deutsche Bibelgesellschaf. 1 Hebrew texts are quoted from Elliger, K & Rudolph, W 1984. Biblia Hebraica Stuttgartensia. Stuttgart: Deutsche Bibelgesellschaf. 2 English texts are quoted from the Revised Standard Version (1971). References to Egypt in the book of Amos Snyman • STJ 2021, Vol 7, No 1, 1–22 5 5 ּהָּלֻּכ רֹאְיַכ הָתְלָעְו ּהָב יֵבְׁשֹוי־לָּכ ּולְבָאְו גֹומָּתַו ץֶרָאָּב ַעֵגֹוּנַה תֹואָבְּצַה הוהי יָנֹדאַו םִיָרְצִמ רֹאיִּכ הָעְקָׁשְו םִיָרְצִמ רֹאיִּכ הָעְקָׁשְו Te Lord, GOD of hosts, he who touches the earth and it melts, and all who dwell in it mourn, and all of it rises like the Nile, and sinks again, like the Nile of Egypt. Te Lord, GOD of hosts, he who touches the earth and it melts, and all who dwell in it mourn, and all of it rises like the Nile, and sinks again, like the Nile of Egypt. Amos 9:5 is an almost verbatim repetition of Amos 8:8 and forms part of the third doxology in the book (Amos 4:13; 5:8–9). It alludes to an earthquake and likens the movement of the earth associated with an earthquake with the movement of the water of the river Nile in Egypt. Te mentioning of Egypt in both Amos 8:8 and 9:5 cannot be regarded as references to the Exodus tradition telling the event of Israel’s deliverance from the hardships of Egypt to the freedom of their own land. In both verses eretz ( )ארץis used as an indication of the land where Israel as the people of God make a living. It is thus rather the tradition of the land or perhaps creation traditions at work here rather than the exodus tradition. Both these verses refer to a geographical phenomenon in the form of an earthquake that will occur. Te ebb and fow of the river Nile in Egypt is used as an example to illustrate the point the author wishes to make. References to Egypt in the book of Amos According to Brueggemann (1997:177) Israel once they began telling their history, “retold all of its experience through the powerful, defnitional lens of the Exodus memory”. Te formulation used by Brueggemann is signifcant. It does not suggest that the Exodus memory was initially a written record of events. It rather refects an initial oral tradition – a position that is adopted in this paper as well. Tis is no diferent in the book of the Twelve where the Exodus event is frequently referred to especially in the book of Hosea (Hos 2:17; 7:11; 7:16; 8:13; 9:3; 9:6; 11:1; 11:5; 11:11; 12:2; 12:10; 12:14; 13:4), but also in other books (Joel 4:19; Micha 6:4; 7:15; Nah 3:9; Hag 2:5; Zech 10:10; 10:11; 14:18; 14:19). Te book of Amos is no exception in this regard. Broadly speaking, the book of Amos can be divided in four major parts. Afer an introduction (1:1–2) a series of prophecies directed at foreign nations and culminating in prophecies against Judah and Israel (1:3–2:16), followed then by another series of prophecies against Israel in Amos 3–6 and fnally Amos 7–9 introduced by fve visions. Te following verses make explicit references to Egypt: Amos 2:10; 3:1; 3:9; 4:10; 8:8; 9:5; 9:7. Two of these texts (Amos 8:8 and 9:5) cannot be related to the Exodus- event and will therefore be excluded from this investigation. הָקְׁשִנְו הָׁשְרְגִנְו ּהָּלֻּכ רֹאָכ הָתְלָעְו ּהָּב בֵׁשֹוי־לָּכ לַבָאְו ץֶרָאָה זַּגְרִת־אֹל תאֹז לַעַה ׃םִיָרְצִמ רֹואיִּכ1 הָקְׁשִנְו הָׁשְרְגִנְו ּהָּלֻּכ רֹאָכ הָתְלָעְו ּהָּב בֵׁשֹוי־לָּכ לַבָאְו ץֶרָאָה זַּגְרִת־אֹל תאֹז לַעַה ׃םִיָרְצִמ רֹואיִּכ1 Shall not the land tremble on this account, and everyone mourns who dwells in it, and all of it rise like the Nile, and be tossed about and sink again, like the Nile of Egypt?”2 Amos 8:8 forms part of a pericope (Amos 8:4–14) where the prophet utters once again a prophecy of doom upon Israel because of social injustices prevailing in society. Te judgement will be experienced in the form of an earthquake. Te coming earthquake is compared to the seasonal rising and falling of the river Nile in Egypt. Exploring the function of the Exodus theme in the book of Amos Tree diferent functions for making use of the Exodus theme in the book of Amos have been determined: Te Exodus as the motive for the prophecies directed at Israel A 2 10 Te Exodus as the motive for the prophecies directed at Israel A Te Exodus as the motive for the prophecies directed at Israel Amos 2:10 ־תֶא תֶׁשֶ֖רָל הָ֔נָׁש םיִ֣עָּבְרַא ֙רָּבְדִּמַּב םֶ֤כְתֶא ְךֵ֨לֹואָו םִיָ֑רְצִמ ץֶרֶ֣אֵמ םֶ֖כְתֶא יִתיֵ֥לֱעֶה יִ֛כֹנָאְו ׃יִֽרֹמֱאָה ץֶרֶ֥א Also I brought you up out of the land of Egypt, and led you forty years in the wilderness, to possess the land of the Amorite. Also I brought you up out of the land of Egypt, and led you forty years in the wilderness, to possess the land of the Amorite. Amos 2:10 is part of the frst major section of the book consisting of six prophecies directed at foreign nations (Amos 1:3–2:3) followed by one directed at Judah (Amos 2:4–5) and culminating in a prophecy against Snyman • STJ 2021, Vol 7, No 1, 1–22 6 Israel (Amos 2:6–16). In the frst part of the prophecy (verses 6–8) directed to Israel YHWH speaks about Israel and her sins. Te sins mentioned are sins committed to their fellow Israelites. All the sins mentioned are related to social injustices done to fellow Israelites. In verses 9–11 YHWH’s redemptive deeds in the history of the people are mentioned. Verse 9 mentioned the granting of the land and it was reiterated again in the second part of verse 10. YHWH also sent the people prophets and Nazirites to guide the people in the ways YHWH wanted them to follow. In verse 10 YHWH addresses Israel changing to second person singular form (“I brought you up from Egypt”) thereby addressing Israel directly (Eidevall 2017:117). What YHWH did to his people in the past is contrasted with the acts of the people now living in the land. YHWH’s act in the Exodus event is in fact rejected by Israel (Hadjiev 2009:58). In this prophecy Israel is reminded of YHWH’s acts of deliverance in the history of the people. YHWH brought ( )הלעhis people up out of the land of Egypt. It is interesting and important to note that this is the only verb used in the book of Amos to describe the deliverance from Egypt (Amos 3:1; 9:7). Exploring the function of the Exodus theme in the book of Amos Te same verb is used in Exodus 3:8, 17 to describe this saving act of YHWH. Te verb suggests a geographical connotation: moving from a lower place to a higher mountainous one (Brueggemann 1997:176; Niehaus 1992:369; Van Leeuwen 1985:88). It indicates not only a movement from the land of Egypt to the promised land, but also from metaphorically speaking, a movement from a situation of slavery to one of freedom. YHWH exalted Israel from a condition where they were slaves in a foreign country to a promised land where they will no longer be slaves but could enjoy freedom. Te people of Israel were brought out of the bondage of Egypt to live in the promised land. Israel is reminded that they were an oppressed people serving as slaves to a foreign nation (Amos 2:10) but now they have become the oppressors not of another foreign nation but of their very own people (Amos 2:6–9) in the land granted to them. Instead of remaining a group of slaves, it is YHWH who made Israel into a people by delivering them from Egypt (Rudolph 1971:146). Garrett (2003:66) notes that the Amorites were mentioned twice creating an “inclusion structure framed by reference to the expulsion of the Amorites. Te implication is that Israel, too, could be expelled”. In other words, just as the Amorites were once destroyed by Snyman • STJ 2021, Vol 7, No 1, 1–22 7 7 YHWH to make room for his people to occupy and make a living in the promised land, the same may now happen to Israel (Amos 2:13–16). Amos 3:1 רׁ ֶש ֲא ה ָחּ ָפׁ ְשּ ִמ ַה־לּ ָכ ל ַע ל ֵא ָרׂ ְשִי י ֵנּ ְב ם ֶכי ֵל ֲע הוהי רּ ֶבּ ִד רׁ ֶש ֲא הּ ֶז ַה ר ָבּ ָד ַה־ת ֶא ּוע ְמׁ ִש ׃ר ֹמא ֵל םִי ַר ְצ ִמ ץ ֶר ֶא ֵמ י ִתי ֵל ֱע ֶה Hear this word that the Lord has spoken against you, O people of Israel, against the whole family which I brought up out of the land of Egypt. Amos 3:1–2 introduces a new section in the book and can be seen as the introduction or prologue to the second part of the book (Amos 3–6). Exploring the function of the Exodus theme in the book of Amos Te unit commences with the familiar “Hear this word” ( שִ ׁמְ עּו אֶ ת־הַדָּבָר הַזֶּה )that is also found in Amos 4:1 and 5:1. Te people are called “children of Israel” and then it is further explicated as “the whole family” (or clan) indicating the close relationship the Israelites have with one another as well as the close relationship with YHWH (Eidevall 2017:123). In Amos 3:1 the people are reminded that YHWH brought them out of Egypt. Te same verb ( )עלהis once again used to describe the deliverance from Egypt. Te fact that the deliverance from Egypt is repeated here serves as a link with the preceding unit (2:6–16). In this case YHWH’s act of salvation is used as the motivation for the prophecies uttered and the punishment announced upon the people in this part of the book. Te deliverance from Egypt was an act of YHWH’s saving power, grace, and kindness to them (Paul 1991:101; Niehaus 1992:375). It is because YHWH rescued his people that they are addressed about their iniquities. As is the case in Amos 2:10, YHWH’s acts in the past on behalf of his people stand in stark contrast to their current behaviour. Amos 3:1–2 introduces a new section in the book and can be seen as the introduction or prologue to the second part of the book (Amos 3–6). Te unit commences with the familiar “Hear this word” ( שִ ׁמְ עּו אֶ ת־הַדָּבָר הַזֶּה )that is also found in Amos 4:1 and 5:1. Te people are called “children of Israel” and then it is further explicated as “the whole family” (or clan) indicating the close relationship the Israelites have with one another as well as the close relationship with YHWH (Eidevall 2017:123). In Amos 3:1 the people are reminded that YHWH brought them out of Egypt. Te same verb ( )עלהis once again used to describe the deliverance from Egypt. י ֵר ָה־ל ַע ּופ ְסָא ֵה ּור ְמ ִאְו םִי ָר ְצ ִמ ץ ֶר ֶאּ ְב תֹונ ְמְרַא־ל ַעְו דֹוּדׁ ְשַאּ ְב תֹונ ְמְרַא־ל ַע ּועי ִמׁ ְש ַה ׃ּהּ ָבְר ִקּ ְב םי ִקּוׁש ֲע ַו ּה ָכֹותּ ְב תֹוּב ַר ת ֹמּוה ְמ ּואְרּו ןֹור ְמׁ ֹש י ֵר ָה־ל ַע ּופ ְסָא ֵה ּור ְמ ִאְו םִי ָר ְצ ִמ ץ ֶר ֶאּ ְב תֹונ ְמְרַא־ל ַעְו דֹוּדׁ ְשַאּ ְב תֹונ ְמְרַא־ל ַע ּועי ִמׁ ְש ַה ׃ּהּ ָבְר ִקּ ְב םי ִקּוׁש ֲע ַו ּה ָכֹותּ ְב תֹוּב ַר ת ֹמּוה ְמ ּואְרּו ןֹור ְמׁ ֹש ׃ּהּ ָבְר ִקּ ְב םי ִקּוׁש ֲע ַו ּה ָכֹותּ ְב תֹוּב ַר ת ֹמּוה ְמ ּואְרּו ןֹור ְמׁ ֹש ׃ּהּ ָבְר ִקּ ְב םי ִקּוׁש ֲע ַו ּה ָכֹותּ ְב תֹוּב ַר ת ֹמּוה ְמ ּואְרּו ןֹור ְמׁ ֹש Proclaim to the strongholds in Assyria, and to the strongholds in the land of Egypt, and say, “Assemble yourselves upon the mountains of Samaria, and see the great tumults within her, and the oppressions in her midst.” Snyman • STJ 2021, Vol 7, No 1, 1–22 8 Amos 3:9 serves as the introduction to a prophetic oracle stretching to verse 15 proclaiming devastation to Israel because of their neglect in terms of social justice. In Amos 3:9 the land of Egypt is mentioned together with Ashdod known as a Philistine city. It seems odd to call upon a country (Egypt) and a city (Ashdod) with the city mentioned frst to witness the unrest and oppression prevailing in Samaria as the capital of the Northern Kingdom. It is also the only instance in the Old Testament/Hebrew Bible where Egypt and Ashdod are mentioned together. It must also be noted that the land of Egypt is called upon but with no direct mentioning of the exodus from Egypt as was the case in Amos 2:10 and 3:1. Te question to consider then is whether mentioning the land of Egypt in Amos 3:9 can be interpreted as a reference to the exodus tradition. To answer this question, one has to briefy pay attention to the mentioning of Ashdod. It is interesting to note that the LXX has a diferent reading in this regard. Te LXX reads “Assyria” instead of Ashdod probably because Assyria would serve as a better parallel to Egypt as a political power than Ashdod as a city-state of the Philistines. Although there is support for the reading of the LXX as the preferred reading (Barthélemy 1992:647), the reading of the MT has to be retained (Wolf 1977:189; Van Leeuwen 1985:124; Paul 1991:115–116; Eidevall 2017:130). To mention Ashdod is a subtle allusion to the land promise and the eventual granting of the land. In Joshua 11:22; 13:3 and 15:47 Ashdod is especially mentioned in connection with the conquest of the land. In Amos 3:9–15 the prophet announces the unthinkable possibility that Israel may lose the land they once occupied. In verse 11 it is said in no uncertain terms that “an adversary shall surround the land and strip you of your defence and your strongholds shall be plundered” (NRSV). ׃ּהּ ָבְר ִקּ ְב םי ִקּוׁש ֲע ַו ּה ָכֹותּ ְב תֹוּב ַר ת ֹמּוה ְמ ּואְרּו ןֹור ְמׁ ֹש Te mentioning of Ashdod serves as a subtle reminder of the initial conquest of the land in stark contrast to the threat of losing the land. Diferent answers were given to answer the question as to why Egypt was called upon as a witness “to see the great unrest within her and the oppression among her people” (Amos 3:9). • Some scholars (Mays 1976:63; Van Leeuwen 1985:124) are of the opinion that Ashdod and Egypt were neighbouring states and therefore they are mentioned together. Snyman • STJ 2021, Vol 7, No 1, 1–22 9 9 • Carroll (1992:193) thinks that the mentioning of Ashdod and Egypt has to do with an idea of some moral consensus with the implication that even these two (pagan) nations known for their acts of violence and injustice would be shocked by the conditions they are about to observe in Samaria. • Other scholars (Rudolph 1971:163; Paul 1991:115) think that Ashdod and Egypt were summoned because of the stipulation in Israelite law that requires at least two witnesses in a lawsuit as proof of reliable evidence (Deut 17:6; 19:15). • Another solution to the problem was to view the call to the entities as a rhetorical device rather than a historical indication (Rudolph 1971:163; Deissler 1981:105). • Another solution to the problem was to view the call to the entities as a rhetorical device rather than a historical indication (Rudolph 1971:163; Deissler 1981:105). It has already been argued that in both Amos 2:10 and 3:1 the deliverance from Egypt is mentioned. Keeping in mind that the exodus tradition was an important theological tradition associated with especially the Northern Kingdom of Israel, it is quite possible that mentioning Egypt in Amos 3:9 is also meant as a reminder of the miraculous exodus from Egypt. Mentioning Egypt here is also perfectly in line with the use of the exodus tradition in the two preceding verses where the Exodus from Egypt is mentioned. Israel, who would be well aware of the hardships of oppression by a foreign power, are now oppressing their own people (Snyman 1994:561). What makes it worse is that the foreign power who once acted as the oppressor is now summoned to witness the oppression executed by Israel on its own people. Te Exodus turned against Israel Te Exodus turned against Israel Amos 4:10 ה ֶל ֲעַא ָו ם ֶכי ֵסּוס י ִבׁ ְש ם ִע ם ֶכי ֵרּוחּ ַב ב ֶר ֶח ַב יּ ִת ְג ַר ָה םִי ַר ְצ ִמ ְך ֶר ֶדּ ְב ר ֶבּ ֶד ם ֶכ ָב יּ ִת ְחּ ַלׁ ִש ׃הוהי־ם ֻא ְנ י ַד ָע םּ ֶת ְבׁ ַש־א ֹלְו ם ֶכּ ְפַא ְבּו ם ֶכי ֵנ ֲח ַמ ׁש ֹאּ ְב I sent among you a pestilence afer the manner of Egypt; I slew your young men with the sword; I carried away your horses; and I made the stench of your camp go up into your nostrils; yet you did not return to me,” says the Lord. Amos 4:10 is part of Amos 4:6–12 which is a prophecy of doom upon Israel and delivered as a “parody of a priestly Torah” (Wolf 1977:211). Te prophecy is carefully structured in fve strophes (verses 6, 7–8; 9, 10, 11) each of them starting with a frst person singular verb introducing YHWH as the one speaking and ending with “Yet you have not returned to me, declares the LORD” ( .)וְלֹא־שַ ׁבְ תֶ ּם עָדַ י נְאֻם־יהוהTe prophecy pertains to diferent agricultural catastrophes that will be experienced as a famine (verse 6), a severe drought (verses 7–8), crop failure due to all kinds of pests, a plague or pest (verse 10) and a national disaster of some sort comparable to what happened with Sodom and Gomorrah (verse 11). Te land promised to the people of God will be a good land, a land fowing with milk and honey (Ex 3:8; 17; 13:5; 33:3; Num 13:27; Deut 6:3; 11:9; 26:9; Josh 5:6). It will be a land with abundant pasture for animals to provide milk and an equally abundant of produce to be harvested as a result of the fruitful soil. In Deuteronomy 8:7–10 the land is described as a land with more than enough water and where wheat and barley, vines and fg trees, pomegranates, olive oil and honey will be available where nobody will lack anything. Indeed, during the time of Amos’s activity as prophet, Israel experienced a time of peace and prosperity. Tere was little threat from foreign powers and trade routes passing up and down Transjordan through Israelite territory contributed to a time of economic prosperity. ׃ּהּ ָבְר ִקּ ְב םי ִקּוׁש ֲע ַו ּה ָכֹותּ ְב תֹוּב ַר ת ֹמּוה ְמ ּואְרּו ןֹור ְמׁ ֹש While the fortresses of Egypt and Ashdod will remain safe, the fortresses of Israel will be plundered (Amos 3:11) because the very fortresses mentioned were used to store up the gains gathered by violent means. In other words, the oppressed people were redeemed from oppression only to become oppressors themselves. Recently, Eidevall (2017:132) came to the same solution but added that Ashdod and Egypt were regarded as Israel’s archenemies par excellence and that will then be the reason why Ashdod and Egypt in particular were selected. Te mentioning of Ashdod and Egypt brought to mind two prominent traditions. Ashdod recalls the conquest of the land while Egypt served as a reminder of the exodus from Egypt as YHWH’s act of salvation par excellence in the history of his people. Snyman • STJ 2021, Vol 7, No 1, 1–22 10 Te Exodus turned against Israel Evidence of this era of economical bloom can be seen from the book of Amos itself. Some Israelites could aford both a summer and winter house (Amos 3:15). Houses were luxuriously furnished and decorated with ivory. Moreover, they could aford it to enjoy the fnest quality food available (Amos 6:1–7). Snyman • STJ 2021, Vol 7, No 1, 1–22 11 In Amos 4:10 YHWH says that he sent ‘a plague like/according to Egypt’ (“ .)דֶּבֶר בְ ּדֶרֶ ְך מִ צְ רַ יִםDeber” or plague is not the only term used in the Exodus narrative to describe YHWH’s actions against pharaoh and the Egyptians. YHWH will act with signs and wonders )(אות מופתand indeed that was the case when the diferent wonders are described as wonders. Te death of the frst born is described with another word .)(נגעNeither of these terms are used by Amos. It is a matter of dispute of what is exactly meant by ‘a plague like/according to Egypt’ .)(דֶּבֶר בְ ּדֶרֶ ְך מִ צְ רַ יִםDoes the term refer to the ffh wonder of the death of the livestock of the Egyptians? Or is it possible that this formulation has the tenth plague (the death of the frstborn) in mind? Another possibility is that it is a reference to the plagues in general. Scholarly opinion on this matter gave diferent answers to the problem of how this phrase has to be understood and at least six possible solutions were proposed. • Wolf (1977:221) thinks of Exodus 9:3–7 reminding the people of the wonder that killed all the livestock of Egypt. • Wolf (1977:221) thinks of Exodus 9:3–7 reminding the people of the wonder that killed all the livestock of Egypt. • Paul (1991:147) opines that the phrase refers to both the disaster that struck the livestock (Ex 9:3–7) as well as the population of Egypt (Ex 9:15). • Rudolph (1971:179) is convinced that the phrase refers only to the death of the frstborn (Ex 12:29) and not to the ffh wonder. • A fourth possibility is that ‘a plague like/according to Egypt’ should be understood as a reference to the plagues in general and not a specifc plague as was suggested by other scholars. Te Exodus turned against Israel • Eideval (2017:147) stated that the “passage alludes to the narrative in its entirety as a long series of calamities (including pestilence) followed by a defeat that wiped out the Egyptian army (Ex 7–15)”. Nogalski (2011:303) agrees with this point of view when he states that verse 10 alludes “to the plagues YHWH used against the Egyptians to force Pharaoh to release Israel to Moses” (Ex 7–12). • Niehaus (1992:401) does not relate this verse with the Exodus events in particular but interprets the verse against a covenantal background referring to Deuteronomy 28:27, 60. Snyman • STJ 2021, Vol 7, No 1, 1–22 12 Te fact that Egypt is mentioned specifcally serves as an undeniable link to the Exodus tradition in Exodus 1–15. In Exodus 5:3 “deber” ( )דֶּבֶרis used in the speech made by Moses and Aaron to the Pharaoh. In this speech they stated that they wish to ofer sacrifces to YHWH “or he may strike us with plagues ( )דֶּבֶרor with the sword”. It is important to note that “deber” ( )דֶּבֶרand the sword are mentioned together here as is the case in Amos 4:10. With the announcement of the death of the livestock of the Egyptians as the ffh plague “deber” ( )דֶּבֶרis used again to describe the plague. In Exodus 9:15 “deber” ( )דֶּבֶרis used to indicate a plague in general when YHWH says: “For by now I could have stretched out my hand and struck you and your people with a plague ( )דֶּבֶרthat would have wiped you of the earth”. Te term “deber” ( )דֶּבֶרis also used in Leviticus 26:25 with no mention of the Exodus but “deber” ( )דֶּבֶרis once again connected to the sword (cf Ex 5:3; Amos 4:10). In Numbers 14:12 the people are threatened with a plague “deber” ( )דֶּבֶרthat will destroy them. Te reason for this action from YHWH is given in the previous verse where YHWH accuses his people they do not believe in him even in spite of all the miraculous signs ( )האתותYHWH performed among them. Te term “otot” ( )אתותis also used to describe the wonders experienced in the plagues that were brought upon Egypt. In Deuteronomy 28:21 the people are threatened with a “deber” ( )דֶּבֶרthat will destroy them should they be disobedient in the promised land. Te Exodus turned against Israel Te Exodus event not unique to Israel Te Exodus turned against Israel Amos 4:10 is not only linked to the Exodus, it is more specifcally linked to the so-called Plague-narrative of Exodus. Te term “deber” ( )דֶּבֶרused in Amos 4:10 does not refer to the ffh plague or the death of frstborn but should be interpreted as referring to the total event of the plague-narrative. In the prelude to the signs and wonders to be played out in ten so-called plagues, the plagues and the sword are foreseen in Exodus 5:3. Amos 4:10 recalls the general reference to plagues and the sword as mentioned in Exodus 5:3 rather than a reference to specifc plagues. A powerful contrast is created by the mentioning of the plagues in the Exodus tradition. In the Exodus tradition the plagues were aimed at the Egyptians. Time and again in the plague-narrative it is said that the plagues did not harm the Israelites (Ex 8:22; 9:7; 9:26; 12:12–13). In Amos 4:10 the plagues are directed at the Israelites, the people of God. Te people who were once guarded from the devasting efects of the plagues will now sufer Snyman • STJ 2021, Vol 7, No 1, 1–22 13 from plagues. Israel, as the people of God, is punished in the same way as the Egyptians, a foreign nation. In short, the exodus is reversed (Hubbard 1989). Secondly, the plagues were witnessed by the Israelites on foreign soil in Egypt. Now they will experience the plagues in the promised land (Snyman 2006:141). Te promised land was supposed to be a land of bounty and fertility. Exactly the opposite will happen now where the people will sufer all kinds of agricultural catastrophes comparable to what happened once in Egypt. Nogalski (2011:303) is right when he observed that YHWH’s past actions of salvation are now turned against Israel. Instead of salvation brought about as a result of the plagues, devastation will now be the result of the plagues. In the plague narrative it is repeatedly said that the Pharaoh and the Egyptians had to sufer the plagues brought upon them because of their disobedience to YHWH to let his people go and worship him. Israel will sufer the plagues because they were also disobedient to the voice of God as is implied in the refrain no less than fve times in this unit: “you have not returned to me, says the LORD” (Amos 4:6; 8; 9; 10; 11). Te Exodus event not unique to Israel ץ ֶר ֶא ֵמ י ִתי ֵל ֱע ֶה ל ֵא ָרׂ ְשִי־ת ֶא אֹול ֲה הוהי־ם ֻא ְנ ל ֵא ָרׂ ְשִי י ֵנּ ְב י ִל םּ ֶתַא םיּ ִיׁ ִש ֻכ י ֵנ ְב ִכ אֹול ֲה ׃ריּ ִק ִמ ם ָר ֲא ַו רֹוּת ְפּ ַכ ִמ םיּ ִיּ ִתׁ ְש ִל ְפּו םִי ַר ְצ ִמ Are you not like the Ethiopians to me, O people of Israel?” says the Lord. “Did I not bring up Israel from the land of Egypt, and the Philistines from Caphtor and the Syrians from Kir?” Amos 9:7 is part of the second last unit in the book consisting of Amos 9:7–10. Amos 9:7 mentions the exodus of Israel from the land of Egypt. As was noted earlier the only verb ( )עלהused in the book of Amos to refer to the Exodus event is used again as was the case in Amos 2:10 and 3:1. YHWH brought his people up from Egypt to the promised land. What is new in this verse is that the Exodus event is put in relief with other similar migrations of other nations. Tree diferent nations are mentioned: the children of Cush, the Philistines, and the Arameans. Mentioning these nations gave rise to the question of why these three nations in particular were mentioned. Snyman • STJ 2021, Vol 7, No 1, 1–22 14 Viewing the text from a literary perspective it is interesting to note that Cush is mentioned frst, followed by Israel and then the Philistines and the Arameans are mentioned last. Israel is sandwiched in between the other nations mentioned. Te verse displays a “kind of envelope structure” starting with a foreign nation (Cush) and concludes with two other foreign nation nations with Israel at the centre (Strawn 2013:112). Strawn (2013:115) in his thorough poetic analysis of 9:7, concluded that a signifcant number of poetic devices indicate that the three lines of this verse belong together. Te only verb used in this verse (“ )הלעstands quite literally at the centre of the unit (Strawn 2013:115) and performs “a triply duty having Israel, the Philistines and Aram as direct objects” (Niehaus 1992:486). Te Exodus event not unique to Israel It is also interesting to note that although Cush is not mentioned in the judgement speeches at the beginning of the book, the Philistines are addressed in the second judgement speech in Amos 1:6–8 while the Arameans are addressed in the frst judgement speech in Amos 1:3–5. Considering the possibility that Amos 9:11–15 is most likely a later addition to the book, a chiastic structure emerged from the mentioning of the Philistines and Arameans at the end of the book: (A) Arameans (1:3–5); (B) Philistines (1:6–8); (B) Philistines (9:7); (A) Arameans (9:7). Why Cush is mentioned remains an intriguing question for scholars (Holter 2015:306–318). Smith (1994:36–37) listed no less than ten diferent answers to this question. Viewing the three nations from a geographical point of view, a universal perspective is created with Israel as the Northern Kingdom, Cush is to be found south of Egypt, Caphtor lies to the west and Kir to the east. YHWH acted on a worldwide scale directing the movement of diferent nations. YHWH indeed rescued his people from Egypt, but he guided and directed the histories of other nations as well (Smith 1994:47). Te people of Cush were held in high regard during the time of the ministry of Amos. Te Cushites were able to subdue the Egyptians during the same time when Amos was a prophet to the Northern Kingdom (Strawn 2013:116– 121). Te Philistines and the Arameans are known as archenemies of Israel (Wolf 1977:347; Van Leeuwen 1985:333). Te Arameans according to 9:7 was once brought from Kir like the Israelites were brought from Egypt. According to Amos 1:5 they will be exiled to Kir. It seems that Aram will be returned by military force to their Snyman • STJ 2021, Vol 7, No 1, 1–22 15 place of origin where they were once brought from by the power of YHWH. Eidevall (2017:236) mentions the possibility that this might be a hint to Israel/Judah that YHWH just might be prepared to reverse the Israelite exodus tradition. Tis passage brings together two vital aspects of who God is in the book of Amos. On the one hand there is the frm conviction that the God of Israel is not only a local God served by the Israelites. Te God of Israel is also the universal God. Te Exodus event not unique to Israel Tis can be seen in Amos 1 and 2 where the moral behaviour of foreign nations does concern YHWH. Social injustices committed by foreign people matter to YHWH. Te idea of God as the universal God is expressed again at the end of book in 9:7 where YHWH’s action is extended from a local to a universal perspective (Tang 2011:187; Wood 2002:90). On the other hand, it was YHWH who brought his people from Egypt to the promised land. Te all-important saving event in the history of God’s people is relativized as simply one event amongst other similar events. YHWH delivered his people from Egypt, but he also brought other people to their respective countries. It is noteworthy that the verb used to describe the deliverance of Israel from Egypt is applied to the Philistines and the Arameans as well. It is equally important to note that Amos 9:7 does not say that YHWH entered into a special relationship with the three nations mentioned as is the case in Amos 3:1–2 where it is said that he only knew ( )ידעthem “of all the families of the earth”. In a novel way Amos reinterpreted the Exodus events and applied it to a diferent situation sometime during the eighth century BC/E. Te way he did it was to relativize this all-important event by comparing the Exodus event with other similar events that happened in the history of other nations in and through YHWH’s guidance. What is even more disturbing is the fact that while no judgement is pronounced upon the three nations, Israel, however, is described as “the sinful kingdom” that will be destroyed (Amos 9:8). The historical context of the book of Amos Determining the historical background of a prophetic book is a risky undertaking. Prophetic books have been edited and updated so that it seldom refects a single historical time. For the purposes of this paper, the historical background refected in the book is taken as that of the 8th Snyman • STJ 2021, Vol 7, No 1, 1–22 16 century BC/E in Israel, the Northern Kingdom. Eideval (2017:16) confrms this consensus among scholars when he states that “With few exceptions they concentrate on one particular period in the history of the kingdom of Israel, namely the last decades of the reign of Jerobeam II (ca 787–747 BCE)”. In Amos 1:1 it is stated that the prophecies in this book were delivered during the time of Jerobeam II, son of Joash, the king of Israel (787/6–747/6 BC/E). Te prophetic activity of the prophet can be dated toward the end of Jerobeam’s reign somewhere around 750 BC/E. Tere was little threat of foreign nations and consequently it was a time of relative peace for both the Northern Kingdom as well as Judah paving the way for economic prosperity (Smith 1994:39–40). Evidence of this time of prosperity could be seen in Amos 3:15 where it is said that some Israelites have both a summer and winter house and that these houses were luxuriously furnished and decorated with ivory where they were feasting on fne quality food (Amos 6:1–7). However, having said this it is also evident that the book was addressed to Judah at a later stage in history. Amos 1:2 states for instance that YHWH roars from Zion (see also Amos 6:1), a tradition more associated with Judah than with Israel. Te last part of the book (Amos 9:11–15) speaks of the fallen tent of David that will be restored, once again a tradition that is more at home in a Judean context of exilic and/or even post-exilic times. Recently, Eideval (2017:18–20) suggested no less than six possible historical contexts for the book of Amos. Conclusion Te Exodus tradition in the book of Amos is utilized in diferent ways. Te investigation yielded the following results: At frst Te Exodus from Egypt is used as the motive for the prophecies directed at Israel. YHWH’s redemptive actions in the past are put in juxtaposition to the current conditions of the people living in the promised land. Secondly, the Exodus is turned against Israel. What happened once to the Egyptians will now happen to the people of God. Just as the Egyptians had to sufer plagues, the Israelites will now sufer plagues. Tirdly, the Exodus event is relativized as an event not unique to Israel. Te Exodus is relativized in the sense that the Exodus “was not a unique Snyman • STJ 2021, Vol 7, No 1, 1–22 17 historical-theological event, but rather a divine routine, to transfer nations from one land to another” (Hofman 1989:181). Barton (2012:72) noted in this regard “precisely because YHWH is a universal God, all the movements of the nations come about through his devising”. While it is true that YHWH has caused the exodus, it is also true that “he is responsible for all the movements of peoples on the face of the earth” (Barton 2010:191). Te three ways in which the exodus tradition featured in the book of Amos reveal a “Steigerung”: at frst the exodus tradition is used as the motivation for the prophecies directed to the people. Te second use intensifes the use of the exodus tradition in the sense that the exodus tradition is now turned against Israel while it is in actual fact one of the major redemptive acts of YHWH in the history of Israel/Judah. In the last instance the intensifcation is even further increased. Te exodus was, afer all, not the unique event peculiar only to the people of YHWH. In fact, what seemed to be the unique saving event in the history of the people is now relativized by the mentioning of similar events that happened to other people as well. Te book of Amos is well aware of the Exodus tradition. Te Exodus tradition is utilized to confrm the major redemptive act of YHWH in the history of Israel and it is then contrasted to the current situation in the promised land. Te book does not only make use of the tradition, it also interprets the tradition and applies it to a new situation. Conclusion In the plague narrative Egypt was the victim but in the book of Amos the people will sufer the fate previously reserved for the Egyptians. Rather than to view Amos 4:10 as a possible allusion to the exodus “but not indicative of Amos’s view on this tradition” (Hofman 1989:177), it seems better to see the reference to the plagues as an interpretation of the plague narrative and applying it to a new situation. In a similar way, the Exodus that was thought of as a unique event that only happened to Israel, is now put in a broader perspective to reveal the surprising insight that other nations also experienced what may be called exodus events. To claim that the exodus tradition was rejected in the book of Amos (Hofman 1989:181) is to press the matter a bit too far. It rather seems that the book afrms the exodus tradition so well-known in the Northern Kingdom reminding the people of this famous event and then utilized it in an innovative way to a new era. Te deliverance from the land of Egypt contrasted with living in the Snyman • STJ 2021, Vol 7, No 1, 1–22 18 promised land. Te familiar event of the miraculous exodus from Egypt gained an unexpected and disturbing message in the book of Amos. Works consulted Barthélemy, D 1992. Critique Textuelle de L’ Ancient Testament 3. Göttingen: Vandenhoeck & Ruprecht. 647. (OBO 50/3). Barton, J 2010. Te Teology of Amos, in Day, J (ed) Prophecy and Prophets in Ancient Israel. Proceedings of the Oxford Old Testament Seminar. London: T & T Clark (Library of Hebrew Bible/Old Testament Studies 531). Barton, J 2012. Te Teology of the Book of Amos. New York: Cambridge University Press. Birch, B C; Brueggemann, W; Fretheim, T E & Petersen, D L 1999. A Teological Introduction to the Old Testament. Nashville: Abingdon Brueggemann, W 1997. Teology of the Old Testament. Testimony, Dispute, Advocacy. Minneapolis: Fortress. Carroll, M D 1992. Contexts for Amos: Prophetic Poetics in Latin American Perspective. Shefeld: Shefeld Academic Press (JSOTSup 132). Deissler, A 1981. Zwölf Propheten. Hosea Joel Amos. Würzburg:Echter Verlag (Neue Echter Bibel). Eideval, G 2017. Amos. A New Translation with Introduction and Commentary. New Haven: Yale University Press (Anchor Yale Bible 24G). Garrett, D A 2008. Amos: a handbook on the Hebrew text. Waco, Texas: Baylor University Press. Hadjiev, T S 2009. Te Composition and Redaction of the book of Amos. Berlin: Walter de Gruyter (BZAW 393). Hofman, Y 1989. A North Israelite Myth and the Judean Historical Tradition: Te Exodus in Hosea and Amos. VT 39:169–182. Snyman • STJ 2021, Vol 7, No 1, 1–22 19 Holter, K 2015. Being like the Cushites: Some Western and African Interpretations of Amos 9:7, in Telle, R I, Stordalen, T & Richardson, M E J (eds). New Perspectives on Old Testament Prophecy and History. Essays in honour of Hans M. Barstad. Leiden: Brill (SVT 168). Hubbard, D A 1989. Joel and Amos. An Introduction and Commentary. Nottingham:Inter-Varsity Press. (TOTC). Jeremias, J 2015. Teologie des Alten Testaments. Göttingen: Vandenhoeck & Ruprecht (ATD Ergänzungsreihe Band 6). Mays, J L 1976. Amos: A Commentary. London:SCM (Old Testament Library). Niehaus, J 1992. Amos, in McComiskey, T E (ed). Te Minor Prophets I. Grand Rapids: Baker. Nogalski, J D 2011. Te Book of the Twelve Hosea – Jonah. Macon, Georgia: Smyth & Helwys Publishing. Paul, S 1991. Amos. Philadelphia: Fortress. (Hermeneia). Rendtorf, 2005. Te Canonical Hebrew Bible. A Teology of the Old Testament. Leiden: Deo Publishing. Rudolph, W 1971. Joel – Amos – Obadja – Jona. Güterloh: Gerd Mohn. (KAT XIII/2). Smith, B K & Page, F S 1995. Amos Obadiah Jonah. Nashville: Broadman & Holman Publishers (NAC). Smith, R 1994. Works consulted A New perspective on Amos 9:7a: “To Me, o Israel, You Are Just Like the Kushites.” Journal of the Interdenominational Teological Center 22:36–47. Snyman, S D 1994. A Note on Ashdod and Egypt in Amos iii 9. VT 44:559–562. Snyman, S D 2006. Eretz and Adama in Amos, in Niemann, H M & Augustin, M (eds). Stimulation from Leiden. Collected communications to the XVIIIth Congress of the International Organization for the Study of the Old Testament, Leiden 2004. Frankfurt am Main: Peter Lang, 137–146. Snyman • STJ 2021, Vol 7, No 1, 1–22 20 Strawn, B A 2013. What is Cush doing in Amos 9:7? Te Poetics of Exodus in the Plural. VT 63:99–123. Tang, R K H 2011. Te Teology of the Land in Amos 7–9. PhD- dissertation University of Gloucestershire. Van Leeuwen, C. 1985. Amos. Nijkerk: Callenbach. (De Prediking van het Oude Testament). Von Rad, G 1975. Old Testament Teology Vol I. London: SCM. Waltke, B K 2007. An Old Testament Teology – an exegetical, canonical and thematic approach. Grand Rapids: Zondervan. Wolf, H W 1977. Joel and Amos. Philadelphia: Fortress. (Hermeneia). Wood, J R 2002. Amos in Song and Book Culture. Shefeld: Shefeld Academic Press (JSOTSup 337). Zimmerli, W 1978. Old Testament Teology in Outline. Edinburgh: T & T Clark.
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Zygote morphogenesis but not the establishment of cell polarity in Plasmodium berghei is controlled by the small GTPase, RAB11A
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PLOS PATHOGENS PLOS PATHOGENS PLOS PATHOGENS OPEN ACCESS Citation: Patil H, Hughes KR, Lemgruber L, Philip N, Dickens N, Starnes GL, et al. (2020) Zygote morphogenesis but not the establishment of cell polarity in Plasmodium berghei is controlled by the small GTPase, RAB11A. PLoS Pathog 16(5): e1008091. https://doi.org/10.1371/journal. ppat.1008091 Editor: Michael J. Blackman, Francis Crick Institute, UNITED KINGDOM Zygote morphogenesis but not the establishment of cell polarity in Plasmodium berghei is controlled by the small GTPase, RAB11A Harshal Patil☯, Katie R. HughesID☯, Leandro LemgruberID, Nisha Philip, Nicholas DickensID, G. Lucas Starnes, Andrew. P. WatersID* Harshal Patil☯, Katie R. HughesID☯, Leandro LemgruberID, Nisha Philip, Nicholas DickensID, G. Lucas Starnes, Andrew. P. WatersID* Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, Scotland, United Kingdom a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 ☯These authors contributed equally to this work. * Andy.Waters@glasgow.ac.uk Abstract Plasmodium species are apicomplexan parasites whose zoites are polarized cells with a marked apical organisation where the organelles associated with host cell invasion and col- onization reside. Plasmodium gametes mate in the mosquito midgut to form the spherical and presumed apolar zygote that morphs during the following 24 hours into a polarized, elongated and motile zoite form, the ookinete. Endocytosis-mediated protein transport is generally necessary for the establishment and maintenance of polarity in epithelial cells and neurons, and the small GTPase RAB11A is an important regulator of protein transport via recycling endosomes. PbRAB11A is essential in blood stage asexual of Plasmodium. Therefore, a promoter swap strategy was employed to down-regulate PbRAB11A expres- sion in gametocytes and zygotes of the rodent malaria parasite, Plasmodium berghei which demonstrated the essential role of RAB11A in ookinete development. The approach revealed that lack of PbRAB11A had no effect on gamete production and fertility rates how- ever, the zygote to ookinete transition was almost totally inhibited and transmission through the mosquito was prevented. Lack of PbRAB11A did not prevent meiosis and mitosis, nor the establishment of polarity as indicated by the correct formation and positioning of the Inner Membrane Complex (IMC) and apical complex. However, morphological maturation was prevented and parasites remained spherical and immotile and furthermore, they were impaired in the secretion and distribution of microneme cargo. The data are consistent with the previously proposed model of RAB11A endosome mediated delivery of plasma mem- brane in Toxoplasma gondii if not its role in IMC formation and implicate it in microneme function. Received: September 13, 2019 Accepted: February 29, 2020 Published: May 28, 2020 Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.ppat.1008091 Copyright: © 2020 Patil et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Editor: Michael J. Blackman, Francis Crick Institute, UNITED KINGDOM Received: September 13, 2019 Accepted: February 29, 2020 Published: May 28, 2020 Received: September 13, 2019 Accepted: February 29, 2020 Published: May 28, 2020 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development Funding: APW received support from The Wellcome Trust (Wellcome.ac.uk) Grant refs: 083811/Z/07/Z; 107046/Z/15/Z, WT104111AIA. HP received support from the European Commission (https://cordis.europa.eu/en) Grant name & ref: Evimalar 242095. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Plasmodium which are passed between human hosts by a mosquito vector. In order to transmit through the mosquito the single-celled parasite undergoes many developmental changes as it morphs from non-motile blood forms to become a polarised and motile ookinete in the mosquito midgut. Transport of proteins within the cell during these criti- cal morphological transitions relies on specific endosome vesicles to correctly target pro- teins within the parasite. We investigated the role of the RAB11A protein which is known to be involved in endosomal vesicle targeting to generate cellular polarity in other organ- isms. Because RAB11A is also essential for parasite growth in the mammalian host we used a promoter swap system to specifically switch off RAB11A in the sexual transmission stages. In the absence of RAB11A parasites were unable to form elongated, motile ooki- netes and were unable to pass through the mosquito. Interestingly the parasites were able to form some of the (polarising) structures specific to ookinetes however full morphologi- cal transformation did not occur and the parasites were not motile. We show that although proteins are still delivered to the parasite surface, secretion is impaired and that the mutant parasites are smaller despite obvious microtubule formation implying that there is a deficit in delivery of membrane to the surface. Competing interests: The authors have declared that no competing interests exist. Introduction All zooites formed by apicomplexan parasites are polarized cells exhibiting an asymmetric dis- tribution of content with defined apical distribution of the organelles (rhoptries and micro- nemes) involved in the recognition and colonisation of host cells. One of the early and critical events during mosquito transmission of malaria parasites (Plasmodium spp) is the initial development from (what is assumed to be) a non-polar zygote to a motile and polarized ooki- nete following fusion of a male and female gamete in the blood meal. This is essential for the parasite to be able to escape the hostile environment of the mosquito midgut and represents the greatest period of time that Plasmodium remains outwith a host cell. Although little is known about the generation of polarity in Plasmodium species, studies in other organisms have established that polarity is vital to carry out specific functions such as cell growth, migra- tion, protein transport and invasion [1]. Indeed, all eukaryotes achieve cell polarity through a conserved set of proteins which includes signalling molecules of the rho family of GTPases, cytoskeleton assembly and recruitment, mobilization of proteins from the intracellular pool to the tip of growth via vesicle delivery [1]. Although, the rho family of GTPases such as Cdc42 and its homologues seem to be conserved in majority of organisms studied, there are species specific varieties of polarity determining proteins with little discernible general conservation [2]. The development and establishment of polarity can be regulated by internal factors such as protein trafficking, microtubules and actin dynamics [reviewed in [3]] and utilise both the exocytic and endocytic pathways to develop polarity [4]. The members of Ras GTPase subfam- ily are central to cell growth, differentiation and survival [reviewed in [5, 6]] and RAB proteins of which there are 11 in Plasmodium [7] belong to a small Ras GTPase family and regulate vesi- cle transport in eukaryotes. RAB11A is involved in regulating vesicular traffic during the recycling of endosomes [8] and may assist in cytokinesis [9]. RAB11A is prenylated and interacts with phosphatidylinosi- tol-4 kinases (PI4Ks) [10, 11] and its effectors such as RAB1-family of interacting proteins (FIPs) [12]. RAB11A has been shown to be essential in all apicomplexans tested including Plas- modium berghei [9]. RAB11A is expressed in all Plasmodium asexual blood stages with punc- tate protein localization in schizonts [7, 11] that by analogy with T. Author summary Author summary According to the WHO there was estimated to be over 200 million cases of malaria in 2017 and nearly half a million deaths. The disease is caused by specific species of Data Availability Statement: Data will be held within a public repository ENA/SRA under accession number PRJEB34537. 1 / 27 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PLOS PATHOGENS PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Introduction gondii may be an PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 2 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development association with rhoptries [13] [9]. T. gondii expressing a ddFKBP-Rab11A dominant negative form (ddFKBP-Rab11ADN) shows reduced invasion of host cells by ~85%, consistent with a role in transport and release of rhoptry content during invasion [14]. Furthermore, preceding cell division, co-localization studies of GAP45 and RAB11A support the notion that RAB11A also mediates the delivery of GAP45 to the Inner Membrane Complex (IMC) and interacts with elements of the motility apparatus Myosin A Tail domain Interacting Protein/Myosin Light chain (MTIP/MLC) but plays no role in the organelle biogenesis and localization of sub-pellicu- lar microtubules [9]. However, in T. gondii, the correct delivery of the major surface antigen SAG1 to the plasma membrane requires functional RAB11A as the ddFKBP-Rab11ADN line showed patchy (abnormal) instead of smooth (normal) localization of SAG1 [9]. RAB11A con- trols the necessary step after biogenesis of secretary organelles but before assembly of the motor complex during cell division [9]. These data suggest that RAB11A along with unconventional myosin controls the IMC assembly and budding of daughter cells. Plasmodium iterates the for- mation of zoites through its life cycle with their attendant features of an IMC and apical organ- elle formation raising the prospect that the roles of RAB11A might be also be reiterated. Indeed, the transcript encoding PbRAB11A is one of 370 transcripts which are stabilized and transla- tionally repressed by the DOZI translational repression complex in gametocytes of the rodent infectious malaria model, Plasmodium berghei [15, 16], indicating its potential role in ookinete development. Therefore, further investigation of PbRAB11A function in the fertilised female gamete (zygote) may reveal insights into the development of polarity in extracellular ookinetes, in P. berghei and avoid the possible influence of its habitual intracellular niche. Here, using a promoter swap strategy we show that PbRAB11A is essential for the transmission of Plasmodium through mosquitoes. Lack of PbRAB11A in ookinetes does not affect the forma- tion of internal, polarised landmarks such as the apical complex and IMC in developing zygotes: meiosis and translation of stored mRNAs is also achieved. However, chromosomes remain decondensed 24 hours post fertilization and zygotes are morphologically arrested and remain spherical. These data suggested that PbRAB11A has no role in the establishment or development of zygote polarity in P. Introduction berghei and instead is necessary for morphological progression in a man- ner consistent with the model of PbRAB11A mediated delivery of plasma membrane proposed for daughter cell formation in T. gondii tachyzoites and Plasmodium asexual blood stage forms. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PbRAB11A is expressed throughout P. berghei life cycle and localizes to the periphery and apical tip of the ookinete Gametocyte expression data is shown as the measurements of Otto et al with the proportions of male (blue) to female (red) expression as reported by [50]. B. Expression of PbRab11A in: A, mixed asexual stages; S, schizonts; G, unactivated gametocytes and O, ookinete C. Expression of PbRab11A post-activation of gametocytes i.e. zygote to ookinete development using rabbit anti-PbRab11A antibody. Asterisks indicate the additional small PbRab11A band in schizont and ookinete. hpa = hours post-activation of gametocytes. D. Localization of Rab11A in WT-GFPCON parasites determined through anti- PbRab11A antibody during blood stage: schizont (separated merozoites), mosquito stages: 6h zygote, ookinete, day 10 oocyst and midgut sporozoites. Insets show magnified images of a segmented merozoite (top) or an ookinete (bottom) tip in their respective panels. Scale bar 5 μm, Inset scale bar 2 μm. https://doi org/10 1371/journal ppat 1008091 g001 Fig 1. Rab11A expression and localization during P. berghei life cycle stages. A. PbRab11A transcription profile in FPKM at ring—R, trophozoite—T, schizont—S, gametocyte—G and ookinete—O stage [49]. Gametocyte expression data is shown as the measurements of Otto et al with the proportions of male (blue) to female (red) expression as reported by [50]. B. Expression of PbRab11A in: A, mixed l S hi G i d d O ki C E i f PbR b11A i i f i Fig 1. Rab11A expression and localization during P. berghei life cycle stages. A. PbRab11A transcription profile in FPKM at ring—R, trophozoite—T, schizont—S, gametocyte—G and ookinete—O stage [49]. Gametocyte expression data is shown as the measurements of Otto et al with the proportions of male (blue) to female (red) expression as reported by [50]. B. Expression of PbRab11A in: A, mixed asexual stages; S, schizonts; G, unactivated gametocytes and O, ookinete C. Expression of PbRab11A post-activation of gametocytes i.e. zygote to ookinete development using rabbit anti-PbRab11A antibody. Asterisks indicate the additional small PbRab11A band in schizont and ookinete. hpa = hours post-activation of gametocytes. D. Localization of Rab11A in WT-GFPCON parasites determined through anti- PbRab11A antibody during blood stage: schizont (separated merozoites), mosquito stages: 6h zygote, ookinete, day 10 oocyst and midgut sporozoites. Insets show magnified images of a segmented merozoite (top) or an ookinete (bottom) tip in their respective panels. Scale bar 5 μm, Inset scale bar 2 μm. https://doi.org/10.1371/journal.ppat.1008091.g001 PbRAB11A is expressed throughout P. berghei life cycle and localizes to the periphery and apical tip of the ookinete The gene encoding pbrab11A (PBANKA_1418900) was transcribed in all stages of the P. ber- ghei life cycle examined and was most abundant in gametocytes [17] (Fig 1A). A polyclonal antibody raised against the C-terminal end of PBRab11A (S4 Table) was used in Western anal- ysis of the WT-GFPCON, [18] line and demonstrated expression of pbrab11a across mixed asexual stages, schizonts, gametocytes and ookinetes. A smaller, ~23kDa band of unknown sig- nificance was detected indicating possible differential regulation or N-terminal processing of PbRAB11A in schizonts and mature ookinetes (asterisked in Fig 1B and 1C). Immunofluores- cence microscopy using the same polyclonal antibody on fixed in WT-GFPCON, parasites showed expression of PbRAB11A in mature schizonts (individual merozoites), 6h zygotes, ookinetes, oocysts as well as midgut sporozoites (Fig 1D). In merozoites, oocysts (day 10) and midgut sporozoites (day 10), the localization of PbRAB11A appeared to be cytoplasmic. In the 6h zygote, PbRAB11A was cytoplasmic and appeared punctate while in the ookinete PbRAB11A was more peripheral and with a focus at the apical tip suggesting a role of PbRAB11A at the apical complex (Fig 1D, S1 Fig). 3 / 27 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development Fig 1. Rab11A expression and localization during P. berghei life cycle stages. A. PbRab11A transcription profile in FPKM at ring—R, trophozoite—T, schizont—S, gametocyte—G and ookinete—O stage [49]. Gametocyte expression data is shown as the measurements of Otto et al with the proportions of male (blue) to female (red) expression as reported by [50]. B. Expression of PbRab11A in: A, mixed asexual stages; S, schizonts; G, unactivated gametocytes and O, ookinete C. Expression of PbRab11A post-activation of gametocytes i.e. zygote to ookinete development using rabbit anti-PbRab11A antibody. Asterisks indicate the additional small PbRab11A band in schizont and ookinete. hpa = hours post-activation of gametocytes. D. Localization of Rab11A in WT-GFPCON parasites determined through anti- PbRab11A antibody during blood stage: schizont (separated merozoites), mosquito stages: 6h zygote, ookinete, day 10 oocyst and midgut sporozoites. Insets show magnified images of a segmented merozoite (top) or an ookinete (bottom) tip in their respective panels. Scale bar 5 μm, Inset scale bar 2 μm. https://doi.org/10.1371/journal.ppat.1008091.g001 NS RAB11A controls Plasmodium ookinete development Fig 1. Rab11A expression and localization during P. berghei life cycle stages. A. PbRab11A transcription profile in FPKM at ring—R, trophozoite—T, schizont—S, gametocyte—G and ookinete—O stage [49]. Rab11A is necessary to generate normal ookinete morphology, motility and for transmission The essential nature of PbRAB11A in the asexual blood stages [9] required a conditional approach for gene disruption to study protein function in the ookinete stage. The promoter swap strategy that has been previously validated [17, 19, 20] is a reliable method to knock PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 4 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development down gene expression during the gametocyte to ookinete transition especially since modifica- tion of the PbRAB11A at the C-terminus would be expected to inactivate the protein. Both the clag (PBANKA_140060) and ama-1 (PBANKA_091500) promoters are known to remain silent in sexual stages whilst maintaining sufficient expression levels during asexual blood stages [17, 19, 20]. 0.9 kb 5’ UpStream Region (USR) of rab11a was replaced by 2 kb 5’USR of clag (referred to as pclag) or 1.7 kb 5’USR of ama-1 (referred to as pama-1) and a 2cmyc N-terminal tag using conventional double crossover homologous recombination in WT-GFPCON para- sites. Mutants were successfully selected and cloned via serial dilution [21]. Both indepen- dently generated pbrab11A promoter-swap mutants: pclag:2cmyc::rab11a (line G480) and pama-1:2cmyc::rab11a (line G481) (henceforth referred as pclag::rab11a and pama-1::rab11a) demonstrated appropriate genomic integration of the introduced constructs (S2 Fig). g g g The two independently generated pbrab11A promoter-swap mutants: pclag::rab11a and pama-1::rab11a showed no apparent growth defects during blood stages and gametocytogen- esis (analysed by morphological comparison of gametocytes, exflagellation of male gameto- cytes, ratio of male to female gametocytes in parasites (S3 Fig). However, visual inspection of in vitro ookinete cultures of pclag::rab11a and pama-1::rab11a parasites revealed a severely impaired zygote to ookinete development by up to 99% and 98% respectively (Fig 2A–2C). Zygotes of both promoter swap lines remained spherical and failed to develop the characteris- tic elongated morphology of a wild type ookinete although the mature ookinete surface marker p25 was expressed and distributed to the surface of both promoter swap lines (Fig 2A–2C). Western analysis of pclag::rab11a and pama-1::rab11a showed normal expression of RAB11A in mixed asexual blood stages, however, PbRAB11A is down-regulated in pclag::rab11a and pama-1::rab11a gametocytes and ookinetes (Fig 2D and 2E). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Rab11A is necessary to generate normal ookinete morphology, motility and for transmission The additional smaller form of PbRAB11A noted in schizonts and mature ookinetes was only detected by the polyclonal PbRAB11A antisera and not by the anti c-MYC antibody indicating that the protein confirm- ing that the smaller isoform lacks the N-terminus of the larger form and therefore the c-MYC epitope that would be present in the promoter swap lines. In addition to the full length protein, a slightly smaller RAB11A product is consistently detected by the anti-c-MYC antibody in the pclag::rab11a line. The reason for this is unclear but may represent a processing event that was not characterised further (Fig 2D). The pclag::rab11a line was arbitrarily chosen for the major- ity of the further analyses and western analysis demonstrated that zygotes of this line failed to produce significant levels of PbRAB11A from 2-24hpa (hours post activation) (Fig 2B, 2D and 2E). Immunofluorescence studies supported the down-regulation of PbRAB11A in pclag:: rab11a “ookinetes” (Fig 2B). The expression of the paralogous PbRAB11B in pclag::rab11a was unaffected during zygote to ookinete development (S4 Fig). Activated-Unfertilized 24h WT-GFPCON Female Gametes (AUFG—treated prior to activation with 2-Deoxy-D-glucose, 2DG [22] showed expression of PbRAB11A and P25 (Fig 2B and 2E) indicating activation of translationally stored mRNAs occurred and was not dependent upon fertilisation (S4 Fig). An imaging flow cytometry (IFC) strategy (S5 Fig, S6 Fig) was developed to quantitate the ooki- nete conversion rate and confirmed the results seen by conventional microscopy (Fig 2F). Using IFC the level of the P25 on the parasite surface was also measured and compared to the degree of ookinete development (stages I-IV as defined by Janse et al, 1985 [23]). This showed that P25, although still strongly expressed was expressed at slightly lower levels in the promoter swap lines compared to the control line (Fig 2G). IFC was also used to measure the perimeter of the parasite as a measure of the surface area of parasites. Mature elongated wild type ooki- netes as expected had an increased perimeter measurement and the predominantly circular parasites of the promoter swap lines retained a lower perimeter measurement similar to imma- ture zygotes and were therefore, of smaller surface area (Fig 2H). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Rab11A is necessary to generate normal ookinete morphology, motility and for transmission Left panel: Dot plot of the ookinete development against a measurement of the periphery of the ookinete using the perimeter measurement feature in IDEAS software for WT-GFPCON (blue) pclag::rab11a (red) and pama1::rab11a (green). Right panel: Graphical representation of the data in the left panel for four gates as indicated below. Bars show median and interquartile range. I. Representative images from gates i-iv for each line showing overlay of channel 2 GFP (green) and channel 3 antiP25-Cy3 antibody (magenta). https://doi.org/10.1371/journal.ppat.1008091.g002 https://doi.org/10.1371/journal.ppat.1008091.g002 2I). The pclag::rab11a zygotes were able to complete meiosis (S7 Fig) although apparently with reduced success compared to WT parasites although this was not a statistically significant dif- ference. Both male and female rab11a alleles appeared to contribute to the full development of the ookinete since crosses with P47ko and P48/45ko lines which make competent male or female gametes respectively only partially restored the ability to generate wild type numbers of mature, morphologically normal ookinetes (S8 Fig). The nucleus of the pclag::rab11a “ooki- netes” appeared decondensed suggesting a qualitative impact on DNA replication or organisa- tion (Fig 2A & S8 Fig). To determine if the mainly spherical pclag::rab11a and pama-1::rab11a ookinete popula- tions were able to complete the life cycle through their invertebrate host, mosquito transmis- sion experiments were performed (Fig 3). Female Anopheles stephensi mosquitoes were allowed to feed on WT-GFPCON, pclag::rab11a or pama-1::rab11a infected mice. Mosquito midguts were examined for the presence of oocysts on day 11 or 14. Mosquito midguts were also analysed on day 17, 18 or 22 assuming that pclag::rab11a and pama-1::rab11a spherical ookinetes might have delayed midgut transversal and oocyst development. The WT-GFPCON showed normal oocyst development in mosquito midguts [median 150, mean 227 oocysts per midgut (n = 3)] while pclag::rab11a (maximum of 4 oocysts per midgut with small size, mean 0.269, median 0 and n = 3) (Fig 3A and 3B) or pama-1::rab11a (maximum of 5 oocysts per midgut with small size, mean 0.31, median 0, n = 2) (independent WT-GFPCON control for pama-1::rab11a showed mean 84, median 130.47, n = 2) showed greatly reduced numbers of oocysts and salivary gland analysis showed a complete absence of pclag::rab11a and pama-1:: rab11a sporozoites (S9 Fig). Rab11A is necessary to generate normal ookinete morphology, motility and for transmission The images of the parasites taken during IFC from the different groups confirmed the accuracy of the classifications (Fig PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 5 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 6 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development Fig 2. Mutant pclag::rab11a and pama-1::rab11a do not make ookinetes and down-regulate PbRab11A. A/B. Microscopy images of immunofluorescence on fixed parasites using anti-RAB11A and/or anti-P25 antibodies as indicated and DAPI as a nuclear stain. B. Fertilized pclag::rab11a spherical ookinetes and Activated Unfertilised Female Gametes (AUFG) i.e. 24h post- activation showing enlarged nucleus (Images taken on Axioplan). Scale bars 5 μm. C. Plot of pclag::rab11a and pama-1::rab11a ookinete development (n = 3, mean +/-SD, two tailed student t test, p-value 0.0001). D. Western blot for Rab11A in pclag::rab11a and pama-1::rab11a parasites at various life cycle stages probed with anti-PbRab11A, anti-c-MYC antibody. GFP is a loading control. Asterisks show the presence of extra bands in schizont and ookinete stages when the blot is probed with anti-PbRab11A antibody. A: Asexual mixed blood stage; S: Schizonts; G: enriched Gametocytes; O: ookinetes. E. Western blots showing the expression of Rab11A in zygotes and ookinetes produced by pclag::rab11a at 2, 4, 6, 8 and 24hpa as well as in AUFG 6 and 24hpa. F-I. Data from live parasites stained with anti-P25-Cy3 antibody, run on an Imagestreamx MkII imaging flow cytometer and analysed in IDEAS software. All figures show analysis of >750 activated cells after gating for activated parasites based on area focus, GFP and P25-Cy3 intensity (See S5 Fig) F. Imaging flow cytometry (IFC) density plots showing the aspect ratio of the masked GFP image (X axis) (AspectRatio_AdaptiveErode(M02, Ch02, 84)) against the circularity of the masked GFP image Fig 2. Mutant pclag::rab11a and pama-1::rab11a do not make ookinetes and down-regulate PbRab11A. A/B. Microscopy images of immunofluorescence on fixed parasites using anti-RAB11A and/or anti-P25 antibodies as indicated and DAPI as a nuclear stain. B. Fertilized pclag::rab11a spherical ookinetes and Activated Unfertilised Female Gametes (AUFG) i.e. 24h post- activation showing enlarged nucleus (Images taken on Axioplan). Scale bars 5 μm. C. Plot of pclag::rab11a and pama-1::rab11a ookinete development (n = 3, mean +/-SD, two tailed student t test, p-value 0.0001). D. Rab11A is necessary to generate normal ookinete morphology, motility and for transmission Western blot for Rab11A in pclag::rab11a and pama-1::rab11a parasites at various life cycle stages probed with anti-PbRab11A, anti-c-MYC antibody. GFP is a loading control. Asterisks show the presence of extra bands in schizont and ookinete stages when the blot is probed with anti-PbRab11A antibody. A: Asexual mixed blood stage; S: Schizonts; G: enriched Gametocytes; O: ookinetes. E. Western blots showing the expression of Rab11A in zygotes and ookinetes produced by pclag::rab11a at 2, 4, 6, 8 and 24hpa as well as in AUFG 6 and 24hpa. F-I. Data from live parasites stained with anti-P25-Cy3 antibody, run on an Imagestreamx MkII imaging flow cytometer and analysed in IDEAS software. All figures show analysis of >750 activated cells after gating for activated parasites based on area focus, GFP and P25-Cy3 intensity (See S5 Fig) F. Imaging flow cytometry (IFC) density plots showing the aspect ratio of the masked GFP image (X axis) (AspectRatio_AdaptiveErode(M02, Ch02, 84)) against the circularity of the masked GFP image (Circularity_AdaptiveErode(M02, Ch02, 84)). Percentage values show proportion of parasites falling into each gate as described. G. Left panel: Dot plot of ookinete development (Circularity_AdaptiveErode(M02,Ch02,84)/AspectRatio(M02,Ch02,84) against P25 intensity (Intensity_MC_Ch03) for the WT-GFPCON (blue) pclag::rab11a (red) and pama1::rab11a (green). Right panel: Bar graph representation of data in left panel split into 4 gates as indicated below. Mean +/-SD and P value 2-tailed t test compared to the control line for each promoter swap line. H. Left panel: Dot plot of the ookinete development against a measurement of the periphery of the ookinete using the perimeter measurement feature in IDEAS software for WT-GFPCON (blue) pclag::rab11a (red) and pama1::rab11a (green). Right panel: Graphical representation of the data in the left panel for four gates as indicated below. Bars show median and interquartile range. I. Representative images from gates i-iv for each line showing overlay of channel 2 GFP (green) and channel 3 antiP25-Cy3 antibody (magenta). (Circularity_AdaptiveErode(M02, Ch02, 84)). Percentage values show proportion of parasites falling into each gate as described. G. Left panel: Dot plot of ookinete development (Circularity_AdaptiveErode(M02,Ch02,84)/AspectRatio(M02,Ch02,84) against P25 intensity (Intensity_MC_Ch03) for the WT-GFPCON (blue) pclag::rab11a (red) and pama1::rab11a (green). Right panel: Bar graph representation of data in left panel split into 4 gates as indicated below. Mean +/-SD and P value 2-tailed t test compared to the control line for each promoter swap line. H. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 https://doi.org/10.1371/journal.ppat.1008091.g002 Rab11A is necessary to generate normal ookinete morphology, motility and for transmission Upon feeding of infected mosquitoes on mice (bite-back) on day 18, 22 or 24, no parasites were observed in pclag::rab11a (n = 3) or pama-1::rab11a (n = 2) infected mice which were monitored until day 14 post infection while WT-GFPCON parasites were observed on day 3 in all experiments (S1 Table and S2 Table). Therefore, PbRAB11A is essential for the transmission of P. berghei and its role in the generation of ookinete morphol- ogy appears critical. gy Due to the inability of pclag::rab11a ookinetes to infect mosquito midguts and their spheri- cal shape, the motility of pclag::rab11a spherical ookinetes was examined in a comparative assay. 24hpa WT-mCherry and GFP-positive pclag::rab11a zygotes (i.e. ookinetes) were PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 7 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development Fig 3. pclag::rab11a parasites are unable to transmit through mosquitoes. A. Plot of oocyst load on day 14 after feeding in dissected midguts of WT-GFPCON or pclag::rab11a fed mosquitoes (n = 3, two tailed student t test, p-value 0.0001). B. Images of dissected midguts and salivary glands from WT-GFPCON and pclag::rab11a parasites fed mosquitoes. C. Speed of WT-mCherry and pclag::rab11a spherical ookinetes. 16 ookinetes for each genotype were measured; bottom and top boxes denote first and third quartiles respectively, whiskers denote minimum and maximum, P<0.0001. D. Representative path of WT-mCherry and pclag:: rab11a ookinetes for 10 minutes. https://doi.org/10.1371/journal.ppat.1008091.g003 Fig 3. pclag::rab11a parasites are unable to transmit through mosquitoes. A. Plot of oocyst load on day 14 after feeding in dissected midguts of WT-GFPCON or pclag::rab11a fed mosquitoes (n = 3, two tailed student t test, p-value 0.0001). B. Images of dissected midguts and salivary glands from WT-GFPCON and pclag::rab11a parasites fed mosquitoes. C. Speed of WT-mCherry and pclag::rab11a spherical ookinetes. 16 ookinetes for each genotype were measured; bottom and top boxes denote first and third quartiles respectively, whiskers denote minimum and maximum, P<0.0001. D. Representative path of WT-mCherry and pclag:: rab11a ookinetes for 10 minutes. Fig 3. pclag::rab11a parasites are unable to transmit through mosquitoes. A. Plot of oocyst load on day 14 after feeding in dissected midguts of WT-GFPCON or pclag::rab11a fed mosquitoes (n = 3, two tailed student t test, p-value 0.0001). B. Images of dissected midguts and salivary glands from WT-GFPCON and pclag::rab11a parasites fed mosquitoes. C. Speed of WT-mCherry and pclag::rab11a spherical ookinetes. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Rab11A is necessary to generate normal ookinete morphology, motility and for transmission 16 ookinetes for each genotype were measured; bottom and top boxes denote first and third quartiles respectively, whiskers denote minimum and maximum, P<0.0001. D. Representative path of WT-mCherry and pclag:: rab11a ookinetes for 10 minutes. https://doi.org/10.1371/journal.ppat.1008091.g003 https://doi.org/10.1371/journal.ppat.1008091.g003 embedded in the same Matrigel preparation (see Materials and Methods) and their motility observed in the red and green fluorescent channels. WT-mCherry ookinetes possessed normal corkscrew like movement and an average speed of ~4 μm/min (range 2–10 μm/min) whereas pclag::rab11a spherical ookinetes were completely immobile (n = 2) (Fig 3C and 3D). This indicates that pclag::rab11a ookinetes are immobile either due to the spherical morphology caused by lack of PbRAB11A and/or possible lack of motility associated proteins and therefore, transmission through mosquitoes is blocked. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 8 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PbRAB11A is not necessary for the generation and deposition of the apical complex and the IMC This suggested that a full (and functional) apical complex was developed by pclag::rab11a zygotes consisting of the IMC and internal organelles (see below) somewhat in contrast to the role for RAB11A in the deliv- ery of surface and IMC markers in T. gondii [9]. The expression and distribution of a number IMC and apical organelle components by developing pclag::rab11a zygotes for which antibody reagents were available was, therefore, examined both by Western blot analysis and where possible immunofluorescence, comparing them to wild type parasites or activated unfertilised female gametes (AUFG) as controls. West- ern analysis of glideosome associated proteins: MTIP, GAP45 and GAP50, MyoA suggested a possible marginal delay in their expression between 6 to 8hpa and overall reduction in protein expression in pclag::rab11a zygotes (Fig 5A). Similarly, the expression of ookinete secreted or surface distributed proteins (chitinase and P28) appeared to be delayed and/or reduced (Fig 5A). The expression of cytoplasmic and more general structural proteins seemed unaffected (DOZI, CITH and alpha-tubulin). The expression of a protein known to be associated with the apical tip of the developing ookinete, the protein phosphatase PPKL seems unaffected in the pclag::rab11a line consistent with the observations that the apical complex is established as nor- mal in the absence of PbRAB11A (Fig 5A, S10 Fig). Immunofluorescence microscopy revealed that all IMC (GAP45, IMCb, MTIP, MyoA), invasive organelle (Chitinase, CTRP) and surface markers (P25) appear to be distributed where expected within the spherical mutant pclag::rab11a matured zygotes (Fig 5, S10 Fig). In addition, PPKL serves as a marker for the apical tip of the mature ookinete and occupies a sim- ilar discrete location in pclag::rab11a matured zygotes alongside evident microtubule forma- tion (S10 Fig). Furthermore, the localised dynamics of IMC protein deposition seemed similar despite the morphological differences between the ookinetes. The localization of GAP45 in pclag::rab11a zygotes was similar at 4h post-fertilization to WT-GFPCON, which indicates an initial focal point or bud development site from which the leading apical end will emerge (S11 Fig) However, although pclag::rab11a 6h zygotes lack a prominent retort outgrowth, GAP45 is deposited in this mutant along the IMC showing an arc-like localization and apparently bor- dering the whole IMC at 24h post fertilization (Fig 5B). The IMC is linked to the subpellicular microtubule network that is critical for parasite motility and morphology. PbRAB11A is not necessary for the generation and deposition of the apical complex and the IMC The demonstration that PbRAB11A production is necessary for the generation of ookinete, morphology, motility and infectivity prompted a further examination of the mutant parasite ultrastructure using electron microscopy. Scanning electron microscopy (SEM) demonstrated that 8h WT-GFPCON zygotes have progressed to the retort form while 8h pclag::rab11a zygotes have a small outgrowth of plasma membrane possibly indicating a site for apical complex development (yellow arrow, Fig 4A). Transmission electron microscopy (TEM) of the same samples demonstrated that the IMC had been fully developed as well as the apical complex in Fig 4. Ultrastructural analysis of pclag::rab11a 8h zygotes. A. SEM images of 8h pclag::rab11a zygotes showing the typical small yet specific membrane extension (see yellow arrow) as compared to retort outgrowth in 8h WT-GFPCON zygotes. B. TEM images of 8h pclag::rab11a zygotes showing integrity of Apical Ring (APR) with aperture (AP), IMC, subpellicular microtubules (Mt) and micronemes (M). C. SEM of left, 24h WT-GFPCON and right, pclag::rab11a “ookinetes”, the apical prominence is arrowed in the latter. D. TEM images of two magnifications of 24hpa pclag::rab11a “ookinetes” demonstrating the fully developed nature of the apical prominence. https://doi.org/10.1371/journal.ppat.1008091.g004 Fig 4. Ultrastructural analysis of pclag::rab11a 8h zygotes. A. SEM images of 8h pclag::rab11a zygotes showing the typical small yet specific membrane extension (see yellow arrow) as compared to retort outgrowth in 8h WT-GFPCON zygotes. B. TEM images of 8h pclag::rab11a zygotes showing integrity of Apical Ring (APR) with aperture (AP), IMC, subpellicular microtubules (Mt) and micronemes (M). C. SEM of left, 24h WT-GFPCON and right, pclag::rab11a “ookinetes”, the apical prominence is arrowed in the latter. D. TEM images of two magnifications of 24hpa pclag::rab11a “ookinetes” demonstrating the fully developed nature of the apical prominence. https://doi.org/10.1371/journal.ppat.1008091.g004 https://doi.org/10.1371/journal.ppat.1008091.g004 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 9 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development 8h pclag::rab11a zygotes with readily identifiable Apical Ring (APR) with an aperture (AP), micronemes (M), Inner membrane complex (IMC) and subpellicular microtubules (Mt) (Fig 4B). EM imaging of parasites after 24 hours of development showed the development of the pclag::rab11a zygotes has barely progressed whereas the WT-GFPCON parasites exhibited the expected, fully elongated form of mature ookinete (Fig 4C and 4D). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PbRAB11A is not necessary for the generation and deposition of the apical complex and the IMC To further investi- gate the development of this tubulin-based structure we used a live-cell permeant tubulin stain to perform IFC analysis on live parasites at different stages of development. Analysis of live parasites showed that activating male gametocytes and male gametes could be clearly visualised and the intensity and distribution of tubulin was unchanged in pclag::rab11a compared to the control (Fig 5C and 5D). At 4 hpa activated females identified by their P25 surface marker showed a discrete focus of tubulin stain representing the formation of the apical complex and site for outgrowth during subsequent parasite development (Fig 5E). This point was clearly present in both WT and mutant parasites, again suggesting that Rab11A is not essential for defining polarity in developing ookinetes. By 24 hpa the tubulin stain was unable to permeate through the membrane of live ookinetes but following partial permeabilisation using L-α- Lysophosphatidylcholine (LysoPC) we were able to visualise the tubulin based cytoskeletal structure in some mature live ookinetes. The promoter swap mutant lines showed tubulin staining around the parasite (Fig 5F) again showing similar intensity and distribution around the periphery of the incompletely formed “ookinetes” compared to WT control ookinetes. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 10 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development Fig 5. Western and immunofluorescence microscopy of ookinete development and structural markers. A. Western blots for WT-GFPCON and pclag::rab11a gametocytes at 2, 4, 6, 8 and 24hpa, and for AUFG at 6 and 24hpa using anti-GAP45, anti- GAP50, anti-P28, anti-MyoA, anti-MTIP, anti-DOZI, anti-CITH, anti-PPKL, anti-αTubulin, anti-Chitinase and anti-actin I Fig 5. Western and immunofluorescence microscopy of ookinete development and structural markers. A. Western blots for WT-GFPCON and pclag::rab11a gametocytes at 2, 4, 6, 8 and 24hpa, and for AUFG at 6 and 24hpa using anti-GAP45, anti- GAP50, anti-P28, anti-MyoA, anti-MTIP, anti-DOZI, anti-CITH, anti-PPKL, anti-αTubulin, anti-Chitinase and anti-actin I Fig 5. Western and immunofluorescence microscopy of ookinete development and structural markers. A. Western blots for WT-GFPCON and pclag::rab11a gametocytes at 2, 4, 6, 8 and 24hpa, and for AUFG at 6 and 24hpa using anti-GAP45, anti- GAP50, anti-P28, anti-MyoA, anti-MTIP, anti-DOZI, anti-CITH, anti-PPKL, anti-αTubulin, anti-Chitinase and anti-actin I Fig 5. Western and immunofluorescence microscopy of ookinete development and structural markers. A. PbRAB11A is not necessary for the generation and deposition of the apical complex and the IMC Cells were gated for area, focus, GFP and absence of P25-Cy3 expression to identify male gametocytes. D. Live parasites 90 min PA gated for area, aspect ratio and tubulin tracker (Invitrogen) stain to identify free male gametocytes. E. Female gametocytes 4 hpa identified by gating for area, focus, GFP and P25-Cy3 expression. Overlaid images are shown for channel2 (GFP) and channel3 (P25-Cy3) and channel2 (GFP) and channel 5 (Tubulin tracker) and single channel images for Tubulin tracker and brightfield. Scale bar (lower left) = 7 μm. >200 female parasites were analysed and there was no difference in the proportion of parasites activating (P25-Cy3 positive) or displaying a prominent tubulin focus. F. Live parasites at 24 hpa stained with tubulin tracker showing non-permeabilised cells (upper) and after partial permeabilisation of cells with LysoPC (lower). Scale bar (for all images) = 7 μm. https://doi.org/10.1371/journal.ppat.1008091.g005 In order to assess possible transcriptional consequences linked to the morphological defects, RNA-seq analysis was performed on both gametocytes and cells resulting from 24 hour cultures of activated gametocytes that would normally generate ookinetes using wild type and pclag::rab11a parasites. Little transcriptional effect was noted in gametocytes (9 transcripts upregulated more than 2-fold and 49 similarly downregulated, S12 Fig) and there was no sig- nificant overlap of the de-regulated transcripts with the pool of transcripts that are destabilised in the absence of CITH or DOZI (1 transcript encoding a conserved protein of unknown func- tion, PBANKA_0707700, S13 Fig). GO-term analysis did not reveal functional classes of tran- script that were affected by the absence of PbRAB11A. There was a slightly stronger effect on ookinete transcription reflected in the number of transcripts with altered steady state level (32 downregulated, 84 upregulated, S14 Fig). In the absence of obviously significant differences in protein expression, deposition and transcription, furthermore taking into account of the expected role of PbRAB11A in micro- neme biogenesis, we examined the functionality of secretion from the apical organelles which is known to be important for the progressive surface distribution of motility associated pro- teins (e.g. CTRP) and soluble enzymes associated with life cycle progression (e.g. chitinase) (reviewed in [23]). Using chitinase as the marker for secretion of apical organelle cargo we compared relative amounts produced by wild type and the two mutants pclag::rab11a and pama1::rab11a parasites after 24 hours of culture of activated gametocytes when mature ooki- netes would normally be present. PbRAB11A is not necessary for the generation and deposition of the apical complex and the IMC Western blots for WT-GFPCON and pclag::rab11a gametocytes at 2, 4, 6, 8 and 24hpa, and for AUFG at 6 and 24hpa using anti-GAP45, anti- GAP50, anti-P28, anti-MyoA, anti-MTIP, anti-DOZI, anti-CITH, anti-PPKL, anti-αTubulin, anti-Chitinase and anti-actin I 11 / 27 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development antibodies. Actin I and α-Tubulin act as loading controls. Asterisks show down-regulated or delayed expression proteins in respective bands. B. Fixed WT-GFPCON ookinetes and pclag::rab11a spherical ookinetes were probed with primary antibodies: anti-GAP45, anti-Chitinase or anti-IMC1b antibodies mixed with FITC-tagged anti-P25 antibody. Images shown are single slices of Deltavision deconvoluted Z stack. Scale bar 5 μm. C-F. Image galleries from IFC analysis. Samples were run on an Imagestreamx MkII imaging flow cytometer were analysed using IDEAS software. Images are representative of over 200 gametocytes analysed. C. Live 30 min post activation (PA) parasites stained with anti-P25-Cy3 and Tubulin tracker (Invitrogen). Cells were gated for area, focus, GFP and absence of P25-Cy3 expression to identify male gametocytes. D. Live parasites 90 min PA gated for area, aspect ratio and tubulin tracker (Invitrogen) stain to identify free male gametocytes. E. Female gametocytes 4 hpa identified by gating for area, focus, GFP and P25-Cy3 expression. Overlaid images are shown for channel2 (GFP) and channel3 (P25-Cy3) and channel2 (GFP) and channel 5 (Tubulin tracker) and single channel images for Tubulin tracker and brightfield. Scale bar (lower left) = 7 μm. >200 female parasites were analysed and there was no difference in the proportion of parasites activating (P25-Cy3 positive) or displaying a prominent tubulin focus. F. Live parasites at 24 hpa stained with tubulin tracker showing non-permeabilised cells (upper) and after partial permeabilisation of cells with LysoPC (lower). Scale bar (for all images) = 7 μm. antibodies. Actin I and α-Tubulin act as loading controls. Asterisks show down-regulated or delayed expression proteins in respective bands. B. Fixed WT-GFPCON ookinetes and pclag::rab11a spherical ookinetes were probed with primary antibodies: anti-GAP45, anti-Chitinase or anti-IMC1b antibodies mixed with FITC-tagged anti-P25 antibody. Images shown are single slices of Deltavision deconvoluted Z stack. Scale bar 5 μm. C-F. Image galleries from IFC analysis. Samples were run on an Imagestreamx MkII imaging flow cytometer were analysed using IDEAS software. Images are representative of over 200 gametocytes analysed. C. Live 30 min post activation (PA) parasites stained with anti-P25-Cy3 and Tubulin tracker (Invitrogen). PbRAB11A is not necessary for the generation and deposition of the apical complex and the IMC We compared levels of parasite-associated protein in gently pelleted parasites and amounts released into the culture supernatant using a soluble non- secreted cytoplasmic protein (DOZI) as a marker for parasite lysis and normalisation. The change in ratio of the amount of chitinase and DOZI in the supernatants indicated reduced production/secretion of chitinase was evident in both mutants (Fig 6). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Discussion Obligate intracellular protozoan parasites such as those represented by the Apicomplexa are likely to have further evolved the endocytic pathway common to all eukaryotes to suit the spe- cialised needs of their intracellular niche. RAB11A is a highly conserved protein that can serve as a marker of both regulated and constitutive secretory pathways that may also ultimately deliver proteins to the cell surface [24]. Plasmodium spp. also have an extended period where they exist as an extracellular parasite in the blood meal of the mosquito following gamete for- mation during the development of the zygote to form the motile ookinete that will subse- quently encyst at the basolaminar side of the mosquito midgut. This extracellular phase of the life cycle offers an opportunity to study the development of a stable, polarised apicomplexan cell without the influence of a surrounding host cell. Secretory activities (including those PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 12 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development Fig 6. Ookinetes deficient in PbRAB11A expression also are relatively deficient in protein secretion. Representative Western blot analysis of culture parasite pellet and supernatants protein content analysing parasite pellets (P) after collection by centrifugation and in the remaining culture supernatant (S). Chitinase is expected to be released and shed into the culture supernatant respectively. DOZI is an abundant cytoplasmic protein that acts as a control for cell lysis. Two representative experiments are shown (A & B). Lower panels are quantitated according to the signals in the upper images and normalized relative to wt parasites. Fig 6. Ookinetes deficient in PbRAB11A expression also are relatively deficient in protein secretion. Representative Western blot analysis of culture parasite pellet and supernatants protein content analysing parasite pellets (P) after collection by centrifugation and in the remaining culture supernatant (S). Chitinase is expected to be released and shed into the culture supernatant respectively. DOZI is an abundant cytoplasmic protein that acts as a control for cell lysis. Two representative experiments are shown (A & B). Lower panels are quantitated according to the signals in the upper images and normalized relative to wt parasites. https://doi.org/10.1371/journal.ppat.1008091.g006 https://doi.org/10.1371/journal.ppat.1008091.g006 https://doi.org/10.1371/journal.ppat.1008091.g006 involving PbRAB11A) will be confined to the delivery of membrane bound or secretory pro- teins to the parasite cell surface or to the specialised organelles associated with ookinete inva- sion (micronemes) for subsequent programmed release. Previous attempts to delete PbRAB11A in haploid blood stages of P. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Discussion berghei were unsuc- cessful indicating essentiality [9]. The abundance of rab11A mRNA in gametocytes [17] and the expectation that this mRNA was translationally repressed [15] suggested a role for PbRAB11A in ookinete development. We employed a c-MYC N-terminal tagging and a pro- moter swap strategy [19, 20] in order to avoid alteration of the C-terminus which contains a highly conserved and essential pair of cysteine residues necessary for the conserved geranylger- anylation required for RAB11A function [25];[26]. Two independent mutant parasite lines: pclag::rab11a (G480) and pama-1:rab11a (G481) exploiting the late schizont clag and ama-1 promoters respectively, were shown to facilitate the blood stage asexual expression of PbRAB11A to normal levels and showed no obvious growth defect. However, rab11a was effectively silenced in the sexual stages allowing examination of protein function during PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 13 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development gametocyte and zygote development. Our results also extended the analysis of the expression of PbRAB11A during the P. berghei lifecycle (Figs 1 & 2) with Western analysis suggesting that two isoforms of PbRAB11A are produced in schizonts and ookinetes due to N-terminal pro- cessing. However, the significance of the observation is unclear and requires further investigation. The absence of PbRAB11A in the pclag::rab11a and pama-1::rab11a lines resulted in the for- mation of spherical ookinetes with an intact apical complex and IMC. Transcription and trans- lation were also shown largely to be uncoupled to cellular development as both protein and transcriptome analyses revealed no striking differences from wild type gametocytes and ooki- netes. Similarly spherical (and developmentally arrested) ookinetes of P. berghei were observed when gap45 KD [27] and pdeδ KO [28] lines were analysed. However, the similarities are superficial given that GAP45 is expressed with only a slight delay and the IMC is correctly anchored in the pclag::rab11a spherical ookinetes unlike in the gap45 KD equivalents where the apical complex was observed to float freely inside the cytoplasm [27]. GAP45 is believed to be delivered to the IMC by Rab11A-mediated vesicles [9] and is also responsible for retort for- mation [27]. Discussion Localization studies of GAP45 suggest the selection of a focal point in pclag:: rab11a 4h zygotes which then disperses along the membrane of pclag::rab11a 6h zygotes lack- ing the WT retort outgrowth and lays down the IMC across the entire cytoplasmic side of the plasma membrane of the spherical pclag::rab11a ookinete (24hpa) indicating the assembly of IMC (S11 Fig and Fig 5B). Our data, however, suggest that delivery of GAP45 does not depend on PbRAB11A mediated vesicles at this stage of parasite development. Equally in ddFKBP-Ra- b11ADN tachyzoites expressing a dominant negative form of TgRAB11A the membrane sur- face protein, SAG1 was not delivered correctly to the cell surface [9] yet delivery of an equivalent surface marker in the developing Plasmodium zygote, P25, seems unaffected and smoothly decorates the surface. SEM analysis revealed a small, cone-like outgrowth in 8h pclag::rab11a zygotes (Fig 4A). Analysis of 8h pclag::rab11a zygotes strongly suggest the outgrowth is associated with the assembly of the collar with an aperture, apical microtubules and the IMC (Fig 4A and 4B). Therefore, assembly of complete set of internal organelles such as IMC, apical complex and micronemes is expected in spherical pclag::rab11a ookinetes and is somewhat comparable with the morphology of round dedifferentiated PDEδ KO P. berghei ookinetes which although they also form apical organelles, possess an incomplete IMC [28]. These round otherwise terminally differentiated PDEδ KO P. berghei ookinetes were shown to rotate rapidly but have little or no forward motility. The same motility assays suggest that pclag::rab11a spherical ookinetes do not exhibit even rotational movement (Fig 3C and 3D) indicating a distinct developmental lesion. ImageStream analysis of pclag::rab11a “ookinetes” indicated that these cells had a smaller surface area than the wild type ookinete equivalents and were therefore smaller. A recent study investigating delayed death phenotype in apicomplexan parasites has implicated a prenylation dependent role for RAB11A in the delivery of vesicular cargo (including GAP45) and intracellular trafficking [30]. Our data would be consistent with a deficit in delivery of lipid to the surface due to the absence of RAB11A implying there is also a stage specificity to the role of RAB11A and its cargo. Sub-pellicular microtubule number varies greatly in the different zooite forms of Plasmo- dium (summarised in [29]) with ookinetes typically expressing around 60 [30] [31], merozoites 3–4 [32] and P. berghei sporozoites 16 [29]. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Discussion The failure of our RAB11A mutant retorts to fully elongate might indicate that there was a physical uncoupling of the IMC from the sub-pellicu- lar microtubules. Direct investigation of this using tubulin tracker in live zygotes/ookinetes and TEM analysis of fixed samples demonstrated an early event at 4hpa visualised as a single centre of polarised nucleation of tubulin subtending the plasma membrane. Unfortunately, PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 14 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development ookinetes become impermeable and live tracking of the microtubule development and organi- sation is not possible. Although TEM evidence was inconclusive it did demonstrate a regular array of microtubule origins around the apical prominence. Furthermore, immune-staining of tubulin indicated that microtubules are formed in parasites in the absence of RAB11A. Micro- tubule length can be a function of type and levels of expression [29], however, there was no apparent impact of lack of RAB11A on tubulin abundance. Despite the abundance of microtu- bules in the ookinete the function of RAB11A does not appear to involve microtubule forma- tion nor tubulin expression. Although no major perturbances in transcription profile were detected in the pclag::rab11a gametocytes and ookinete forms, there was a minor temporal delay in protein expression of certain proteins assayed with our panel of antibodies. Furthermore, the expression of micro- neme proteins CTRP (also associated with ookinete motility) and chitinase appears to be reduced in pclag::rab11a and pama1::rab11a ookinetes than WT-GFPCON ookinetes although micronemes are clearly formed (Fig 4D). Secretion assays confirmed the reduced expression of chitinase and demonstrated that there was no obvious secretion of chitinase indicating func- tional impairment of apical organelle secretion. A deficiency in secretion is also supported by the immunofluorescence data which indicate that both CTRP and chitinase localise in a pat- tern consistent with deposition in the apical organelles. Based on current results and past studies, we propose a model for developmental block of pclag::rab11a spherical ookinetes (Fig 7). The essential apical marker ISP1 is polarised in late female zygotes indicating pre-selection of the focal point of ookinete [33]. Published data [27] and our results (Fig 5, S11 Fig) suggest that GAP45 is also important for further development of the focal point, however, our data demonstrate that along with GAP45, PbRAB11A is critical for the retort outgrowth of P. berghei zygote. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Discussion Once the focal point is marked through ISP1, GAP45 might start assembling at the focal point 4h post-fertilization along with as yet unknown focal point markers but which might include components of the IMC, collar and MTOC [34–36] through which microtubules extend. Subsequently, PbRAB11A along with cytoskeletal components such as actin as well as microtubules assist in the retort shape forma- tion. Specifically, PbRAB11A endosomes might provide plasma membrane to the growing tip or to the joint of the retort and the main body of the zygote (here we refer to it as the ‘neck’ region) (Fig 7) and anticipate a role for Rab11A in the secretion, delivery of membrane synthe- sis components e.g. PI4K [11] and other necessary proteins while donating plasma membrane to assist the intended morphological transformation. Along with plasma membrane, the PbRAB11A endosome might help directly or indirectly in the incorporation of marker(s) at the neck region forming a transition point segregating the initial spherical body of the zygote from the retort outgrowth. Forces might be generated at the transition point that pushes the growing apical complex outwards by donating plasma membrane. Furthermore, the transition point ‘neck marker/s’ may act as a centre for pulling the plasma membrane during ookinete development. In pclag::rab11a zygotes, all characterised developmental and structural markers are formed normally however, we hypothesise that PbRAB11A-mediated endosomes are responsible for delivering the additional plasma membrane required to form the ookinete as it is larger than the female gamete and early zygote. Normally such membrane structures would be both recycled and de novo synthesised and made available for the growing apical complex. In the absence of Rab11A this does not occur, neck markers are probably mis-localized how- ever, apical bud formation is achieved but not further outgrowth. The zygote developmental processes described here serve as models for the developmental events of intracellular forms of Plasmodium such as sporozoites and merozoites as well as other apicomplexans that might be exploited for disease interventions. Our data highlight, PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 15 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development Fig 7. Proposed Model: Rab11A mediated delivery of plasma membrane in P. berghei. Rab11A mediated vesicles are involved in the delivery the plasma membrane and transmembrane proteins to the growing tip or to the neck region of retort / zygote. Animal procedures and parasite reference line Parasites were maintained in Theiler’s original (TO) or NIH Swiss outbred female mice, approximately weighing 25 g and > 6 weeks old. Ethics statement All animal work was approved by the University of Glasgow’s Animal Welfare and Ethical Review Body and by the UK’s Home Office (PPL 60/4443). The animal care and use protocol complied with the UK Animals (Scientific Procedures) Act 1986 as amended in 2012 and with European Directive 2010/63/EU on the Protection of Animals Used for Scientific Purposes. Discussion These are also possibly involved in secretion, development and maintenance of cell shape, protein trafficking coordinating with cytoskeletal components. Blue dots with ‘?’ suggest possible numbers of spindle poles in a zygote. WT-GFPCON 6hpa retort showing possible site for membrane expansion either at the apical tip or neck region. Expanded cartoons of the apical regions of mutant and wild type parasites at 6hpa highlight the vesicles that lack RAB11A. Fig 7. Proposed Model: Rab11A mediated delivery of plasma membrane in P. berghei. Rab11A mediated vesicles are involved in the delivery the plasma membrane and transmembrane proteins to the growing tip or to the neck region of retort / zygote. These are also possibly involved in secretion, development and maintenance of cell shape, protein trafficking coordinating with cytoskeletal components. Blue dots with ‘?’ suggest possible numbers of spindle poles in a zygote. WT-GFPCON 6hpa retort showing possible site for membrane expansion either at the apical tip or neck region. Expanded cartoons of the apical regions of mutant and wild type parasites at 6hpa highlight the vesicles that lack RAB11A. however, that there may well be stage and species-specific features to even these essential processes. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PCRs were performed using Taq DNA polymerase (Invitrogen) as per manufacturer’s instructions. PCRs were performed using Taq DNA polymerase (Invitrogen) as per manufacturer’s instructions. 3’UTR of the snare (PBANKA_141880) was amplified from genomic (g)DNA of WT P ber- ghei by using forward primer GU1620 and reverse primer GU1621 (S3 Table) and re-cloned into pG72 to generate pclag:2cmyc::rab11a construct (‘p’ stands for promoter). Construct pama-1:2cmyc::rab11a was obtained by replacing clag 5’UTR in pclag:2cmyc::rab11a with PCR amplified 1.7 Kb 5’UTR of ama-1 (PBANKA_091500) ORF from gDNA of WT P. berghei using forward primer GU1622 and reverse primer GU1623 (S3 Table). Plasmids pclag:2cmyc:: rab11a and pama-1:2cmyc::rab11a were verified by restriction digestion as well as Sanger sequencing (Eurofins MWG biotech). Purified and HindIII-NotI (New England Biolabs) line- arised genomic constructs were obtained by gel extraction (QIAquick Gel Extraction Kit) and subsequent ethanol precipitation. >5μg of linearized genomic constructs were transfected into WT-GFPCON P. berghei [18] schizonts as described in [21] and [37] to express PbRab11A under the control of either clag (PBANKA_140060) or ama-1 promoter respectively. (Note: pclag:2cmyc::rab11a and pama-1:2cmyc::rab11a were referred as pclag::rab11a and pama-1:: rab11a throughout respectively.) Generation of mutant parasites All the genes, 5’UTRs and 3’UTRs amplifications were performed using either Expand High Fidelity PCR System (Roche) or KAPA HiFi PCR system (KAPA Biosciences) and diagnostic PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 16 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Plasmodium berghei infections, cultures and stage enrichment Mice were infected by intraperitoneal (i.p.) injection either by fresh infected blood with PBS or by approximately 200 μl of blood suspension having parasitaemia 3–5% from thawed cryovials. Post-infection mice develop parasitaemia approximately 0.5–3% on day 3, and for some exper- iments, mice were given a single dose of 100 μl phenylhydrazine (12.5 mg/ml) (mice body- weight ratio 125 mg/kg) i.p. to enhance numbers of reticulocytes usually 48 h prior infection. Parasitaemia was monitored daily by Giemsa staining of thin smears of mouse tail blood [21] and parasites were observed under oil immersion (Invitrogen) 100x objective of light micro- scope (Primo Star- Zeiss). Images were captured through PAXcam5 camera using PAXcam software and processed using Fiji/ImageJ software (National Institute of Health, http://fiji.sc/ Fiji). Schizonts were generated as described in [21]. For enrichment of gametocytes, post 72 h of infection mice were treated with sulfadiazine (30 mg/litre) in drinking water for 48h to kill asexual parasite stages. For ookinete cultures, cardiac blood containing gametocytes was placed into ookinete culture medium (RPMI1640 containing 25 mM HEPES, 5 mM hypoxan- thine, 20% FCS, 10 mM sodium bicarbonate, 100 μM xanthurenic acid at pH 7.6) and incu- bated at 21˚C for 24h. Schizonts, gametocytes and ookinete development was observed by Giemsa staining. Ookinete conversion rates were calculated either from Giemsa staining or immunofluorescence microscopy using Cyanine3-tagged anti-P25 antibody (see immunofluo- rescence assay methods) of ookinete culture. Ookinete conversion rates were calculated according to the following formula: % ookinete conversion ¼ number of ookinetes analysed through morphology number of ookinetes þ number of female or zygotes   % ookinete conversion ¼ number of ookinetes analysed through morphology number of ookinetes þ number of female or zygotes   To analyse activation centres cardiac blood was placed immediately into ookinete culture medium (1:30 blood to ookinete medium ratio) and 10 μl was placed on a haemocytometer at 21˚C. After 15 minutes, activation centres defined as actively moving clumps of cells were counted using 10X objective on the light microscope (Primo Star- Zeiss). Fertility of mutant gametes was assessed through in-vitro cross fertilization with P. berghei parasites able to pro- duce either only fertile male (P47 KO) [38] or female (P48/45 KO) gametes [39], respectively. Motility assay MACS-purified ookinetes were embedded in Matrigel and incubated for 1h at 21˚C before imaging. Time-lapse movies were acquired every 10 seconds for 10 minutes on a Leica M205 FA fluorescence stereomicroscope employing the GFP and mCherry filter sets (0.5 second exposure for each). Ookinete speeds were calculated on Fiji software (NIH, http://fiji.sc/Fiji) using the MtrackJ plugin [40]. Inhibition of gametocyte fertilisation To prevent fertilization of female gametes, unactivated gametocytes were cultured in enriched PBS (PBS supplemented with 2mM HEPES, 2mM Glucose, 0.4mM NaHCO3, 0.01% BSA) containing 100 mM 2-Deoxy-D-glucose (Sigma) for 45 minutes [22] and filtered through Plas- modipur filters (EuroProxima), washed with ookinete medium and re-cultured in ookinete medium without 2-Deoxy-D-glucose (2DG) for 24h. Female gametocytes activate but fertiliza- tion is prevented due to a blockage in male gamete exflagellation [22]. Plasmodium berghei infections, cultures and stage enrichment PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 17 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development The male to female gametocyte ratio was calculated by examining under 100x oil immer- sion lens Giemsa stained slides made from tail blood taken from phenylhydrazine and sulfadi- azine treated mice 72 hrs post-infection having similar parasitaemia. Five different fields with well separated cells were counted from each of the two Giemsa slides per experiment per para- site line (i.e. ten fields per experiment per parasite line). Six biological replicates were per- formed for pclag::rab11a vs WT-GFPCON and four replicates for pama-1::rab11a vs WT-GFPCON. Transmission Transmission of parasites was performed by feeding 200 or 300 Anopheles stephensi mosqui- toes on anaesthetized, infected mice having 2–8% parasitaemia. Mosquitoes were dissected on day 11 or 14 post-feeding for oocyst counting and on day 17, 18 and 22, 27 post-feeding for oocysts and sporozoite counting. Midguts and salivary glands were examined with Leica M205 FA Fluorescence Stereomicroscope and images were captured using Leica DFC340FX camera and through LAS AF Lite 2.2.0 build 4758 (Leica Microsystems Ltd.) and processed through ImageJ/Fiji software (National Institute of Health). Oocyst numbers were counted by live imaging. Scanning and transmission electron microscopy For scanning and transmission electron microscopy P. berghei gametocytes 8 hours post-acti- vation (hpa) and 24hpa in ookinete medium were processed as described in [41]. SEM samples were examined on a JEOL6400 SEM running at 10kV and tiff images captured using Olympus Scandium software. TEM samples were examined either on Tecnai T20 (FEI) running at 200kV or Leo 912AB TEM running 120kV and images captured using Gatan Digital Micro- graph Software (Gatan, Japan). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Western Blotting For analysis of PbRAB11A and ookinete development markers, P. berghei schizonts were enriched with 55% Nycodenz solution in PBS; gametocytes and ookinetes were enriched by 53% Nycodenz solution in PBS following density gradient centrifugation [21]. Mixed asexual blood stage parasites collected from an infected mouse by cardiac puncture were filtered through CF11 cellulose columns (Whatman-GE Healthcare Life Sciences) to exclude mice PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 18 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development white blood cells and immediately lysed with ice-cold erythrocyte lysis buffer (1.5M NH4Cl, 0.1M KHCO3, 0.01 EDTA) for 15 minutes on ice. Equal amounts of parasite material from mixed asexual stage, schizonts, gametocytes and ookinetes were lysed in Net2+ buffer (140 mM NaCl, 50 mM Tris- pH 7.4, 4mM Dithiothreitol, 0.01% Nonidet P-40) supplemented with complete EDTA free Protease Inhibitor Cocktail Tablets (Roche) (1 tablet/10ml) and sus- pended in 2X Laemmli sample buffer containing 15% (v/v) β-mercaptoethanol and separated on 10 or 12% SDS polyacrylamide gels (Flowgen Biosciences) and visualized using ECL and X- ray films as described by [42]. Blots were probed with primary antibodies (S4 Table & S5 Table) and HRP coupled secondary antibodies either Polyclonal Goat anti-Rabbit or anti- mouse Ig/HRP (Dako) (1:10000). For infrared based visualization, appropriate secondary anti- bodies were used (IRDye 680LT Goat anti-mouse IgG and IRDye 800CW Goat anti-rabbit IgG antibodies) and nitrocellulose blots were scanned on Odyssey Sa Infrared Imaging System (LI-COR Biosciences). Blots were stripped twice for 5 minutes each with 0.2M NaOH solution and intermittent washing with distilled water and re-blocked in 5% milk in PBS-Tween before re-probing with further antibodies (S4 Table & S5 Table). Microneme secretion assays were performed as described by [41], parasite secretion supernatant samples were either concen- trated on an Amicon-ultra centrifugal filter, 30 kDa cut-off (Millipore), suspended in Laemmli sample buffer and analysed as above or loaded and analysed directly. Immunofluorescence assay Air dried thin smears of P. berghei ookinete or schizont or sporozoites and oocysts, obtained from midgut of P. berghei infected Anopheles stephensi crushed in PBS, were fixed with 4% EM grade paraformaldehyde (Electron Microscopy Science) for 10 minutes. Permeabilisation, blocking and incubation with primary and appropriate secondary antibodies (S4 Table & S5 Table) was performed as described by [41] with additional last washes with 70% ethanol and absolute ethanol 1 min each, air-dried and mounted in VectaShield (Vectorlabs) containing DAPI (4’, 6-diamidino-2-phenylindole) in glycerol for nuclear staining. Parasites were exam- ined either under Delta Vision Epifluorescence microscope (Applied Precision). 100x objec- tive, images were captured with CoolSNAP HQ camera (Photometrics) and deconvoluted using SoftWoRx software (Applied Precision) or under Axioplane2 (Zeiss) 100x objective, images were taken through HAMAMATSU ORCA_ER camera (HAMAMATSU) and Veloc- ity software 4.1.0 (PerkinElmer). Images were processed using Fiji (NIH) as well as SoftWoRx explorer 1.3. Super-resolution images were captured through Elyra PS.1 super-resolution microscope (Zeiss) under 60x objective with sCMOS PCO camera and images were visualized with ZEN Black software (Zeiss) and processed with ZEN LITE software (Zeiss). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Flow Cytometry analysis WT-GFPCON, activated unfertilised WT-GFPCON female gametes (AUFG) and pclag::rab11a gametes were collected 4hpa and 24hpa in ookinete media and purified using 53% Nycodenz density gradient centrifugation, washed with enriched PBS twice and vigorously vortexed three times 10 seconds each to break the zygote/ookinete clumps. Parasites were incubated with anti-P25 monoclonal antibody (mAb) (1:1000) diluted in enriched PBS for 30 minutes, washed and re-probed with secondary antibodies Goat anti-mouse Alexa Fluor 633 (1:1000) and erythroid cell marker anti-Ter119 PE/Cy5 antibody (eBioscience) (1:500) diluted in enriched PBS (see S5 Table for antibodies) supplemented with 5 μM Hoechst 33342 for 30 minutes, washed twice with enriched PBS and once with FACS buffer (2% (v/v) Fetal Bovine Serum (defined), 0.05% (w/v) sodium azide (NaN3) and 2 mM EDTA in PBS) vortexed. Para- sites were re-suspended in 1ml FACS buffer and parasite aggregates were removed by filtering PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 19 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development through nylon filtration fabric NITEX 40 μm pore size (Cadisch Precision Meshes). Samples were run on a FACS CyAn (Beckman Coulter) equipped with a 405 nm, 488 nm and 633 nm laser and 5,000 to 10,000 events were acquired. Post-acquisition analysis was performed using Kaluza software (Beckman Coulter). The gating strategy was implemented to identify female gametes, zygote and ookinetes (GFP, P25 and Hoechst positive, Ter119 PE/Cy5 negative) from negative controls of uninfected RBCs (Ter119 PE/Cy5 positive), infected RBCs with asexual stages of parasites (Ter119 PE/Cy5 and Hoechst positive) and unstained samples. The DNA content was analysed by comparing the Hoechst 33342 stain levels of these parasites. Differen- tiation between mutant male and female gametocytes was not possible due to lack of two-col- our background of mutants as shown by [43]. Imaging flow Cytometry (IFC) Ookinetes for IFC were prepared by harvesting ookinete cultures and disrupting cell clumps by passing through a 26g needle. Cells were stained with an anti-P25 antibody conjugated to the Cy3 fluorophore (αP25-Cy3) in enriched PBS for 45 minutes at room temperature. Para- sites were washed in enriched PBS and resuspended in Magnesium and Calcium free Dulbec- co’s PBS (DPBS) and passed through 40 μm pore nitex (Cadisch Precision Meshes). Samples were run on an Imagestreamx MkII (Merck) equipped with one camera and 4 lasers (405 nm, 488 nm, 561 nm and 633 nm). Single colour compensation controls were also acquired and post-acquisition analysis and gating was performed in IDEAS software (S4 Fig). Parasites stained for tubulin for IFC were harvested at indicated time points and incubated with 1:2000 dilution of Tubulin Tracker Deep Red (Invitrogen) and αP25-Cy3 in enriched PBS for 45 min- utes at room temperature then resuspended in DPBS and filtered through nitex before acquisi- tion on an ImagestreamX MkII. 24 hour ookinete cultures were permeabilised by addition of L-α-Lysophosphatidylcholine at a final concentration of 250 μg/ml for 2 minutes in enriched PBS then washed in enriched PBS before staining as above. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Supporting information S1 Fig. Distribution of Rab11A in wild type ookinete. Localization of Rab11A in WT- S1 Fig. Distribution of Rab11A in wild type ookinete. Localization of Rab11A in WT- GFPCON ookinete. The first column shows magnified images of apical tip of ookinete (taken from the images in the second column) stained with anti-PbRab11A antibody. Scale bar 5 μm. (TIF) S2 Fig. Genomic introduction of pbrab11a promoter swap constructs. A. P. berghei RNA- Seq data for rab11a, clag and ama-1 shown in FPKM [49]. B. Schematic of the generation of pclag::rab11a and pama-1::rab11a parasites (Not to Scale). Diagnostic PCRs for integration of (C) pclag::rab11a and (D) pama-1:: rab11a constructs into WT-GFPCON gDNA, respectively, showing the 5’ and 3’ integration of respective constructs (PCR fragment as annotated in the schematic in B). W indicates a fragment present only in WT-GFPCON parasites. DNA ‘+’ is an unrelated positive PCR control (P28) and ‘-’ is a no DNA template negative PCR control. Abbreviations: USR, upstream region; SM, selectable marker. (TIF) S3 Fig. Development of sexual stages of pclag::rab11a and pama-1::rab11a parasites mirrors that of wild type parasites. A. Images of Giemsa stained pclag::rab11a and pama-1::rab11a gametocytes; M, male gametocytes; F, female gametocytes. B. Exflagellation count of male gametocytes of pclag::rab11a (n = 4, mean +/-SD, two tailed student t test, p-value 0.9891) and pama-1::rab11a (n = 3, mean +/-SD, two tailed student t test, p-value 0.4337). C. Ratio of male to female gametocytes in pclag::rab11a (n = 6, mean +/-SD, two tailed student t test, p value 0.00046) and pama-1::rab11a (n = 3, mean +/-SD, two tailed student test, p-value 0.0111) para- sites compared to WT-GFPCON. (TIF) S4 Fig. Expression of PbRAB11B is unaffected by downregulation of PbRAB11A in Pclag:: rab11a mutant parasites. A. Western blot analysis of PbRAB11B expression following activa- tion of gametocytes comparing wild type parasites with Pclag::rab11a and Activated Unferti- lised Female Gametocytes (AUFG) across the time course of zygote to ookinete transition sampling at times indicated in hours. B. Immunofluorescence imaging of PbRAB11B expres- sion at 24hpa in the same parasite lines when mature ookinetes should be present. Scale bar = 5μm. S5 Fig. Imaging flow cytometry gating strategy to quantitate ookinete conversion rate. Dot plots and histograms showing the sequential gating strategy pipeline used to identify ookinetes and quantitate conversion rate. Files were acquired separately then merged in IDEAS software. Transcriptomics Differential expression was carried out using cuffdiff (version 2.2.1). Sub- sequent analyses were carried out using the CummeRbund package (http://compbio.mit.edu/ cummeRbund/, version 2.0). Generic GO slim terms were obtained through PlasmoDB.org and only Biological Process terms were shown for simplicity. Transcriptomics Unactivated gametocytes were immediately filtered through Plasmodipur filters at 37˚C before enrichment step or used to set up ookinete cultures. All samples were enriched with Nycodenz density gradient centrifugation and mixed vigorously with 1 ml TRIzol (Ambion-Life Tech- nologies) and stored at -80˚C or immediately used for RNA isolation using RNAeasy Universal Mini kit (Qiagen) with on-column DNAse digestion by RNase-free DNase set (Qiagen) according to manufacturer’s instructions. RNA quality was assessed through reverse transcrip- tase PCR performed using SuperScript III Reverse Transcriptase kit (Life Technology) before transcriptomic analysis (Glasgow Polyomics: www.polyomics.gla.ac.uk). RNA Sequencing (RNA-Seq) reads were prepared (Please see S6 Table and S7 Table for parameters of RNA-Seq) using Life Technologies stranded mRNA library kit and sequencing was carried out on Life Technologies Ion Proton platform. Fastq files were quality controlled using FastQC (http://www.bioinformatics.babraham.ac. uk/projects/fastqc/, version 0.10.1) and trimmed for adapters and with a quality threshold >2 = 20 using cutadapt [[44], version 1.6 version, “-m 16 -b GGCCAAGGCG -q 20”]. Reads were then aligned to the Plasmodium berghei ANKA genome [[45] PlasmoDB version 11.1] using Tophat [[46]. Version 2.0.12, “–keep-fasta-order -b2-D 20 –b2-R 3 –b2-N 1 –b2-L 20 – b2-I S,1,0.50 -g 10 -I 5000–-library-type fr-firststran”"]. In order to have maximum sensitivity to low abundance or divergent transcripts reads that failed to align with Tophat2 were extracted using bed tools (http://bedtools.readthedocs.org/en/latest/, version 2.19.1,“"bamto- fast”") and aligned to the same reference using bowtie2 local alignments [[47], version 2.2.1, PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 20 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development “–-local -D 20 -R 3 -N 1 -L 20 -i S,1,0.50–-m”"]. The Tophat accepted hits and bowtie2 aligned reads were then merged to form the alignment for that sample using Picard tools (http:// broadinstitute.github.io/picard/, version 1.112). Gene-level expression analysis was carried out using the cufflinks2 package [[48] version 2.2.1] using annotated genes only (PlasmoDB VER- SION 11.1 GFF file). Differential expression was carried out using cuffdiff (version 2.2.1). Sub- sequent analyses were carried out using the CummeRbund package (http://compbio.mit.edu/ cummeRbund/, version 2.0). “–-local -D 20 -R 3 -N 1 -L 20 -i S,1,0.50–-m”"]. The Tophat accepted hits and bowtie2 aligned reads were then merged to form the alignment for that sample using Picard tools (http:// broadinstitute.github.io/picard/, version 1.112). Gene-level expression analysis was carried out using the cufflinks2 package [[48] version 2.2.1] using annotated genes only (PlasmoDB VER- SION 11.1 GFF file). PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Supporting information Step 1 –gate R1 defined objects within a broad size range that includes infected RBC, gameto- cytes and ookinetes. Step 2- R2 includes cells positive for GFP. Step 3 –R3 gates on cells in PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 21 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development focus on the Brightfield image. This gate is broad as we observe that some activated female gametocytes displayed a lower gradient RMS that is normal for focussed cells. Step 4—Gate R4 allows us to select cells in focus in the GFP channel. Step 5—Gate R5 selects for cells positive for P25-Cy3. The proportion of GFP positive cells that were also positive for P25-Cy3 was sim- ilar for the WT and the promoter swap lines. Step 6—The next gate selects cells also in focus in the P25-CY3 channel. GFP positive cells include asexual stages and non-activated gametocytes. Events positive for GFP and Cy3 not included for analysis include uninfected RBC that are autofluorescent as a result of the phenylhydrazine treatment given to enhance parasitaemia. Step 7—To help exclude images containing debris or overlapping cells a mask was generated to allow selection of cells where the area of the brightfield image was sufficiently larger than that of the area of the GFP image (Area_adaptiveErode(M05,Ch05) And not Area (M02, Ch02)). (Other strategies to exclude debris included using a spot count feature to identify images containing a single object, or the threshold feature to analyse only the object within the image that was within the size and intensity criteria. In some cases, images including doublets and debris were manually selected for exclusion from analysis). Step 8- To separate out the three merged files the object number vs time is plotted and three populations from the individ- ual samples can be separated. Step 9 –Finally the circularity and aspect ratio features were gener- ated on the adaptive erode (84%) mask for the GFP image and used to plot ookinete conversion. Similar strategies using the brightfield image and the Cy3 image were also successful and gave similar results. All gating strategies were justified by examining images of objects falling outwith the gates. Step 10 –In order to plot the ookinete development against other features the aspect ratio and circularity features were combined onto one axis. Statistics below show the number of cells included and the % of each population falling into each gate. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Supporting information Fluorescent and bright field images of 22 / 27 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development WT-GFPCON and pama-1::rab11a infected midguts and salivary glands. (TIF) S10 Fig. Immunofluorescence microscopy for ookinete development and structural mark- ers. Fixed WT-GFPCON ookinetes and pclag::rab11a spherical ookinetes were probed with pri- mary antibodies: anti-DOZI, anti-CITH, anti-PPKL, anti-CTRP, anti-MyoA and anti-MTIP antibodies mixed with either FITC-tagged anti-P25 or anti-α tubulin antibodies. Except PPKL, all images shown are single slice of Deltavision deconvoluted Z stack. For PPKL, single slice images of Z stacks obtained from ELYRA 3D SIM microscope is shown. Scale bar 5 = μm. (TIF) S11 Fig. Dynamic localization of GAP45. Time course immunofluorescence of WT-GFPCON and pclag::rab11a zygotes for GAP45 and P25 [4hpa timepoint images are taken through Axio- plan and 6hpa timepoint images are single slices of deconvoluted Z stack taken from Deltavi- sion microscope]. Scale Bar = 5 μm. (TIF) S12 Fig. Significantly deregulated genes in WT gametocytes vs pclag::rab11a gametocytes. Summary of the expression levels of genes that are more than 2 fold altered in a comparison of wild type and rab11a KD gametocytes as assessed by RNAseq analysis. (TIF) S13 Fig. The altered transcription profile of pbrab11a KD gametocytes does not signifi- cantly overlap with that of either DOZI and CITH KO gametocytes. Venn diagram repre- sentation of the extent of similarity between the transcriptomes of pclag::rab11a, cithko and doziko gametocytes. (TIF) S14 Fig. Significantly deregulated genes in WT ookinetes vs pclag::rab11a 24hpa forms. Summary of the expression levels of genes that are more than 2 fold altered in a comparison of wild type and rab11a KD ookinetes as assessed by RNAseq analysis. (TIF) S1 Table. Showing pclag::rab11a parasites are unable to transmit through mosquitos. (XLSX) S2 Table. Showing pama1::rab11a parasites are unable to transmit through mosquitos. (XLSX) S3 Table. Primers used for PCR amplifications, generation of plasmids and diagnostic PCRs. (XLSX) S4 Table. Peptide raised primary antibodies from Proteintech used for immunofluores- cence or western blotting. (XLSX) S5 Table. Primary antibodies obtained from external sources, their dilutions used for immunofluorescence, western blotting or FACS analysis. (XLSX) S6 Table. RNASeq reads trimmed and raw for three sets of parasite samples. (XLSX) S10 Fig. Immunofluorescence microscopy for ookinete development and structural mark- ers. S1 Table. Showing pclag::rab11a parasites are unable to transmit through mosquitos. (XLSX) S1 Table. Showing pclag::rab11a parasites are unable to transmit through mosquitos. (XLSX) Supporting information Fixed WT-GFPCON ookinetes and pclag::rab11a spherical ookinetes were probed with pri- mary antibodies: anti-DOZI, anti-CITH, anti-PPKL, anti-CTRP, anti-MyoA and anti-MTIP antibodies mixed with either FITC-tagged anti-P25 or anti-α tubulin antibodies. Except PPKL, all images shown are single slice of Deltavision deconvoluted Z stack. For PPKL, single slice images of Z stacks obtained from ELYRA 3D SIM microscope is shown. Scale bar 5 = μm. (TIF) S11 Fig. Dynamic localization of GAP45. Time course immunofluorescence of WT-GFPCON and pclag::rab11a zygotes for GAP45 and P25 [4hpa timepoint images are taken through Axio- plan and 6hpa timepoint images are single slices of deconvoluted Z stack taken from Deltavi- sion microscope]. Scale Bar = 5 μm. (TIF) S12 Fig. Significantly deregulated genes in WT gametocytes vs pclag::rab11a gametocytes. Summary of the expression levels of genes that are more than 2 fold altered in a comparison of wild type and rab11a KD gametocytes as assessed by RNAseq analysis. (TIF) S13 Fig. The altered transcription profile of pbrab11a KD gametocytes does not signifi- cantly overlap with that of either DOZI and CITH KO gametocytes. Venn diagram repre- sentation of the extent of similarity between the transcriptomes of pclag::rab11a, cithko and doziko gametocytes. (TIF) S14 Fig. Significantly deregulated genes in WT ookinetes vs pclag::rab11a 24hpa forms. Summary of the expression levels of genes that are more than 2 fold altered in a comparison of wild type and rab11a KD ookinetes as assessed by RNAseq analysis. (TIF) wild type and rab11a KD ookinetes as assessed by RNAseq analysis. (TIF) S1 Table. Showing pclag::rab11a parasites are unable to transmit through mosquitos. (XLSX) S2 Table. Showing pama1::rab11a parasites are unable to transmit through mosquitos. (XLSX) S3 Table. Primers used for PCR amplifications, generation of plasmids and diagnostic PCRs. (XLSX) S4 Table. Peptide raised primary antibodies from Proteintech used for immunofluores- cence or western blotting. (XLSX) S5 Table. Primary antibodies obtained from external sources, their dilutions used for immunofluorescence, western blotting or FACS analysis. (XLSX) S6 Table. RNASeq reads trimmed and raw for three sets of parasite samples. (XLSX) PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 Supporting information In this figure 507 refers to WT-GFPCON, G480 refers to pclag::rab11a and G481 refers to pama1::rab11a. (TIF) S6 Fig. IFC Images. Gallery of representative images from the ookinete gate IV (Fig 2G) for the WT parasite line (top) and the promoter swap mutant lines. Scale bar (lower left) 7 μm. (TIF) S7 Fig. pclag::rab11a spherical ookinetes undergo meiosis. A. Flow cytometry analysis on FACsCYAN to illustrate DNA content of pclag::rab11a gametocytes 4hpa. Parasites stained with DNA stain Hoechst 33342 were gated for activation using anti-P25 antibody and DNA content in these compared to WT-GFPCON gametocytes 4hpa and WT-GFPCON activated unfertilized female gametes (AUFG) 4hpa. FACS plots showing results of one of three inde- pendent experiments. B. bar graph shows percentage of 4N (zygotes completed meiosis), 2N (fertilized female gametes, meiosis is incomplete or blocked) and 1N (gametocytes or asexual) parasites. Data from AUFG was used to verify the gating strategy (n = 3, mean +/-SD, two tailed student t test, p-value 0.129292). S8 Fig. Active rab11a is contributed by both male and female gametes. A. Cross-fertilization of pclag::rab11a with male defective (P48/45-) and female defective (p47-) mutants (n = 3, mean +/- SD, two tailed student t test, p value 0.0001) and B. Representative Giemsa images of ookinetes and zygotes obtained 24h after (cross) fertilisation. The decondensed nuclei of the pclag::rab11a zygotes are arrowed. Scale bar = 3μm. (TIF) S8 Fig. Active rab11a is contributed by both male and female gametes. A. Cross-fertilization of pclag::rab11a with male defective (P48/45-) and female defective (p47-) mutants (n = 3, mean +/- SD, two tailed student t test, p value 0.0001) and B. Representative Giemsa images of ookinetes and zygotes obtained 24h after (cross) fertilisation. The decondensed nuclei of the pclag::rab11a zygotes are arrowed. Scale bar = 3μm. (TIF) S9 Fig. pama-1::rab11a parasites are unable to transmit through mosquitoes. A. Plot of oocyst load in dissected midguts of WT-GFPCON and pama-1::rab11a fed mosquitoes (n = 2, two tailed student t test, p-value 0.0001). B. Fluorescent and bright field images of S9 Fig. pama-1::rab11a parasites are unable to transmit through mosquitoes. A. Plot of oocyst load in dissected midguts of WT-GFPCON and pama-1::rab11a fed mosquitoes (n = 2, two tailed student t test, p-value 0.0001). B. References 1. Nelson WJ. Adaptation of core mechanisms to generate cell polarity. Nature. 2003; 422(6933):766–74. https://doi.org/10.1038/nature01602 PMID: 12700771; PubMed Central PMCID: PMC3373010. 2. Chant J. Cell polarity in yeast. Trends Genet. 1994; 10(9):328–33. 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Quevillon E, Spielmann T, Brahimi K, Chattopadhyay D, Yeramian E, Langsley G. The Plasmodium fal- ciparum family of Rab GTPases. Gene. 2003; 306:13–25. Epub 2003/03/27. https://doi.org/10.1016/ s0378-1119(03)00381-0 PMID: 12657463. 8. Ullrich O, Reinsch S, Urbe S, Zerial M, Parton RG. Rab11 regulates recycling through the pericentriolar recycling endosome. J Cell Biol. 1996; 135(4):913–24. Epub 1996/11/01. https://doi.org/10.1083/jcb. 135.4.913 PMID: 8922376; PubMed Central PMCID: PMC2133374. 9. Agop-Nersesian C, Naissant B, Ben Rached F, Rauch M, Kretzschmar A, Thiberge S, et al. Rab11A- controlled assembly of the inner membrane complex is required for completion of apicomplexan cytoki- nesis. PLoS Pathog. 2009; 5(1):e1000270. https://doi.org/10.1371/journal.ppat.1000270 PMID: 19165333; PubMed Central PMCID: PMC2622761. 1. Nelson WJ. Adaptation of core mechanisms to generate cell polarity. 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Showing pama1::rab11a parasites are unable to transmit through mosquitos. (XLSX) S3 Table. Primers used for PCR amplifications, generation of plasmids and diagnostic PCRs. (XLSX) S4 Table. Peptide raised primary antibodies from Proteintech used for immunofluores- cence or western blotting. (XLSX) S5 Table. Primary antibodies obtained from external sources, their dilutions used for immunofluorescence, western blotting or FACS analysis. (XLSX) S6 Table. RNASeq reads trimmed and raw for three sets of parasite samples. (XLSX) 23 / 27 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development S7 Table. Number of reads aligned to the genome of P. berghei ANKA for comparison with the original read counts. S7 Table. Number of reads aligned to the genome of P. berghei ANKA for comparison with the original read counts. (XLSX) S7 Table. Number of reads aligned to the genome of P. berghei ANKA for comparison with the original read counts. (XLSX) Conceptualization: Katie R. Hughes, Andrew. P. Waters. Conceptualization: Katie R. Hughes, Andrew. P. Waters. Formal analysis: Nicholas Dickens. Investigation: Harshal Patil, Katie R. Hughes, Leandro Lemgruber, Nisha Philip. Methodology: Katie R. Hughes, Nisha Philip. Investigation: Harshal Patil, Katie R. Hughes, Leandro Lemgruber, Nisha Philip. Methodology: Katie R. Hughes, Nisha Philip. Project administration: Andrew. P. Waters. Project administration: Andrew. P. Waters. Resources: G. Lucas Starnes. Supervision: Katie R. Hughes, Andrew. P. Waters. Supervision: Katie R. Hughes, Andrew. P. Waters. Validation: Katie R. Hughes. Validation: Katie R. Hughes. Writing – original draft: Harshal Patil, Andrew. P. Waters. Writing – review & editing: Katie R. Hughes, Nicholas Dickens, Andrew. P. Waters. 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Nat Rev Microbiol. 2014. https://doi. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 50. Yeoh LM, Goodman CD, Mollard V, McFadden GI, Ralph SA. Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates. BMC Genomics. 2017; 18(1):734. Epub 2017/09/18. https://doi.org/10.1186/s12864-017-4100-0 PMID: 28923023; PubMed Central PMCID: PMC5604118. References org/10.1038/nrmicro3184 PMID: 24384598. 37. Orr RY, Philip N, Waters AP. Improved negative selection protocol for Plasmodium berghei in the rodent malarial model. Malar J. 2012; 11:103. Epub 2012/04/03. https://doi.org/10.1186/1475-2875-11-103 PMID: 22463060; PubMed Central PMCID: PMC3364864. 38. van Dijk MR, van Schaijk BC, Khan SM, van Dooren MW, Ramesar J, Kaczanowski S, et al. Three members of the 6-cys protein family of Plasmodium play a role in gamete fertility. PLoS Pathog. 2010; 6 (4):e1000853. 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PLoS One. 2014; 9(9):e108930. Epub 2014/10/03. https://doi.org/10.1371/ journal.pone.0108930 PMID: 25275500; PubMed Central PMCID: PMC4183507. 43. Mair GR, Lasonder E, Garver LS, Franke-Fayard BM, Carret CK, Wiegant JC, et al. Universal features of post-transcriptional gene regulation are critical for Plasmodium zygote development. PLoS Pathog. 2010; 6(2):e1000767. https://doi.org/10.1371/journal.ppat.1000767 PMID: 20169188; PubMed Central PMCID: PMC2820534. 44. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBLnet Journal Bioinformatics in action. 2011; 17. 45. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, et al. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2009; 37(Database issue):D539–43. https://doi.org/10.1093/nar/gkn814 PMID: 18957442; PubMed Central PMCID: PMC2686598. 46. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of tran- scriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4):R36. https://doi.org/10.1186/gb-2013-14-4-r36 PMID: 23618408; PubMed Central PMCID: PMC4053844. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 26 / 27 PLOS PATHOGENS RAB11A controls Plasmodium ookinete development 47. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie2. Nat Methods. 2012; 9(4):357–9. https://doi.org/10.1038/nmeth.1923 PMID: 22388286; PubMed Central PMCID: PMC3322381. 48. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1008091 May 28, 2020 47. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie2. Nat Methods. 2012; 9(4):357–9. https://doi.org/10.1038/nmeth.1923 PMID: 22388286; PubMed Central PMCID: PMC3322381. 48. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013; 31(1):46–53. https://doi.org/10. 1038/nbt.2450 PMID: 23222703; PubMed Central PMCID: PMC3869392. 49. Otto TD, Bohme U, Jackson AP, Hunt M, Franke-Fayard B, Hoeijmakers WA, et al. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol. 2014; 12:86. Epub 2014/11/02. https://doi.org/10.1186/s12915-014-0086-0 PMID: 25359557; PubMed Central PMCID: PMC4242472. References Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013; 31(1):46–53. https://doi.org/10. 1038/nbt.2450 PMID: 23222703; PubMed Central PMCID: PMC3869392. 49. Otto TD, Bohme U, Jackson AP, Hunt M, Franke-Fayard B, Hoeijmakers WA, et al. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol. 2014; 12:86. Epub 2014/11/02. https://doi.org/10.1186/s12915-014-0086-0 PMID: 25359557; PubMed Central PMCID: PMC4242472. 50. Yeoh LM, Goodman CD, Mollard V, McFadden GI, Ralph SA. Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates. BMC Genomics. 2017; 18(1):734. Epub 2017/09/18. https://doi.org/10.1186/s12864-017-4100-0 PMID: 28923023; PubMed Central PMCID: PMC5604118. 27 / 27
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https://www.research-collection.ethz.ch/bitstream/20.500.11850/325548/2/640-3052-1-PB.pdf
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Uncertainty quantification and global sensitivity analysis for economic models
Quantitative economics
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ETH Library Journal Article This page was generated automatically upon download from the ETH Zurich Research Collection. For more information, please consult the Terms of use. This page was generated automatically upon download from the ETH Zurich Research Collection. For more information, please consult the Terms of use. Quantitative Economics 10 (2019), 1–41 1759-7331/20190001 Daniel Harenberg: dharenberg@ethz.ch Stefano Marelli: marelli@ibk.baug.ethz.ch Bruno Sudret: sudret@ibk.baug.ethz.ch Viktor Winschel: viktor.winschel@gmail.com We are very grateful to Antoine Bommier for helpful discussions and support. We thank three anonymous referees for their very valuable comments and suggestions. We also thank Johannes Brumm, Felix Kübler, Christoph Winter, and participants at the CEF 2016, IWcee16, PASC16, and the University of Zurich ACEF seminar for helpful comments. Daniel Harenberg and Viktor Winschel gratefully acknowledge financial support of Swiss Re Foundation and ETH Zurich Foundation. Most of this work was completed while Viktor Winschel was at the ETH Risk Center, ETH Zurich. Uncertainty quantification and global sensitivity analysis for economic models Daniel Harenberg Center for Economic Research, ETH Zurich and Oxford Economics Ltd Stefano Marelli Department of Civil, Environmental and Geomatic Engineering, ETH Zurich Bruno Sudret Department of Civil, Environmental and Geomatic Engineering, ETH Zurich © 2019 The Authors. Licensed under the Creative Commons Attribution-NonCommercial License 4.0 Available at http://qeconomics.org. https://doi.org/10.3982/QE866 1. Introduction The question whether quantitative results of an economic model are sensitive to spe- cific parameterization assumptions is important, not only for the credibility of a spe- cific study but also for the general advancement of a quantitative approach to economic analysis. Since many studies have implications for policymakers, there is a strong case to be made for structured sensitivity analyses to become an essential part of quantita- tive studies of economic models. Moreover, a sensitivity analysis can go beyond simple robustness checks and answer more detailed questions such as which parameters—and which interactions between them—are driving the conclusions derived from an eco- nomic model. Such an importance ranking informs the researcher on which parts to fo- cus on when calibrating or extending a model, or the policymaker on which parameters need further scrutiny. The economic literature is well aware of the need for a structured sensitivity analysis for quantitative models.1 However, with few exceptions, current practice involves a high degree of subjective and somewhat arbitrary judgments. Typically, some parameters are chosen and individually changed to a different value to assess the partial influence on the results. Such “one-at-a-time” approaches tend to be unstructured and, more im- portantly, suffer from the fact that they are only local, that is, highly dependent on the chosen parameter values. Moreover, they cannot account for possible interactions be- tween parameters and nonlinear relationships that are often encountered in economic models. The present paper proposes methods for global sensitivity analysis that overcome the mentioned deficiencies of local approaches. Specifically, we employ Sobol’ indices and univariate effects, which—in contrast to the local sensitivity analyses typically used in economics—accurately identify nonlinearities and interactions in the mapping from parameters to model outcomes. Such global methods have been developed in the last decades in the engineering and applied mathematics fields as part of the more general topic of uncertainty quantification.2 While local sensitivity analyses rely on compar- isons of model outcomes at few selected parameter values, global methods quantita- tively formalize the uncertainty surrounding parameter values and propagate it through the model to evaluate the importance of each parameter, as well as interactions between parameters. The methods we propose are easy to deploy because they are nonintrusive, meaning that they treat the economic model as a black box, and thus require no changes to existing code. Also, they are implemented in various freely available software tool- boxes. Oxford Economics Ltd We present a global sensitivity analysis that quantifies the impact of parame- ter uncertainty on model outcomes. Specifically, we propose variance-decompo- sition-based Sobol’ indices to establish an importance ranking of parameters and univariate effects to determine the direction of their impact. We employ the state- of-the-art approach of constructing a polynomial chaos expansion of the model, from which Sobol’ indices and univariate effects are then obtained analytically, using only a limited number of model evaluations. We apply this analysis to sev- eral quantities of interest of a standard real-business-cycle model and compare it to traditional local sensitivity analysis approaches. The results show that local sensitivity analysis can be very misleading, whereas the proposed method accu- rately and efficiently ranks all parameters according to importance, identifying interactions and nonlinearities. Keywords. Computational techniques, uncertainty quantification, sensitivity analysis, polynomial chaos expansion. JEL classification. C60, C63. JEL classification. C60, C63. 2 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) y y p y 2See, for example, Sudret (2007) or Borgonovo and Plischke (2016) for an overview. 3See Iooss and Lemaître (2014) for a comprehensive review. 1See Leamer (1985), Kydland (1992), Canova (1995), Hansen and Heckman (1996), among others, who advocate a structured sensitivity analysis. Canova (1994) and Gregory and Smith (1995) propose global sen- sitivity analysis as a means to partly answer to the statistical weaknesses of calibration. 2See, for example, Sudret (2007) or Borgonovo and Plischke (2016) for an overview. 1. Introduction Many global sensitivity analysis methods are described in the literature, character- ized by varying degrees of complexity, as well as underlying assumptions.3 For an in- depth unifying view of most global sensitivity measures, the reader is directed to Bor- gonovo, Hazen, and Plischke (2016). In this paper, we are interested in the class of im- portance measures, as our aim is that of providing a robust quantitative assessment of Uncertainty quantification and global sensitivity Quantitative Economics 10 (2019) 3 the importance of each of the input parameters with respect to the model outcomes. Arguably one of the most widely accepted importance measures in the engineering and applied mathematics communities is variance decomposition, also known as analysis of variance (ANOVA). Based on the functional model decomposition introduced in Sobol’ (1993), variance decomposition allows one to compute total Sobol’ indices, which rep- resent the fraction of the variance of the outcome that is explained by each parameter. Total Sobol’ indices contain a parameter’s direct impact as well as its impact due to in- teractions with other parameters. First-order Sobol’ indices isolate the direct impact, while higher-order Sobol’ indices identify the contributions due to the joint effects of groups of parameters at a time, thereby exposing interactions in an economic model. As a result, we get a complete, global importance ranking of all parameters and their interactions, which can be helpful for interpreting model mechanics, as well as guiding model calibration and further model development. A second sensitivity question of central economic interest is in which direction each parameter affects the outcomes, not just locally but globally. We answer this with so- called univariate effects, which display the slope of that relationship for each parameter over its range, averaging over all other parameters. They help a researcher to find regions of high and low sensitivity, and can be interpreted as a robust direction of change under parameter uncertainty. Thus, they can be very useful for economic policy analysis. The global approach we propose starts by representing the uncertainty about each parameter by a (potentially bounded) probability distribution. This parameter uncer- tainty is propagated through the economic model by repeated evaluation at randomly drawn parameter vectors. The required sampling from the parameter distributions could be done by Monte Carlo simulation. 4For example, Aruoba, Fernández-Villaverde, and Rubio-Ramírez (2006) use it to compare different so lution methods. Den Haan, Judd, and Juillard (2011) do the same for the multicountry extension. 4 Harenberg, Marelli, Sudret, and Winschel 4 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) We find that the local sensitivity measures typically employed in economics can be highly misleading. For example, the relative importance of variance and autocorrela- tion of total factor productivity (TFP) shocks in determining the production variance ratio flips depending on which parameter vectors are considered. Of course, we know that it is the combination of both that drives the unconditional variance of TFP and production, but this interaction cannot be picked up by a local measure where one pa- rameter at a time is changed individually. Another wide-spread local method is scenario analysis, which—as we show—suffers from similar weaknesses. By contrast, the global Sobol’ indices we compute establish an unambiguous ranking of autocorrelation and standard deviation and accurately quantify the contribution of the interaction between the two parameters. More generally, our global analysis shows that only few parame- ters and interactions matter for each quantity of interest. Therefore, when calibrating or estimating such an RBC model, a researcher can focus on a small subset of the parame- ters. The univariate effects uncover a nonlinear relationship between autocorrelation and the variance of production, with the impact becoming stronger the higher the value of the autocorrelation parameter. Thus, the empirically much researched question of the value of the autocorrelation of TFP shocks is of paramount importance for the results of the RBC model. Another interesting nonlinearity is found for the depreciation rate, whose impact on the capital-output ratio is decreasing and convex. This exemplifies the importance of univariate effects for understanding model properties, but also for economic policy analysis if the parameter under consideration is a policy variable, for example, a tax rate. In the economic literature, there are only few papers that perform a global sensitiv- ity analysis (GSA). An early example is Harrison and Vinod (1992) who assumed distri- butions over the elasticities of a static, deterministic general equilibrium model of the macroeconomy to study robustness of their simulation results. A specific field where GSA has received a bit more attention is the economics of climate change. Anderson, Borgonovo, Galeotti, and Roson (2014) computed various global sensitivity indices for the DICE model of Nordhaus (2008). Saltelli, Annoni, Azzini, Campolongo, Ratto, and Tarantola (2010) showed that the sensitivity analysis of the Stern (2007) report is not ro- bust. 1. Introduction However, due to the slow convergence prop- erties of Monte Carlo simulations, a very large number of draws would be required, in particular if higher-order Sobol’ indices and univariate effects are to be estimated. We overcome this problem by approximating the mapping from parameters to quantities of interest with a so-called sparse polynomial chaos expansion. The Sobol’ indices and univariate effects are then computed analytically from the coefficients of the polynomial with high accuracy and at no additional cost (see Sudret (2008)). We exemplify the approach for the canonical real-business-cycle (RBC) model with capital adjustment costs. This model has been widely studied and is well understood.4 We consider several quantities of interest, that is, endogenous outcomes, that are fre- quently found in the traditional RBC literature. In the main part of the paper, we focus on the capital-output ratio, because it is often used as a calibration target, and the ratio of the variance of log production in the model over its empirical counterpart. This sec- ond variable, which we will refer to as the production variance ratio, has often been em- ployed to assess how much of the observed fluctuations can be explained by the model (see, e.g., Canova (1995) or Eichenbaum (1991)). Results for other quantities are then summarized to show the broad applicability of global sensitivity analysis. 5The following derivations however hold whatever the PDF (e.g., Gaussian, Beta, etc.) of these input pa- rameters. 4 Harenberg, Marelli, Sudret, and Winschel In a highly complex model, Cai, Judd, and Lontzek (2015) performed an extensive sensitivity analysis of the social cost of carbon using local methods on a wide range of parameter vectors. Canova (1994, 1995) proposed a global sensitivity analysis to put the macroeconomic calibration approach on a statistically more rigorous footing. He analyzes the RBC model and puts great effort into specifying the distributions over the parameters, for which he uses existing studies. All of the above papers rely on Monte Carlo simulations and, therefore, cannot (accurately) compute interactions or univariate effects. Ratto (2008) employed first-order Sobol’ indices to study the influence of structural parameters on reduced form estimation of linear or linearized DSGE models. More re- cently, Scheidegger and Bilionis (2017) proposed Gaussian process machine learning to solve economic models with very high-dimensional state spaces. They show how this framework lends itself naturally to uncertainty quantification. The main advantage of Quantitative Economics 10 (2019) 5 Uncertainty quantification and global sensitivity polynomial chaos expansions as proposed in the present paper lies in the very fast con- vergence rate of the estimation of Sobol’ indices of first and higher orders (Sudret (2008), Le Gratiet, Marelli, and Sudret (2016)). In addition, the presented methodology is non- intrusive, thus requiring no changes to existing code. The paper is structured as follows: in Section 2, we introduce a general framework for uncertainty quantification, followed by the theory and numerical techniques em- ployed in global sensitivity analysis. Section 3 first presents the economic model and then the parameterization for the sensitivity analyses. In Section 4, we present and dis- cuss results for local sensitivity analyses, and in Section 5 for our global sensitivity anal- ysis. Section 6 concludes. Code and data are available in the Supplemental Material on the journal website as a supplementary file (Harenberg, Marelli, Sudret, and Winschel (2019)). 2.1 Introduction • In Step B, the uncertainty in the input parameters is described by a joint PDF that best represents the available information. In the present case, bounds on the various parameters will be selected based on literature review; see details in Section 3.3. Alter- natively, the PDF could result from a previous estimation of the economic model. • In Step B, the uncertainty in the input parameters is described by a joint PDF that best represents the available information. In the present case, bounds on the various parameters will be selected based on literature review; see details in Section 3.3. Alter- natively, the PDF could result from a previous estimation of the economic model. • In Step C, uncertainty propagation is carried out so as to analyze the moments and distributions of the QoI, for instance by plotting histograms, or calculating low- probability events. • Finally, in Step C′, sensitivity analysis is carried out to rank the input parameters according to their impact onto the prediction uncertainty, or to identify the direction of change of that impact. The acquired knowledge can be used to focus a more detailed analysis on a subset of the input variables (dimensionality reduction), hence mitigating the computational costs associated with the curse of dimensionality. • Finally, in Step C′, sensitivity analysis is carried out to rank the input parameters according to their impact onto the prediction uncertainty, or to identify the direction of change of that impact. The acquired knowledge can be used to focus a more detailed analysis on a subset of the input variables (dimensionality reduction), hence mitigating the computational costs associated with the curse of dimensionality. The above procedure can be carried out using Monte Carlo simulation (MCS), which is a standard technique to estimate statistical properties based on random number generation. However, when dealing with computationally expensive models, the well- known slow convergence rate of MCS methods hinders their application in many prac- tical scenarios. An alternative, much more efficient approach is given by spectral repre- sentations and, in particular, polynomial chaos expansions. 2.1 Introduction Uncertainty quantification aims at identifying the sources of uncertainty or lack of knowledge that can affect parameters of a model and, subsequently, the predictions ob- tained from this model. In this paper, we call the computational model a mapping: θ ∈Dθ ⊂RM →y = M(θ) ∈RQ (1) (1) θ ∈Dθ ⊂RM →y = M(θ) ∈RQ To simplify the presentation, we assume in this section Q = 1, that is, we consider a scalar quantity of interest (QoI) y. Due to uncertainties in the model parameters, the latter are represented by a random vector Θ of prescribed joint probability density func- tion (PDF) fΘ defined over a probabilistic space {ΩFP}, where Ω is the space of out- comes, F is the associated σ-algebra, and P is the probability measure associated with the PDF fΘ. For instance, without any further information, the various input parame- ters {Θii = 1M} may be considered as statistically independent, and be assigned prescribed ranges.5 Uncertainty propagation techniques aim at characterizing the statistical properties of the (random) output of the model Y = M(Θ) (2) (2) that is, estimate its statistical moments (mean μY , variance σ2 Y ) or its probability density function fY . Sensitivity analysis aims at determining which input parameters {Θii = 1M} (or combination thereof) contribute the most to the uncertainty of the QoI. In particular, methods for global sensitivity analysis developed in the sequel aim at ap- portioning the variance σ2 Y to each input parameter Θi, pairs (ΘiΘj), etc., in order to determine those parameters whose uncertainty explain most of the QoI’s variance, as well as to detect those whose uncertainty has no impact on the predictions. Figure 1 summarizes the different concepts presented above (after Sudret (2007)): Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019 Figure 1. Uncertainty quantification framework. Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) 6 Harenberg, Marelli, Sudret, and Winschel Figure 1. Uncertainty quantification framework. • In Step A, the computational model M is defined, which requires to identify input parameters and output quantities of interest. • In Step A, the computational model M is defined, which requires to identify input parameters and output quantities of interest. • In Step A, the computational model M is defined, which requires to identify input parameters and output quantities of interest. 2.2 Polynomial chaos expansions Instead of being represented through samples as in Monte Carlo simulation, the model output may be represented as a series expansion in an abstract space of random vari- ables (spectral representation). More specifically, assuming that Y has finite variance, it belongs to the Hilbert space of second-order random variables and may be cast as Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 7 Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 7 follows (Soize and Ghanem (2004)): follows (Soize and Ghanem (2004)): follows (Soize and Ghanem (2004)): follows (Soize and Ghanem (2004)): follows (Soize and Ghanem (2004)): Y = ∞  j=0 bjZj (3) (3) (3) In the above equation, {Zj}∞ j=0 is a numerable set of random variables (which form a ba- sis of the Hilbert space), and {bj}∞ j=0 are coefficients to be computed. The latter may be interpreted as the coordinates of Y in this basis. In the sequel, we focus on polynomial chaos expansions (PCE), in which the basis terms {Zj}∞ j=0 are multivariate orthonormal polynomials w.r.t. the joint PDF of the input random vector Θ.6 Note that, while equa- tion (3) is exact, approximations are in practice obtained by truncating the series to a finite number of terms. We relegate the construction of the basis to Appendix B, because it is formally iden- tical to other orthonormal polynomials that are often used in economics, for example, Chebyshev polynomials.7 Let us stress, however, that a crucial difference is that, in the case of polynomial chaos expansions, the weight functions are given by fΘ, so that the polynomials efficiently capture the uncertainty in the model parameters. Once such a basis is constructed, and a truncation scheme is selected (typically, the maximum total polynomial degree p, cf. Appendix B, or more sophisticated truncation schemes as in Blatman and Sudret (2010a)), the spectral expansion in equation (3) becomes: Y =  α∈A bαΨα(Θ) (4) (4) where α = (α1αM) is a multiindex that identifies the polynomial degree in each input variable θi, Ψα is a multivariate orthogonal polynomial built by tensor product of the underlying univariate polynomials of degree αi and A is the selected truncation set. 2.2.1 Computation of coefficients by least-squares The literature on polynomial chaos expansions proposes many alternative approaches to compute the expansion coeffi- cients denoted by {bαα ∈A}. 6See, for example, Ghanem and Spanos (2003) or Ghanem and Spanos (2003). 7See Judd (1998). 2.2 Polynomial chaos expansions Even when limiting the scope to so-called nonintrusive approaches, which rely upon repeated evaluations of the model M for selected realiza- tions of the input vector, one can mention projection methods (Le Maître, Knio, Najm, and Ghanem (2001)), sparse grids (Keese and Matthies (2003), Ganapathysubramanian and Zabaras (2007)), stochastic collocation (Xiu and Hesthaven (2005)), and least-square minimization (Berveiller, Sudret, and Lemaire (2006)). In this paper, we focus on the lat- ter approach for several reasons. First, thanks to recent advances in the field of compres- sive sensing (see, e.g., Chen, Donoho, and Saunders (1998), Efron, Hastie, Johnstone, and Tibshirani (2004)), sparse regression-based PCE (Blatman and Sudret (2010a)) has become a staple method in applied sciences due its efficiency when a limited compu- tational budget is available, even in high dimensional problems. Second, no dedicated sampling algorithm is required to generate the pool of full model evaluations needed to calculate the PCE coefficients (as opposed, e.g., to sparse-grid-based methods). As Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Harenberg, Marelli, Sudret, and Winschel 8 Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) a matter of fact, sparse PCE can be seen as a post-processing step of an existing MCS. Finally, this family of methods allows for some noise in the QoI, which is useful in eco- nomic applications and which we discuss further in the context of the real-business- cycle model in Section 3.2. Considering a truncation set A ⊂NM, the series expansion in equation (4) is cast as the sum of the truncated series and a residual ε: Y = M(Θ) =  α∈A bαΨα(Θ) + ε (5) (5) The least-square minimization approach consists of finding the set of coefficients B = {bαα ∈A} which minimizes the mean square error E[ε2]. This set is computed at once by solving: The least-square minimization approach consists of finding the set of coefficients B = {bαα ∈A} which minimizes the mean square error E[ε2]. 2.2 Polynomial chaos expansions This set is computed at once by solving: B = arg min b∈RcardAE  M(Θ) −  α∈A bαΨα(Θ) 2  (6) (6) In practice, one replaces the expectation operator in equation (6) by the empirical mean over a sample set: ˆB = arg min b∈RcardA 1 N N  i=1  M  θ(i) −  α∈A bαΨα  θ(i)2  (7) (7) In this expression, XED = {θ(i)i = 1N} is a sample set of points called experimen- tal design (ED) that is typically chosen so as to cover the input parameter space DΘ. To solve the least-square minimization problem in equation (7), the computational model M is first run for each point in the ED, and the results are stored in a vector Y = {y(1) = M(θ(1))y(n) = M(θ(N))}T. Then one calculates the information matrix by evaluating the basis polynomials on each point in the ED: A = Aij def = Ψj  θ(i) i = 1Nj = 1cardA  (8) (8) The solution of the least-square minimization problem finally reads ˆB =  ATA −1ATY (9) (9) The ED may be built from Monte Carlo simulation, Latin Hypercube Sampling (LHS, see McKay, Beckman, and Conover (1979)) or quasi-random sequences (Niederreiter (1992)). The size of the ED is of crucial importance for a robust analysis. Typical over- sampling rates (N/cardA) = 2 to 3 are used in practice (Berveiller, Sudret, and Lemaire (2006)). The ED may be built from Monte Carlo simulation, Latin Hypercube Sampling (LHS, see McKay, Beckman, and Conover (1979)) or quasi-random sequences (Niederreiter (1992)). The size of the ED is of crucial importance for a robust analysis. Typical over- sampling rates (N/cardA) = 2 to 3 are used in practice (Berveiller, Sudret, and Lemaire (2006)). 2.2.2 Error estimation and sparse PCE As discussed above, the proper truncation set (e.g., the maximal degree of polynomials to be included in the truncated series) depends on the problem under consideration. In order to assess the accuracy of any truncated Uncertainty quantification and global sensitivity 9 Uncertainty quantification and global sensitivity 9 Quantitative Economics 10 (2019) series, the generalization error E[ε2] in equation (6) shall be estimated. 2.2 Polynomial chaos expansions This could be done using a validation set Xval = {θkk = 1nval} as follows: err(Xval) def = 1 nval nval  k=1  M(θk) −  α∈A bαΨα(θk) 2  (10) (10) where the validation points may be sampled by Monte Carlo simulation and where nval is large enough, typically equal to 104 or 105. Such an estimator is, however, not affordable in the general case since the very principle of constructing PC expansions is to limit the number of runs of the original model M. Reusing the ED XED in the above equation is not a viable option due to overfitting. Indeed, doing so, the so-called empirical error, err(XED), would strongly underestimate the true error E[ε2]. A good compromise between accuracy and efficiency is obtained by using the leave- one-out error estimator (Blatman and Sudret (2010a), Le Gratiet, Marelli, and Sudret (2016)). The principle is the following: a PC expansion MPC\i is constructed using an experimental design XED\θ(i) def = {θ(1)θ(i−1)θ(i+1)θ(N)}, and the error is com- puted on the point that has been left apart: i def = M  θ(i) −MPC\i θ(i)  (11) (11) Then the operation is repeated for i = 1N excluding each point in turn. The leave- one-out error is defined by errLOO def = 1 N N  i=1 2 i = 1 N N  i=1  M  θ(i) −MPC\i θ(i)2 (12) (12) and turns out to be, after basic algebra: and turns out to be, after basic algebra: errLOO = N  i=1 M  θ(i) −MPC θ(i) 1 −hi 2  (13) (13) where hi is the ith diagonal term of matrix A(ATA)−1AT (matrix A is defined in equation (8)) and MPC(·) is now the PC expansion built up at once from the full experimental design XED. The error in equation (13) requires neither additional model evaluations nor additional PCEs and can thus be computed at very low cost. As a conclusion, as soon as an experimental design is available, the size of which is sufficiently large compared to the number of unknown PCE coefficients, the latter can be computed from a mere least- square minimization (equation (9)) and a very good and cheap error estimator is given by equation (13). This error estimator allows for degree-adaptive PCE construction. 8In economics, this truncation scheme is also known as complete polynomials; cf. Judd (1998). 2.2 Polynomial chaos expansions To see how, de- fine the standard truncation scheme by AMp = {α ∈NM : |α| ≤p}; see Appendix B for details.8 For a given ED, different AMp are tried out by varying the maximal polynomial degree p, and the best expansion according to equation (13) is finally retained. Values 10 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) of errLOO ≤10−2 guarantee a sufficient accuracy in practice for moment- and sensitivity analysis. We corroborate this for the real-business-cycle model in Sections 5.2 and 5.4.3. When the number of input parameters is large (e.g., M ≥10), the standard truncation set AMp may easily contain thousands to even millions of basis elements. Due to the necessity of oversampling (i.e., having N > cardAMp), the basic least-squares approach detailed above may not be practically feasible anymore due to the associated compu- tational costs, especially in the presence of expensive-to-evaluate modern computa- tional codes, which may take hours to execute even on dedicated high-performance- computing hardware. In the last few years, algorithms for deriving sparse expansions have been proposed: in these approaches, instead of computing a possibly big set of co- efficients the majority of which are eventually close to zero, one searches directly for the nonzero coefficients. Techniques such as compressive sensing (e.g., orthogonal match- ing pursuit (Pati, Rezaiifar, and Krishnaprasad (1993)) or least-angle regression (Efron et al. (2004))) have proven effective in selecting only a few basis polynomials out of a large candidate basis set, and then compute the associated coefficients (Blatman and Sudret (2011), Doostan and Owhadi (2011)). A detailed description can be found in these publications and the literature therein. In the real-business-cycle model of Section 3.1, degree-adaptive sparse PCE based on least-angle regression (LAR) (see Blatman and Su- dret (2011)) is used. 2.2.3 Post-processing of PC expansions As mentioned previously, the truncated PC ex- pansion 2.2.3 Post-processing of PC expansions As mentioned previously, the truncated PC ex- pansion ˆY = MPC(Θ) =  α∈A ˆbαΨα(Θ) (14) (14) is a sample-free representation of the model output. It contains all the information about the statistical properties of the random output Y = M(Θ). 2.3 Sensitivity analysis 2.3.1 Global sensitivity analysis Global sensitivity analysis aims at quantifying which are the input parameters {Θi}M i=1 or combinations thereof that best explain the variabil- ity of the quantity of interest Y = M(Θ) (Saltelli, Chan, and Scott (2000), Saltelli, Ratto, Andres, Campolongo, Cariboni, Gatelli, Saisana, and Tarantola (2008)). This variability being described by the variance Var[Y], the question reduces to apportioning the lat- ter to each input parameter {Θ1ΘM}, pairs (ΘiΘj), etc. For this purpose, variance decomposition techniques (a.k.a. functional ANOVA) have gained interest since the mid 90s. The Sobol’ decomposition (Sobol’ (1993)) states that any square integrable function M with respect to a probability measure associated with a PDF fΘ(θ) = M i=1 fΘi(θi) (in- dependent components9) may be cast as 2.3.1 Global sensitivity analysis Global sensitivity analysis aims at quantifying which are the input parameters {Θi}M i=1 or combinations thereof that best explain the variabil- ity of the quantity of interest Y = M(Θ) (Saltelli, Chan, and Scott (2000), Saltelli, Ratto, Andres, Campolongo, Cariboni, Gatelli, Saisana, and Tarantola (2008)). This variability being described by the variance Var[Y], the question reduces to apportioning the lat- ter to each input parameter {Θ1ΘM}, pairs (ΘiΘj), etc. For this purpose, variance decomposition techniques (a.k.a. functional ANOVA) have gained interest since the mid 90s. The Sobol’ decomposition (Sobol’ (1993)) states that any square integrable function M with respect to a probability measure associated with a PDF fΘ(θ) = M i=1 fΘi(θi) (in- dependent components9) may be cast as M(θ) = M0 + M  i=1 Mi(θi) +  1≤i<j≤M Mij(θiθj) + ··· + M12M(θ) (16) (16) that is, as a sum of a constant M0, univariate functions {Mi(θi)1 ≤i ≤M}, bivariate functions {Mij(θiθj)1 ≤i < j ≤M}, etc. Using the set notation for indices, that is, as a sum of a constant M0, univariate functions {Mi(θi)1 ≤i ≤M}, bivariate functions {Mij(θiθj)1 ≤i < j ≤M}, etc. Using the set notation for indices, u def = {i1is} ⊂{1M} (17) (17) the Sobol’ decomposition in equation (16) reads decomposition in equation (16) reads M(θ) = M0 +  u⊂{1M} u̸=∅ Mu(θu) (18) (18) 9Extensions of functional ANOVA to the case of dependent random variables exist; see, for example, Kucherenko, Tarantola, and Annoni (2012), Mara and Tarantola (2012), Caniou and Sudret (2013). However, their interpretation is more complex due to the need to distinguish between contributions due to interac- tion and to correlation. 2.2 Polynomial chaos expansions Due to the orthog- onality of the PC basis, mean and standard deviation of ˆY may be computed directly from the coefficients ˆB (see details in Le Gratiet, Marelli, and Sudret (2016)): ˆμY def = E[ ˆY] = E  α∈A ˆbαΨα(Θ)  = ˆb0 ˆσ2 Y def = Var[ ˆY] = E ( ˆY −ˆb0)2 =  α∈A α̸=0 ˆb2 α (15) (15) In other words, the mean and variance of the random response may be obtained by a mere combination of the PCE coefficients once the latter have been computed. This property, together with the close relation to Sobol’ indices and univariate effects pre- sented in detail in Section 2.3, significantly distinguish PCE from formally similar poly- nomial approximation methods (as used, e.g., in Cai and Judd (2010)). Indeed, especially in the context of moment- and sensitivity analysis, the polynomial expansion in equa- tion (14) is never used directly to approximate the full model. Rather, it is the coefficients themselves that are directly used to give a fast-converging estimate of the statistics of the underlying model. Quantitative Economics 10 (2019) 11 Uncertainty quantification and global sensitivity From a functional point of view, however, the function θ →MPC(θ) in equation (14) can still be viewed as a surrogate of the original model M, that is, an analytical, easy- to-evaluate function that gives a good approximation of the true model output M(θ). The quality of the approximation is not ensured pointwise uniformly, but in the mean- square sense, as can be seen from the derivation of the PC coefficients (equations (6)– (9)). Importantly, the construction of PCE using the parameters’ input distributions en- sures that the stochastic properties of the uncertainty are retained, which is crucial for the GSA we propose in this paper. One can take advantage of this feature to obtain accu- rate plots of the output distribution, that is, the PDF of the output random variable Y = M(Θ). For this purpose, a large Monte Carlo sample set X = {θ1θn} is drawn from the input distribution fΘ, say n = 106. Then the surrogate model MPC is run onto this sample set in no time. The sample set of PCE outputs YPC = {MPC(θ1)MPC(θn)} is then plotted as a histogram, or using kernel density smoothing techniques (Wand and Jones (1995)). 2.3 Sensitivity analysis An important class of global sensitivity measures that do not rely on the indepen- dence of the input parameters is that of moment-independent measures, first introduced by Borgonovo (2007). Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Harenberg, Marelli, Sudret, and Winschel 12 Quantitative Economics 10 (2019) where θu is a subvector of θ which only contains the components that belong to the index set u. It can be proven that the Sobol’ decomposition is unique when the orthogo- nality between summands is required, namely E Mu(θu)Mv(θv) = 0 ∀u v ⊂{1M} u ̸= v (19) (19) Orthogonality with the constant term M0 implies in particular that E[Mu(θu)] = 0 ∀u ⊂ {1M}. The existence and uniqueness of equation (16) together with the orthogonal- ity property in equation (19) now allow one to decompose the variance D def = Var[M(Θ)] as follows: D = Var   u⊂{1M} u̸=∅ Mu(Θu)  =  u⊂{1M} u̸=∅ Var Mu(Θu) =  u⊂{1M} u̸=∅ Du (20) (20) where the partial variances are defined by where the partial variances are defined by where the partial variances are defined by Du def = Var Mu(Θu) = E M2 u(Θu)  (21) (21) 2.3.2 Sobol’ indices The so-called Sobol’ indices Su are defined as the ratio of the partial variances Du to the total variance D. Due to equation (20) they obviously sum up to 1. Hence each index is interpreted as the share of variance that is explained by the group of parameters Θu. The first-order indices correspond to single input variables, that is, u = {i}: Si = Di D = Var Mi(Θi) Var[Y]  (22) (22) The second-order indices (u = {ij}) read The second-order indices (u = {ij}) read The second-order indices (u = {ij}) read Sij = Dij D = Var Mij(ΘiΘj) Var[Y]  (23) (23) etc. Note that the total Sobol’ index ST i , which quantifies the total impact of a given pa- rameter Θi including all interactions with other parameters, may be computed by the sum of the Sobol’ indices of any order that involve Θi: ST i =  i∈u Su (24) (24) Sobol’ indices allow for an in-depth analysis of the relative impact of the uncertainties affecting the model predictions. 2.3 Sensitivity analysis The formulæ above are interpreted as follows: • Factor setting: the total Sobol’ index ST i indicates the share of the total variance D explained by the input parameter θi, alone or in combination with any other parame- ter(s). If this is negligible (in pratice, if ST i < 1%), this means that parameter θi could be set to a deterministic value without changing the distribution of the quantity of interest. Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) 13 Uncertainty quantification and global sensitivity • Screening: the first-order Sobol’ index Si indicates by what percentage the total vari- ance D would be reduced, should the parameter θi be perfectly known and set to a fixed value. It allows to determine which parameter(s) shall be investigated in priority, should one want to decrease the prediction variability. Classically, Sobol’ indices are evaluated by Monte Carlo simulation. Detailed expres- sions of the estimators of first-order and total indices can be found in Sobol’ (1993), Sobol’ (2001), Janon, Klein, Lagnoux, Nodet, and Prieur (2014). In practice, two sam- ple sets of the input vector Θ are used for computing each first-order (resp., total) in- dex. Typically, nS = 103 to 104 samples are needed for accuratey estimating each index, leading to a total cost of (M + 1) · nS. This high computational cost is affordable when the considered model M is analytical, or at least very fast to evaluate. Fortunately, the technique of polynomial chaos expansions presented above allows for a straightforward evaluation of Sobol’ indices. 2.3.3 PC expansion-based Sobol’ indices Sobol’ indices are considered as the most ver- satile sensitivity measures for general computational models, since they do not rely on any assumption of linearity nor monotonicity of the model M (Saltelli et al. (2008)). Their estimation by Monte Carlo simulation is, however, computationally demanding, as mentioned above. A number of recent approaches has been proposed to reduce the computational burden associated to their estimation, mostly based on recent develop- ments of stochastic collocation techniques (Ma and Zabaras (2010), Yang, Choi, Lin, and Karniadakis (2012)). In this paper, we choose to follow the approach proposed by Sudret (2008), where the Sobol’ indices are derived by directly post-processing the co- efficients of the PCE. 2.3 Sensitivity analysis When combined with their sparse-regression-based calculation, this approach has been extensively shown to be computationally very efficient (see, e.g., Blatman and Sudret (2010b), Deman, Konakli, Sudret, Kerrou, Perrochet, and Benabder- rahmane (2016)). Indeed, the Sobol’ decomposition (equation (16)) of a truncated PC expansion MPC(θ) =  α∈A ˆbαΨα(θ) can be derived analytically, as shown below. ∈A For any subset of variables u = {i1is} ⊂{1M}, let us define the set of multi- variate polynomials Ψα which depend only on u by Au = {α ∈A : αk ̸= 0 if and only if k ∈u} (25) (25) One can observe that the Au’s form a partition of A since One can observe that the Au’s form a partition of A since  u⊂{1M} Au = A (26) (26) Thus a truncated PC expansion such as in equation (14) may be rewritten as follows by simple reordering of the terms: Thus a truncated PC expansion such as in equation (14) may be rewritten as follows by simple reordering of the terms: MPC(θ) = b0 +  u⊂{1M} u̸=∅ MPC u (θu) (27) (27) Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Harenberg, Marelli, Sudret, and Winschel 14 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2 14 Quantitative Economics 10 (2019) where where where where MPC(θ ) def  b Ψ (θ) (28) MPC u (θu) def =  α∈Au bαΨα(θ) (28) (28) Consequently, due to the orthogonality of the PC basis, the partial variance Du in equa- tion (21) reduces to Du = Var MPC u (Θu) =  α∈Au b2 α (29) (29) that is, again, a mere sum of squares of selected coefficients. The Sobol’ indices Su can then be computed by dividing the above results by the total variance (equation (15)). In other words, from a given PC expansion, the Sobol’ indices of any order may be obtained by a mere combination of the squares of the coefficients. 2.3 Sensitivity analysis As an illustration, the first- order PC-based Sobol’ indices read SPC i =  α∈Ai b2 α/D Ai = {α ∈A : αi > 0αj̸=i = 0} (30) (30) whereas the total PC-based Sobol’ indices are whereas the total PC-based Sobol’ indices are STPC i =  α∈AT i b2 α/D AT i = {α ∈A : αi > 0} (31) (31) As a conclusion, polynomial chaos expansions not only provide a surrogate model for a possibly computationally expensive model as those used nowadays in economics, but also yield at no cost the full set of sensitivity indices that are useful for a better un- derstanding of the single and joint effects of input parameters on quantities of interest. 2.3.4 Univariate effects While Sobol’ indices provide quantitative insight on the im- portance of a parameter, they do not include information about the direction in which it affects the quantities of interest. Which parameters have an overall positive, which a negative relationship? Is the relationship of the input parameter to the model out- come linear or nonlinear? In which regions of the parameter range is the sensitivity the largest? These questions can be answered with univariate effects, originally introduced by Younes, Mara, Fajraoui, Lehmann, Belfort, and Beydoun (2013). Univariate effects can be defined as the conditional expectation of a quantity of interest as a function of a single parameter, where expectations are taken over all other parameters: M(1) i (θi) = E M(Θ|Θi = θi)  (32) (32) They can thus be interpreted as an average or robust relationship between an input pa- rameter and the quantity of interest. In the case of PCE models, univariate effects have an analytical closed form that is closely related to the first-order Sobol’ decomposition in equation (30) (Deman et al. (2016)): They can thus be interpreted as an average or robust relationship between an input pa- rameter and the quantity of interest. In the case of PCE models, univariate effects have an analytical closed form that is closely related to the first-order Sobol’ decomposition in equation (30) (Deman et al. (2016)): M(1) i (θi) = b0 +  α∈Ai bαΨα(θi) Ai = {α ∈A : αi > 0αi̸=j = 0} (33) (33) All the techniques described will be applied to the economic model of Section 3.1. Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 15 15 Uncertainty quantification and global sensitivity 2.4 Relevance for structural estimation Sobol’ indices and univariate effects can play a major role in structural estimation. The identification of a parameter (or a set thereof) through structural estimation is only pos- sible if the corresponding total Sobol’ index is significant. A negligible total Sobol’ index means that the QoI under scrutiny is not affected by the value of the underlying random variable. Thus, additional empirical evidence on such QoI cannot constrain the param- eter’s value. On the other hand, while a large total Sobol’ index means that the paremeter affects the QoI, it is possible that its effect is highly nonlinear, hence leading to multiple lo- cal maxima in the corresponding likelihood function. In other words, a significant total Sobol’ index is a necessary but not sufficient condition for the identifiability of a param- eter in structural estimation. Univariate effects can provide an effective tool to identify this particular scenario. The PCE-based approach presented here could be particularly useful as a prestep in structural estimation because of its efficiency and accuracy in identifying irrelevant parameters. Showing this in an economic application would, in our view, be very in- teresting, but is outside the scope of the present paper, so that we leave it for future research. 3. Economic model and parameterization The presented tools for uncertainty quantification are generically applicable to any eco- nomic model. To illustrate their use, we apply them to a canonical real-business-cycle (RBC) model with capital adjustment costs, because this model has often been used as a test bench for introducing new numerical methods; see, for example, Den Haan, Judd, and Juillard (2011), Brumm and Scheidegger (2017), or Winschel and Kraetzig (2010). In the subsection on the RBC model, we also define the QoIs for which we perform uncertainty quantification. In the subsection on the parameterization, we also include parameter bounds, which are essential to the local and global sensitivity analyses later on. 3.1 Real-business-cycle model and quantities of interest We first summarize the standard RBC model before defining the quantities of interest. The allocation problem is described by the dynamic optimization We first summarize the standard RBC model before defining the quantities of interes The allocation problem is described by the dynamic optimization max {ctltit}∞ t=0 E0 ∞  t=0 βt  cχ t (1 −lt)1−χ1−1 τ  1 −1 τ   (34) (34) The objective function is a discounted sum of utilities of consumption ct and leisure 1 −lt in each period, where β is the discount factor, τ is the intertemporal elasticity of substitution (IES), and χ is the leisure share parameter in utility. The decision variables Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) 16 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2 Harenberg, Marelli, Sudret, and Winschel 16 Quantitative Economics 10 (2019) are consumption ct, labor lt, and investment it. The aggregate resource constraint is qt = ct + it + φ 2 kt  it kt −δ 2  (35) (35) where qt denotes the quantity of produced goods, kt the capital stock, and δ the depre- ciation rate of capital. Production qt can be used for consumption and investment, the latter being subject to a convex adjustment cost. These investment adjustment costs are modeled like in Den Haan, Judd, and Juillard (2011), with φ governing the size of the costs. The production technology qt = exp(zt)kα t l1−α t (36) (36) depends on productivity zt, capital kt, labor lt and the capital share α. The capital tran- sition and stochastic productivity processes are given by kt+1 = it + (1 −δ)kt (37) zt+1 = ρzt + et+1 (38) (37) (38) where ρ is the autocorrelation coefficient of the productivity process with independent, identically and normally distributed shocks et+1 ∼N(0σ). where ρ is the autocorrelation coefficient of the productivity process with independent, identically and normally distributed shocks et+1 ∼N(0σ). Using the notation of the uncertainty quantification framework introduced above, we have a parameter vector containing eight parameters, θ = {βτχαδρφσ} (39) (39) From an uncertainty quantification perspective, the parameter vector is the input to the RBC model, which itself can be treated as a black box, M(θ).10 In this model, all pa- rameters are continuous, but for the GSA methods we propose it is no problem to have discrete parameters, for example, the number of countries, as an input. 10This is different from the literature that considers robust decision making under model uncertainty; cf. our discussion in the concluding Section 6. Under that approach, the agent takes the parameter uncertainty into account such that the optimization problem in equation (34) needs to be modified accordingly. 3.1 Real-business-cycle model and quantities of interest From an uncertainty quantification perspective, the parameter vector is the input to the RBC model, which itself can be treated as a black box, M(θ).10 In this model, all pa- rameters are continuous, but for the GSA methods we propose it is no problem to have discrete parameters, for example, the number of countries, as an input. Turning to the quantities of interest, let us first repeat that the basic RBC model was chosen for illustrating the methodology, not because it features particularly insightful QoIs. For most of the paper, we consider just two quantities of interest, y = {y1y2} = M(θ), to keep the exposition clear. The first QoI is the average capital-output ratio, y1 = E kt qt   (40) (40) which is often used as a calibration target, for example, Kydland and Prescott (1982) or Cooley and Prescott (1995). Our sensitivity analysis can help identify which parameters are most relevant for calibrating it (and which are not), and—by looking at univariate 10This is different from the literature that considers robust decision making under model uncertainty; cf. our discussion in the concluding Section 6. Under that approach, the agent takes the parameter uncertainty into account such that the optimization problem in equation (34) needs to be modified accordingly. Quantitative Economics 10 (2019) 17 Uncertainty quantification and global sensitivity effects—in which regions of the parameter space the capital-output ratio is particularly sensitive.11 The second QoI is the ratio of the variance of log production in the model over its empirical counterpart. This second variable, which we will refer to as the production variance ratio, is frequently the quantity of interest in standard RBC models, where it is used to assess how much of the observed fluctuations can be explained by the model (see, e.g., Eichenbaum (1991), King and Rebelo (1999), or Canova (1995)). Denoting by ˆσ2 q the empirical variance of log production in the data, the variance ratio is y2 = 1 ˆσ2 q Var log(qt)  (41) (41) We set ˆσ2 q = 328, a standard value in the literature (see, e.g., King and Rebelo (1999)). In Section 5.6, we discuss and present results for other quantities of interest. 13If the error is large relative to the variance of the QoIs, or if it is biased, then the model results are likel to be unreliable independently of sensitivity analysis. 11Alternatively, one can first calibrate the model to match the capital-output ratio and then study how sensitive the results are. This is relevant, since the empirical values found in the literature range from 25 to 4 and higher (cf., e.g., McGrattan and Prescott (2017)), which deliver different parameter values. 11Alternatively, one can first calibrate the model to match the capital-output ratio and then study how sensitive the results are. This is relevant, since the empirical values found in the literature range from 25 to 4 and higher (cf., e.g., McGrattan and Prescott (2017)), which deliver different parameter values. 12In addition, if the model cannot be solved to the desired accuracy at a given parameter vector, for example, due to nonconvergence for numerical reasons, the vector can simply be discarded from the ex- perimental design. 13If the error is large relative to the variance of the QoIs, or if it is biased, then the model results are likely to be unreliable independently of sensitivity analysis. 4 and higher (cf., e.g., McGrattan and Prescott (2017)), which deliver different parameter values. 12In addition, if the model cannot be solved to the desired accuracy at a given parameter vector, for example, due to nonconvergence for numerical reasons, the vector can simply be discarded from the ex- perimental design. 13If the error is large relative to the variance of the QoIs, or if it is biased, then the model results are likely 3.2 Accuracy of model solution for global sensitivity analysis The Sobol’ decomposition in equation (16) is exact when there is no error in the QoIs. Nonetheless, the methods we propose are robust to some numerical error in the evalua- tion of the model for the following important reasons. First, as discussed in Section 2.2.1, we compute the PCE by least-squares regression, which allows for small noise in the data.12 Second, Sobol’ indices and univariate effects are based on conditional expecta- tions; see equations (22) and (32). As long as numerical error in the model evaluation is unbiased and small relative to the variance of the QoIs, the error is integrated out and the results of the GSA are unaffected.13 Third, for Sobol’ indices and univariate effects to be used as a sensitivity measure, it is not necessary that their values be known exactly. For example, it does not matter whether the total Sobol’ index of the capital share, α, is 083 or 084, because small differences do not affect the interpretation in a sensitivity context. The interpretation would rather be that,for example, the variance of the QoI ex- plained by α is “between 80 and 85 percent,” and α is “clearly more important than” or “approximately of equal importance as” another parameter. Thus, while the canonical RBC model presented above can be solved easily at high accuracy, our methods are well suited to more expensive models that are harder to eval- uate. For the reasons mentioned in the previous paragraph, it is not necessary to solve expensive models at very high accuracy. On top of that, we employ a degree-adaptive, sparse PCE, as explained in Section 2.2.2, meaning that a small number of model eval- uations is often sufficient. We discuss this further in Section 5.4.3, where we study the convergence of Sobol’ indices with respect to the experimental design. 11Alternatively, one can first calibrate the model to match the capital-output ratio and then study how sensitive the results are. This is relevant, since the empirical values found in the literature range from 25 to 4 and higher (cf., e.g., McGrattan and Prescott (2017)), which deliver different parameter values. 12 12In addition, if the model cannot be solved to the desired accuracy at a given parameter vector, for example, due to nonconvergence for numerical reasons, the vector can simply be discarded from the ex- perimental design. 3.2 Accuracy of model solution for global sensitivity analysis Harenberg, Marelli, Sudret, and Winschel 18 Quantitative Economics 10 (2019) We solve the RBC model with global nonlinear methods (Cai and Judd (2010)) using the generic toolbox of Miranda and Fackler (2002). Specifically, we use a time iteration algorithm to solve the Euler equation for optimal choices. We employ Chebyshev col- location with a polynomial of degree 11 (Judd (1992)). To compute our QoIs, the model is simulated for 5000 periods, discarding the first 1000. This is sufficient for an accurate and stable solution of the model.14 Relative Euler equation errors, evaluated along the simulation path for all parameter vectors and reported in log10-scale, are in the range of −50 to −62 for the average error and in the range of −30 to −41 for the maximum error. This is in line with other studies (e.g., Aruoba, Fernández-Villaverde, and Rubio-Ramírez (2006)). To illustrate the robustness of the global sensitivity measures, we reduced the de- gree of the Chebyshev polynomial to three. Average Euler errors increase markedly to a range of [−23−42] in log10-scale. While small changes in the Sobol’ indices and uni- variate effects are observable, the results in terms of importance ranking, interactions, and direction of change do not change at all. 15Canova (1994) considers log utility and therefore does not have bounds for the IES. Instead, we cove the same range of the IES as Juillard and Villemot (2011). 14Increasing the order of the polynomial to 15 and the number of simulation periods to 10,000 does no affect our results at all. 15 14Increasing the order of the polynomial to 15 and the number of simulation periods to 10,000 does not affect our results at all. 15Canova (1994) considers log utility and therefore does not have bounds for the IES. Instead, we cover the same range of the IES as Juillard and Villemot (2011). 14Increasing the order of the polynomial to 15 and the number of simulation periods to 10,000 does not affect our results at all. 15Canova (1994) considers log utility and therefore does not have bounds for the IES. Instead, we cover 3.3 Parametrization for sensitivity analysis Generally, the parameter vector, θ, can be determined either by estimation or by cali- bration of the model. Since we do not want to distract from the paper’s contribution, we will simply parametrize the model by setting θ to values that are common in the liter- ature. However, it is important to note that the methods for uncertainty quantification and global sensitivity analysis proposed in this paper are just as applicable and relevant when the parameters are first calibrated or estimated. Our baseline parameterization, θ0, closely follows Cooley and Prescott (1995), whose values are considered standard in the literature. They are displayed in the second col- umn of Table 1. Since Cooley and Prescott (1995) do not have adjustment costs, we take the value for φ from Juillard and Villemot (2011). As is typical in the RBC literature, the values are for quarterly data. The lower and upper bounds for each parameter, θi and θi, are set symmetrically around each baseline value. In the context of sensitivity analysis, the bounds should be chosen to represent values at the upper and the lower end of what most economists would still find reasonable. For example, in an RBC model, a value for the capital share of α = 09 is theoretically possible, but would not be considered plausible and is thus not included in our range. The restriction that the bounds be symmetric around the mean is not necessary, but facilitates the discussion of the local sensitivity analysis. It does, however restrict the ranges that we can consider, for example, for the discount factor β, since β < 1 is also required. The bounds are displayed in the third and fourth column of Table 1. We base them on Canova (1994), who performs an extensive literature review of the parameter values of this RBC model.15 Uncertainty quantification and global sensitivity 19 19 Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 19 Table 1. Parameter values. Parameter Baseline, θ0 i Lower bound, θi Upper bound,θi Discount factor, β 098 097 099 IES, τ 06 02 1 Leisure share in utility, χ 03 02 04 Capital share, α 035 02 05 Depreciation rate, δ 002 001 003 Capital adjustment cost, φ 05 000 100 Autocorrelation of TFP, ρ 095 092 098 Standard deviation of TFP, σ 0007 0005 0009 Table 1. Parameter values. 4. Local sensitivity analysis This section presents two local sensitivity measures that are often encountered in quan- titative economic work, namely one-at-time finite differences and scenario analysis.16 Thereby, we can compare them to the global sensitivity measures that are presented in Section 5. Generally, local measures are intuitive and easy to implement, but suffer from three important drawbacks. First, they are valid only locally at the chosen evalu- ation points and may differ substantially for other, even close-by points. Second, they typically rely on a linear approximation of the slope, so that nonlinearities are not ac- counted for. And third, they either do not capture interactions between the parameters, or if they do, they cannot isolate them. Because of these important drawbacks, this sec- tion only presents the methods without giving economic interpretation. The economic interpretation is instead given in the section on the global sensitivity measures. 3.3 Parametrization for sensitivity analysis The three values θ0 i , θi, and θi for each parameter are used in the local sensitivity analysis in the next section. The global sensitivity analysis also uses them, but addition- ally specifies a distribution over each parameter; cf. Section 5.1. 16Elasticities are another local sensitivity measure, which is conceptually related to OAT analysi 4.1 One-at-a-time finite differences One of the most common sensitivity analyses in numerical economics consists of chang- ing a single parameter value, while keeping all others fixed, and reporting the change in the quantity of interest. Often this is interpreted as a robustness check. When performed for all parameters in turn, this procedure is known in the uncertainty quantification lit- erature as one-at-a-time (OAT) finite differences (e.g., Borgonovo and Plischke (2016)). Since OAT is a local measure, we compute it for two different points. Specifically, we first change one parameter at a time from its lower bound to its baseline value given in Table 1, while keeping all other parameters fixed at their lower bound values. The corresponding change in each QoI is OAT 1 i = M  θ∼iθ0 i  −M(θ) (42) (42) 20 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) (a) Average capital-output ratio (b) Production variance ratio Figure 2. One-at-a-time (OAT) sensitivity indices, showing the impact of changing a single pa- rameter while keeping all others fixed (cf. equations (42) and (43)). Red bars represent parameter changes from lower bound to baseline value, blue bars from baseline value to upper bound; cf. Table 1. 20 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) (b) Production variance ratio (a) Average capital-output ratio (a) Average capital-output ratio (a) Average capital-output ratio (b) Production variance ratio Figure 2. One-at-a-time (OAT) sensitivity indices, showing the impact of changing a single pa- rameter while keeping all others fixed (cf. equations (42) and (43)). Red bars represent parameter changes from lower bound to baseline value, blue bars from baseline value to upper bound; cf. Table 1. where θ∼i means that all parameters but i take their lower bound values. We then do the same starting at the baseline values in Table 1 and changing one parameter at a time to its upper bound, thereby keeping the same direction and size of change as in equation (42): where θ∼i means that all parameters but i take their lower bound values. 4.1 One-at-a-time finite differences We then do the same starting at the baseline values in Table 1 and changing one parameter at a time to its upper bound, thereby keeping the same direction and size of change as in equation (42): OAT 2 i = M  θ0 ∼iθi  −M  θ0  (43) (43) Figure 2 plots the values of OAT 1 i in red and OAT 2 i in blue. Turning first to average capital-output ratio in the left-hand panel, we observe that only three of the eight pa- rameters have a nonzero impact. When looking at the first evaluation point, OAT 1 i , rep- resented in red, it is clear that capital share, α, is the most important parameter, fol- lowed by discount factor, β, and depreciation rate δ. However, when we move to the second evaluation point, OAT 2 i , represented in blue, α and β are much more similar in their impact, because the importance of β has increased whereas the effect of α remains unchanged. The reason is that for β, nonlinearities, interactions, or both are at work, whereas capital share, α, seems to have a linear impact on the average capital-output ratio. Turning to the production variance ratio in the right-hand panel, we similarly ob- serve that only three parameters matter. However, the set of parameters impacting this QoI is quite different. By comparing the two evaluation points, OAT 1 i in red and OAT 2 i in blue, we see clearly the main weakness of local analysis: not only does the impact of au- tocorrelation, ρ, change dramatically between OAT 1 and OAT 2, but also the importance ranking of ρ and σ is reversed. The reasons are, again, nonlinearities and interactions, which cannot be identified or accounted for with the OAT sensitivity measure. Joint vari- ation of multiple parameters is known as scenario analysis, discussed next. Uncertainty quantification and global sensitivity 2 Quantitative Economics 10 (2019) 21 17See, for example, Stern (2007). 18 4.2 Scenario analysis Scenario analysis is another very common form of sensitivity analysis in economics.17 In a scenario, typically several parameter values are changed simultaneously to reflect some change in the economic environment.18 This is intuitively appealing and allows for more complex parameter changes than the one-at-a-time finite differences of the previous section. Thereby, scenario analysis is able to capture interactions between pa- rameters, but it is not straightforward to isolate the effect of such interactions. We consider three scenarios based on the parameter values in Table 1. Due to the simplicity of the canonical RBC model, the scenarios are not meant to capture a particu- larly plausible economic environment, but rather to exemplify the approach. One draw- back that becomes apparent is the high level of discretion typically involved in choosing scenarios and corresponding parameter values, which is due to the local nature of this sensitivity measure. The scenarios are: 1. Scenario “Baseline”: all parameters take their baseline values. 2. Scenario “High risk and risk aversion”: σ, and ρ are at their upper bounds and τ is at its lower bound, so that risk aversion 1 τ is high. All other parameters are at their baseline values. 3. Scenario “High capital utilization and frictions”: α, δ, and φ are at their upper bounds, all other parameters are at their baseline values. Figure 3 plots the three scenarios in a graph with the two quantities of interest, av- erage capital-output ratio and production variance ratio, on the axes. Therefore, we can compare the scenarios and evaluate the impact of joint parameter changes on the two Figure 3. Scenario analysis, each scenario representing a set of parameter values as explained in the enumerated list in the main text. Figure 3. Scenario analysis, each scenario representing a set of parameter values as explaine in the enumerated list in the main text. See, for example, Stern (2007). 18More generally, a scenario can be defined as a set of assumptions. As long as the assumptions can be nested using a real-valued parameter, they can be analyzed with the tools discussed in this paper. p 18More generally, a scenario can be defined as a set of assumptions. As long as the assumptions can b nested using a real-valued parameter, they can be analyzed with the tools discussed in this paper. Harenberg, Marelli, Sudret, and Winschel 22 Quantitative Economics 10 (2019) quantities of interest. 5. Global sensitivity analysis In this section, we present the results of the global sensitivity analysis for the canoni- cal RBC model. In contrast to the local sensitivity measures of the previous section, the global measures do not depend on a specific evaluation point. In addition, they fully capture the nonlinearity in the mapping from parameters to quantities of interest and allow us to analyze interactions between parameters. All calculations in this section are performed with UQLab©, an actively maintained Matlab© toolbox for uncertainty quan- tification (Marelli and Sudret (2014, 2017)).19 20It is, for example, possible to use discrete distributions with mass points. 4.2 Scenario analysis However, scenario analysis does not allow us to tell which param- eter or which interaction between parameters is important in each case. For example, the “Baseline” scenario has the lowest level of both QoIs. The “High risk and risk aversion” scenario has a much higher variance ratio, but we cannot say whether this is mostly due to the increase in autocorrelation, ρ, or standard deviation, σ, of TFP shocks. From the results in the previous section, it could be either; cf. Figure 2. One solu- tion would be to combine the scenario analysis with OAT finite differences to tease out individual parameter effects and interactions, known as scenario decomposition or gen- eralized Tornado diagrams (see, e.g., Borgonovo (2010) and Borgonovo, Castaings, and Tarantola (2011)). However, such Tornado diagrams are rarely encountered in economic studies and are outside the scope of this paper, since they also suffer from the fact that they are local and linear. 19The toolbox can be freely downloaded from www.uqlab.com. 20 5.1 Parameter distributions As explained in Section 2, we need to specify a distribution that represents the uncer- tainty about the value of each parameter. This is a crucial step in GSA, as the sensitivity results depend on it, and should thus be done carefully. Methodologically, there is no limitation on what distributions are allowed.20 This is determined by the research ques- tion and data availability. In our case, the research question is how sensitive outcomes are with respect to the parameters, and there is only little data on parameter values of RBC models. The most widely used approach to determine the most suited distributions to rep- resent the lack of knowledge of the specific value of a parameter in the absence of em- pirical data is given by the principle of maximum entropy (Jaynes (1982)), commonly used to define prior information in Bayesian analysis. The rationale behind this prin- ciple is that if only a set of constraints is available regarding the value of an unknown variable, for example, its maximum and minimum bounds, its moments, or its sign, the distribution that maximizes the information entropy (a measure of the variability of a random variable) while respecting the constraints should be used to represent its sta- tistical uncertainty. Common examples of such distributions for continuous variables include the uniform distribution when the minimum and maximum values are known, Quantitative Economics 10 (2019) 23 Uncertainty quantification and global sensitivity the Gaussian distribution when the first two moments are known, or the exponential distribution when the variable is strictly positive but unbounded. In our particular case, we have identified the available information on the parame- ters of the RBC model as the minimum and maximum bounds on the admissible param- eters based on the work of Canova (1994), who derives “a least informative (Bayesian) density” for each parameter of the RBC model using a comprehensive literature review. Since we assume that the only knowledge we have are the bounds of each parameter, applying the maximum entropy principle results in the choice of uniform distributions to represent our lack of knowledge on the actual parameter values. Of course, the avail- able information for other economic models may not be the same, hence requiring dif- ferent distributions to parametrize the corresponding uncertainty. Since often data on parameter values may not be available, the use of literature review, expert opinion, and “commonly used values” is perfectly acceptable. 5.1 Parameter distributions In such circumstances, the uncertainty about a parameter value is usually represented using a continuous distribution rather than point mass for discrete values, unless the parameter is known to have a discrete nature. It should also be noted that the maximum entropy distributions can be updated through Bayesian analysis in the case empirical data were to become available. A uni- form distribution is also adequate for our research question, where we want to under- stand the model sensitivities over plausible ranges of parameters. We do not—and for lack of data could not—ask what empirical parameter distributions would mean for the distribution of the quantities of interest. Therefore, we assume that all parameters of our model are independently and uniformly distributed with support given by the lower and upper bounds in Table 1.21 For this approach, it does not matter whether the values for the baseline parameter vector, θ0, are taken from the literature or are calibrated to some empirical targets. If the model was calibrated, we could proceed in the same fashion by specifying distribu- tions and performing our global sensitivity analysis. If, instead, a structural model was estimated with data, then one could additionally use the marginal distributions of the parameter estimates as the parameter distributions. 21As mentioned in footnote 9, assuming dependence between parameter distributions makes it difficult to disentangle the effects of parameters. 5.2 Polynomial chaos expansion of the economic model We first demonstrate the convergence of the polynomial chaos expansion of the real- business-cycle model, since the following GSA is based on it. Due to the computa- tional cost of the RBC model, a maximum computational budget of 500 model eval- uations was available, which allowed us to run both GSA and additional convergence analysis. We therefore generated a set of nested experimental designs of increasing size NED = {5060500} using nested Latin Hypercube Sampling (Blatman and Sudret (2011)). For each set, a sparse PCE was calculated based on least-angle-regression with an adaptive degree selection in the range 3 ≤p ≤20; cf. Section 2.2.2. The resulting set of PCEs was then compared based on their leave-one-out error estimator calculated with equation (13). 24 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Figure 4. Convergence of the PCE leave-one-out error estimator (equation (13)) as a function of the size of the experimental design for both QoIs. Figure 4. Convergence of the PCE leave-one-out error estimator (equation (13)) as a function of the size of the experimental design for both QoIs. The resulting convergence plot for each of the two QoIs is displayed in Figure 4. The error for the average capital-output ratio drops very quickly, while the production variance ratio converges at a slower rate. Based on the guidelines given in Le Gratiet, Marelli, and Sudret (2016), a leave-one-out error errLOO ≤005 was deemed sufficient for the purposes of first and total Sobol’ indices. Therefore, a computational budget of N = 150 model evaluations was selected for all the subsequent analyses, unless explicitly specified. As shown below, this budget suffices to achieve a very high accuracy of Sobol’ indices. However, for more sophisticated economic models, a more realistic computa- tional budget may be in the order of 101−2. This is typically sufficient for GSA for the reasons discussed in Sections 3.2 and 5.4.3. 5.4 Sobol’ indices 5.4.1 Total and first-order Sobol’ indices As described in Section 2.3.2, Sobol’ indices are an important tool to establish an importance ranking of input parameters and their interactions. Total Sobol’ indices (equation (24)) represent the fraction of the variance of a quantity of interest that is explained by the variability of each input parameter, in- cluding nonlinearities and interactions. Therefore, small total indices are indicative of unimportant variables. First-order indices (equation (22)) instead only account for the direct contribution of each parameter, including nonlinearities but excluding interac- tions terms. It is common to compare the two sets of indices to identify the importance of interactions between input variables: if total and first-order indices are very similar, the model is mostly additive (no interactions), otherwise interactions play an important role. Figure 6 shows this comparison between total (in red) and first-order (in blue) in- dices for both QoIs. 5.4.1 Total and first-order Sobol’ indices As described in Section 2.3.2, Sobol’ indices are an important tool to establish an importance ranking of input parameters and their interactions. Total Sobol’ indices (equation (24)) represent the fraction of the variance of a quantity of interest that is explained by the variability of each input parameter, in- cluding nonlinearities and interactions. Therefore, small total indices are indicative of unimportant variables. First-order indices (equation (22)) instead only account for the direct contribution of each parameter, including nonlinearities but excluding interac- tions terms. It is common to compare the two sets of indices to identify the importance of interactions between input variables: if total and first-order indices are very similar, the model is mostly additive (no interactions), otherwise interactions play an important role. Figure 6 shows this comparison between total (in red) and first-order (in blue) in- dices for both QoIs. The left-hand panel displays the indices for the average capital-output ratio. The first thing to notice is that only three of the eight parameters have an influence. The other Sobol’ indices are zero, meaning that we can fix them to any value without influencing the capital-output ratio. To some extent, this is surprising, because in a general equilib- rium of a dynamic, stochastic economy with rational expectations, as considered here, all parameters can, in principle, affect all endogenous outcomes. Due to the complexity of such models, obtaining the insight that only few parameters matter is generally dif- ficult. 5.3 Histograms of the quantities of interest To see how the the parameter uncertainty propagates through the model, first consider the resulting histograms of the two quantities of interest. To get the histograms, we eval- uate the surrogate model on a Monte Carlo sample of size one million. Such a large num- ber of evaluations would be prohibitively expensive for the RBC model. For smaller sam- ple sizes, the histograms of the surrogate and the original model are virtually identical. Figure 5 displays the histograms of average capital-output ratio (left) and production variance ratio (right). Both distributions have a notable dispersion and are right-skewed. The values corresponding to the baseline, θ0, are indicated by vertical lines. For these two QoIs, the baseline values are close to the respective modes of the distribution, but that need not generally be the case. The left-hand figure shows that typical target values for the capital-output ratio in [2535] can be achieved with many different parame- ter combinations, whereas the more extreme value of 6 considered by McGrattan and Prescott (2017), while still being in the range considered here, substantially limits the possible parameter values. The right-hand figure is very similar to Figure 5 in Canova (1994), who, however, had only 1000 Monte Carlo-based model evaluations, too few to perform a global sensitivity analysis, as we do next. Uncertainty quantification and global sensitivity 25 Quantitative Economics 10 (2019) 25 (a) Average capital-output ratio (b) Production variance ratio Figure 5. Histograms of the QoIs, calculated by drawing a Monte Carlo sample of size 1,000,000 from the parameter distributions and evaluating each parameter vector with the PCE surrogate of the RBC model. The straight line represents the value if the model is evaluated at the baseline parameter values; cf. Table 1. (a) Average capital-output ratio (b) Production variance ratio (b) Production variance ratio Figure 5. Histograms of the QoIs, calculated by drawing a Monte Carlo sample of size 1,000,000 from the parameter distributions and evaluating each parameter vector with the PCE surrogate of the RBC model. The straight line represents the value if the model is evaluated at the baseline parameter values; cf. Table 1. 5.4 Sobol’ indices Moreover, local analysis would not help, as any results are valid only locally. We can, of course, derive the deterministic steady state of the RBC model, where is easy to see that τ, χ, and φ drop out of the equations (and by definition of deterministic steady state, ρ and σ play no role). But that this transfers to the stochastic economy is not im- mediately clear. Turning to the three parameters with nonzero indices, we first observe that they are of substantial (not just minor) importance. The capital share, α is clearly 26 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) (a) Average capital-output ratio (b) Production variance ratio Figure 6. Total Sobol’ indices, ST i , in red and first-order Sobol’ indices, Si, in blue. The total Sobol’ indices are larger by construction, as they include all interactions. Based on N = 150 eval- uations of the RBC model. Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) 26 (a) Average capital-output ratio (b) Production variance ratio (b) Production variance ratio Figure 6. Total Sobol’ indices, ST i , in red and first-order Sobol’ indices, Si, in blue. The total Sobol’ indices are larger by construction, as they include all interactions. Based on N = 150 eval- uations of the RBC model. the most important, indicating that most effort should go into that parameter when cal- ibrating the RBC model. Since estimates of the capital share depend a lot on data qual- ity, period considered, and the measure of capital (or labor) income employed, a global sensitivity analysis should be an integral part of quantitative studies using a neoclassical production function.22 Typically, when calibrating the RBC model, α is fixed to a value taken from other studies. Given that α is so fixed, we see that the discount factor β and the depreciation rate δ are equally important in determining the capital-output ratio. The production variance ratio in the right-hand panel displays a similar pattern in that again only three parameters are nonzero. Note, however, that the set of parameters governing capital-output ratio and variance ratio is quite different. 22For example, estimates of the capital share depend on whether nonfarm proprietors’ income or in- tellectual property rights are included in the measure of capital. Also, the capital share has increased over time, cf. Karabarbounis and Neiman (2014) or Elsby, Hobijn, and ¸Sahin (2013). 5.4 Sobol’ indices While it is not sur- prising that autocorrelation, ρ, and standard deviation, σ, of TFP shocks are the most important parameters for the variance of production, it is to some extent unexpected that no other parameters play a role (α being the only other nonzero parameter, but unimportant compared to ρ and σ). As argued above, in a rational expectations general equilibrium of a dynamic economy, preference parameters could, in principle, have an impact on this QoI. In addition, for such a variance-related QoI, it would be hard to de- rive insights by resorting to a deterministic steady state. The conclusion we can draw from the figure is that preferences and technology do not matter for determining one of the most relevant quantities of interest of the early RBC literature—it is only the shock process that matters. Thus, the assumption of log-utility found in many papers (e.g., Cooley and Prescott (1995)) is innocuous, at least when the variance ratio is the focus. Last, recall that in the local OAT analysis of Section 4.1, the results on which param- eter was more important—ρ or σ—were ambiguous and depended on the evaluation Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 27 point. There is no such ambiguity here: over the intervals specified, ρ is more impor- tant. As there is substantial disagreement in the literature on the empirical value of ρ, GSA should be performed.23 For all nonzero parameters, the total Sobol’ index in red and the first-order Sobol’ in- dex in blue behave very similarly. The total index is larger by construction, as it contains all interactions, whereas the blue bar represents the direct impact of each parameter (excluding interactions). The difference represents the interactions of each parameter. While nonnegligible, the interactions are, overall, surprisingly small, given that this is a general equilibrium model, where all parameters could potentially interact. Such inter- actions are of substantial interest economically, since they help explain the model’s me- chanics, which often cannot be derived analytically. The figure therefore confirms the inadequacy of OAT measures since they cannot take interactions into account. To see which of any two parameter combinations interact, we next study second-order Sobol’ indices. 5.4.2 Second-order Sobol’ indices From an economic perspective, interactions be- tween parameters are particularly interesting. However, accurate computation of higher-order indices requires an experimental design of bigger size. 23Estimates of the stochastic process of TFP depend, for example, on how aggregate time series are de- ended; cf. Canova (1998). 5.4 Sobol’ indices It is due to the fact that these two inter- actions offset each other that the local OAT for α does not change between evaluation points in Figure 2(a). Turning to the production variance ratio, we find that the interaction between auto- correlation ρ and standard deviation σ is very important, which is not surprising as these two parameters determine the unconditional variance of TFP, and thus of production. That both parameters interact with α is due to the standard modeling of the TFP shocks being multiplicative to production technology, which in turn is determined mainly by α. The result that Sαρ is much larger than Sασ reflects the corresponding finding for first- order Sobol’ indices, namely that ρ is more important than σ. Finally, recall that local OAT analysis cannot identify such interactions. The ambigu- ous results it provided regarding the relative importance of ρ versus σ were in part due to this deficiency, as these two parameters turn out to interact strongly. Since the eco- nomic literature typically uses local sensitivity measures, there are nearly no studies that identify interactions.24 The fast, accurate, and nonintrusive identification of parameter interactions is an important advantage of the global methods we propose. 5.4.3 Convergence of Sobol’ indices As discussed in Section 5.2, the main rationale for choosing a minimum experimental size is to achieve a sufficiently low generalization error for the PCE. However, it is worth giving further insight on the convergence behavior of the Sobol’ indices, as these are of central interest and tend to converge very fast.25 Therefore, in this section we look at the estimates of the Sobol’ indices as a function of the experimental design size. The convergence study consists of estimating total, first-order, and second-order in- dices for a set of increasingly larger experimental designs with a maximum of of N = 500. The experimental designs are constructed as described in Section 5.2. Confidence bounds for each index estimate are calculated as the 95% empirical inter-quantile ranges by means of NB = 100 bootstrap replications of the underlying PCE coefficients. The main results are reported in Figure 8 for the two largest first-order Sobol’ indices (left panel) and the two largest second-order indices (right panel). Total Sobol’ indices are not shown because their convergence behavior is essentially identical to that of their first-order counterparts. 5.4 Sobol’ indices To estimate second- order indices, we choose—based on the convergence shown in Figure 4—a sample size of N = 250, corresponding to errLOO ≈2 · 10−3 for the production variance ratio. The three second-order Sobol’ indices corresponding to the three parameters that had nonzero total Sobol’ indices are displayed in Figure 7 for each of the two QoIs. Gen- erally, they are not large, but, as we show in the next section, they are estimated at very high precision, meaning that we can confidently interpret them. (a) Average capital-output ratio (b) Production variance ratio Figure 7. Second-order Sobol’ indices, representing the importance of interactions between any two parameters. Only the three largest are shown for each of the two quantities of interest. Based on N = 250 evaluations of the RBC model. 23Estimates of the stochastic process of TFP depend, for example, on how aggregate time series are de- trended; cf. Canova (1998). (a) Average capital-output ratio Figure 7. Second-order Sobol’ indices, representing the importance of interactions between any two parameters. Only the three largest are shown for each of the two quantities of interest. Based on N = 250 evaluations of the RBC model. Figure 7. Second-order Sobol’ indices, representing the importance of interactions between any two parameters. Only the three largest are shown for each of the two quantities of interest. Based on N = 250 evaluations of the RBC model. 23Estimates of the stochastic process of TFP depend, for example, on how aggregate time series are de- trended; cf. Canova (1998). 28 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) For average capital-output ratio, the strongest interaction turns out be between those two parameters that, individually, had less of an impact, namely β and δ. The in- teraction means that, for example, increasing the discount factor will directly increase the capital output ratio (first-order Sobol’ index), but this effect is dampened due to de- preciation. In other words, the smaller δ, the larger the effect of β. While this interaction can also be seen in the analytic solution for the deterministic steady state, it is not obvi- ous from the deterministic solution that this is the most important interaction, and what that means for the stochastic economy. Another interesting point is that the indices Sβα and Sαδ are of essentially the same magnitude. 25See also our discussion relating to the robustness of Sobol’ indices in Section 3.2. 24One exception is Anderson et al. (2014) who compute second-order Sobol’ indices for a subset of the parameters of the climate change model of Nordhaus. 24One exception is Anderson et al. (2014) who compute second-order Sobol’ indices for a subset of the parameters of the climate change model of Nordhaus. 25See also our discussion relating to the robustness of Sobol’ indices in Section 3.2. Uncertainty quantification and global sensitivity 29 Uncertainty quantification and global sensitivity 29 Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) 29 Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 29 (a) First-order Sobol’ indices (b) Second-order Sobol’ indices Figure 8. Convergence of estimates of first- and second-order Sobol’ indices. The left panel shows the two largest nonzero first-order indices for each QoI. The right panel shows the two largest second-order indices for each QoI. Error bounds are calculated by bootstrap resampling of the PCE coefficients. ( ) Fi t d S b l’ i di (b) S d d S b l’ i di (a) First-order Sobol’ indices (b) Second-order Sobol’ indices Figure 8. Convergence of estimates of first- and second-order Sobol’ indices. The left panel shows the two largest nonzero first-order indices for each QoI. The right panel shows the two largest second-order indices for each QoI. Error bounds are calculated by bootstrap resampling of the PCE coefficients. evaluations, whereas second-order indices require approximately N = 220 model evalu- ations. 2 Therefore, the empirical error bounds of errLOO ≤5 · 10−2 for total and first-order indices as well as errLOO ≤5 · 10−3 for second-order indices are appropriate. For more expensive models, it is possible to adopt a greedy strategy by gradually enriching the experimental design until the target errLOO for the desired analysis is reached. In realistic scenarios with highly complex models, the available computational bud- get can be much lower than the 500 model evaluations we could afford for this model. However, the combination of sparse PCE and Sobol’ indices is widely regarded as one of the most computationally effective tools available to perform global sensitivity anal- ysis and can often be performed with affordable experimental designs. This efficiency is largely due to the effectiveness of sparse PCE, whose convergence is very fast globally, a crucial property for the unbiased estimation of Sobol’ indices. Further considerations on convergence, even for models that show a relatively poor point-wise convergence of the PCE surrogates, are discussed in Le Gratiet, Marelli, and Sudret (2016). Recent applica- tions with complex, high dimensional and/or highly computationally expensive models can be found, for example, in Deman et al. (2016), Le Gratiet, Marelli, and Sudret (2016) and Chiaramello, Parazzini, Fiocchi, Ravazzani, and Wiart (2017). 5.4 Sobol’ indices From the convergence behavior in Figure 8, it is clear that esti- mators of first-order (and total) indices converge already with as few as N = 120 model 5.5 Univariate effects As described in Section 2.3.4, univariate effects are conditional expectations functions of a parameter that provide a robust magnitude and sign of the parameter’s impact on the QoIs. The univariate effects for the eight input parameters are shown in Figure 9 for average capital-ouput ratio (left) and production variance ratio (right), respectively. The mean effect is included in each, so that the y-axis directly shows the corresponding value of the quantity of interest; cf. equation (32). For example, as β ranges from 097 to 099, 30 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) 30 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) (a) Average capital-output ratio (b) Production variance ratio Figure 9. Univariate effects, which are conditional expectation functions, showing the direc- tion in which a parameter impacts each quantity of interest. Because the mean effect is included, the y-axis represents the expected value of the quantity of interest. Quantitative Economics 10 (2019) (b) Production variance ratio (b) Production variance ratio (a) Average capital-output ratio Figure 9. Univariate effects, which are conditional expectation functions, showing the direc- tion in which a parameter impacts each quantity of interest. Because the mean effect is included, the y-axis represents the expected value of the quantity of interest. expected average capital-output ratio increases from approximately 22 to 4, where the expectation is taken over all other parameters. For capital-output ratio, the parameters which had a total Sobol’ index of zero ac- cordingly have univariate effects that are flat. The univariate effect for the discount rate β is increasing and convex. The convexity reflects, of course, the exponential discount- ing in the agent’s objective. The impact of capital share α is very close to linear over the whole range. This is because—even though α enters as an exponent in the produc- tion function—the quantity of interest here is the ratio of capital over output, both of which are affected similarly by α. Finally, the univariate effect of the depreciation rate δ is falling and convex. The result that β and δ are nonlinear, while α is close to linear, cor- responds to the findings of the local OAT analysis of Section 4.1. However, we now get a much clearer picture as to the exact shape of (non)linearities over the respective ranges. 5.5 Univariate effects Together with the insights on interactions that we get from the second-order Sobol’ in- dices, we can only now fully understand and interpret the results of the OAT analysis. For the production variance ratio, shown in the right panel, we again observe that parameters with first-order Sobol’ indices close to zero display univariate effects that are zero or negligibly small, while those corresponding to higher indices (α, ρ, and σ) display sizeable effects. Unsurprisingly, both ρ and σ display a positive slope, but the Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 31 univariate effect of σ on the variance ratio is close to linear while that of ρ is strongly convex. Therefore, when setting ρ to a high value, for example, to 0975, it is much more important to be careful and put effort in obtaining an accurate estimate than it is for low values. Empirically, the discussion centers a lot around values approaching a unit root, which, in light of our results, indeed is an important question when studying how much of the business cycle a given model can explain. All univariate effects of the RBC model turn out to be monotone in the ranges we specified. Of course, nonmonotonic behavior is possible and would be highly relevant for calibrating a model. For example, a parameter could first have a negative impact on a quantity of interest and, after crossing some threshold value, a positive impact. Iden- tifying and interpreting such relationships should typically be of substantial economic relevance. As a point in case, an interesting application of univariate effects would be the study of a policy reform, where the reform is governed by a real-valued parameter, say a tax rate. If the quantity of interest is, for example, social welfare, then the univariate effect can be interpreted as the robust impact of the tax rate on welfare, which often will be nonmonotonic and have local or global maxima.26 Finding such global optima that are robust to parameter uncertainty should make policy recommendations stemming from economic models more credible to policy makers. 26As discussed in our concluding Section 6, robustness in our context refers to the sensitivity of the model’s quantities of interest under parameter uncertainty. In particular, this is complementary to the ro- bust decision making under model uncertainty as studied, for example, in Hansen and Sargent (2007). 6. Conclusion This paper introduces Sobol’ indices and univariate effects as tools for global sensitivity analysis (GSA) and uncertainty quantification in economics and shows how to accu- rately compute them with a limited computational budget using polynomial chaos ex- pansions. We apply this methodology to the canonical real-business-cycle model with capital adjustment costs and compare it to traditional local methods, such as one-at- a-time parameter changes and scenario analyses. The comparison shows that the tradi- tional local sensitivity analysis can be misleading as it depends on the chosen evaluation points. Only the global analysis captures nonlinearities and identifies interactions, both of which are central to economic models. For univariate effects, which are conditional expectation functions of each parameter, it is worth emphasizing the economic signifi- cance for public policy evaluation. For example, the policy parameter could be a tax rate and the quantity of interest could be social welfare. Then the univariate effect could be interpreted as the robust impact of the tax on welfare under parameter uncertainty.27 With respect to robust economic policy analysis, a related strand of the economic literature has studied the impact of model uncertainty, where the decision maker can- not assign probabilities to different, competing economic models because of funda- mental, irreducible uncertainty. In that strand of literature, non-Bayesian approaches to decision making are used, such as min-max (e.g., Hansen and Sargent (2007)) or min- max regret (e.g., Brock, Durlauf, and West (2003), Brock, Durlauf, Nason, and Rondina (2007)), yielding optimal policies that perform sufficiently well under all—and, in par- ticular, adverse—model specifications.28 The sensitivity analysis we propose is comple- mentary, as it can be applied to a min-max (regret) model in order to understand the importance of the parameters that are not part of the fundamental model uncertainty, for example, the parameters in the decision maker’s utility function. Combining model uncertainty and parameter uncertainty is an interesting undertaking that we leave for future research. While we parameterized the model with standard values from the literature to fo- cus on the sensitivity analysis, the methods we propose are equally well suited if the model is calibrated to empirical targets or even structurally estimated. For a structurally estimated model, one can use the moments of the parameter estimates to specify the distributions needed for uncertainty quantification, or even the posterior marginal dis- tributions (obtained, e.g., through kernel density estimation). 28An insightful study comparing different approaches is Cai and Sanstad (2016). 32 Harenberg, Marelli, Sudret, and Winschel 2 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Other QoIs that would be of economic interest and for which GSA may yield impor- tant insights are, for example, welfare, inequality, or bankruptcies. Such questions are, of course, not in the scope of the canonical RBC model, which is used here to explain the methodology. 27A nice example is the ongoing work of Gersbach, Liu, and Tischhauser (2018), who apply the methods we propose to study robustness of forward guidance for monetary policy. 27A nice example is the ongoing work of Gersbach, Liu, and Tischhauser we propose to study robustness of forward guidance for monetary policy. 28 27A nice example is the ongoing work of Gersbach, Liu, and Tischhauser (2018), who apply the methods we propose to study robustness of forward guidance for monetary policy. 28An insightful study comparing different approaches is Cai and Sanstad (2016). 5.6 Other quantities of interest We have focused on two quantities of interest, average capital-output ratio and produc- tion variance ratio, to explain the methodology of GSA. In Appendix A, we extend the analysis to four more QoIs that are frequently found in the traditional RBC literature: the variance ratio of log consumption, the correlation of consumption and output, the variance of consumption growth, and the correlation of investment with output. Our aim is to showcase how the methodology applies broadly, picks up the individually dif- ferent characteristics of the QoIs, and presents them in an easy to convey manner. It is important to note that extending the analysis with more QoIs can be done at very small cost as long as either the QoIs have already been calculated or—in the case of stochastic models like our RBC model—the model simulations have been saved. In that case, there is no need to create a new experimental design and run the model. We find that there is substantial variation as to which parameters are important for each QoI. One result worth highlighting is that the utility leisure share, χ, and the capital adjustment costs, φ, do not impact any of the QoIs we studied. As mentioned previously, these two parameters drop out in the steady state equation of the capital-output ratio, but that this transfers to the stochastic economy and all other QoIs, for which analytical solutions do not exist, is not obvious. One conclusion is that the functional specification of adjustment costs, which is frequently used in the literature (cf. Den Haan, Judd, and Juillard (2011)), is not well suited for studying these QoIs. Depending on the research question, it should be modified or extended. 26As discussed in our concluding Section 6, robustness in our context refers to the sensitivity of the model’s quantities of interest under parameter uncertainty. In particular, this is complementary to the ro- bust decision making under model uncertainty as studied, for example, in Hansen and Sargent (2007). 6. Conclusion For a calibrated model, uncertainty quantification puts the calibration procedure on a more rigorous statistical Quantitative Economics 10 (2019) 33 Uncertainty quantification and global sensitivity footing, as argued by Eichenbaum (1991), Gregory and Smith (1995), and in particular Canova (1994, 1995). There are several freely available toolboxes that implement GSA and uncertainty quantification. The analysis in this paper is done with the Matlab© toolbox UQLab, which is nonintrusive, that is, it treats the model as a black box. Therefore, no changes have to be made to an existing model solution code and the proposed methods can read- ily be deployed. In addition, the methods in this paper are straightforward to parallelize by distributing the experimental design points. For academic research, the insights offered by GSA can help economists understand mechanisms and interactions in complex models and inform them as to where to di- rect efforts, for example, when extending the model or calibrating it. For policy-oriented work, a GSA is crucial for assessing the plausibility and credibility of policy recommen- dations. Appendix A: Other quantities of interest In this section, we present results for the quantities of interest discussed in Section 5.6. These are the variance ratio of log consumption, y3 = 1 ˆσ2c Var[log(ct)], the correlation of consumption and output, y4 = corr(ctqt), the variance of consumption growth, y5 = var( ct+1 ct −1), and the correlation of investment with output, y6 = corr(itqt). t Figure 10 displays the total Sobol’ indices for all four QoIs. The Sobol’ indices for consumption variance are, as expected, very similar to those of production variance. The variance of consumption growth, by contrast, depends mostly on the standard de- viation of TFP shocks, σ, and only very little on the autocorrelation, ρ. Turning to the correlations of consumption and investment with output, it is well known that the stan- dard RBC model has difficulty matching the data (cf. King and Rebelo (1999)). The Sobol’ indices show that, while both are influenced by the same set of parameters, the impor- tance of the parameters differs strongly. This knowledge can help to calibrate the model. The corresponding univariate effects are displayed together in Figure 11. When the univariate effects for different QoIs are plotted together, it is common to scale them by Figure 10. Total Sobol’ indices for other QoIs. Figure 10. Total Sobol’ indices for other QoIs. 34 Harenberg, Marelli, Sudret, and Winschel Quantitative Economics 10 (2019) Figure 11. Univariate effects. Figure 11. Univariate effects. mean and variance, since otherwise some effects may be hard to see due to scaling is- sues. This is different of how we represented the univariate effects in Section 5.5, but the advantage here is that the direction of change can easily be compared. The information on the importance of each parameter is given by the Sobol’ indices of the previous figure. For example, Figure 11 shows a positive impact of φ on three of the QoIs, but the corre- sponding total Sobol’ indices are essentially zero, meaning that these univariate effects can be ignored. On the other hand, the capital share α has nonzero Sobol’ indices for all QoIs, and we see that its univariate effects have positive slope for the consumption variance ratio and the correlation of investment with production, while having a nega- tive impact on the variance of consumption growth and the correlation of consumption with production. Appendix A: Other quantities of interest Also, one can see that the impact is close to linear for some parameters and nonlinear for others. mean and variance, since otherwise some effects may be hard to see due to scaling is- sues. This is different of how we represented the univariate effects in Section 5.5, but the advantage here is that the direction of change can easily be compared. The information on the importance of each parameter is given by the Sobol’ indices of the previous figure. Appendix B: Polynomial basis In this Appendix, we provide details on how to construct a polynomial basis in Sec- tion 2.2. While this can also be found in, for example, Judd (1998), we restate it here as the context is very different, and because the construction is crucial to the PCE. In this Appendix, we provide details on how to construct a polynomial basis in Sec- tion 2.2. While this can also be found in, for example, Judd (1998), we restate it here as the context is very different, and because the construction is crucial to the PCE. A suitable basis for equation (3) is given by orthonormal polynomials with respect to a weight function that corresponds to the PDF of the input random variables. In the sequel, we assume that the input variables are statistically independent, so that the joint PDF is the product of the M marginal distributions: fΘ(θ) = M i=1 fθi(θi), where fθi’s are the marginal distributions of each variable {θii = 1M} defined on DΘi. For each variable Θi and any two functions φ1φ2 : θ ∈DΘi →R, we define the functional inner Quantitative Economics 10 (2019) Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 35 Uncertainty quantification and global sensitivity 35 Quantitative Economics 10 (2019) Uncertainty quantification and global sensitivity 35 35 product by the following integral (provided it exists): product by the following integral (provided it exists): ⟨φ1φ2⟩i def = E φ1(Θi)φ2(Θi) =  DΘi φ1(θ)φ2(θ)fΘi(θ)dθ (44) (44) where E[·] is the expectation operator. Using the above notation, classical algebra allows one to build a family of orthogonal polynomials {P(i) k k ∈N} satisfying  P(i) j P(i) k  i def = E P(i) j (Θi)P(i) k (Θi) = a(i) j δjk; (45) (45) see, for example, Abramowitz and Stegun (1970). In the above equation, subscript k de- notes the degree of the polynomial P(i) k , δjk is the Kronecker symbol equal to 1 when j = k and 0 otherwise and a(i) j def = ∥P(i) j ∥2 i = ⟨P(i) j P(i) j ⟩i corresponds to the squared norm of P(i) j . For standard distributions, the associated families of orthogonal polynomials are wellknown. For instance, if Θi ∼U(−11) has a uniform distribution over [−11], the re- sulting family is that of the so-called Legendre polynomials (Xiu and Karniadakis (2002)). Appendix B: Polynomial basis The obtained polynomials may be normalized as follows: ψ(i) j = P(i) j /  a(i) j  i = 1dj ∈N (46) (46) From the sets of univariate orthonormal polynomials, one can now build multivari- ate orthonormal polynomials by tensor product. For this purpose, let us define the multi- indices α ∈NM, which are ordered lists of natural integers α = (α1αM), αi ∈N. One can associate a multivariate polynomial Ψα to any multiindex α by Ψα(θ) def = M  i=1 ψ(i) αi (θi) (47) (47) where the univariate polynomials {ψ(i) k k ∈N} are defined in equation (46). Due to equa- tion (45) and the above tensor product construction, the multivariate polynomials in the input vector Θ are also orthonormal, that is, where the univariate polynomials {ψ(i) k k ∈N} are defined in equation (46). Due to equa- tion (45) and the above tensor product construction, the multivariate polynomials in the input vector Θ are also orthonormal, that is, E Ψα(Θ)Ψβ(Θ) def =  DΘ Ψα(θ)Ψβ(θ)fΘ(θ)dθ = δαβ ∀αβ ∈NM (48) (48) where δαβ is the Kronecker symbol which is equal to 1 if α = β and zero otherwise. With this notation, it can be proven that the set of all multivariate polynomials in the input random vector Θ forms a basis of the Hilbert space in which Y = M(Θ) is represented (Soize and Ghanem (2004)): Y =  α∈NM bαΨα(Θ) (49) (49) The representation of the random response in equation (49) is exact when the in- finite series is considered. However, in practice, only a finite number of terms can be computed. For this purpose, a truncation scheme A has to be selected. Since the basis consists of multivariate polynomials, it is natural to consider all the polynomials up to Harenberg, Marelli, Sudret, and Winschel 36 Quantitative Economics 10 (2019) a given maximum degree. Let us define the total degree of a multivariate polynomial Ψα by |α| def = M i=1 αi. The standard truncation scheme consists in selecting all polynomials such that the total degree |α| is smaller than or equal to a given p. The maximal poly- nomial degree p may typically be equal to 3–10 in practical applications. 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https://openalex.org/W4283011808
https://jamane.marospub.com/index.php/journal/article/download/16/39
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Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat dan Kawasan Permukiman
Jurnal Akuntansi, Manajemen dan Ekonomi
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cc-by-sa
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Abstrak Penelitian ini didasari oleh suatu kondisi yaitu belum maksimalnya penyerapan anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara. Oleh karena itu masalah ini harus segera diatasi, salah satunya melalui penelitian untuk menemukan faktor-faktor yang mempengaruhi penyerapan anggaran ini bisa maksimal. Penelitian ini merupakan penelitian kualitatif untuk meneliti faktor-faktor yang mempengaruhi penyerapan anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara. Fokus penelitian ini adalah menjelaskan faktor- faktor yang mempengaruhi penyerapan anggaran yaitu faktor perencanaan, faktor administrasi, faktor sumber daya manusia, faktor pengadaan barang/jasa, faktor regulasi dan faktor komitmen organisasi. Sampel seluruh pegawai pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara dengan jumlah sampel sebanyak 17 orang. Metode penelitian yang digunakan yaitu riset deskriptif kualitatif yaitu riset didasarkan pada data kualitatif dalam pernyataan-pernyataan. Hasil penelitian merekomendasikan untuk lebih cepat dalam pengesahan anggaran oleh DPRD dan Pemerintah Daerah sehingga memiliki waktu untuk penyerapannya, melibatkan masing-masing SKPD dalam merencanakan anggaran sehingga tidak terdapat kegiatan penting yang terlewatkan dan perlu perhatian dari segi sarana dan prasana yang kurang memadai karena akan mempengaruhi kinerja pegawai. Kata kunci: analisis, penyerapan anggaran, dinas perumahan rakyat, kawasan permukiman JURNAL AKUNTANSI, MANAJEMEN DAN EKONOMI (JAMANE) Vol. 1, No. 1, Mei (2022),IPage 77-88 P-ISSN (2829-8888) & E-ISSN (2829-8462) Abstract This research is based on a condition that is not yet maximal budget absorption at the Department of Public Housing and Settlement Areas of North Nias Regency. Therefore, this problem must be addressed immediately, one of which is through research to find the factors that influence the maximum absorption of this budget. This research is a qualitative research to examine the factors that affect the absorption of the budget at the Department of Public Housing and Settlement Areas of North Nias Regency. The focus of this study is to explain the factors that influence budget absorption, namely planning factors, administrative factors, human resources factors, goods/services procurement factors, regulatory factors and organizational commitment factors. The sample is all employees at the Department of Public Housing and Settlement Areas of North Nias Regency with a total sample of 17 people. The research method used is descriptive qualitative research, namely research based on qualitative data in statements. The results of the study recommend that it is faster to ratify the budget by the DPRD and the Regional Government so that it has time for absorption, involve each SKPD in planning the budget so that no important activities are missed and need attention in terms of inadequate facilities and infrastructure because it will affect performance employee. Keywords: analysis, budget absorption, public housing service, residential area Submitted Accepted Published : https://doi.org/10.56248/jamane.v1i1.16 05-05-2022 27-05-2022 28-05-2022 PENDAHULUAN sehingga belanja pemerintah menjadi pendorong utama laju pertumbuhan ekonomi. Untuk kegiatan yang langsung menyentuh kepentingan masyarakat luas, semakin awal pelaksanaan kegiatan, manfaat serta efek stimulusnya juga makin besar. Jika pelaksanaannya mundur ke akhir tahun padahal seharusnya bisa dilaksanakan lebih awal, maka yang dirugikan adalah masyarakat, karena tertunda menerima manfaat. Kegagalan target penyerapan anggaran memang berakibat hilangnya manfaat belanja, karena dana yang dialokasikan ternyata tidak semuanya dapat dimanfaatkan, yang artinya terjadi idle money. Penyerapan anggaran menjadi topik menarik akhir-akhir ini. Fenomena APBN dan APBD yang kurang terserap di awal tahun, tapi di genjot penyerapannya di akhir tahun sering terjadi. Kondisi ini sering menjadi diskusi hangat di kalangan pemerintahan, masyarakat, akademisi dan media. Pengertian Noviwijaya & Rohman (2013), penyerapan anggaran yang sederhana adalah membandingkan anggaran dengan realisasinya, misalnya anggaran sebesar Rp. 100 juta terealisasi sebesar Rp. 90 juta, berarti tingkat penyerapan anggaran sebesar 90%. Fenomena yang terjadi, menjelang akhir tahun anggaran, instansi pemerintah berusaha menyerap anggaran mendekati 100%, agar tidak dinilai penyerapan anggarannya rendah. Jika ingin lebih proporsional dalam menilai penyerapan anggaran, perlu juga di lihat target penyerapan anggaran yang telah di susun di awal, apakah telah sesuai target atau tidak (Halim & Kusufi, 2016). Ukuran kinerja yang juga harus dicermati adalah capaian output serta outcome. Penyerapan anggaran yang tinggi tanpa adanya output serta outcome yang optimal akan menunjukkan kinerja yang kurang baik. Selain itu, dikemukakan juga adanya proporsionalitas persentase penyerapan anggaran, seperti banyak diberitakan di media, penyerapan anggaran cenderung menumpuk di akhir tahun, hal ini dibuktikan dengan kecenderungan persentase penyerapan anggaran pada akhir triwulan III kurang dari 75%. Bank Dunia menyebut negara-negara berkembang termasuk Indonesia punya permasalahan dalam penyerapan anggaran yang di sebut “slow back-loaded”, artinya penyerapan rendah pada awal sampai tengah tahun anggaran, namun melonjak memasuki akhir tahun anggaran (Nursahidin, 2017). j j y g g Anggaran Pendapatan Belanja Daerah (APBD) adalah rencana keuangan tahunan daerah yang di bahas dan disetujui bersama oleh Pemerintah Daerah dan DPRD dan ditetapkan dengan Peraturan Daerah (Permendagri, 2017). APBD merupakan hal yang sangat penting bagi pemerintah yang berkaitan dengan uang di mana pada saat tertentu manfaatnya bisa benar-benar dirasakan oleh masyarakat. Dalam struktur Anggaran Pendapatan Belanja Daerah (APBD) proses pengeluaran anggaran dipergunakan untuk membangun kesejahteraan pelayanan oleh pemerintah terhadap publik. Dalam kerangka penganggaran berbasis kinerja, sebenarnya penyerapan anggaran bukan merupakan satu-satunya target pengalokasian anggaran (Sudastri, 2016). Submitted 05-05-2022 Published 28-05-2022 : https://doi.org/10.56248/jamane.v1i1.16 Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat Dan Kawasan Permukiman Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 7 Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat Dan Kawasan Permukiman Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 78 METODE Jenis penelitian yang digunakan dalam penelitian ini adalah riset deskriptif kualitatif yang didasarkan pada data kualitatif yaitu berbentuk pernyataan- pernyataan (Sugiyono, 2018). Populasi dalam penelitian ini adalah pegawai pada Dinas Perumahan Rakyat dan Kawasan Permukiman sebanyak 17 orang. Jenis data yang digunakan dalam penelitian ini adalah data primer dan sekunder. Teknik pengumpulan data dengan angket, wawancara, observasi, ujian (test) dokumentasi. Teknik analisis data dengan melakukan metode deskriptif dan deduktif. PENDAHULUAN Performance based budgeting lebih menitikberatkan pada kinerja suatu kegiatan, yang di lihat adalah output dan outcome-nya (Abdurrohman & Marsus, 2017; Eton, 2019; Nugraheni, Wardayanti, & Kustono, 2016; Rakhman, 2019; Sari, Yuesti, Sudja, & Kepramareni, 2019). Hanya saja variabel dominan pendorong pertumbuhan dalam kondisi perekonomian Indonesia saat ini adalah faktor konsumsi, Dalam realisasinya masih banyak terdapat Satuan Kinerja Perangkat Daerah (SKPD) dalam Penyerapan anggarannya belum maksimal menyebabkan kurang optimalnya kinerja pemerintah. Di sisi lain penyerapan anggaran merupakan suatu hal yang vital guna mendorong proses Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 79 responden di lokasi penelitian. Untuk mendapatkan data yang dibutuhkan dari responden sesuai pertanyaan wawancara yang telah disiapkan berdasarkan faktor- faktor yang mempengaruhi penyerapan anggaran. Hasil pengamatan telah di buat dalam bentuk deskriptif. pembangunan sumber daya yang dapat membangun kinerja pemerintah secara lancar (Utomo, 2014; Zarinah, Darwanis, & Abdullah, 2016). Salah satu faktor penyebab penyerapan anggaran belum maksimal adalah dikarenakan masih terdapatnya kehati-hatian dan keraguan yang berlebihan dalam menggunakan anggaran sehingga memicu untuk terjadinya penyerapan anggaran yang belum maksimal hingga 100%. Pemerintah yang baik merupakan pemerintah yang dapat merealisasikan seluruh anggaran dengan efektif serta efisien bagi kesejahteraan masyarakat. Wawancara yang diajukan kepada responden dilakukan berdasarkan daftar pertanyaan yang telah di susun. Informasi atau data yang sama dari setiap responden tidak lagi dijelaskan satu persatu pada hasil penelitian guna mempersingkat hasil penelitian ini. Hasil yang diperoleh adalah: Berdasarkan data atau informasi yang diperoleh dari Bapak Yulius Zai, S.T., M. Eng. Sebagai Kepala Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara yang diwawancarai pada tanggal 04 September 2019 bahwa: “Penyerapan anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara telah terlaksana sampai 97 % dari program yang telah direncanakan dari awal. Penyerapan anggaran ini memang belum sepenuhnya terlaksana dari semua program, hal ini disebabkan karena keterlambatan pengesahan anggaran yang diajukan kepada DPRD dan Pemerintahan Daerah. Selain itu munculnya kehati-hatian kepada seluruh SKPD terkait dalam menyerapkan anggaran akibat waktu yang sangat singkat dalam penyerapan anggaran itu sendiri. Namun, anggaran yang tidak terserap pada tahun anggaran tersebut akan dijadikan silva untuk dimanfaatkan pada tahun kedepannya. Lebih lanjut beliau mengatakan bahwa akibat dari kurangnya penyerapan anggaran ini yaitu kegiatan tidak sesuai dengan target, sehingga output berkurang”. Hasil Dalam penelitian ini metode yang digunakan adalah metode deskriptif, di mana metode deskriptif adalah cara pengumpulan data dan penyajian data sehingga mudah dipahami”. Metode deskriptif hanya berhubungan dengan hal menguraikan atau memberikan keterangan- keterangan mengenai suatu data atau keadaan. Dengan metode deskriptif dapat menerangkan keadaan, gejala atau persoalan. Dalam mengelola keuangan daerah Rencana Kerja dan Anggaran disahkan terlebih dahulu menjadi jadi Dokumen Pelaksanaan Anggaran baru bisa dilakukan pelaksanaan anggaran. Pelaksanaan anggaran adalah salah satu kegiatan melalui Data deskriptif dalam penelitian ini diperoleh secara langsung melalui pengamatan dan wawancara kepada Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat Dan Kawasan Permukiman Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 80 sebuah rencana yang di tata secara matang dan terperinci. Menurut Thomas (2018) mengemukakan bahwa apabila rencana anggaran sudah dilaksanakan dengan baik maka pelakasanaan anggaranpun ikut tercapai. Manajemen Daerah sebagai kegiatan untuk mendukung capaian indikator-indikator kinerja meningkatkan tingkat opini BPK terhadap LKPD. Adapun tujuan pengembangan Program Aplikasi Sistem Informasi Manajemen Daerah ini yaitu : Adapun tujuan pengembangan Program Aplikasi Sistem Informasi Manajemen Daerah ini yaitu : Lebih lanjut beliau menjelaskan mengenai proses administrasi yang diterapkan pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara yaitu proses administrasi yang digunakan sudah berbasis tekonologi yaitu dengan menggunakan aplikasi sistem informasi manajemen daerah sehingga betul-betul membantu dalam pengelolaan keuangan daerah secara terintegrasi yang meliputi penganggaran, penatausahaan, akuntasi dan pelaporan. a. Menyediakan database mengenai kondisi di daerah yang terpadu baik dari aspek keuangan, aset daerah, kepegawaian atau aparatur daerah maupun pelayanan publik yang dapat digunakan untuk penilaian kinerja instansi pemerintah daerah (Laia, Halawa, & Lahagu, 2022). b. Menghasilkan informasi yang komprehensif, tepat dan akurat kepada manajemen pemerintah daerah. Informasi ini dapat digunakan sebagai bahan mengambil keputusan. p p Dari penjelasan di atas terkait dengan aplikasi yang digunakan pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara sesuai dengan VISI BPKP sebagai Auditor Presiden yang responsif, interaktif dan terpercaya untuk memujudkan akuntabilitas keuangan negara yang berkualitas dalam mentransformasikan manajemen pemerintah menuju pemerintahan yang baik dan bersih serta sesuai amanat PP 60 tahun 2008 pasal 59 ayai (2) dan Inpres Nomor 4 Tahun 2011, BPKP dalam hal ini Deputi Pengawasan Bidang Penyelenggaraan Keuangan Daerah memandang perlu untuk memfasilitasi pemerintah daerah dalam mempersiapkan aparatnya menghadapi perubahan, mendorong pelaksanaan tata kelola keuangan daerah sesuai dengan peraturan yang berlaku, efisien, efektif, transparan, akuntabel dan auditabel. Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 81 tidak sesuai dengan rencana kegiatan”. Berdasarkan penjelasan di atas dapat disimpulkan bahwa aturan yang diterapkan berdasarkan dari Undang-Undang yang berlaku pada Pemerintahan Kabupaten Nias Utara. dengan defenisi penempatan kerja menurut Danang (2012), penempatan kerja merupakan proses atau pengisian jabatan atau penugasan kembali pegawai pada tugas atau jabatan baru atau jabatan yang berbeda. Hasil wawancara selanjutnya terkait akibat dari penyerapan anggaran yang tidak tercapai pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara, Beliau menjelaskan bahwa “penyerapan anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara memang belum terealisasi seratus persen, ini disebabkan karena keterlambatan persetujuan anggaran dari pihak terkait sehingga waktu yang dibutuhkan untuk merealisasikannya kurang, hal ini mengakibatkan pelayanan yang diberikan kepada masyarakat kurang maksimal, akan tetapi angggaran yang belum terealisasi tersebut akan dijadikan silva untuk dilanjutkan pengerjaannya pada tahun mendatang”. Untuk pertanyaan selanjutnya mengenai realisasi anggaran pengadaan barang dan jasa pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara, bahwa realisasi anggaran terkait pengadaan barang dan jasa pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara sudah dilaksanakan dengan sebaik mungkin, karena hal ini penting dalam menunjang pekerjaan pada Dinas ini. Berdasarkan penjelasan di atas dapat disimpulkan bahwa pengadaan barang dan jasa telah dilaksanakan sesuai dengan rencana yang telah ditetapkan sebelumnya sehingga mempengaruhi daripada kinerja pegawai pada dinas perumahan rakyat dan kawasan permukiman Kabupaten Nias Utara. Selanjutnya terkait pertanyaan wawancara mengenai pegawai dalam bekerja, Beliau menjelaskan bahwa “pegawai yang ada pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara betah dan senang bekerja, hal ini dapat dilihat dari tingkat kehadiran pegawai yang cukup bagus dan hasil pelaksanaan kegiatan yang sudah direncanakan sudah maksimal”. Berdasarkan paparan di atas dapat dijelaskan bahwa realisasi anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara belum terealisasi sepenuhnya namun tetap berupaya untuk merealisasikan pada tahun yang akan datang. 2. Menurut Pendapat Riman K. Harefa, S.AP., M. AP sebagai Kepala Bidang Pertanahan Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara yang diwawancarai pada hari yang sama yaitu pada tanggal 04 September 2019, dari pertanyaan yang diajukan dapat diketahui bahwa sejalan dengan apa yang disampaikan oleh Kepala Dinas Perumahan Rakyat Kabupaten Nias Utara tentang ketercapaian penyerapan anggaran yang belum maksimal. Namun beliau menyarankan kepada pihak terkait dalam hal ini DPRD dan Pemerintah Daerah agar persetujuan anggaran yang diajukan 2. Menurut Pendapat Riman K. Harefa, S.AP., M. Hasil Hal ini penting guna meningkatkan kualitas Laporan Keuangan pemerintah daerah menuju terwujudnya good govermance. c. Mempersiapkan aparat daerah untuk mencapai tingkat penguasaan dan pendayagunaan teknologi informasi yang lebih baik. d. Memperkuat basis pemerintah daerah dalam melaksanakan otonomi daerah. Kemudian terkait penetapan pegawai pada bidang pekerjaan, beliau mengatakan bahwa “Pegawai yang ada pada Dinas Perumahan Rakyat dan Kawasan Permukiman pada umumnya sudah ditempatkan sesuai dengan kemampuannya meskipun ada sebagian yang tidak sesuai, hal ini disebabkan karena keputusan mutlak penempatan pegawai ditetapkan oleh Bupati. Namun berdasarkan kualifikasi pendidikan yang layak, semua pegawai mampu beradaptasi dengan bidang pekerjaan masing-masing sehingga sejauh ini sedikit pekerjaan yang tertunda pengerjaannya. Berdasarkan pendapat di atas dapat disimpulkan bahwa pegawai pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara sudah ditempatkan pada bidang pekerjaan sesuai dengan kualifikasi dan keterampilan yang dimiliki oleh para pegawai. Hal ini sejalan Selanjunnya penjelasan di atas sejalan dengan RPJM Tahun 2010-2014 dalam Renstra tahun 2010-2014, Deputi Pengawasan Bidang Penyelenggaraan Keuangan Daerah yang telah menetapkan Pengembangan Sistem Informasi Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 81 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 81 AP sebagai Kepala Bidang Pertanahan Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara yang diwawancarai pada hari yang sama yaitu pada tanggal 04 September 2019, dari pertanyaan yang diajukan dapat diketahui bahwa sejalan dengan apa yang disampaikan oleh Kepala Dinas Perumahan Rakyat Kabupaten Nias Utara tentang ketercapaian penyerapan anggaran yang belum maksimal. Namun beliau menyarankan kepada pihak terkait dalam hal ini DPRD dan Pemerintah Daerah agar persetujuan anggaran yang diajukan Berdasarkan penjelasan di atas dapat disimpulkan bahwa pegawai yang ada pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara betah dan senang bekerja pada dinas tersebut. Selanjutnya hasil wawancara terkait pertanyaan mengenai peraturan yang diterapkan, Beliau menjelaskan bahwa “dalam melaksanakan program kerja sudah direncanakan pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara dilaksanakan sesuai dengan Undang-undang yang berlaku, hal ini dilakukan untuk menghindari temuan- temuan BPK terkait program kerja yang Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat Dan Kawasan Permukiman Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 82 oleh masing-masing SKPD untuk segera disetujui pada awal tahun sehingga memberikan waktu yang cukup panjang bagi masing-masing SKPD dalam penyerapan anggaran dimaksud. permukiman bahwa “penyerapan anggaran khusus bidang ini sudah dilaksanakan sesuai rencana anggaran yang ada, kita kan fokus pada pembangunan rumah tak layak huni dan kita sudah melakukannya berdasarkan data yang diperoleh dari masing-masing desa dan teah dilakukan survei langsung ke lapangan untuk melihat kelayakannya”. Terkait dengan akibat penyerapan anggaran yang tidak tercapai, beliau menjelaskan bahwa “memang hal ini bukan suatu hal yang baru karena hampir setiap tahunnya anggaran yang ada tidak mampu direalisasikan pada tahun tersebut, ini dikarenakan perencanaan anggaran yang sangat lamban dan persetujuan anggaran yang lama dari DPRD dan Pemerintahaan Daerah, kita sudah berusaha untuk merealiasasikannya, namun waktunya kurang dan kita pun perlu hati-hati dalam merealisasikannya”. Berdasarkan penjelasan di atas dapat disimpulkan bahwa penyerepan anggaran khusus bidang perumahan rakyat dan kawasan permukiman telah direalisasikan sesuai dengan rencana kegiatan yang ada. Terkait pertanyaan wawancara selanjutnya, penjelasan beliau serupa dengan penjelasan responden yang telah dijelaskan sebelumya, sehinggan pada bagian ini tidak lagi mengulangi penjelasan dari hasil wawancara tersebut. Berdasarkan pendapat di atas dapat disimpulkan bahwa penyerapan anggaran yang tidak tercapai pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara disebabkan karena keterlambatan perencanaan anggaran dan persetujuan angggaran dari DPRD dan Pemerintahan Daerah. Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 83 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 83 dan Pelaporan pada tanggal 04 September 2019, mengemukakan “bahwa “pegawai yang ada pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara rata- rata sudah sarjana bahkan ada beberapa yang sudah strata dua, mengenai kesesuaian pegawai pada posisi/jabatan dengan keahlian masing-masing sudah sesuai, berbicara masalah kualitas pegawai untuk masing-masing bidang kerja, para pegawai sudah tidak diragukan lagi, hal ini disebabkan karena pegawai terus melakukan pelatihan terkait pekerjaan di bidang masing- masing” akan mempengaruhi daripada kinerja pegawai itu sendiri. Di mana kinerja pegawai merupakan suatu hasil yang dicapai oleh pegawai tersebut dalam pekerjaanya menurut kriteria tertentu yang berlaku untuk suatu pekerjaan tertentu (Baharuddin et al., 2022; Laoli & Ndraha, 2022; Sarumaha, 2022; Wau, 2022; Zebua, 2022; Zega, 2022). Hasil wawancara terkait daftar pertanyaan yang telah disiapkan dan belum termuat pada penjelasan ini, disebabkan karena penjelasannya sama dari penjelasan responden sebelumnya. 5. Berdasarkan hasil wawancara kepada Bapak Syukur R. Telaumbanua, S.T. sebagai Kepala Seksi Peralatan Teknis mengemukakan bahwa “realisasi aggaran barang dan jasa pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara sudah sesuai, namun terdapat sedikit kendala yaitu kurangnya perencanaan anggaran dari barang dan jasa tersebut sehingga setiap tahunnya daerah memiliki utang kepada pihak yang menyediakan barang dan jasa. Ianya berharap kepada Pemerintah Daerah supaya dalam perencanaan anggaran tersebut perlu pengkajian akan kebutuhan selama satu tahun” 7. Hasil wawancara kepada Muhammad Hanafi, salah seorang staf pegawai pada Dinas Perumahan Rakyat Kabupaten Nias Utara pada hari yang sama yaitu tanggal 04 September 2019 mengatakan bahwa “peraturan yang diterapkan pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara telah dilaksanakan, hanya saja regulasi dari yang tidak sempurna sehingga beberapa program yang sudah direncanakan namun program tersebut tidak layak atau kurang bermanfaat dialihkan dengan kegiatan yang lain yang lebih dibutuhkan pada saat itu”. 7. Hasil wawancara kepada Muhammad Hanafi, salah seorang staf pegawai pada Dinas Perumahan Rakyat Kabupaten Nias Utara pada hari yang sama yaitu tanggal 04 September 2019 mengatakan bahwa “peraturan yang diterapkan pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara telah dilaksanakan, hanya saja regulasi dari yang tidak sempurna sehingga beberapa program yang sudah direncanakan namun program tersebut tidak layak atau kurang bermanfaat dialihkan dengan kegiatan yang lain yang lebih dibutuhkan pada saat itu”. Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 81 Beliau menambahkan lagi bahwa “proses administrasi yang dilakukan pada Dinas Perumahan Rakyat dan Kawasan Permukiman khususnya pada Bidang Pertanahan telah dilaksanakan sesuai dengan aturan yang berlakuk”. 4. Wawancara kepada Bapak Fransiscus N. Telaumbanua, S.T. M.M. sebagai Kepala Seksi Sertifikat Tanah Bidang Pertanahan mengemukan hal yang sama seputar penyerapan anggaran, akibat dan proses administrasi. Mengenai proses administrasi yang dilakukan pada Dinas Perumahan Rakyat dan Kawasan permukiman lebih khusus pada bidang sertifikat tanah, beliau menjelaskan bahwa “proses administrasi pada bidang ini menggunakan aplikasi yaitu SIMDA jadi kita tinggal menginput data, aplikasi ini sangat membantu pekerjaan pegawai khususnya dalam pembuatan administrasi”. 3. Selanjutnya wawancara kepada Bapak Kristian F Harefa, ST. M.M. sebagai Kepala Bidang Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara mengemukakan bahwa “dalam melakukan aktivitas pengelolaan administrasi sudah menggunakan aplikasi Sistem Informasi Manajemen Keuangan Daerah (SIMDA) sehingga memudahkan dalam penyampaian laporan pertanggung jawaban setiap akhir tahun”. Mengenai kenyamanan pegawai dalam bekerja, beliau mengatakan bahwa pegawai yang bekerja pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara sudah cukup bagus dan betah bekerja di kantor walaupun sarana kantor yang masih belum memadai jika di lihat dari kapasitas ruangan yang masih sempit. Beliau menambahkan, besar harapan pihak pemerintah lebih memperhatikan juga hal ini karena jelas Selanjutnya Beliau menjelaskan terkait penyerapan anggaran khusus bidang perumahan rakyat dan kawasan Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 83 Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat Dan Kawasan Permukiman Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 8 Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat Dan Kawasan Permukiman Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 8 84 penjelasan responden sebelumnya, namun beliau menyarankan terkait penyerapan anggaran yaitu “kita dalam menyerapkan anggaran tentu sesuai dengan perencanaan yang ada, jadi agar penyerapan anggaran bisa terealisasi semaksimal mungkin setiap tahunnya diharapkan perencanaan dan persetujuan anggaran tersebut sudah selesai awal tahun sehingga memberikan waktu yang panjang dari masing-masing satuan kerja untuk mengeksekusinya dan terhindar dari kehati-hatian karena memberikan waktu yang banyak untuk mengevaluasi pekerjaan tersebut”. Kemudian terhadap penyesuaian atau revisi mata kegiatan membutuhkan revisi DIPA yang menyebabkan satuan kerja harus bolak balik dalam ketidakpastian kapan anggaran yang di blokir harus di buka. Termasuk lamanya birokrasi di DJA dalam revisi anggaran menyebabkan sebuah kegiatan harus menunggu anggaran blokir dibuka. Berdasarkan penjelasan di atas dapat disimpulkan bahwa keterlambatan penyerapan anggaran juga disebabkan oleh Direktoral Jenderal Anggaran dalam merevisi anggaran sehingga satuan kerja harus menunggu lama dalam mengeksekusi kegiatan tersebut. Dari penjelasan di atas dapat disimpulkan bahwa agar penyerapan anggaran masing-masing satuan kerja dapat terlaksana dengan maksimal maka perlu kerjasama yang baik dari pihak pemerintah daerah dalam mempercepat perencanaan dan persetujuan anggaran. 9. Berdasarkan hasil wawancara kepada Bapak Temazaro Hulu, S.E. dapat disimpulkan bahwa dari daftar pertanyaan yang di ajukan sejalan dengan penjelasan responden sebelumnya, namun beliau lebih menekankan pada betah tidaknya pegawai dalam bekerja. Beliau menjelaskan bahwa “pada umumnya pegawai sudah merasa nyaman bekerja pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara, namun perlu juga perhatian pemerintah terkait sarana yang digunakan pada Dinas ini, dimana ruangan kerja yang digunakan masih terlihat sempit sehingga mempengaruhi kepuasan pegawai dalam bekerja”. 9. Berdasarkan hasil wawancara kepada Bapak Temazaro Hulu, S.E. dapat disimpulkan bahwa dari daftar pertanyaan yang di ajukan sejalan dengan penjelasan responden sebelumnya, namun beliau lebih menekankan pada betah tidaknya pegawai dalam bekerja. Beliau menjelaskan bahwa “pada umumnya pegawai sudah merasa nyaman bekerja pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara, namun perlu juga perhatian pemerintah terkait sarana yang digunakan pada Dinas ini, dimana ruangan kerja yang digunakan masih terlihat sempit sehingga mempengaruhi kepuasan pegawai dalam bekerja”. 1.Berdasarkan hasil wawancara kepada Bapak Aferli Hulu, S.E. sebagai Kepala Sub Bagian Umum dan Keuangan sesuai dengan daftar pertanyaan yang telah disiapkan, juga menjelaskan sesuai dengan hasil wawancara kepada responden sebelumnya, namun beliau lebih menekankan pada akibat dari penyerapan anggaran yang tidak tercapai. Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 83 Guna mempercepat proses penyerapan anggaran yang berdampak pada mekanisme pembayaran perlu pengadaan barang dan jasa yang efektif dan efisien. Kesalahan sasaran penyerapan anggaran mengenai pengadaan barang dan jasa mengakibatkan kurangnya manfaat belanja sebab dana yang telah direncakan sebagian kecil tidak dapat dimanfaatkan. Menurut Alumbida, Saerang & Ilat (2016) mengemukakan bahwa “realisasi atas pembayaran kegiatan adalah serapan anggaran”. 8. Selanjutnya hasil wawancara kepada Rasidi Ziliwu, S.T. sejalan dengan hasil wawancara kepada responden sebelunya, namun beliau lebih menekankan pada penyebab keterlambatan anggaran, Beliau menjelaskan bahwa “realitasnya di lapangan bahwa ada hal-hal yang sifatnya teknis implementatif penyebebab rendahnya penyerapan APBN yaitu adanya oknum DJA yang meminta jatah anggaran sehingga menyebabkan satuan kerja enggan untuk mengeksekusi kegiatan dan terkadang posisi satuan kerja seperti pengemis anggaran di DJA”. 6. Berdasarkan hasil wawancara kepada Bapak Irvan Hutagalung, S.T. sebagai Kepala Sub Bagian Program, Evaluasi 6. Berdasarkan hasil wawancara kepada Bapak Irvan Hutagalung, S.T. sebagai Kepala Sub Bagian Program, Evaluasi Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 85 12.Berdasarkan hasil wawancara kepada Arimby Samosir sebagai Staf pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara dapat disimpulkan bahwa dari pertanyaan yang telah di susun juga memberikan penjelasan yang sama dari penjelasan responden sebelumnya. Beliau menyarankan “dalam perencanaan anggaran perlu melibatkan setiap satuan kerja terlebih dalam merencanakan kegiatan-kegiatan setiap tahunnya, berdasarkan pengalaman masih terdapat rangkaian kegiatan yang tidak sesuai untuk dilaksanakan sedangkan kegiatan-kegiatan penting diabaikan, sehingga terkadang satuan kerja mengalihkan rangkaian kegiatan yang tidak sesuai tersebut pada kegiatan yang penting, tentu hal ini berpengaruh pada hasil yang dicapai yang tidak maksimal karena kurangnya perencanaan”. 12.Berdasarkan hasil wawancara kepada Arimby Samosir sebagai Staf pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara dapat disimpulkan bahwa dari pertanyaan yang telah di susun juga memberikan penjelasan yang sama dari penjelasan responden sebelumnya. Beliau menyarankan “dalam perencanaan anggaran perlu melibatkan setiap satuan kerja terlebih dalam merencanakan kegiatan-kegiatan setiap tahunnya, berdasarkan pengalaman masih terdapat rangkaian kegiatan yang tidak sesuai untuk dilaksanakan sedangkan kegiatan-kegiatan penting diabaikan, sehingga terkadang satuan kerja mengalihkan rangkaian kegiatan yang tidak sesuai tersebut pada kegiatan yang penting, tentu hal ini berpengaruh pada hasil yang dicapai yang tidak maksimal karena kurangnya perencanaan”. 15.Berdasarkan hasil wawancara kepada Saudari Ellen Agustina Gea, sebagai staf pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara dari daftar pertanyaan yang telah disiapkan juga memberikan penjelasan yang sama. 16.Agustina Gulo dan Hermasyah Gea pada tanggal 04 September 2019 juga menyampaikan hal yang sama seperti yang sudah dijelaskan di atas terkait daftar pertanyaan yang sudah disiapkan, intinya penyerapan anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara sudah berjalan namun belum maksimal yang diakibatkan oleh keterlambatan persetujuan anggaran dari DPRD dan Pemerintah Daerah, perencanaan kegiatan yang tidak maksimal dan belum termuat dalam anggaran sehingga terdapat kegiatan yang dialihkan penyerapannya pada kegiatan lain yang lebih dibutuhkan. 16.Agustina Gulo dan Hermasyah Gea pada tanggal 04 September 2019 juga menyampaikan hal yang sama seperti yang sudah dijelaskan di atas terkait daftar pertanyaan yang sudah disiapkan, intinya penyerapan anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara sudah berjalan namun belum maksimal yang diakibatkan oleh keterlambatan persetujuan anggaran dari DPRD dan Pemerintah Daerah, perencanaan kegiatan yang tidak maksimal dan belum termuat dalam anggaran sehingga terdapat kegiatan yang dialihkan penyerapannya pada kegiatan lain yang lebih dibutuhkan. Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 85 13.Berdasarkan hasil wawancaran kepada Amenesi Telaumbanua sebagai staff pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara dapat disimpulkan bahwa penjelasan dari daftar pertanyaan yang telah disiapakn masih sejalan dengan penjelasan responden sebelumnya. Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat Dan Kawasan Permukiman Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 8 Ianya menjelaskan bahwa “akibat penyerapan anggaran yang tidak maksimal pada tahun ini berpengaruh terhadap kinerja pegawai yang kurang maksimal juga output kepada masyarakat tidak berhasil sehingga menimbulkan perasaan kurang senang dari masyarakat karena pelayanan yang tidak baik dari kami pegawai, walaupun pada dasarnya hal ini semata-mata bukan sepenuhnya kesalahan kami sebagai pegawai tetapi lebih kepada keterlambatan pengesahan anggaran dari pemerintah daerah, kami kan cuma menjalankan rangkaian program yang telah direncanakan”. Berdasarkan penjelasan di atas dapat disimpulkan bahwa pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara perlu perhatian pemerintah khususnya pada ruang kerja yang masih sempit sehingga para pegawai sedikit terganggu dalam melaksanakan aktivitasnya. 10.Berdasarkan hasil wawancara kepada Imansyah Lase, S.H. dapat disimpulkan dari daftar pertanyaan yang telah disiapkan bahwa sejalan juga dengan Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 85 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 85 Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa anggaran oleh DPRD dan Pemerintah Daerah. penyediaan barang dan jasa telah terlaksana dengan baik, pegawai merasa nyaman dan betah bekerja di kantor, dan peraturan yang ada pada Dinas Perkim tetap dipatuhi dan dijalankan, serta penyerapan anggaran yang tidak tercapai mengakibatkan kegiatan tidak sesuai target dan output berkurang. 2. Pegawai dalam bekerja sudah merasa aman namun perlu perhatian mengenai sarana yang masih sempit dan kurang layak. 3. Penyediaan barang dan jasa sudah terlaksana dengan baik dan membantu para pegawai dalam melaksanakan kegiatannya. Namun terdapat hal yang perlu dievaluasi terkait penyediaan barang dan jasa yaitu kurangnya perencanaan anggaran dari setiap kegiatan sehingga setiap tahunnya masih ada utang daerah untuk memenuhi kekurangan tersebut. DAFTAR PUSTAKA Abdurrohman, A., & Marsus, S. (2017). Factor Analysis for Slow Budget Realization. International Journal of Innovation and Economic Development, 3(1), 28-50. https://doi.org/10.18775/ijied.1849- 7551-7020.2015.31.2002 4. Terkait dengan aturan yang pada Dinas telah dilaksanakan sesuai Perbup yang ditetapkan oleh Pemerintah Daerah. Alumbida, D. I., Saerang, D. P. E., & Ilat, V. (2016). Pengaruh Perencanaan, Kapasitas Sumber Daya Manusia Dan Komitmen Organisasi Terhadap Penyerapan Anggaran Belanja Daerah Pada Pemerintah Kabupaten Kepulauan Talaud. Jurnal Accountability, 5(2), 141-151. https://doi.org/10.32400/ja.14431.5.2. 2016.141-151 5. Akibat dari penyerapan anggaran yang tidak maksimal yaitu kegiatan tidak sesuai dengan target yang telah direncanakan dan kurangnya output yang diberikan kepada masyarakat. 6. Proses administrasi pada Dinas Perumahan Rakyat dan Kawasan Permukiman sudah cukup bagus karena sudah manggunakan aplikasi sehingga mempercepat penyelesaian pekerjaan. Baharuddin, A. A., Musa, M. I., & Burhanuddin. (2022). Pengaruh Motivasi Dan Kompetensi Kerja Terhadap Prestasi Kerja Karyawan Sales. Jurnal Akuntansi, Manajemen Dan Ekonomi, 1(1), 55–62. https://doi.org/10.56248/jamane.v1i1. 13 Sejalan dengan Tiganasu et al. (2018), menunjukkan bahwa kualitas kelembagaan dan kinerja manajemen memiliki pengaruh positif terhadap tingkat penyerapan dana struktural dan telah berhasil mendukung pembangunan ekonomi. Sedangkan Thomas (2018), menunjukkan proses penganggaran, kompetensi pegawai, kapasitas sektor swasta dan bantuan dana berpengaruh positif dan signifikan terhadap penyerapan anggaran. Danang, Sunyoto. (2012) Manajemen Sumber Daya Manusia. Jakarta: PT. Buku. Eton, M. (2019). Internal Control and Budget Implementation in Kabale District Uganda. International Journal of Science and Research (IJSR), 8(1), 815-821. Pembahasan Berdasarkan data yang telah dijelaskan di atas dan sekaligus membandingkan dengan landasan teori dibuat dalam bentuk data deduktif yang membahas tentang bagaimana menerangkan sekumpulan data dalam bentuk toeri yang tulisan yang mudah dibaca dan cepat memberikan informasi kepada pembaca, sehingga yang menjadi data deduktif pada penelitian ini adalah untuk mengetahui faktor-faktor yang mempengaruhi Penyerapan Anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara, sehingga dari informasi yang telah didapatkan dapat disimpulkan yaitu: 14.Berdasarkan hasil wawancaran kepada Saudari Fertin Sri Juinta Gea, SE. sebagai staf pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara terkait dengan keberadaan pegawai. Ianya menjelaskan bahwa “kami pegawai merasa senang bekerja di kantor, adanya komunikasi yang baik antara pegawai sehingga para pegawai betah dan senang dalam melaksanakan pekerjaan”. Dari penjelasan tersebut dapat disimpulkan bahwa pegawai betah dan senang bekerja pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara. 14.Berdasarkan hasil wawancaran kepada Saudari Fertin Sri Juinta Gea, SE. sebagai staf pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara terkait dengan keberadaan pegawai. Ianya menjelaskan bahwa “kami pegawai merasa senang bekerja di kantor, adanya komunikasi yang baik antara pegawai sehingga para pegawai betah dan senang dalam melaksanakan pekerjaan”. Dari penjelasan tersebut dapat disimpulkan bahwa pegawai betah dan senang bekerja pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara. 1. Penyerapan anggaran pada Dinas Perumahan Rakyat dan Kawasan Permukiman Kabupaten Nias Utara sudah terlaksana namun belum maksimal, hal ini disebabkan karena keterlambatan persetujuan rencana Analisis Faktor-Faktor Yang Mempengaruhi Penyerapan Anggaran Pada Dinas Perumahan Rakyat Dan Kawasan Permukiman 86 KESIMPULAN Supaya penyerapan anggaran terlaksana dengan baik maka perlu perencanaan anggaran yang tepat dan persetujuan yang cepat dari DPRD dan Pemerintah Daerah. Realisasi anggaran Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 87 Copyright © 2022 Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) P-ISSN (2829-8888) & E-ISSN (2829-8462) Jurnal Akuntansi, Manajemen Dan Ekonomi (Jamane) 1 (1), Mei 2022 - Jeliswan Berkat Iman Jaya Gea, Odaligoziduhu Halawa 87 Halim, A., & Kusufi, S. (2016). Teori, Konsep, dan Aplikasi Akuntansi Sektor Publik dari Anggaran hingga Laporan Keuangan, dari Pemerintah hingga Tempat Ibadah. (Salemba Empat, Ed.) (2nd ed.). Jakarta: Salemba Empat. Peraturan Menteri Dalam Negeri Nomor 33 (2017). Tentang Pedoman. Penyusunan Anggaran dan Belanja Daerah. Rakhman, F. (2019). Budget Implementation In A Risky Environment: Evidence From The Indonesian Public Sector. Asian Review of Accounting, 27 (2), 162- 176. https://doi.org/10.1108/ARA-01- 2018-0020 Laia, O., Halawa, O., & Lahagu, P. (2022). Pengaruh Sistem Informasi Manajemen Terhadap Pelayanan Publik. Jurnal Akuntansi, Manajemen Dan Ekonomi, 1(1), 70–76. https://doi.org/10.56248/jamane.v1i1. 15 Sari, L. G. E., Yuesti, A., Sudja, I. N., Kepramareni, P. (2019). Analysis of Budget Planning, Competence of Human Resources and Implementation of the Viii Lldikti Region Budget with Organizational Commitment as A Moderation. International Journal of Contemporary Research and Review, 10(2), 21273-21288. https://doi.org/10.15520/ijcrr.v10i02. 655 Laoli, E. S., & Ndraha, T. P. (2022). Pengaruh Sistem Pengendalian Manajemen Terhadap Kinerja Pegawai. Jurnal Akuntansi, Manajemen Dan Ekonomi, 1(1), 15– 20. https://doi.org/10.56248/jamane.v1i1. 8 Noviwijaya., A. & Rohman., A. (2013). Pengaruh Keragaman Gender dan Usia Pejabat Perbendaharaan Terhadap Penyerapan Anggaran Satuan Kerja (Studi Empiris pada Satuan Kerja Lingkup Pembayaran KPPN Semarang I). Diponegoro Journal of Accounting, 2(3), 1-12. Sudastri, D. (2016). Pengaruh Perencanaan Anggaran dan Kompetensi Sumber Daya Manusia Terhadap Penyerapan Anggaran. Jurnal Akuntansi, 4(1), 1– 22. Sugiyono. (2018). Metode Penelitian Kuantitatif, Kualitatig, dan R&D. Alfabeta: Bandung. Nugraheni, P. P. A., Wardayanti, S. M., & Kustono, A. S. (2016). The Effect of Organizational Commitments, Understanding of Management, External Pressure and Human Resources on Budgeting Absorption and Performance at Financial and Asset Management Board District Jember. International Journal of Science and Research (IJSR), 7(12), 1510-1515. Sarumaha, W. (2022). Pengaruh Budaya Organisasi dan Kompetensi Terhadap Kinerja Pegawai. Jurnal Akuntansi, Manajemen Dan Ekonomi, 1(1), 28– 36. https://doi.org/10.56248/jamane.v1i1. 10 Tiganasu, R., Incalțarau, C., & Pascariu, G. C. (2018). Administrative capacity, structural funds absorption and development. Evidence from central and eastern European Countries. Nursahidin. (2017). Problem Penyebab Rendahnya Penyerapan Anggaran Di Daerah. Jurnal Publika, 5 (1), 60-71. 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Proposing a Supply Chain Collaboration Framework for Synchronous Flow Implementation in the Automotive Industry: A Moroccan Case Study
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information Article Proposing a Supply Chain Collaboration Framework for Synchronous Flow Implementation in the Automotive Industry: A Moroccan Case Study Imane Ibn El Farouk 1 , Imane Moufad 2 , Youness Frichi 2, * , Jabir Arif 2,3 1 2 3 * and Fouad Jawab 2 Laboratory of Studies and Research in Economics and Management, Chouaib Doukalli University, El Jadida 24000, Morocco; imane-ibn-el-farouk@outlook.com Laboratory of Technologies and Industrial Services, High School of Technology, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco; imane.moufad@usmba.ac.ma (I.M.); jabir.arif@usmba.ac.ma (J.A.); fouad.jawab@usmba.ac.ma (F.J.) Laboratory of Modeling and Optimization of Industrial Systems, National School of Applied Sciences, Tetouan 93040, Morocco Correspondence: youness.frichi@usmba.ac.ma; Tel.:+212-670144244 Received: 30 July 2020; Accepted: 2 September 2020; Published: 7 September 2020   Abstract: The present paper reports on studying synchronous flow implementation, as a lean supply chain tools, through a collaborative relationship with suppliers. This involves consolidating with a new contribution to the development and application of a supply chain collaboration framework between automotive constructor and first-tier equipment suppliers to achieve the synchronous flow of components. The objective is to provide the automotive companies with a decision-making tool for selecting strategic suppliers to collaborate with, examining the collaboration context in terms of motivators, drivers, and barriers and evaluating the collaboration performance. Therefore, our contribution is structured as follows. As a first step, an overview of papers reporting on collaboration, lean supply chain, and synchronous flow is provided to identify the key elements of successful collaboration relationships. As a result, a preliminary framework is elaborated. The second step described the case study of a leading automotive firm “RENAULT” and its suppliers in Morocco. Based on semi-structured interviews conducted with participants from these companies, the preliminary framework was improved. The next section discusses the obtained results as well as the improved framework. Finally, conclusions and suggestions for further works are included. Keywords: lean supply chain; supply chain collaboration; synchronous flow; framework; Morocco 1. Introduction The automotive industry is becoming increasingly competitive due to, among others, the evolving nature of the products, the variety of models, and customer requirements. The tough competitiveness has pushed automotive manufacturers to revisit various established strategies and reassess their viability under the lean lens [1]. The implementation of lean practices aims at eliminating wastes and reducing inventory costs [2]. Lean tools applied in the automotive industry include, but are not limited to, cellular manufacturing, 5S, total productive maintenance, work standardization, quality management, visual control, statistical processes control, pull production, long-term relationships with suppliers, and synchronous flow [1]. Particularly synchronous flow in the automotive industry has gained importance with the increasing complexity and diversity of components and sub-assemblies that suppliers deliver to their contractors. The sequence of arrival of the spare parts on the assembly line must be perfectly synchronized to allow a coherent, efficient, and effective assembly. The synchronous flow approach implies absolute respect of the requisition time—i.e., the manufacturer’s advance Information 2020, 11, 431; doi:10.3390/info11090431 www.mdpi.com/journal/information Information 2020, 11, 431 2 of 24 notice to its suppliers so that they can manufacture the planned spare parts, in the right sequence, at the right time and with the correct quantity. The whole vehicle assembly relies on the timely delivery of components. Sequential Just In Time (JIT) makes it necessary for suppliers to transport customer-ordered components in the same sequence and synchronized with the final assembly process [3]. Synchronous flow is qualified as a high JIT supply strategy and requires a robust logistical organization. It takes the JIT approach to the extreme. Numerous studies have shown the benefits of implementing lean practices in the automotive industry [1]. However, for a company, being lean is not sufficient to gain full competitive advantages, the company’s suppliers are also required to pursue a lean strategy for better performance [4]. Hence, lean tools and practices must be extended down through the supply chain to achieve a lean supply chain [5]. It focuses on continuous improvement through the elimination of non-added-value activities along the supply chain [4]. Thus, the lean methods, which are extensively applied in the automotive industry, need to be extended to the auto-component suppliers so that the whole supply chain becomes lean [1]. For that purpose, several authors have identified the collaboration with suppliers as the main factor for the successful implementation of lean tools and practices among the supply chain [6,7]. In this paper, the aim is to study the possibility of implementing synchronous flow, as a lean supply chain tool, via the collaboration with suppliers. To this end, a framework of supply chain collaboration is established in the automotive industry for implementing the synchronous flow approach. The purpose of this framework is to provide the automotive firms with a decision-making tool for, first, selecting strategic suppliers to collaborate with; second, examining the collaboration environment in terms of key drivers and barriers; third, assessing the collaboration performance regarding the synchronous flow approach. Seeking competitive advantages, most of the leading automotive firms relocate to emerging markets such as Morocco due to the governments’ overall low cost of manufacturing and incentive measures. For instance, the Moroccan government has structured the automotive industry sector around industrial ecosystems that group together industry leaders and small and medium-sized enterprises (SMEs) in industrial areas. The objective is to create genuine technological fields around targeted collaboration, leading to long-term supply contracts and technology transfers [1]. Thanks to this strategy, the Moroccan automotive industry has reached sustained growth levels over the last few years. Its performance is particularly remarkable in terms of exports and job creation. Given the strategic importance of such an industry, investigating the benefits of adopting and applying lean practices, in particular synchronous flow, is worthwhile. Thus, we aim to develop the supply chain collaboration framework based on the literature, and a case study of an international automotive firm operating in Morocco and its suppliers. It is important to note that this paper is based on a preliminary analysis of an article published in a conference proceeding [8]. In this paper, more analysis and insights are provided that go beyond the conference paper regarding implementing the synchronous flow in the automotive firm. The remainder of this paper is organized as follows. The next section reviews the literature on the lean supply chain, collaboration, and synchronous flow to provide an overview of key components of successful supply chain collaboration. Section 3 presents the working methodology, which consists of two main subsections. The first one describes the studied case study of a leading automotive firm and its suppliers in Morocco. The second subsection describes the data collection process, which relied on semi-structured interviews. Section 4 provides the research results and the elaborated framework of supply chain collaboration. Section 5 discusses the obtained results as well as the elaborated framework. The last section concludes the paper and gives insights into future research. 2. Literature Review In this section, a literature review is provided on supply chain collaboration, its drivers, motivators, benefits, and the key elements in lean synchronization with suppliers. The literature review helped us Information 2020, 11, 431 3 of 24 Information a2020, 11, x FOR PEER REVIEW for supply chain collaboration, particularly for the implementation 3 of 24 establish preliminary framework of lean practices. 2.1. Supply Chain Collaboration 2.1. Supply Chain Collaboration Supply chain collaboration admits different definitions [9–11]. However, one of the most widely adopted definitions of supply chain is “two[9–11]. or more independent work Supply chain collaboration admitscollaboration different definitions However, one ofcompanies the most widely jointly todefinitions plan andofexecute supply chain operations with greater successcompanies than when acting in adopted supply chain collaboration is “two or more independent work jointly isolation” Somesupply researchers the term collaboration is chosen to describe the close to plan and[12]. execute chain underline operationsthat with greater success than when acting in isolation” [12]. cooperation among autonomous engaged in a joinedtoinitiative to effectively meet the end Some researchers underline that thepartners term collaboration is chosen describe the close cooperation among customer’s needs with minimum cost [13,14]. Collaboration occurs when two or more organizations autonomous partners engaged in a joined initiative to effectively meet the end customer’s needs with exchange information, share responsibilities for planning, manage, execute,exchange and monitor supply minimum cost [13,14]. Collaboration occurs when two or more organizations information, chain responsibilities performance [14–16]. Singh etmanage, al. [17] consider that monitor supply chain collaboration is a responsible share for planning, execute, and supply chain performance [14–16]. relationship among partners, whochain sharecollaboration information, a collective performance, and Singh et al. [17] consider that supply is adevelop responsible relationship among partners, reconfigure business practices improve profit margin.and Recent literature is focusing on antoimproved who share information, developto a collective performance, reconfigure business practices improve characterization of the collaborative supply chain. According to Marqui et al. [18], collaboration is profit margin. Recent literature is focusing on an improved characterization of the collaborative supply much more complicated than a set ofcollaboration techniques and systems; behaviors chain. According to Marqui et al. [18], is much moreseveral complicated thanand a setcharacteristics of techniques are required makebehaviors the collaborative supply chain reality. The authors also considersupply cooperating and systems; to several and characteristics arearequired to make the collaborative chain and coordinating operations with strategically selected partners to achieve collaboration within the a reality. The authors also consider cooperating and coordinating operations with strategically selected supply chain. However, cooperation is supply necessary, butHowever, not a sufficient condition to achieve partners to achieve collaboration within the chain. cooperation is necessary, but not which istonecessary, but not a requirement achieve collaboration. Additionally, Ma et acoordination, sufficient condition achieve coordination, which is to necessary, but not a requirement to achieve al. [19] have added that, besides collaboration, therethat, are besides many other conceptsthere currently usedother that collaboration. Additionally, Ma et al. [19] have added collaboration, are many involve an interestused in collaborative such as coordination, cooperation, alliance, and concepts currently that involve relationships, an interest in collaborative relationships, such as coordination, joint venture,alliance, as outlined Figure 1. According to Spekman [20], cooperation is where cooperation, andin joint venture, as outlined in Figureet1.al. According to Spekman et al.firms [20], exchange basic information and havebasic someinformation long-term relations limited number of critical cooperation is where firms exchange and havewith somea long-term relations with a suppliers or customers. addition, higher degree is coordination involving a continuous flow of limited number of criticalIn suppliers or acustomers. In addition, a higher degree is coordination involving andflow critical information provided information technology. Collaboration is a stage aimportant continuous of important and critical using information provided using information technology. higher than coordination that requires a high levelthat of commitment, trust, and Collaboration is a stage higher than coordination requires a high level of information-sharing commitment, trust, [21,22]. Therefore, cooperation, and collaboration are different concepts because they and information-sharing [21,22]. coordination, Therefore, cooperation, coordination, and collaboration are different involve various of trust and commitment [23]. and commitment [23]. concepts becauselevels they involve various levels of trust Terms describing collaborative relationships Lowest Coordination Cooperation Collaboration Alliance Joint-venture Highest Figure 1. Levels of collaboration. Source: adapted from Ma et al. [19]. Figure 1. Levels of collaboration. Source: adapted from Ma et al. [19]. Furthermore, we align with the point of view that collaboration relationships occur when more we align with the point that collaboration relationships occur when more than Furthermore, one organization work together for of a view mutual objective and distinguish collaboration from than one organization workthe together for functionalities: a mutual objective and distinguish collaboration from coordination, which serves following establishing collaborative organizations, coordination, which serves the following functionalities: establishing collaborative organizations, collecting and sending information, planning collaborative activities, identifying the allocation of demand, assessing performance, and managing changes [12]. In this respect, there are two dimensions of supply chain collaboration [24]: vertical collaboration, which involves collaboration Information 2020, 11, 431 4 of 24 collecting and sending information, planning collaborative activities, identifying the allocation of demand, assessing performance, and managing changes [12]. In this respect, there are two dimensions of supply chain collaboration [24]: vertical collaboration, which involves collaboration between suppliers and customers; horizontal collaboration, which includes collaboration with competitors and other supply chain actors. 2.2. Drivers of Collaborative Relationships The drivers represent the key factors that make collaboration more successful [17]. Nevertheless, in the implementation process, it is necessary to analyze the presence of barriers that may hinder the initiative’s implementation or the achievement of expected benefits [25]. This literature review has not discussed the barriers because they are overcome if the drivers are available. According to Marqui et al. [18], the main characteristics required for collaborative relationships in the supply chain are communication, interdependence, transparency, flexibility, leadership, synchronized decision-making, commitment, and organizational culture compatibilities. Additionally, Freitas et al. [25] have proposed to characterized the supply chain collaboration using five elements, which include appropriate performance system, information sharing, decision synchronization, incentive alignment, and streamlined inter-enterprise business processes. In the same light, Mofokeng and Chinomona [10] have outlined seven key dimensions of collaborative relationships, namely information sharing, decision synchronization, incentive alignment, resource sharing, communication, and joint knowledge creation. In the context of the automotive industry, information sharing, joint decision making, and electronic data interchange positively influence the supply chain [26,27]. Additionally, trust is considered an essential mechanism in collaborative relationships [25]. Developments in information technology are making it easier for companies to share planning information [17,28]. Effective collaborative planning depends on the quality of the information shared between the companies [29]. In this context, Panahifar et al. [30] talked about enablers that can improve collaboration. They studied the following enablers: trust, information readiness, and secure sharing of information. Based on these studies, we compiled Table 1, which summarizes the drivers of collaborative relationships and their founding references. Table 1. Drivers of collaboration in the supply chain. Drivers of Collaborative Relationships X X X X X X X X X Communication Interdependence Transparency Flexibility Leadership Synchronization decision-making Commitment Organizational culture compatibility X X X X X Appropriate performance system Information sharing Decision synchronization Incentive alignment Streamlined inter-enterprise business processes X X X X X X X Information sharing Goal congruence Decision synchronization Incentive alignment Resource sharing Communication Joint knowledge creation Reference [18] [25] [10] Information 2020, 11, 431 5 of 24 Table 1. Cont. Drivers of Collaborative Relationships X X X X Information sharing Joint decision making Electronic data interchange positively Influences operational performance of SC X X X Trust Information readiness Secure sharing of information X X X X X X X X X X Commitment Trust Competition, Technology Innovative SC process Joint long-term relations Better Information sharing Joint decision making Incentive alignment Resource sharing Appropriate Performance measure, Globalization X X X Quality of information shared between the companies Trust Information readiness and secure sharing of information Reference [26] [30] [17] [29] 2.3. Motivators of Collaborative Relationships According to Freitas et al. [14], the motivators behind adopting collaborative relationships can be classified into two categories: 1. Economic motivators: represent market-related factors that influence the supply chain and push companies to adopt collaborative initiatives. They include [25]: • • • • 2. Intense competition: the fierce inter-company competition and the emergence of new firms are forcing companies to develop new practices to improve their efficiency and ensure competitiveness. Product and market characteristics: a consistent element in collaborative relationships is the challenge for companies to reduce their life cycle. Economic globalization: it represents a significant factor in the adoption of collaborative relationships. Market reaction: as companies establish collaborative initiatives in their markets, it can help them boost their competitiveness, and then other firms see the need to follow them. Organizational motivators: they are internal factors related to the company’s organization and among the supply chain companies that lead to the adoption of collaborative initiatives. Organizational motivators comprise supply chain problems, previous experiences, and pressure from the partners. They are associated with the companies’ structure, either internally or between companies, which allows for the adoption of collaborative relationships [14]. 2.4. Benefits of Collaborative Relationships Another important element in the process of implementing collaborative relationships is benefits. They represent the efficiency and effectiveness offered to the overall supply chain [17]. Additionally, collaboration in the supply chain can improve performance by minimizing the demand and supply uncertainty, improve revenue, reduce cost, and increase flexibility [31]. Many studies have found that a higher level of supply chain collaboration can improve the firms’ performance, especially in logistics activities [32,33]. Other studies have identified cost reduction, profit, forecast accuracy, and inventory Information 2020, 11, 431 6 of 24 control as the benefits of collaboration in the supply chain [10,15]. As a conclusion of a literature review by Singh et al. [17], the authors listed the benefits of supply chain collaboration as follow: inventory turns, increased revenues, costs reduction, product availability, on-time delivery, responsiveness, advanced economy, capital utilization, decreased time to market, improved quality, reduced inventory, improved customer services, better supply chain relationships, increased information sharing, accurate forecasting, and enhanced competitiveness. 2.5. Key Elements in Lean Synchronization with Suppliers From reducing lead times, increasing productivity, reducing inventory, improving quality, and making efficient use of space, lean has helped various organizations achieve their operational objectives [34]. Lean synchronization or JIT works toward satisfying customers’ demands in the right quality, time, and eliminating any activity that does not add value to the production process. Synchronous supply is when the requisition is sent to the supplier a few hours in advance. The brevity of the anticipation of this requisition has led to the setting up of specific organizations, particularly in the automotive industry [35,36]. The increasing rate of adopting lean practices in the supply chain has been noticed, particularly in the automotive industry. This has created a need for geographical proximity of the supplier to the assembler. Here we provide the key elements for effective implementation of lean supply chain practices [37]: • • • • • Collaboration with suppliers: the implementation of lean practices relies primarily on long-term and reliable relationships with suppliers. Thus, the success of lean is based on collaboration with suppliers. Tuli and Shankar [6], and Huang et al. [7] have identified important drivers of significant stakeholders’ collaboration that include: trust, information sharing, goal congruence, resource sharing, coordinating actions, and willingness to collaborate. Boonsthonsatit and Jungthawan [38] argued that suppliers’ participation in lean, which results from collaboration, can improve the company’s performance and present opportunities to gain competitive advantages. Training: when a manufacturer is aware of the benefits of collaboration with its suppliers, it promotes the application of collaboration in the supply chain through training initiatives for the benefit of the suppliers. Training initiatives end up by suppliers appreciating how important collaboration is. Manfredsson et al. [2] have studied the outcomes of manufacturers providing training and sharing knowledge with its suppliers on promoting collaboration. The authors found that suppliers’ commitment and willingness to learn are crucial for the excellent implementation of lean practices. Training is proven to increase engagement regarding the application of lean tools and structure the way of working for continuous improvement [39]. Resources: insufficient resources do not allow the implementation of lean supply chain practices. Some companies use expert consulting to implement these practices, so resources for consulting are essential [40]. Proximity: JIT delivery is an obvious and important outcome of lean production. However, it is challenged by geographic dispersion. Thus, suppliers with proximity are perfect candidates for JIT delivery [41]. Other factors: Other key factors for succeeding in applying the lean approach include leadership supporting initiatives, linking improvement to strategic goals, practicing continuous improvement daily, employee involvement and satisfaction, continuous learning, etc. [11,42]. From this literature review, we have drawn in Figure 2 the preliminary framework, based on lean practices, for implementing the synchronous flow approach via supply chain collaboration. The present framework provides the key elements of successful collaboration relationships. The first step concerns the analysis of motivators and drivers. The second step involves the selection of lean supply chain practices. The third one concerns examining the collaboration environment in terms of key elements in lean synchronization, namely the proximity, the information-sharing Information 2020, 11, 431 7 of 24 requirements, and the resources requirements. Once all steps are validated, we implement and assess the collaboration performance regarding the synchronous flow approach. Information 2020, 11, x FOR PEER REVIEW 7 of 24 Figure 2. A preliminary framework for supply chain collaboration in the implementation of lean Figure 2. A preliminary framework for supply chain collaboration in the implementation of practices. lean practices. 3.3. Materials and Methods Materials and Methods The methodology proposed The methodology proposedininthis thispaper paperisisorganized organizedaround aroundthe thefollowing followingsteps steps(see (seeFigure3). Figure 3). The is is firstly based on on a literature review to identify the motivation factors, the drivers, the Theproposal proposal firstly based a literature review to identify the motivation factors, the drivers, benefits of collaborative relationships, and the of lean synchronization. As aAs result, a the benefits of collaborative relationships, andkey the elements key elements of lean synchronization. a result, preliminary framework is developed. Secondly, an an analysis of aofcase study of of five a preliminary framework is developed. Secondly, analysis a case study fivecompanies companiesisis conducted conductedtotohighlight highlightthe theautomotive automotiveindustry’s industry’scontext contextand anddetermine determinethe thespecific specificelements elementsofof collaboration results of of these collaborationtotoenrich enrichthe thepreliminary preliminaryframework. framework.The The results thesetwo twosteps stepsallow allowfor forthe the proposition propositionofofa arevised revisedframework frameworkadapted adaptedtotothe thecase casestudy studycontext. context. Information 2020, 11, 431 Information 2020, 11, x FOR PEER REVIEW Literature 8 of 24 8 of 24 Motivators of Drivers of collaborative collaborative relationship relationship Benefits of collaborative Key elements in Lean relationship synchronization review Preliminary framework Case study Specific constructs of collaborative relationship Revisited framework Figure 3. Steps of the proposed methodology. Figure 3. Steps of the proposed methodology. 3.1. 3.1.Case CaseStudy StudyDescription Description This Thisstudy studyaims aimstotodevelop developa aframework frameworkfor forcollaboration collaborationbetween betweenautomotive automotiveconstructors constructorsand and first-tier first-tierequipment equipmentsuppliers supplierstotoachieve achieveaasynchronous synchronousflow flowofofcomponents. components.The Thebasic basicidea ideaisistoto synchronize synchronizethe thecomponents’ components’deliveries deliveriesand andthe thevehicle vehicleassembly assemblyflow flowtotoreduce reduceororeliminate eliminateparts parts inventory in the manufacturer’s plant. According to Piekkari et al. [43] and Seawright and Gerring inventory in the manufacturer’s plant. According to Piekkari et al. [43] and Seawright and Gerring [44], [44], the single holistic case-study is appropriate to phenomena explore phenomena withinunit a single unit in of a the single holistic case-study is appropriate to explore within a single of analysis analysis a complex Case study research examine multiple and understand complexincontext. Casecontext. study research is mostly used is to mostly examineused and to understand complex multiple complex Besides, in a holistic and in-depth investigation, case study research isas issues. Besides, in issues. a holistic and in-depth investigation, case study research is widely recommended widely recommended as a[45]. robust research methodto[45]. according Jastistudy and Kodali [46], a robust research method Besides, according JastiBesides, and Kodali [46], thetocase is considered the case study is considered as the most famous empirical research methodological approach in the as the most famous empirical research methodological approach in the lean research field. lean research field. has an applied, qualitative, and exploratory nature. It is organized on a single case This research This research qualitative, and exploratory nature. is organized on a single case study made up ofhas onean ofapplied, RENAULT’s automobile plants and five of itsItfirst-tier component suppliers. study made up of one of RENAULT’s automobile plants and five of its first-tier component suppliers. To save confidentiality, we have named them A, B, C, D, and E. All of them play an essential role To confidentiality, havebecause namedof them B, C, D, E. All ofofthem play an essential in insave RENAULT’s supplywe chain the A, vitality andand criticality the components theyrole supply. RENAULT’s supplyof chain because of the vitality companies and criticality the components The characteristics the five studied suppliers’ are of provided in Table 2.they supply. The characteristics the five studied suppliers’ are providedwere in Table 2. under a traditional Until theofstudy time, the five first-tiercompanies component suppliers working push flow. To provide a plan with subassembly, suppliers follow a daily firm order received from Table 2. Characteristics ofFigure the five4.first-tier suppliers. RENAULT’s planning unit, as explained in (1), theequipment supplier has three days as notice to plan, manufacture, and deliver the order (2), (3), (4). Firm order considers the initial sequence of vehicles, Supplier A increased by B C all components D are used in theE assembly introduced in sheet metal, a safety margin. Since Characteristic line, and regarding the diversity level, internal picking activities are used to supply the workstations Multinati Multinational Local Multinational following the sequence of vehicles introduced in theMultinational assembly line (5), (6). Finally, empty packaging Category onal company company company company is returned to the customer (6). Figure 4 shows this mechanism and the location of inventory in the company plant. So, the main factor that motivated the study is that push flow may cause a high inventory level, Design, Automotive metal especially in an uncertain demandSheet context. Indeed, uncertainty comes from two factors: diversity and products: air Stamping, manufacture, Climate, customer needs changing [47]. transformation conditioners, exhaust sale, after-sales electronic by cutting, system, service of plastic heaters, electrical Activity s, and stamping, and and electronic and systems for the interior manufacturing of devices, fuel bulkhead management of systems. metal parts. management on-board fluids Global Size (Number of Information 2020, 11, 431 employees) Component Characteristic DiversityCategory (number of parts) Plastic and leather systems, and ITS devices. 6113 170,932 27,000 and gases and their components 120 Specific Characteristic of the studies companies Table 2. Characteristics of the five first-tier equipment suppliers. Interior Plastic and Exhaust trim Air conditioners Supplier leather B system D C elements A 6 Multinational company Multinational 155company Multinational 9 company Automotive Sheet metal Assembly products: air Assembly line Assembly line transformation conditioners, line Climate, by cutting, Local 12 company 32,000 9 of 24 Fuel system E Multinational 6 company Assembly line Stamping, Design, Assembly sale, line manufacture, after-sales service of heaters, electrical plastic systems for exhaust stamping, and electronics, and electronic UntilActivity the study time, the first-tier component suppliers were working a traditional the management of system, and under manufacturing andfive interior devices, fuel on-board fluids from and bulkhead of metal parts. systems. push flow. To provide a plan with subassembly, suppliers follow a daily firm order received management gases and their Plastic and systems, and ITS RENAULT’s planning unit, as explained in Figure to plan, components leather 4. (1), the supplier has three days as notice devices. Use point manufacture, and deliver the order (2), (3), (4). Firm order considers the initial sequence of vehicles, Global Size (Number 27,000 120 32,000 in the introduced in sheet metal, increased by a 6113 safety margin.170,932 Since all components are used of employees) assembly line, and regarding the diversity level, internal picking activities are used to supply the Specific Characteristic of the studies companies workstations following the Interior sequence Exhaust line (5), (6). Finally, trim of vehicles Plastic and introduced in the assembly Fuel system Air conditioners Component system and the location of leather empty packaging is returned elements to the customer (6). Figure 4 shows this mechanism Diversity (number parts) So, the main 6 155 motivated the 9 study is that12push flow may 6 cause a inventory in the ofplant. factor that Assembly Assembly high inventory demand context. uncertainty comes from Use pointlevel, especially in an uncertain Assembly line Assembly Indeed, line Assembly linetwo line line factors: diversity and customer needs changing [47]. Figure 4. 4. Current Current push push flow flow with with suppliers. suppliers. Figure The project’s essence is to study the possibility of implementing the synchronous flow between The project’s essence is to study the possibility of implementing the synchronous flow between RENAULT’s plant and suppliers. Synchronization concerns components’ flow from suppliers and RENAULT’s plant and suppliers. Synchronization concerns components’ flow from suppliers and vehicle sequence stage of the assembly process. Implementing the synchronous link “Input vehicle sequenceininthe thefinal final stage of the assembly process. Implementing the synchronous link Assembly” mainly concerns the voluminous and/or highly parts. Asparts. explained in Figurein 5; “Input Assembly” mainly concerns the voluminous and/ordiversified highly diversified As explained suppliers will receive two types of requests from the plant. A provisional request gives information Figure 5; suppliers will receive two types of requests from the plant. A provisional request gives about all flows located upstream of the Thisassembly information allows to organize information about all on flows located on assembly upstreamline. of the line. This suppliers information allows and make production planning. The second request is the firm requisition order, and it is issued when the vehicle passes through the “assembly entry” point. The firm requisition order represents the only information that triggers the supplier’s supply of the assembly line. In synchronous flow, all the logistics picking is outsourced to the suppliers who deliver ready-made handling units directly to the workplace. As mentioned in Figure 6, the handling unit becomes multi-reference. suppliers to organize and make production planning. The second request is the firm requisition order, and it is issued when the vehicle passes through the “assembly entry” point. The firm requisition order represents the only information that triggers the supplier’s supply of the assembly line. In synchronous flow, all the logistics picking is outsourced to the suppliers who deliver readymade handling units directly to the workplace. As mentioned in Figure 6, the handling unit becomes Information 2020, 11, 431 10 of 24 multi-reference. Figure 5. Synchronous flow mechanism. Source: adapted from RENAULT document. In this type of flow, the frozen horizon becomes very short (a few hours). The time available to the supplier to prepare a packaging and ship the parts directly to the assembly point (Tp) corresponds to the time between the moment when the vehicle enters assembly (Ti) and that of its passage at the assembly point of the delivered part synchronously (Tc). That is why proximity is the first criteria to be fulfilled in a synchronous flow. According to RENAULT’s service, less than 5 km must separate the plant and suppliers. Figure 5. Synchronous flow mechanism. Source: adapted from RENAULT document. Figure 5. Synchronous flow mechanism. Source: adapted from RENAULT document. In this type of flow, the frozen horizon becomes very short (a few hours). The time available to the supplier to prepare a packaging and ship the parts directly to the assembly point (Tp) corresponds to the time between the moment when the vehicle enters assembly (Ti) and that of its passage at the assembly point of the delivered part synchronously (Tc). That is why proximity is the first criteria to be fulfilled in a synchronous flow. According to RENAULT’s service, less than 5 km must separate the plant and suppliers. Figure Figure 6. 6. Handling unit composition. In this type of flow, the frozen horizon becomes very short (a few hours). The time available to the supplier to prepare a packaging and ship the parts directly to the assembly point (Tp) corresponds to the time between the moment when the vehicle enters assembly (Ti) and that of its passage at the assembly point of the delivered part synchronously (Tc). That is why proximity is the first criteria to be fulfilled in a synchronous flow. According to RENAULT’s service, less than 5 km must separate the plant and suppliers. Figure 6. Handling unit composition. 3.2. Data Collection Process Data collection processes used the following sources: semi-structured interviews, consultation of internal RENAUTLT’s documents, and observations. Semi-structured interviews allow collecting data by interviewing participants using an interview guide [48], which contains all covered topics (Table 3). The interview guide was elaborated based on the literature review, which identified motivators, barriers, benefits, and prerequisites for implementing synchronous flow. On the side of the client plant (RENAULT’s plant), the interviews were carried out with several participants in different departments—namely purchasing managers of each equipment manufacturer, plant logistics manager, Information 2020, 11, 431 11 of 24 supply manager, transportation manager, engineering department, human resources department, IT department, and environment department. On the supplier’s side, the logistics manager was the primary contact designated as the project manager. Participants were met individually at their offices. The interviews were started by introducing the study’s objective and asking for permission to record the interviews. At the end of each interview, the participants had the opportunity to add other elements not discussed and which can serve to deepen the study. The interviews lasted, on average, between 30 to 60 min. A thematic analysis was carried out for data analysis. The recorded interviews were transcribed, and the exciting features of the textual data were coded using QSR NVivo 10 qualitative data analysis software. Table 3. Interview guide. Participant Collected Data Location requirements Supplier Project manager Handling unit requirements Cost structure Plant supply manager Purchasing department Suppliers selection Suppliers Categorization Negotiation elements Transport manager Current transportation value Supply manager Average inventory level of each component IT department RENAULT’s network connection device Necessary configuration of the logistic system HR department Requirements to manage supplier staff in plant Environment department Environment requirements Flow circulation requirements Engineering department Packaging requirements Handling requirements 4. Results 4.1. Application of the Preliminary Framework In this subsection, the elaborated preliminary framework of Figure 2 is applied to study the possibilities of implementing synchronous flow with the five equipment suppliers. In-depth practical investigations have brought out other constructs to consider. Table 4 summarizes the application of the three first steps of the preliminary framework. Regarding the proximity criterion, it was necessary to split the study into two parts. Through the proposed framework for supporting the adoption of a collaborative supply chain with a focus on supply chain lean practice, different aspects of motivators are analyzed to encourage companies’ involvement with suppliers and thus to allow the initiation of the collaboration in the supply chain. Following this analysis, the motivators of launching the collaboration prospect are varied and led us to their classification into two categories—economic and organizational motivators. Economic motivators are identified through optimization of inventory level within supply chain prospect. For that purpose, optimization must be achieved in a win–win perspective concurrently with the customer and the supplier. Organizational motivators are reflected through increased flexibility and reactivity, especially in the automotive context characterized by the demand uncertainty. Information 2020, 11, 431 12 of 24 Table 4. Application of the preliminary framework. A B C D E Economic motivators Optimization of inventory level within the supply chain Optimization of inventory level in the supply chain Optimization of inventory level in the supply chain Optimization of inventory level in the supply chain Optimization of inventory level in the supply chain Organizational motivators Flexibility and reactivity Flexibility and reactivity Flexibility and reactivity Flexibility and reactivity Flexibility and reactivity Suppliers Categorization strategic strategic strategic strategic strategic Presence of Drivers yes yes yes yes yes Proximity to plant 500 km 400 km 400 km 20 km 230 km Proximity Action plan Study a second type of synchronous flow with a firm request from sheet metal workshop Study a second type of synchronous flow with a firm request from sheet metal workshop Study a second type of synchronous flow with a firm request from sheet metal workshop Study the possibility of locating the supplier in the plant. Study a second type of synchronous flow with a firm request from sheet metal workshop The practical investigation showed that it is judicious to categorize the suppliers before considering eligibility for the synchronous flow. Suppliers categorization was done according to the Kraljic Matrix [49–52]. According to the purchasing department’s interviews, we concluded that all suppliers are classified as strategic suppliers. Their impact on profit is considerable, given the relatively high purchase price and the consumption rate. On the supply risk side, suppliers’ scarcity and the criticality of the parts they deliver are two factors making them at high risk. Suppliers can be qualified as a single source. The literature on suppliers’ categorization shows that maintaining relationships is the best strategy for this category. Implementing supply chain lean practice is a way to achieve this relationship. According to Table 4, after testing the proximity requirements, we deducted those for all the suppliers except suppliers D. The synchronous flow from assembly line input will not be possible, so a second type of synchronous will be tested for those suppliers. Consequently, it is synchronous with the sheet metal input. In what follows, we separated the two studies, respectively, into two studies: S1: synchronous input metal sheet tested with suppliers A, B, C and E; S2: synchronous input assembly line tested with supplier D. As proximity requirements were decisive, subsequent studies consist of applying other elements of the preliminary framework, namely information-sharing requirements, resource requirements, KPI, and continuous improvement. Accordingly, for each supplier, those key elements will be tested with the aim is to verify the possibility of implementing synchronous flow and, if necessary, identify the barriers preventing this implementation. To this end, data collected from interviews and observations were compiled to answer each key element. Results are exposed in the following sections in table form, giving the decision about implementation possibility of synchronous flow. 4.2. S1: Synchronous Input Metal Sheet Study (Suppliers A, B, C, and E) As mentioned previously, this type of synchronous flow was tested with four suppliers: A, B, C, and E. The flow is programmed, based directly on the vehicle film’s firming and the emission of a firm message by vehicle to the supplier. These firm messages are accompanied by a forecast order in gross need grouped by production day and by chain. The Frozen period (horizon of which the needs and orders are firm and unchangeable) begins from the sheet metal workshop, which is two working possibility of synchronous flow. 4.2. S1: Synchronous Input Metal Sheet Study (Suppliers A, B, C, and E) As mentioned previously, this type of synchronous flow was tested with four suppliers: A, B, C, and E. The 11, flow Information 2020, 431is programmed, based directly on the vehicle film’s firming and the emission of a 13 of 24 firm message by vehicle to the supplier. These firm messages are accompanied by a forecast order in gross need grouped by production day and by chain. The Frozen period (horizon of which the needs andFigure orders are firm andthis unchangeable) begins fromfirm the sheet workshop, which is two working days. 7 explains mechanism. Since ordermetal is based on the initial vehicle sequence, Figure 7 explainstothis mechanism. Since firm order is based the initial vehicle sequence, the from the days. principal condition achieve this synchronous flow is theon respect of the vehicle sequence principal condition to achieve this synchronous flow is the respect of the vehicle sequence from sheet sheet metal to assembly line. This respect is measured by SSAR (Standard Sequence Achievement metal to assembly line. This respect is measured by SSAR (Standard Sequence Achievement Ratio). Ratio). This measures the percentage of vehicles that keep their place between the time they go into This measures the percentage of vehicles that keep their place between the time they go into production and the time they are finished. This rate reflects the capacity to meet operations planning. production and the time they are finished. This rate reflects the capacity to meet operations planning. According to Renault’s instructions, to accomplish a synchronous flow according to the initial sequence, According to Renault’s instructions, to accomplish a synchronous flow according to the initial SSAR must be more than 95%. Otherwise, the sequenced deliveries from the suppliers will sequence, SSAR must be more than 95%. Otherwise, the sequenced deliveries from the suppliers willnot be adapted the flow of vehicles. not beto adapted to the flow of vehicles. Figure Synchronousinput input metal mechanism. Figure 7. 7. Synchronous metal mechanism. After applying the preliminary preliminaryframework, framework, we conclude After applyingelements elements from from the andand fromfrom TableTable 5, we5,conclude that that none of the four suppliershas has been been selected selected for flow. Financial benefits that can none of the four suppliers forthe thesynchronous synchronous flow. Financial benefits that can RENAULT achieve from the synchronous flow is between EUR 20,000 and EUR 27,000. It includes RENAULT achieve from the synchronous flow is between EUR 20,000 and EUR 27,000. It includes average inventorycost. cost.Information Information sharing since the the fourfour suppliers have ahave certified the the average inventory sharingisisachieved achieved since suppliers a certified information system specific to synchronous flow. They can receive all required orders viaintegrated an information system specific to synchronous flow. They can receive all required orders via an integrated system. Nevertheless, two principal criteria were unpromising: system. Nevertheless, two principal criteria were unpromising: 1. Resource: the principal resource here is the handling unit. This unit must be multi-reference and Resource: the to principal here the at handling unit. This be multi-reference be suitable supportresource all shapes of is parts the same time. Forunit twomust suppliers, the current and be handling suitable to support all shapes parts at the same time. two suppliers, the investment current handling unit is inadequate forofsuch flow. Regarding the For estimated benefits, the amount is not justified. unit is inadequate for such flow. Regarding the estimated benefits, the investment amount is 2. notPlanning achievement: this is about SSAR; unfortunately, in the Renault plant, this rate is below justified. the required level. 2. Planning achievement: this is about SSAR; unfortunately, in the Renault plant, this rate is below the required level. 1. Table 5. Synchronous input metal study. A B C E Benefits in inventory EUR 27,000 EUR 21,000 EUR 20,000 EUR 20,000 Information sharing requirement X X X X Resources requirements 7 X X 7 Action plan = investment to adapt handling unit EUR 255,000 0 0 EUR 22,000 SSAR 7 7 7 7 Final decision 7 7 7 7 Resources requirements Action plan = investment to adapt handling unit SSAR Information 2020, 11, 431 Final decision  EUR 255,000   ✓ ✓ 0 0      EUR 22,000   14 of 24 4.3. S2: 4.3. S2: Synchronous Synchronous Input Input Assembly Assembly Line Line (Suppliers (Suppliers D) D) The following followingsection sectionisisdevoted devoted testing possibility of implementing synchronous flow The to to testing thethe possibility of implementing synchronous flow from from assembly line input with Supplier D. In the same way as other suppliers, elements of the assembly line input with Supplier D. In the same way as other suppliers, elements of the preliminary preliminarywill framework willBenefits be applied. and requirements will be evaluated, decision framework be applied. and Benefits requirements will be evaluated, and a decisionand willa be made will be made to implement or not synchronous flow. to implement or not synchronous flow. Figure 88 explains explains the the projected projected flow flow to to achieve achieve with with suppler suppler D. D. The The supplier supplier will will continuously continuously Figure receive forecasts from RENAULT’s service planning (1). Those forecasts are used to upstream plan the receive forecasts from RENAULT’s service planning (1). Those forecasts are used to plan the upstream of the supply chain (2), (3). A delivery flow between supplier D plant and its workshop in of the supply chain (2), (3). A delivery flow between supplier D plant and its workshop in the the RENAULT to supply components required for manufacturing operations (4),A(5). A RENAULT plantplant serveserve to supply components required for manufacturing operations (4), (5). firm firm requisition is sent to the supplier via the printer each time a vehicle is captured at the entrance requisition is sent to the supplier via the printer each time a vehicle is captured at the entrance to the to the assembly (6). Then, picking from the inventory done according theorder firm and order and assembly line (6).line Then, picking from the inventory is doneis according to the to firm every every exhaust component is designed for a specific vehicle and identified withequivalent the equivalent exhaust systemsystem component is designed for a specific vehicle and identified with the VIN VIN ( Vehicle Identification Number ) (7). Finally, a reverse logistic flow concerns empty packaging to to (Vehicle Identification Number) (7). Finally, a reverse logistic flow concerns empty packaging supplier D D plant plant (8). (8). supplier Figure 8. Synchronous flow in the plant for supplier D. Figure 8. Synchronous flow in the plant for supplier D. 4.3.1. Benefits According to the preliminary framework, the implementation of synchronous flow starts absolutely with benefits highlighting. Here, only financial benefits are discussed. From a lean perspective, benefits come from cost and waste avoiding. Regarding flow, the idea is to analyze all costs which can be avoiding through synchronous flow implementation. All benefits are summarized in Table 6, and singly explained as follows: 1. Inventory Financial Cost: With the synchronous flow, there would be no stock of exhaust lines in the RENAULT plant, and zero stock is reached. The stock’s financial cost is calculated according to the rate of return on capital practiced by the banks. As Morocco’s interest rate is about 5%, Information 2020, 11, 431 2. 3. 4. 15 of 24 and with an average annual inventory amount of EUR 149,292 financial savings from inventory is about EUR 74,646 per year. Inventory Deterioration Cost: It is incurred due to the deterioration of the parts while staying in stock. This cost depends on the nature of the part. Exhaust Systems, the subject of the present study, are very exposed to oxidation. As mentioned in Table 6, the cost related to waste because of oxidation is about EUR 6,600,000 per year. This represents the cumulative value of all the quantity of parts damaged during the year. Upstream Transport Cost: In push flow, Renault supports the upstream transport reserved for the exhaust system. In the case of synchronous flow, this type of transport will no longer be supported by the plant; consequently, all the cost is considered a benefit. Human Resource Cost: In push flow, the picking agent is present to prepare the handling unit adequate to the vehicle sequence. In synchronous flow, this task will be done by the supplier so that RENAULT will save the salary of the picking agent. By analyzing the expected benefits structure, it is noticed that they are high due to inventory-related costs. Especially deterioration cost with 98%. As mentioned previously, Exhaust System is very exposed to oxidation. It should be noted that an oxidized part is irreparable and is automatically confused. Consequently, a financial loss is generated equivalent to the purchase price of the part. The loss becomes more and more consequent when it comes to an expensive part and represents a significant percentage of the vehicle’s price, as is the case for the exhaust line. One of the best solutions to avoid this waste is limiting the constitution of stock as much as possible and to tend towards 0 stock. This solution can be achieved through the synchronous flow since the supply flow will be precisely synchronized with the parts’ consumption flows, and the stock of the exhaust lines would be eliminated. Table 6. Benefits from synchronous flow with supplier D. N◦ Elements Annual Amount (Euros) 1 Financial cost 74,646 2 Inventory deterioration cost 6,600,000 3 Upstream transportation fees 67,782 4 Human resource for Handling 37,752 4.3.2. Requirements and Investments Hereabouts, all investments required for implementation are evaluated. Table 7 summarized those elements: 1. Proximity action plan: The first requirement to be studied is proximity. This supplier is located at 20 km from the plant. Depending on the part’s assembly point, the supplier has only 2 h (Tc-Ti = 120 min) to prepare and deliver a complete exhaust package. To overcome this constraint, the supplier was welcomed to the RENAULT plant’s premises, installing its production and delivery units according to the following guidelines: • • • Installation of suppliers in the same industrial park as the manufacturer. The supplier will transfer its activity to the manufacturer’s plant. The supplier will use its resources to provide components. All fees related to room layout and rent is in charge of RENAULT for whom it costs nothing since the premises are already fitted out and fully amortized. 2. Information sharing: Initially, the suppliers must be linked to the client factory’s information system via an internet application. The application requires an investment, in our case. Since the Information 2020, 11, 431 16 of 24 supplier is located in the client’s site, the solution was to link the supplier to the customer network via a physical cable by installing printers used to print requisition orders. Information on the progress of the firm film and the current vehicle sequences are provided daily by the IT department via email. Resources: both human and material resources are concerned. 3. • • • 4. Material resources: These are packages that must be multi-reference to support all the diversity of exhaust lines at the same time. There is also the tractor, which would be used to handle these packages to the workstation. Human resources: this consists of recruiting a workshop foreman and physical flow agent dedicated to this flow. Training: Working in synchronous flow differs from normal flow; this requires special training for all the team dedicated to this flow. RENAULT’s services provided the training. Safety/environment specifications: Since RENAULT is ISO14000 certified, and the supplier settles on the customer’s site, the supplier must comply with the requirements of this certification. Requirements aim to protect welding stations through fire-resistant curtains, extraction at the source for the smoke emitted from the welding, either by extractors or by a suction torch. The supplier has agreed to take charge of all related investments. Table 7. Investments for synchronous flow with supplier D. N◦ Investments Element Annual Amount (Euros) Total Annual Amount (Euros) 1 Proximity action plan room layout rent 0 0 Information sharing requirement printer 4500 2 other information sharing 0 4500 Human 3 team leader 10,000 handling agent 180,000 training 0 Resources 206,000 Physical 4 Environment Handling Equipment 6000 Picking trolley 10,000 Fire-resistant curtains, extraction at the source for the smoke emitted from the welding, either by extractors or by a suction torch. 0 0 4.3.3. Final Decision and Implementation After analyzing expected benefits and investments, a decision has to be made about the implementation or not of synchronous flow. Table 8 shows all the elements identified and presents the balance between gain and investment. Regarding the benefits, and as mentioned previously, inventory is a significant cost item, mostly due to the high deterioration risk of the exhaust system. Considering the investments induced by requirements, the information sharing tool represents only 2% of total investment cost, taking into account the simple solution chosen to link suppliers with the plant information system. The important part of investments is in other resources. There is the recruitment of specific teams regarding this project and specific handling material. Compliance with environmental requirements could have constituted a hefty cost item for the customer if the supplier had not taken Information 2020, 11, 431 17 of 24 the initiative to take charge of it. The final decision was a convenient agreement to start the project with an annual global net benefit of approximately EUR 6500. Regarding vehicle transformation cost, RENAULT can save approximately EUR 75/vehicle. Table 8. Balance of implementing synchronous flow with supplier D. Annual Amount (Euros) Benefits 67,129,986 Investment 210,500 Final decision Balance (Euros) 6,502,499 OK for implementation According to the preliminary framework (Figure 2), two constructs are to be achieved after implementation: Suppliers performance measurement system and continuous improvement practice. 1. 2. • Performance measurement: from the previous literature review, an appropriate performance measurement system is a vital driver in a supply chain relation [53]. According to Bigliardi and Bottani [54], supplier performance measurement indicators are among a whole supply chain performance measurement system. They are summarized in: efficiency, responsiveness, reliability, and price offered [55]. For RENAULT, equipment suppliers’ performance is measured by service rate, document accuracy, logistic quality, product quality, and price productivity. These indicators join those identified in the literature. In the specific case of synchronous flow, the supplier is judged only on the logistics quality, price, and product quality. This difference comes from the fact that integration with the supplier reaches the ultimate point in the synchronous flow, which is reflected in the performance indicators. The respect of the delivery time is no longer a significant criterion since the delivery delay is intolerable. The supplier delivers the components directly for use, so there is no margin to absorb any delay. Documentation accuracy serves to guarantee the documentary reliability, which is used to feed the stock status. In synchronous flow, the stock no longer exists, so this indicator is no longer useful. Table 9 illustrates the evolution of indicators from a high flow to synchronous flow. Continuous improvement: To ensure continuous improvement, it is necessary to permanently and systematically identify the failures and risks which can block the fluidity of the flow. Hence, we have proposed an audit tool and a tool for risk management. Self-audit tool Table 9. Comparison of Indicators. Indicators Objective Push Flow Synchronous Flow Service rate Measure respect of delivery time X 7 Documentation accuracy Guarantee inventory update reliability X 7 Logistic quality Measure logistical incidents, such as chain shutdown or missing X X Price Capacity to optimize continuously the cost structure X X Product quality Compliance with quality requirements. X X Continuous self-audit is an effective way to guarantee the continuity of a system [56]. It makes it possible to detect faults and correct them permanently. We have proposed an audit tool to verify the correct application of all the synchronous flow requirements. We designed it in light of the interviews with the various actors who expressed, each in their field, the critical points which risk blocking Information 2020, 11, 431 18 of 24 the fluidity of flows. Table 10 shows the audit tool organized in five axes: firm film, information, human resources, handling material, and procedures. For each question, an actor is designed as responsible for answering it. Table 10. Self-audit tool. Source: Ibn El Farouk and Jawab [8]. Self-Audit Checklist Process N◦ Supply Mount Point in a Synchronous Flow Parameters Questions Actor What is the information procedure you are applying in case of changing the firm film? Logistic department 2 How do you guarantee the real-time information-sharing on the film firm with the supplier? Logistic department 3 What is the frequency of preventive control you have planned for the printer? Supplier 4 Do you have a back-up printer on-site? Supplier How do you ensure the printer’s continuous supply of consumables? Supplier 6 Do you meet the quality requirements of consumables used? Supplier 7 How do you act in any failure of network connection? Supplier 8 How a network failure is handled? IT 9 How do you guarantee the maintenance of the delivery trolleys? Supplier How do you guarantee the maintenance of self-propelled tractors? Supplier How is your trolley loop calculated? How do you update it? Supplier How do you ensure the application of business requirements at the workplace? Supplier How do you manage the versatility of the picking post? Supplier Do you guarantee that the picking agent is constantly present next to the printer? Supplier 1 Firm film 5 10 Information Handling 11 12 Procedure 13 14 • Human resources Risk management tool The synchronous flow saves costs related to inventory management, but this strength constitutes, at the same time, its weakness. The absence of the stock makes the system very weak and sensitive to the slightest disturbance. The most severe risk that may arise is the disruption of the assembly line replenishment. With zero safety stock, the only consequence is the production activity shutdown, which is considered an intolerable incident due to the immense losses. The risk analysis we have associated with this project would help control this risk and avoid it happening. The idea is to manage risks by identifying their possible causes and controlling them by implementing appropriate action plans. In this regard, a Fault Tree Analysis of deliveries breakdown was made thanks to brainstorming that led to a mapping of undesirable events to be monitored (Figure 9). Those events concern three axes: information-sharing, inventory management, and resource availability. Information-sharing includes two elements: network quality and material availability. Network quality can be considered an external factor, under which both the supplier and RENAULT have no control. Contrariwise, material availability, especially printer, is the supplier’s responsibility. Inventory management aim at managing operations to guarantee a smooth flow of material from upstream to downstream. Effective inventory management must avoid an out-of-stock situation and also guarantee financial savings. Resources availability concerns both material and human resources. Human resources are the events concern three axes: information-sharing, inventory management, and resource availability. Information-sharing includes two elements: network quality and material availability. Network quality can be considered an external factor, under which both the supplier and RENAULT have no control. Contrariwise, material availability, especially printer, is the supplier’s responsibility. Inventory management aim at managing operations to guarantee a smooth flow of material from Information 2020, 11, 431 19 of 24 upstream to downstream. Effective inventory management must avoid an out-of-stock situation and also guarantee financial savings. Resources availability concerns both material and human resources. most critical key inare anythe leanmost practice since those practices require more and special Human resources critical key in any lean practice since rigor, those implication, practices require more skills. implication, As mentioned previously, synchronous flow requires a specific handlingflow tool requires whose availability rigor, and special skills. As mentioned previously, synchronous a specific ensures the assembly line’s continuity. Thus, is vital toline’s guarantee a rigorous system of handling tool whose availability ensures the itassembly continuity. Thus,management it is vital to guarantee tools,management especially regular maintenance operations. athose rigorous system of those tools, especially regular maintenance operations. Figure 9. Risks mapping. Source: Source: adapted adapted from from Ibn Ibn El El Farouk Farouk and Jawab [8]. The preliminary preliminary framework’s framework’s application application on on the the case case study study has has revealed The revealed other other essential essential factors factors that should be taken into consideration in the implementation of synchronous flow within aa supply supply that should be taken into consideration in the implementation of synchronous flow within chain. Thus, Thus, the the preliminary preliminary framework framework was was revisited revisited and The resulting resulting framework chain. and improved. improved. The framework is is provided in Figure 10. provided in Figure 10. Information 2020, 11, 431 Information 2020, 11, x FOR PEER REVIEW 20 of 24 20 of 24 Figure 10.10. Proposed supply chain collaboration framework forfor thethe implementation of synchronous flow. Figure Proposed supply chain collaboration framework implementation of synchronous flow. Information 2020, 11, 431 21 of 24 5. Discussion Through the proposed framework to support the implementation of synchronous flow, via collaborative practice between a car manufacturer and component suppliers, the lessons can only be numerous and constructive. The financial balance was clearly in favor of the project. However, the financial dimension would not have been sufficient without a firm commitment from the customer and the supplier to bring this project to fruition. A commitment reflected in that of all the teams whose conviction of the well-founded nature of the project has made it a success. It can be confirmed that mutual trust between customer and supplier has amply increased the project’s success chances. The supplier settled on the client’s premises without being worried about losing his know-how, and the client was ready enough to welcome the supplier and put in place all the favorable conditions for its installation. The second crucial lesson is that the supplier’s size is not a determining criterion for starting a collaborative practice. Among the five suppliers involved in the study, the only selected one with whom the project worked was the smallest supplier. Additionally, it is the supplier with the oldest relationship with the client. Through this study, it can be confirmed that collaboration, especially in lean practice, should be considered particularly with strategic suppliers. In the present case study, the delivered component and the exhaust line, is a critical component for the assembly process with a high price, which represents a considerable impact on the profit margin. Additionally, supply sources are scarce in this sector. In this study, two frameworks were proposed. The preliminary framework, resulting from the literature review, highlighted the main elements to be considered and monitored during a lean supply chain collaborative practice. The second framework enriched the first one with specific construct to the case study, namely, the need to categorize the suppliers before starting such a practice, considering the sustainability data reflected in the framework with respect to environmental standards. Risk management and establishing an audit system are two tools that will guarantee the continuity of the system after its start-up. Finally, a specific effort has to be made concerning the mutation of the supplier measurement performance system. As it has been advanced, this system was completely changed after the implementation of synchronous flow. Thanks to this project, supplier-customer relation has evolved, and the traditional performance indicators have become obsolete. 6. Conclusions This study’s objective was to analyze a collaborative practice within the framework of the synchronous flow between the automotive manufacturer and its equipment manufacturers. Two frameworks were proposed. The first one resulted from a literature review that focused on supply chain collaboration and lean practices between supplier and customer. Through this preliminary framework, the primary constructs of a lean supply chain collaboration were identified and organized in a decision support tool that can orient the efforts during the implementation of synchronous flow. Regarding the specificity of synchronous flow, the practical experimentation was essential to enrich the preliminary framework. The experiment was carried out in the form of a case study, consisting of a RENAULT’s plant and five of its equipment manufacturers. The obtained result, namely the revised framework, confirmed the critical aspect of trust, commitment, and information sharing as a pillar of all collaborative practices. The conducted case study enriched the catalog of practices to be adopted with strategic suppliers. The safety and environment data were strongly highlighted and only confirmed the obligation to make all the lean project stakeholders adhere to the same requirements. Another important conclusion is the change in the performance measurement system after joining a lean supply chain project. This change reveals that performance measurement is a fundamental management tool for customer–supplier relationships within the supply chain. It is not fixed but evolves with the maturity of this relationship. As a perspective and as part of a win–win approach, the flow must evolve towards synchronous production. In this way, the stock level would be optimized even on the supplier side. Synchronous Information 2020, 11, 431 22 of 24 production would only be possible if the manufacturing cycle time is less than the Tc-Ti interval. This objective necessitates the deployment of more lean manufacturing practices to improve the production flow by eliminating non-value-added steps. Author Contributions: Conceptualization, I.I.E.F., I.M., Y.F., J.A. and F.J.; Data curation, I.I.E.F., I.M. and Y.F.; Formal analysis, I.I.E.F., I.M., Y.F. and J.A.; Investigation, I.I.E.F., I.M., Y.F. and J.A.; Methodology, I.I.E.F., I.M., Y.F. and J.A.; Project administration, I.I.E.F., I.M., Y.F., J.A. and F.J.; Resources, I.I.E.F., I.M, Y.F. and J.A.; Software, Y.F.; Validation, I.I.E.F., I.M., Y.F. and J.A.; Visualization, F.J.; Writing—original draft, I.I.E.F., I.M., Y.F. and J.A.; Writing—review & editing, I.I.E.F., I.M., Y.F. and J.A. All authors have read and agreed to the published version of the manuscript. Funding: This research received no external funding. Acknowledgments: The authors would like to thank the participants from the studied companies for their availability, precious time, and valuable contribution. Conflicts of Interest: The authors declare no conflict of interest. References 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. Sahoo, S. 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Portuguese
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Volume da gota dos colírios comerciais nacionais
Arquivos brasileiros de oftalmologia
1,994
cc-by
1,635
(I) Pós-graduandos do Departamenlo de Oftalmologia e Otorrinolaringologia da Faculdade de Medicina de Ribeirão Prelo - USP. (2) Prof. Doutor do Departamenlo de Oftalmologia e Otorrinolaringologia da Faculdade de Medicina de Ribeirão preto-USP Enderµ para correspondêncla:Dr.FabianoAnsekllO Hueb de Menezes - Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto -USP -Departamento de Oftalmologia e Olorrinolaringologia - 1 2· andar - . Campus da. USP de Ribeirão Preto - Monte Alegre - CEP 14049 - Ribeirão Preto - São Paulo - Brasil RESUMO o volume da gota de oito classes de colírios disponíveis no mercado nacional, foi aferido, com uma precisão de 0,5 "I, e, paralelamente, compa­ rado com o padrão volumétrico de quatro classes de colírios americanos. Em relação aos colírios nacionais analisados, seis deles apresentaram volu­ mes de gotas estatisticamente iguais entre si e aos das gotas americanas, isto é, 20 a 25 "I, ao passo que, dois deles, mostraram gotas com o dobro do volume considerado necessário e ideal. Esses achados são discutidos e, suas implicações médicas e econômicas, são abordadas. MATERIAL E MÉTODOS Palavras-<:have: colírio, volume, gota. Volume da gota dos colírios comerciais nacionais Eyedrops' size in Brazil Fabiano Anselmo Hueb de Menezeslll Fernando Cenci Guimarãesl'l Habib Nahmatalah Obeidl'l Jacob Moyses Cohen III Antônio Augusto Velasco e Cruz l'" Fabiano Anselmo Hueb de Menezeslll Fernando Cenci Guimarãesl'l Habib Nahmatalah Obeidl'l Jacob Moyses Cohen III Antônio Augusto Velasco e Cruz l'" RESULTADOS A figura I mostra os volumes mé­ dios e intervalo de confiança encontra­ dos para as gotas dos oito colirios estu­ dados. Análise de variância unifa­ torial, com medidas repetidas, mostrou diferenças significativas entre as gotas dos colirios (F = 60.413, p< 0.00001). Análises Post-Hock pelo teste de Tukey indicaram que as gotas dos colírios G e H eram diferentes entre si e também dos demais, os quais não diferiram significativamente entre si. As gotas dos colírios americanos não eram significativamente diferentes en­ tre si. Na figura I , o intervalo de con­ fiança da média das gotas destes colirios é representado pelas duas li­ nhas pontilhadas. INTRODUÇÃO Até 1 985, O volume da gota dos colírios comerciais americanos era de 50 a 70 "I (1,2). Após essa data, com o intuito de minimizar efeitos colaterais, Brown & cols.6 introduziram modifi­ cações nos conta-gotas dos frascos e reduziram o volume das gotas para cer­ ca de 20-25 ,,1. Como a literatura nacio­ nal a este respeito é nula, e o assunto além da importância médica tem, para o paciente oftalmológico, implicações econômicas, deciֱimos medir o vo­ lume das gotas de alguns colírios usa­ dos comercialmente no Brasil. Espe­ cificamente, procuramos verificar se, no Brasil, existe uma padronização volumétrica como a existente no mer­ cado americano. · Nossos resultados indicam que, se por um lado a maioria dos colírios estudados apresentou uma constância volumétrica da gota com­ parável à existente nos E.U.A., por ou­ tro algumas marcas apresentaram gotas com volumes até 1 00% maiores do que o desejável. A fim de se medirem volumes da ordem de microlitros, confeccionou-se um cone de vidro com 8 cm de com­ primento, diâmetro externo superior de 1 3 mm e diâmetro externo inferior de 5 mm. A graduação deste cone foi feita de 0,5 em 0,5 Ljl até 0,1 mI,; posteriormente de 10 em l O LjI até, 0,3 mI. O volume da gota foi medido di­ retamente após sua instilação no in­ terior do tubo. Foi aferido o volume da gota de oito colírios distintos (A, B, C, D, E, F, a, H). Para cada colírio, mediu-se uma gota de 1 0 frascos diferentes. Os colírios eram fabricados por 3 labora­ tórios (A, B, C = laboratório I ; D, E = laboratório 2, e F,a,H = laboratório 3). Paralelamente, mediu-se, a título de controle, o volume da gota de 4 colírios utilizados comercialmente nos E.U.A, pertencentes a um mesmo laboratório. Em três destes, mediu-se 6 frascos e, no último, 4 frascos_ ARQ. BRAS. OFfAL. 57(1), FEVEREIRO/I994 http://dx.doi.org/10.5935/0004-2749.19940072 34 Volume da gota dos colírios comerciais nacionais Volume da gota dos colírios comerciais nacionais Volume da gota dos colírios comerciais nacionais coincidentemente ou não, como no caso do colirio H, que é usado no trata­ mento do glaucoma. Como se essa dis­ crepância na padronização dos colírios não bastasse, as bulas de colírios e os catálogos de laboratórios orientam a instilação de 2 gotas de colirio em cada olho por vez, fazendo duplicar novamente os gastos financeiros do paciente. centração da droga no filme lacrimal. Portanto, a redução do volume de uma gota de 50-70 para 20Lj1 não diminui sua eficácia (3,4). Além da virtual inutili­ dade terapêutica, gotas de grande volu­ me, excedendo sobremaneira a capaci­ dade volumétrica da fenda palpebral, induzem a maior toxicidade, uma vez que grande quantidade de fármaco é perdida. As perdas ocorrem devido ao extravasamento da medicação e\ou dre­ nagem pelas vias lacrimais e posterior absorção pela mucosa nasal. Essa ab­ sorção nasal é possivelmente, a princi­ pal fonte de efeitos colaterais (I). O re­ gistro norte americano de efeitos cola­ terais, induzidos por drogas topica­ mente usadas, documentou mais de 1 500 casos de toxicidade sistêmica por colírios de fi-bloqueadores (3). Nestes dados estão incluídas 13 mortes por es­ tado asmático, algumas vezes logo após a instilação do colírio no consultório do oftalmologista. Recentemente, caso se­ melhante ocorreu no sul do Brasil. Em relação aos colírios nacionais analisa­ dos, a maioria (A a F) apresentou volu­ me das gotas estatisticamente igual ao das gotas americanas, isto é 20 a 25 Ljl (notar a superposição dos intervalos de confiança). Já os colírios G e especial­ mente o H mostraram gotas com o do­ bro do volume considerado ideal. A importância médica da falta de padro­ nização, verificada nesse tipo de coli­ rio, não é clara. Em relação à toxi­ cidade supramencionada, pode-se obje­ tar que se trata de reações idiossin­ cráticas e, portanto, imprevisíveis qual­ quer que seja o volume das gotas. En­ tretanto a implicação econômica é indiscutível. Colírios cujas gotas sejam o dobro do ideal acabam na metade do tempo do que os padronizados. Esse fato é ainda mais importante quando a droga a ser instilada é de uso crônico, SUMMARY The size of eight commercial brazilians eyedrops was measured and comparade with the size of four americans eyedrops. Measurements \Vere calibrated in steps of O. 5 pI. The size of six brazilians eyedrops \Vere significantly different between then and from americans eyedrops (20-25 pI). The size of the two remaining brazilians eyedrops were mllch larger (45-50 pi ). The medical and socio-economic importance of these findings were discussed. 55 50 3 45 !! 40 o Q Labor.tOrlo 0 · 1 c • 2 .. . 3 .. 35 .., • 30 E ѷ 25 :::::::::::::::::::::::::::F::::l:::::ƅ2.::::::::;:::::::::::: ::::::: [ [ > 20 1 5 b ColTrio Figura 1 DISCUSSÃO 55 50 3 45 !! 40 o Q Labor.tOrlo 0 · 1 c • 2 .. . 3 .. 35 .., • 30 E ѷ 25 :::::::::::::::::::::::::::F::::l:::::ƅ2.::::::::;:::::::::::: ::::::: [ [ > 20 1 5 b ColTrio F gu a 1 . KeyK'ords: eyedrops, siza. KeyK'ords: eyedrops, siza. I . SHELL, JW. Pharmacokinetics of Topically Applied Ophlhalmic Drugs. SI/TV. Ophlhalmol. 26:207,1 982. 2. CHRAI, SS; PATION, TF; MEHTA, A; RO­ BINSON, JR . Lacrimal and Insti l l ed Fluid Dynamics in Rabbit Eyes. J. Plrann. Sei. 62:1 1 1 2, 1 973. 3. NAGATAKI, S & MISHIMA, S. Phannaco­ kinetics ofInstilled Drugs in lhe Human Eye. lnl. Ophtlralmol. Clin. 20:33, 1 980. 4. MAURICE, DM. Factors In fluencing lhe Penetration of Topically Applied Drugs. lnt. Ophthalmol. Clin. 20:21 , 1 980. 5. FIT..E, RR & PATION, TF. Topically Applied Pilocarpine. Areh. Ophthalmol. 98: 1 12, 1 9 80. 6. BROWN, RH; HOTCHKISS, ML; DAVIS, EB. Creating Smaller Eyedrops by Reducing Eye­ dropper Tip Dimensions. Am. J. Ophlhalmol. 99:460-464, 1 985. 6. BROWN, RH; HOTCHKISS, ML; DAVIS, EB. Creating Smaller Eyedrops by Reducing Eye­ dropper Tip Dimensions. Am. J. Ophlhalmol. 99:460-464, 1 985. p 5. FIT..E, RR & PATION, TF. Topically Applied Pilocarpine. Areh. Ophthalmol. 98: 1 12, 1 9 80. H pr 4. MAURICE, DM. Factors In fluencing lhe Penetration of Topically Applied Drugs. lnt. Ophthalmol. Clin. 20:21 , 1 980. F I . SHELL, JW. Pharmacokinetics of Topically Applied Ophlhalmic Drugs. SI/TV. Ophlhalmol. 26:207,1 982. REFERÊNCIAS BIBLIOGRÁFICAS W I . SHELL, JW. Pharmacokinetics of Topically Applied Ophlhalmic Drugs. SI/TV. Ophlhalmol. 26:207,1 982. I . SHELL, JW. Pharmacokinetics of Topically Applied Ophlhalmic Drugs. SI/TV. Ophlhalmol. 26:207,1 982. 2. CHRAI, SS; PATION, TF; MEHTA, A; RO­ BINSON, JR . Lacrimal and Insti l l ed Fluid Dynamics in Rabbit Eyes. J. Plrann. Sei. 62:1 1 1 2, 1 973. n 2. CHRAI, SS; PATION, TF; MEHTA, A; RO­ BINSON, JR . Lacrimal and Insti l l ed Fluid Dynamics in Rabbit Eyes. J. Plrann. Sei. 62:1 1 1 2, 1 973. n 3. NAGATAKI, S & MISHIMA, S. Phannaco­ kinetics ofInstilled Drugs in lhe Human Eye. lnl. Ophtlralmol. Clin. 20:33, 1 980. 3. NAGATAKI, S & MISHIMA, S. Phannaco­ kinetics ofInstilled Drugs in lhe Human Eye. lnl. Ophtlralmol. Clin. 20:33, 1 980. Estudos farmacocinéticos têm mos֯ trado que o aproveitamento máximo das drogas, veiculadas por colírios, ocorre quando o volume da gota é de cerca de 20 Ljl (3). Ou seja, aumentando­ se o volume da gota ou o número de instilações, não se obtém maior con- 4. MAURICE, DM. Factors In fluencing lhe Penetration of Topically Applied Drugs. lnt. Ophthalmol. Clin. 20:21 , 1 980. F 5. FIT..E, RR & PATION, TF. Topically Applied Pilocarpine. Areh. Ophthalmol. 98: 1 12, 1 9 80. H 6. BROWN, RH; HOTCHKISS, ML; DAVIS, EB. Creating Smaller Eyedrops by Reducing Eye­ dropper Tip Dimensions. Am. J. Ophlhalmol. 99:460-464, 1 985. ARQ. BRAS. OITAL. 57(1), FEVEREIRO/1994 35 ARQ. BRAS. OITAL. 57(1), FEVEREIRO/1994
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“The Opposite of Treatment”: A qualitative study of how patients diagnosed with psychosis experience music therapy
Nordic journal of music therapy
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“The Opposite of Treatment”: A qualitative study of how patients diagnosed with psychosis experience music therapy Hans Petter Sollia,b* and Randi Rolvsjordb aLovisenberg Diakonale Hospital, Oslo, Norway; bGAMUT, The Grieg Academy, University of Bergen, Bergen, Norway (Received 27 June 2013; accepted 29 January 2014) aLovisenberg Diakonale Hospital, Oslo, Norway; bGAMUT, The Grieg Academy, University of Bergen, Bergen, Norway (Received 27 June 2013; accepted 29 January 2014) Previous research studies regarding music therapy and severe mental illness have mainly adopted quantitative methodologies in order to study the effec- tiveness of music therapy interventions. Studies that have explored service users’ experiences of participation in music therapy are small in number, and almost nonexistent in the field of psychosis. This study aimed to explore how mental health patients with a diagnosis of psychosis experienced parti- cipation in music therapy, in general, and more specifically how they experienced music therapy in relation to their current mental state and life situation. Nine inpatients with psychosis were interviewed using a semi- structured interview focusing on the participants’ experiences of music therapy in individual sessions, groups, and performances. Through the use of interpretative phenomenological analysis, four super-ordinate themes cen- tral to the participants’ experiences were found: freedom, contact, well- being, and symptom reduction. Based on the findings, mental health recov- ery, positive mental health, and agency are proposed as constituting a better framework for music therapy in mental healthcare than a primary focus on symptom remission and functional improvement. Keywords: music therapy; mental health; psychosis; recovery; user-perspective; agency *Corresponding author. Email: hpsolli@gmail.com Nordic Journal of Music Therapy, 2014 http://dx.doi.org/10.1080/08098131.2014.890639 “The Opposite of Treatment”: A qualitative study of how patients diagnosed with psychosis experience music therapy Hans Petter Sollia,b* and Randi Rolvsjordb aLovisenberg Diakonale Hospital, Oslo, Norway; bGAMUT, The Grieg Academy, University of Bergen, Bergen, Norway (Received 27 June 2013; accepted 29 January 2014) Introduction Psychosis is characterized by crucial changes in thoughts and perceptions as well as in a person’s emotional and social life. The lifetime prevalence of all psychotic disorders has been found to be up to 3%, and around 1% for schizophrenia (Perälä et al., 2007). Despite promising developments in medical treatment and psychosocial rehabilitation, there are growing calls for other, more effective approaches to help and support people with psychosis (Bentall, 2009; Fledderus, Bohlmeijer, Smit, & Westerhof, 2010; Herrman, Saxena, & Moodie, 2005; Slade, 2009). Within the last decade, outcome studies have documented positive effects of music therapy on symptoms and functioning for people © 2014 The Grieg Academy Music Therapy Research Centre H.P. Solli and R. Rolvsjord 2 diagnosed with schizophrenia and the wider condition of psychosis (Gold, Solli, Krüger, & Lie, 2009; Gold et al., 2013; Mössler, Chen, Heldal, & Gold, 2011). As a consequence of this emerging evidence base, music therapy is now being recommended in national treatment guidelines for people with psychosis in UK and Norway (National Collaborating Centre for Mental Health, 2010; The Norwegian Directorate of Health, 2013). However, while an increasing number of such quantitative outcome studies have documented the effectiveness of music therapy in regard to various stan- dardized outcome measures (mainly measures of symptom reduction), the service user-perspective of these patients1 has been explored to a much lesser extent. Recent qualitative studies involving people with severe mental illness have primarily focused on development of theoretical and clinical frameworks (De Backer, 2004; Odell-Miller, 2007; Pedersen, 2006), and case studies and case reports have mainly addressed the therapy process from the music therapist’s perspective (e.g. Bruscia, 2012; Jensen, 1999; Metzner, 2003; Næss & Ruud, 2007; Odell-Miller, 1991; Silverman, 2003; Solli, 2008). Some surveys and questionnaires have been conducted (e.g. Baines, 2003; Baines & Danko, 2010; Choi, 1997; Eyre, 2011; Reker, 1991; Silverman, 2006), but their pre- determined focus has resulted in limited opportunities for exploring service users’ own perspectives. A few personal narratives written by users can also be found (Hibben, 1999; Tyson, 1981). Existing research studies containing first-hand accounts of users’ experiences in music therapy are either conducted with informants who have nonpsychotic illnesses (Carr et al., 2011; Rolvsjord, 2010; Stige, 1999, 2012a) or with a broader group of mental health clients (Ansdell & Meehan, 2010; Baines & Danko, 2010; Clemencic-Jones, 1998; Grocke, Bloch, & Castle, 2009; Hammel- Gormley, 1995; Jampel, 2007). 1In this text the term patient is used because the music therapy takes place in a hospital setting. Additionally, the terms user and participant are applied when referring to research and general mental health-care contexts. 2Related terms frequently used in literature include personal recovery (Slade, 2009), recovery in mental illness (vs. recovery from mental illness) (Davidson et al., 2009), and social recovery (Repper & Perkins, 2003; Tew et al., 2012). Introduction First-hand accounts from patients diagnosed with psychosis can be found in Moe’s (2000; Moe, Roesen, & Raben, 2000) doctoral thesis, but the study is limited to the guided imagery and music (GIM) method. Finally, Silverman’s (2010) mixed-method study contains a small section where participants with psychosis have commented upon sessions in interviews. To our knowledge, a qualitative in-depth study on how patients with psychosis experi- ence music therapy in general has not previously been conducted. The limited interest in the user perspective found in music therapy may reflect a general trend in research literature on mental illness, where mental health service users’ subjective experiences have been neglected (Jenkins & Barrett, 2004; Strauss, 2008). Critical voices claim that this lack of first-person accounts has resulted in the silencing of a whole group of people who have thus been left subject to the perspectives of others (Geekie, Randal, Read, & Lampshire, 2012). While nomothetic, generalized knowledge has been prized, Nordic Journal of Music Therapy 3 this provides us with only “half the story” (Slade, 2012). Consequently, there is a need for more research which can contribute idiographic, subjective knowledge. Psychosis is, first and foremost, a human experience, in the sense that the psychotic experiences are only immediately accessible to the person who is psychotic (Geekie et al., 2012; Slade, 2012). Research on users’ experiences is therefore able to contribute to the overall scientific quality of research related to severe mental illness (Strauss, 2008). During the last decade, attention has increasingly been paid to user perspec- tives from people experiencing mental health difficulties, with these perspectives being accorded value across health care politics, research, and practice (Thornicroft & Tansella, 2005). This development is closely related to the growing influence of the notion of mental health recovery2 (Anthony, 1993; Slade, 2009). Mental health recovery is a critical and user-oriented paradigm that has arisen from first-person accounts from people with mental health difficulties, contributing rich “insider” perspectives on what it is like to live with a severe mental illness, and what helps and hinders processes of recovery (Davidson et al., 2005; Deegan, 1996; Read & Reynolds, 1996). This knowledge has led to radical changes in the understanding of mental health and illness and in the content of mental health services being proposed, and is increasingly permeating international mental health policy (Slade, Adams, & O'Hagan, 2012). Introduction A much cited definition describes recovery as: a deeply personal, unique process of changing one’s attitudes, values, feelings, goals, skills and/or roles. It is a way of living a satisfying, hopeful, and contributing life, even with limitations caused by the illness. Recovery involves the development of new meaning and purpose in life as one grows beyond the catastrophic effects of mental illness. (Anthony, 1993, p. 7) a deeply personal, unique process of changing one’s attitudes, values, feelings, goals, skills and/or roles. It is a way of living a satisfying, hopeful, and contributing life, even with limitations caused by the illness. Recovery involves the development of new meaning and purpose in life as one grows beyond the catastrophic effects of mental illness. (Anthony, 1993, p. 7) This notion of mental health recovery differs radically from clinical recovery, especially regarding the significance of symptoms. While clinical recovery refers to full symptom remission (Liberman, Kopelowicz, Ventura, & Gutkind, 2002), mental health recovery is less about the cure and treatment of illness, and more about the challenges and possibilities of living with various degrees of illness and problems. Additionally, the process of recovery is linked to a higher degree with contextual and social aspects of a person’s life, where social relationships, social roles, and social inclusion are seen as crucial elements for a better life (Repper & Perkins, 2003; Tew et al., 2012; Topor, Borg, Di Girolamo, & Davidson, 2011). Essentially, mental health recovery highlights how people with mental health difficulties must be considered responsible and active agents in their own life and recovery process. Thus, the professional’s engagement related to users’ recovery is closely linked to the promotion of 4 H.P. Solli and R. Rolvsjord self-determination, hope, and community inclusion (Davidson, Tondora, Lawless, O’Connell, & Rowe, 2009). The recovery orientation has clear similarities to community music therapy and resource-oriented perspectives in music therapy. However, the notion of recovery has not gained much attention in music therapy literature, although within the last few years there seems to be an growing interest (Chhina, 2004; Grocke, Bloch, & Castle, 2008; Jensen, 2008; Kaser, 2011; Kooij, 2009; Maguire & Merrick, 2013; McCaffrey, Edwards, & Fannon, 2011; Solli, 2009, 2012; Solli & Rolvsjord, 2008). Introduction In a meta-synthesis of studies of service users’ experiences of music therapy (Solli, Rolvsjord, & Borg, 2013), a central finding was that music therapy contributed to many of the central aspects found important for a person’s recovery process. However, the data material on which this meta-synthesis was based varied in quality and richness, and contained few participants with psychosis. This article reports on a study which features data provided by mental health patients with ongoing psychosis and analyzed using interpretative phenomeno- logical analysis (IPA). The primary purpose of the study was to gain first-hand accounts from people diagnosed with psychosis who were participating in music therapy. This article addresses: (1) what it is like for inpatients with psychosis to participate in music therapy; and (2) how participants with psychosis experience music therapy in relation to their mental health and current life challenges. Downloaded by [Universitetsbiblioteket i Bergen] at 01:53 04 March 2014 The music therapy offered to participants in this study can be characterized as humanistic (Ruud, 2010), resource-oriented (Rolvsjord, 2010), and with influ- ences from community music therapy (Stige & Aarø, 2012). Each participant was offered a 30–60-min weekly individual session in a music therapy room, a weekly 45-min open group session in the ward TV-room, and opportunities to perform music at the hospital’s “season parties” (see Table 1 for actual participa- tion). The therapeutic collaboration involved a wide variety of musical engage- ment, based on the preferences of the participants, but including structured and free improvisations, playing and singing from song-books, learning to play instruments, music listening, song-writing, recording and mixing of music, production of CDs, and uploading songs to the Internet. In addition, verbal conversations were a natural part of all sessions. Participants and setting Prior to data collection, the study received ethical approval from the Regional Committee for Medical and Health Research Ethics, and was reported to the local health and social services ombudsman. Nine participants were recruited from the first author’s music therapy practice at a closed inpatient intensive psychiatric unit at a hospital in Norway. Selection of participants was done purposively, choosing people who were expected to offer insight into the research question (Smith, Flowers, & Larkin, 2009). Participants had to meet the following inclusion criteria: (1) diagnosed with a psychotic illness, and/or have experienced psychosis within the past year; (2) motivated for music ther- apy; and (3) verbally capable of expressing her/himself in an interview. Patients in an acute psychotic phase were excluded or included once acute symptoms had been ameliorated. Criteria for inclusion and exclusion were assessed by the researcher and a psychiatrist or psychologist, based on information collected by the clinical team on the ward. A letter of informed consent was signed by all participants. Three interviews with each patient were intended, but due to practical factors such as sudden discharge and rapid changes in mental condition, an unequal number of interviews were completed with each patient. All partici- pants in the study had a strong interest in music, although this was not a criterion of inclusion. For more characteristics of the participants, see Table 1. Nordic Journal of Music Therapy 5 Table 1. Participant information. Table 1. Participant information. Gender Female 4 Male 5 Age in years Range 21–41 Mean 32 Diagnosis (ICD-10) Paranoid schizophrenia 7 Schizoaffective disorder 1 PTSD and undifferentiated psychosis 1 Hospitalization§ Compulsory 8 Voluntary 1 Contact with mental health services in years Range 2–20 Mean 10 Duration of music therapy in months Range 3–34 Mean 13 Number of sessions Range 14–55 Mean 31 Music therapy format Individual sessions only P2, P6 Individual sessions and groups P4, P7, P8 Individual sessions, groups, and performances P1, P3, P5, P9 Data collection A semi-structured interview guide with open questions was developed through discussion between the present authors (Kvale & Brinkmann, 2009). The sche- dule was intended to capture a wide range of the participants’ subjective experi- ences within music therapy, both musical and relational. The two initial questions were: “What kind of role does music play in your life?” and “Can you tell me about your experiences with music therapy the last couple of weeks?” A flexible and nondirective interview approach was adopted in order to enable the partici- pants to express their experiences in ways that best suited their personal narrative H.P. Solli and R. Rolvsjord 6 style. Strategies for minimizing the level of stress for people with cognitive and verbal challenges whilst maximizing the quality of the interviews was used (Kirkevold & Bergland, 2007). Participants were interviewed individually by the first author in durations of 15–40 min adjusted to their mental and emotional state and response. As a rule, the interviews were done in separate sessions, but due to the participant’s mental and emotional states some interviews were conducted in the continuations of the music therapy sessions. All interviews were recorded and transcribed. The double role as therapist and researcher was experienced as advantageous in order to lower the stress level of the participants, and in gaining a deeper understanding of their context. However, this double position called for a reflexivity (Finlay & Gough, 2003; Stige, Malterud, & Midtgarden, 2009) and review of attitudes and positions throughout the project. The use of reflexivity notes, clinical supervision, and regular conversations with the research super- visor (second author) was important in this process. Alternation between the closeness that gave access to vital knowledge and the reflection that allowed critical thinking was of great importance. It was also important to be reflexive about possible tendencies for participants to withhold negative experiences and exaggerate positive aspects when being interviewed by their therapist. Analysis The data was analyzed using IPA, as outlined by Smith et al. (2009). The goal of the analysis was to learn something from the participants’ psychological world, and to try to understand the meaning of the content by engaging in an inter- pretative relationship with the text. First, each interview transcript was read a number of times and relevant parts were marked. Remarks and initial codes were noted in the right-hand margin, using the software Atlas.ti. After several rounds of reading transcripts while editing and developing emerging codes, there was a process of grouping codes into associated families or clusters. Then, code families that were closely connected were merged and renamed, before the clusters most prominent in terms of illuminating the research question were chosen as key themes. The final step of the data analysis was the writing phase, where the selection of extracts for each theme was processed into larger parts of text. At all stages of this analytic interpretative process, there was a constant alternation in focus, moving back and forth between details in the text, the wholeness of each interview, the sum of all interviews and the project as a whole, as well as various theoretical perspectives, often referred to as the hermeneutic circle or spiral (Alvesson & Sköldberg, 2000). Findings Four super-ordinate themes were drawn from the analysis, as presented in Table 2. 7 Nordic Journal of Music Therapy Table 2. Key themes and sub-themes. Theme 1: Freedom Theme 2: Contact Table 2. Key themes and sub-themes. Theme 1: Freedom Freedom from illness Freedom from stigma Freedom from treatment Theme 2: Contact Contact with oneself Contact with aliveness Contact with emotions Contact with other people Theme 3: Well-being Enjoyment and satisfaction Motivation Mastery Hope Theme 4: Symptom relief The psychotic state Disturbing thoughts and voices Visual hallucinations Freedom from illness Freedom from stigma Freedom from treatment Contact with oneself Contact with aliveness Contact with emotions Contact with other people Enjoyment and satisfaction Motivation Mastery Hope The psychotic state Disturbing thoughts and voices Visual hallucinations Theme 2: Contact Theme 3: Well-being aded by [Universitetsbiblioteket i Bergen] at 01:53 04 March 2014 Theme 4: Symptom relief Theme 1: Freedom Freedom from illness: Most of the participants stated some kind of ambivalence in relation to music and music therapy being connected to their diagnosis and treatment of their condition. Rather, they described music therapy as a place where they managed to take their mind off the illness: P1: There’s a freedom from all possible illness, then… and psychosis and everything that’s bothersome. There’s something good and creative in this room. HP: Did you notice that when you came into the room now? P1: Yeah, I mean I've always noticed that it's good to be here. It’s peaceful, you know. It’s peaceful in this room. There’s no disease in this room. There are no negative spirits here, somehow. There’s peace. The everyday situation at the ward was described as extremely demanding, both because living in a closed ward together with other people in crisis was a challenging experience, but also because major parts of the treatment focused strongly on their diagnosis and deficits. In this context music therapy was experienced as a sanctuary, a setting that afforded experiences of freedom and peace, or at least some distance from their everyday struggle. I haven’t had the feeling of mastering so much while I’ve been here at the hospital. It’s mostly been complicated stuff that I’m supposed to relate to … and learn from, so I don’t end up where I started, sort of thing… so I don’t end up at the doctor's office again. But I’ve sort of forgotten about that when I play. I don’t think about those things. I suppose I think less and less about the difficult things the more I play…or the more I listen to music… (P9) H.P. Solli and R. Rolvsjord 8 Several participants expressed skepticism about the idea of music being used as treatment, as if this would be a way of intruding into one of the few illness-free zones they had left. I think that it [music therapy] should be an area that is free from analyzing and stuff. It should just be about music. Not necessarily what … kind of diagnosis you have. You shouldn’t have to talk about such things here. I think that’s the best, you know… (P4) In contrast, one participant (P3) expressed that she would like to discuss her psychotic experiences more frequently in music therapy. Theme 1: Freedom Freedom from stigma: The staff’s general focus on illness at the hospital was often experienced as overwhelming and intense, leaving some participants with a struggle of identity, fighting against the stigmatic role of being a “psychiatric patient”. In contrast, music therapy was experienced as helpful in rebalancing self-perception, enabling participants to discover or reawaken their own interests and abilities. Being able to demonstrate their musical resources to other patients and staff, whether via music therapy groups, performances, or recorded CDs, was experienced as a means of fighting stigma. Once I come here [to the hospital], I’ve got “sick” written on my forehead. And then there’s lots of staff-members who talk to me like I'm really sick and stuff. (…) Because I often feel like a misfit, that there’s sort of so much wrong with me, you know? And when I'm here [in music therapy], then I don’t feel that there’s so much wrong. (P3) Freedom from treatment: Most of the participants said that they enjoyed the fact that music therapy sessions did not focus strongly on their illness and problems: “Because there’s enough of that elsewhere” one woman remarked (P2). Paradoxically, music therapy was often experienced as a break from treatment: Freedom from treatment: Most of the participants said that they enjoyed the fact that music therapy sessions did not focus strongly on their illness and problems: “Because there’s enough of that elsewhere” one woman remarked (P2). Paradoxically, music therapy was often experienced as a break from treatment: HP: Did you think that music therapy was a part of the treatment you got here, or did you think of it as something else? P7: Hmm … I suppose I thought of it as something different … actually. In fact, I think of it almost the opposite way. It’s not a part of the treatment, it is an alternative to treatment. It is something else … more like a break from treatment. Most of the music therapy processes did include engagement with difficult themes and emotions in the patient’s present situation. However, music therapy was experienced as handling these themes differently than other treatment approaches at the hospital. A woman whose individual sessions included the writing and recording of a song about her self-harming reflected: 9 Nordic Journal of Music Therapy I think I got to express some thoughts and stuff without necessarily having some- one trying to fix it. Theme 1: Freedom Just see how it is…(…) Often when someone talks … or if I say something … almost always someone will suggest what I should do with it, or give me extra pills, or whatever… Whereas when we made up [a] song, then it wasn’t … there wasn’t any answer… it was just a sort of expression. (P2) Theme 2: Contact So the only thing I can do, then, is to cut myself, because then I can feel my body. (…) But as soon as I start to beat the drums then …there is something that works (…) I feel … you know … a little bit … actually a bit the way I feel when I have harmed myself. That sort of … well … I'm here, sort of [touches her hand]. Here it ends in a way, and here it begins. (P2) Contact with emotions: Music as a promoter of emotional contact was high- lighted by all participants and constituted the greatest number of coded sections. Accounts pointed toward music therapy as an arena where emotions (and feel- ings) are noticed, created, developed, and expressed. Music is releasing. It can bring so many emotions. (…). Creates feelings. Gives feelings. It is feelings. So that you get feelings. You get new feelings, get inspired. Or just feel something or think something, reflect a bit, think something new, change yourself, get associations, immerse yourself in something, remember … have memories … (P8) Music was highlighted as a particularly good way of connecting with, and expressing, emotions connected to pain, anger, and aggression. Using swearing and rude words in song-lyrics and raps, and hitting drums, and playing on distorted guitars, were given as examples of ways of getting in contact with and expressing these emotions. Performing and producing CDs provided oppor- tunities for communicating emotions and experiences to other people both inside and outside the hospital. Because I… I feel… when I sing and stuff, then I get a lot out… like anger and dirt, in a way. So I feel I’ve become more like conscious, then, and … stronger … (…) I feel it has helped me very much to dare to say “Fuck you, Child welfare!” and show it to others. You know, to show them that I'm aggressive and angry because someone’s done something wrong. And that… that what they’ve done is not right, in a way. (P3) Contact with other people: That music was a way of making contact with other people was also a major finding in this study. Musical interplay was experienced as an arena where contact was important in order to make the music flow and groove. I try to look at you sometimes then to see where I am… and see what you think… about where we are. (P6) Theme 2: Contact Contact with oneself: Music was described as a personal matter by all of the participants. Accounts suggested that some music was experienced as touching closely on personal and social identity, and that music could provide a strong sense of being oneself and having an inner core. For me it [the music] … is therapeutic because it … it hits a nail within myself… in a way, that tells me… that the music hits me in a way … that gives me a feeling of that…I belong in the music, this is me, the music is me – exactly the music I hear now, it’s me. (…) I find a real sense of identity in music. And a feeling of being home… and personal … personal … re-involvement in myself … every time I listen to music. (P6) Music therapy was also connected to positive change and development regard- ing participants’ own identity, self-awareness, self-confidence, and self-esteem. I feel I've become a different person after having these sessions. Because it's … I feel like I've been more like… Before I was a bit like shy and stuff… and I was maybe not that present and stuff. But after these sessions, I felt I’d really got more guts inside me. (P3) Contact with aliveness: Experiences related to a sense of aliveness and presence were reported by several of the participants. These sensations were described as being manifested through bodily sensations, “sparkling” feelings, experiences of taking up space in the room, and awareness of becoming “a new human being”. HP: How does it feel to sing it, then? P8: It's like being in love. It tickles in my stomach and it …. My heart beats and I feel the pulse in my fingers and in my body and I feel alive, happy for life, and full of emotions and strength, and that I’m master- ing something, and that I’m expressing something … that I really mean. One of the participants experienced loud improvisations on a drum kit as enabling her to become more alive and aware of her body and breath, helping her to separate herself from the rest of the world – experiencing sensations similar to when she cut herself with razor blades. 10 H.P. Solli and R. Rolvsjord I don’t know my body that well … it's sort of numb. Theme 2: Contact Musical and social relationship with the music therapist was experienced as an important first social step, and for some of the participants an eye-opener that made them more aware of the importance of being social. When I'm alone then it [the rap] doesn’t work at all. But when I'm here, then I always come up with something. (…) When you're sitting there with the drums, then something … it's like something … I’m rapping. If you left, the rap would disappear, really. But when you come here, then it's there, right? (P1) I try to look at you sometimes then to see where I am… and see what you think… about where we are. (P6) 11 Nordic Journal of Music Therapy Several participants talked about music as a way of connecting to the world outside the hospital. Some of them had experienced giving a CD with their own recordings to other patients, staff, friends, or family as a way of connecting socially or maintaining social relationships with others. Accounts also included making friends at public concerts, joining a choir or band, uploading music to the web, and chatting with people who listened to it, or trying to get a gig. I was out a couple of days ago. Then I went into a pub. So I started talking to a guy there, you know. Then it turned out he was the man responsible for the music, you know. So he got my email and my phone number. (…) Maybe I'll get a gig, then. (P5) Theme 3: Well-being Enjoyment and satisfaction were the most prominent aspects referred to by participants in this study. Many of the participants used words like fun, amusing, and happy to describe their participation in music therapy. No, I think it's been fun, pure and simple. (P4) It’s been a rush of happiness really. It’s been positivity all the time. There’s not been anything negative, you know? That struck me as a bit unusual … (P9) Being admitted to a closed ward for several months was referred to as inactive, boring, and de-motivating. In this context the enjoyable qualities of music therapy were highly valued. So it [music therapy] has been positive in that phase where I was stuck in the hospital, then. I didn’t have much else to do here. At that time I had nothing else to do at the hospital. Just walked back and forth in the hallway, and ate and slept and didn’t do much else. It filled the day a little bit anyhow. Made it a better stay. (P9) Yes, the music is something that pulls me up. Music pulls me up. It's therapeutic for me. It’s a pity I don’t do it more often because I benefited from it. I get very much pleasure from it. (P6) Although participants highlighted that music therapy made them feel better, more satisfied, and healthy, music therapy was not experienced as diminishing all worries and problems, but rather as bringing more wellness into life despite the challenges caused by the illness. I’ve felt very well when I've been here [in music therapy], you know. Even though I have seen things and stuff. But I've felt very healthy and well, you know. (P3) Motivation: A majority of the participants talked about music therapy as a motivating activity, something they looked forward to and therefore managed 12 H.P. Solli and R. Rolvsjord to attend, even when having a bad day. Often music therapy was highlighted as being more motivational than other forms of therapy at the hospital, and a general complaint was that one session a week was too little. I think it’s much easier to wake up to music therapy than to other boring stuff. Conversations and stuff, I’m almost not capable of that. (P3) I've been looking forward to it. It's the only thing I've been looking forward to here. To succeed, or be able to complete a project, you know … that makes you feel better automatically. That it is you who has done it, and that it was actually good, and that others like it … then you’ve done something that points in the right direction. (P5) Theme 3: Well-being But I had no joy, there was nothing … I thought it sounded insanely better when I did it myself: then when you recorded it, I got a fucking disappointment, that is. (…) I know for myself that I sounded better than that … I know that because I used to take lessons. (…) It was a heavy disappointment. I became very depressed. P6: No, I was admittedly very poorly prepared then. But I had no joy, there was nothing … I thought it sounded insanely better when I did it myself: then when you recorded it, I got a fucking disappointment, that is. (…) I know for myself that I sounded better than that … I know that because I used to take lessons. (…) It was a heavy disappointment. I became very depressed. Hope: It was evident in this study that participation in music therapy was connected to experiences of hopes and dreams for many participants. In a life situation described as full of obstacles, mental health threats and pain, music and music therapy were connected to an amplified hope for a better future. So I feel that it gives me huge joy and lots of hope. I somehow look forward [to the future] when I'm doing music. (P3) So I feel that it gives me huge joy and lots of hope. I somehow look forward [to the future] when I'm doing music. (P3) Several of the participants spoke about their plans for continued musical engage- ment, for playing and performing music after discharge. Some plans were perceived as more realistic, while other statements were interpreted as dreams or wishes with more unrealistic outlooks. However, they all depicted music as a strong facilitator of hopefulness. Yes, it’s my dream to work as an artist and make money out of it. And make a living of it. Maybe do some concerts now and then, and… some gigs, who knows? Theme 3: Well-being (P8) As a majority of the participants were compulsorily detained at the hospital, their motivation for receiving help was initially quite small. However, music therapy was described as a service that contributed to reconsideration of their resistance against hospitalization. One woman said that if she could have had music therapy every day, she would have admitted herself voluntarily (P8). Another participant said: Yeah, I really mean it. If it weren’t for the music therapy, I wouldn’t have been able to stand being here. Then I would have run off long ago, maybe… (P5) Some of the participants compared music therapy to other forms of therapy, conveying that they found music therapy more motivating because of its physi- cal, active, social, and enjoyable nature. You get the chance to develop a part of yourself, not just be passive. Because I often find that a lot of the verbal treatment, conversations with the doctor and psychologist, it’s very passive, you …become very superficial and very pas- sive. (P7) Mastery: Most participants talked about experiences of mastery in music therapy. These experiences were often related to their own sensations of coping with an instrument or a piece of music, but were also connected to reactions from other people during a group session or a performance. I think I mastered the tam-tam drums. Like Mona [a fellow patient], she came up to me and said “you're really good at playing”, you know. That’s nice. So I try to be nice in return. It’s positivity. It leads to something positive. (P9) Recordings and performances experienced as successful by the participants were reported to give sensations of mastery, to promote feelings of wellness and afford better self-esteem: To succeed, or be able to complete a project, you know … that makes you feel better automatically. That it is you who has done it, and that it was actually good, and that others like it … then you’ve done something that points in the right direction. (P5) 13 Nordic Journal of Music Therapy In contrast, two of the participants in this study had negative experiences of their not having achieved mastery when listening to recordings of themselves. For one man this was very hard to cope with: HP: When you played the saxophone – it was not just positive for yo P6: No, I was admittedly very poorly prepared then. Theme 4: Symptom relief3 The psychotic state: Many participants did not want to go into detail about their psychotic experiences and how these related to music. Several reasons were given for this: that, as psychotic experiences were not a common theme in music therapy sessions, it felt strange to start talking about them in the interviews (P7); that psychotic experiences were so complex that a lot more time would be needed to explain them (P6), or that psychosis or illness should not be a part of music therapy at all (P4). These responses can clearly be linked to the issue of freedom, as described under theme 1. For participants who shared their accounts about how music and music therapy related to the condition of psychosis, each story had a personal and unique character. One participant said that, in general, treatment had made her become sceptical toward the reality of the world around her, but that music therapy was different. aded by [Universitetsbiblioteket i Bergen] at 01:53 04 March 2014 Downloaded by [Universitetsbiblioteket i Bergen] at 01:53 04 March 2014 P2: What's scary with this ….. to be told that you have this kind of diagnosis, is that suddenly you can’t rely on the world, you can’t rely on yourself, because it’s not all that is there for real (…) P2: What's scary with this ….. to be told that you have this kind of diagnosis, is that suddenly you can’t rely on the world, you can’t rely on yourself, because it’s not all that is there for real (…) HP: Does music therapy do anything in relation to … to it, sort of, you being more sceptical or less sceptical, in a way? P2: No, what’s nice, maybe especially, is that here it doesn’t matter if it’s true or not, it … it's good anyway. It doesn’t matter to me if it’s real or not. One participant said that music had a positive and transformative impact on what he called “the spell”: One participant said that music had a positive and transformative impact on what he called “the spell”: HP: How is it to play music or listen to music? P6: It can amplify the spell in a positive way. Theme 3: Well-being (P5) Having a hobby that theoretically has the potential of bringing success and fame, no matter how unrealistic that dream may seem at the moment, was an aspect of playing music that was inspiring for one participant: Having a hobby that theoretically has the potential of bringing success and fame, no matter how unrealistic that dream may seem at the moment, was an aspect of playing music that was inspiring for one participant: I'm thinking, damn, I may not be the next Madonna, but I'm not going to be the next Madonna … I do have an alter ego name, though… But I… You do want to have a hobby, and then you sometimes get some stars in your eyes. But it's fun to dream! And maybe you can develop it one day into something big (…) But now I’m on social security, so I can keep on with it on my spare time. (P8) For one participant, music was experienced as so important that he could not imagine managing life without it, referring to music as being the essence, nourishment, sound, hobby, and creativity in his life. 14 H.P. Solli and R. Rolvsjord It [the music] has saved me many times, I guess…that I've always had a hobby. (…) Creating something instead of being destructive, kind of. (P5) 3To some degree, themes 2 and 3 could also be related to the relief of symptoms, particularly negative symptoms. This category is to a larger degree about psychotic experiences, also referred to as positive symptoms. Theme 4: Symptom relief3 The psychosis may become pleasurable and with, with, with … it may seem … like … a healthy nerve activity (…) compared to a negative nerve activity as psychosis is often found to be, you know, for humans… In contrast, one of the participants had no experience of music affecting psycho- tic experiences. When asked if music therapy and music therapy were helpful for her in relation to her illness and health, she connected music to emotional states, but doubted that it could influence psychosis in any way (P7). 15 Nordic Journal of Music Therapy Disturbing thoughts and voices: Participation in music therapy was described as having a vital impact on what were referred to as thoughts by some and as voices by others. These thoughts or voices were often characterized as threaten- ing, destructing, and disturbing, and were constantly present in the participant’s everyday life. In particular, active music playing and improvising on instruments were reported to moderate or even eliminate annoying thoughts and voices whilst playing, and sometimes for a few hours after a session. Playing music together with the therapist was reported to be better than listening to music at home. I've stopped thinking destructive thoughts, at least when I've been playing music, then. (P9) I've stopped thinking destructive thoughts, at least when I've been playing music, then. (P9) Patients’ explanations of why music and music therapy were helpful included calming down, being distracted, concentrating, and refocusing. It’s one of the few things that really helps me get rid of these driving thoughts. Maybe it’s just about focusing on something else. Calming down and focusing on something else, simply. You follow the music instead of grinding round and round in your head all the time. (P2) One participant said that playing loud music helped her to drown out what she experienced as loud and annoying sounds around her. P2: The beauty of playing drums is that it drowns out, in a way … all the annoying sounds that bother me otherwise, as… HP: Yes. Voices that you hear, or..? P2: Yes, sort of … kind of, the way that clock [points at the clock on the wall], it becomes difficult to concentrate … when it keeps on like that… HP: Because you hear it very loudly? P2: I hear it very well. Also the hiss from … HP: From the radiator? Theme 4: Symptom relief3 P2: Yes HP: So the drum set really takes up all the space? P2: Yes, it feels so good! P2: The beauty of playing drums is that it drowns out, in a way … all the annoying sounds that bother me otherwise, as… HP: Yes. Voices that you hear, or..? P2: Yes, sort of … kind of, the way that clock [points at the clock on the wall], it becomes difficult to concentrate … when it keeps on like that… HP: Because you hear it very loudly? P2: I hear it very well. Also the hiss from … HP: From the radiator? P2: Yes HP: So the drum set really takes up all the space? P2: Yes, it feels so good! Only two participants talked unreservedly about hearing voices (P1 and P3). One participant reported that music was so important to her that she gained strength to battle and take control over the voices. HP: What happens with the voices then, when you're doing music? P3: With my voice? 16 H.P. Solli and R. Rolvsjord HP: No, the voices you hear … you just said that you hear voices inside your head. What happens when we’re singing and stuff down here? P3: No, then I say like: Fuck you! Now it's my turn! HP: Really? P3: Yes! HP: Do they say something back, then? P3: Yes, they say: “No. You listen!” And I just say: “No, fuck you, it's my turn now!” HP: And then you sing? P3: Yes! HP: No, the voices you hear … you just said that you hear voices inside your head. What happens when we’re singing and stuff down here? P3: No, then I say like: Fuck you! Now it's my turn! HP: Really? P3: Yes! HP: Do they say something back, then? P3: Yes, they say: “No. You listen!” And I just say: “No, fuck you, it's my turn now!” HP: And then you sing? P3: Yes! aded by [Universitetsbiblioteket i Bergen] at 01:53 04 March 2014 Downloaded by [Universitetsbiblioteket i Bergen] at 01:53 04 March 2014 Visual hallucinations: One participant talked about seeing things in the room that she knew were not real, usually referred to as visual hallucinations (P3). Theme 4: Symptom relief3 For this woman, improvising on the drum kit together with the music therapist on bass guitar became a way of battling what she first experienced as shadows and later called “dead people” present in the room. In an interview done immediately after a session she explained how such an improvisation on drums and bass had had an impact on her visions. HP: How was it just now when we came into the room and talked together? P3: Well, I had a belief that I have become a spirit. So I had to help those in the church cemetery. And just then I saw a dead body … who was sitting behind you. But when I started playing and so on then I started thinking about other things, and then suddenly I looked there, and it was gone. HP: What was it that happened then, do you think? P3: I don’t know, but I think my brain wanted to focus on something else because I was thinking very strongly that I had to get rid of this image. Discussion Our analysis highlighted four super-ordinate themes central to participants’ experiences in music therapy: freedom, contact, well-being, and symptom relief. The overall impression of our findings is that music therapy is highly appreciated amongst patients, and is experienced as positive and supportive in relation to their life situation and health in multiple ways. In this respect, we may say that the users’ perspective outlined in this article does not diverge from previous findings in outcome studies of music therapy for patients with psychosis, but rather confirms previous accounts of the effectiveness of music therapy. However, as will be discussed, our findings, and in particular those connected to the “freedom” theme, at the same time challenge and even question the role of music therapy as part of treatment provision. 17 Nordic Journal of Music Therapy A prominent finding was that music therapy was experienced as engaging, motivating, and enjoyable by all of the participants. Psychotic illness (i.e. schizophrenia) is in general characterized by apathy, lack of motivation, and emotional flatness (Faerden et al., 2009), referred to as negative symptoms, or as a necessary coping strategy (Boevink, 2012). These are serious aspects of psychotic illness which prognosticate poor functioning and quality of life (Katschnig, 2000), and where standard treatments show limited progress (Kirkpatrick, Fenton, Carpenter, & Marder, 2006). Given these premises, the participants’ reports of how music therapy made them feel more vital, uplifted, joyful, hopeful, and motivated, and enabled them to become more active parti- cipants in their everyday lives, constitute an important and promising finding. Here too, we may say that the present study confirms results from outcome studies with regard to the significant effects of music therapy on negative symptoms for people with severe mental illnesses (Gold et al., 2009, 2013; Mössler et al., 2011), although in our findings such aspects were linked to experiences of well-being (that is, to an increase of positive health) rather than to a reduction of negative symptoms. In the light of the users’ experiences, we may therefore suggest that it is more appropriate to describe recovery processes in terms of the level of positive health (i.e. as described by Provencher and Keyes (2013) on a continuum from languishing to flourishing) than in terms of symp- tom reduction. A second prominent finding was the participants’ experiences of being in contact. Discussion The fact that some of the participants joined group music therapy while other did not (see Table 1) could be a factor that affected how music therapy’s role in facilitating such contact was perceived, but no clear tendencies were identified. Experiences of contact may be discussed in relation to a vital but undervalued aspect of the development and character of psychosis: the sub- jective experience of alterations of the first-person dimension (Davidson & Strauss, 1992; Lysaker, Buck, & Lysaker, 2012). Such alterations are described as “a sense that I had lost myself, a constant feeling that my self no longer belonged to me” (Kean, 2009, p. 1034). This lost or weakened capacity for intrapersonal and interpersonal dialogue, often referred to as ipseity disturbance (Pérez-Álvarez, García-Montes, Vallina-Fernández, Perona-Garcelán, & Cuevas-Yust, 2011), was also reported among participants in our study. Here, music was experienced as something that was closely connected to identity and a sense of having an inner core, whilst music therapy was reported to help in regaining contact with a sense of self, identity, and aliveness. With a missing vital presence in one’s own life, interpersonal contact becomes overwhelming: hence a diminished personal identity and sense of self are closely connected to social agency (Lysaker et al., 2012). We found that many participants related music therapy to a renewed motivation for being in contact with others. These findings suggest that music therapy is an approach that can meet some of the core challenges for people who are experiencing psychosis in a promis- ing way. 8 H P S lli d R 18 H.P. Solli and R. Rolvsjord In general, there is a lack of knowledge about potential harmful conse- quences in art-based therapy for patients with psychosis (Ruddy & Milnes, 2005). In our study seven patients reported no harmful or negative experiences related to their participation in music therapy. The two remaining participants, who in general found music therapy helpful, reported negative experiences from listening back to audio recordings of their own musical performance. They both expected their singing or playing to sound qualitatively better than it did to them on listening back to the recording, and consequently they felt intimidated by the recording. This can be understood in terms of a “reality check” for people with an unrealistic estimation of their own skills, or a reaction to a sudden realization that prior skills are no longer intact. Discussion 7) and the relation between the interventions and symptoms (de l’Etoile, Nordic Journal of Music Therapy 19 2002) are generally the focus of attention. Our analysis of firsthand accounts demonstrates that participants were generally less concerned with how music therapy reduced symptoms and increased functioning, instead emphasizing more experiences related to their own well-being, hope, or meaning, and indeed sometimes even resisting the very notion of music therapy as concerned with illness and treatment. These factors are all highlighted as important for mental health recovery (Leamy, Bird, Le Boutillier, Williams, & Slade, 2011; Provencher & Keyes, 2013). More traditional “clinical outcomes” (such as decreases in anxiety and disturbing thoughts) were mentioned by some of the participants, but these had the character of being of secondary importance. This harmonizes with Davidson et al.’s (2009) understanding of the relationship between mental health recovery and clinical recovery: Processes involved in a person’s entering into and being in recovery include the processes that appear to lead to a reduction in the illness as well. The opposite, however, would not necessarily be true. In other words, if we begin with describing the processes involved in minimizing deficit, disability, and dysfunction, we may never arrive at a process of maximizing the person’s health and everyday life. Beginning with the person’s everyday life and his or her efforts to live with the illness, on the other hand, naturally extends to efforts to minimize the illness as disrupting or posing barriers to that life. In brief, minimizing illness is not the same as maximizing health, and our model must incorporate both. (p. 34) Such a perspective might shed light on the paradoxical “opposite of treatment” health-promoting experiences of our participants. In our study, the participants found themselves “treated” by a professional to a certain extent, but they never- theless experienced music therapy as an invitation into a non-clinical arena for music making that made them feel more “normal” and well. This points to a discrepancy between how participants in our study experienced music therapy, and the top-down rationale represented in many outcome studies and clinical models, where professionals provide methods, techniques, and interventions aimed at the improvement of the patient’s symptoms and functioning (Odell- Miller, 2007). Discussion Either way, these experience triggered emotions that were difficult to process in the participants’ current life situations. In this respect, music therapists need to exercise a high degree of reflexivity and caution when recording music with this group of patients. We must emphasize, however, that such singular episodes of negative experiences in the context of an overall positive experience call for qualified and mindful music therapy practice, rather than disfavoring music therapy in work with people diagnosed with psychosis. The most conspicuous finding in this study was that, despite the overall positive user experiences of music therapy as supportive and helpful, several of the participants did not consider music therapy to be a treatment, instead emphasizing its representation of freedom from illness, stigma, and treatment. This was connected to experiences of music being one of the few illness-free spaces or zones in their lives. In consequence, several of our participants expressed strong opposition toward the mixing of music and psychiatric treat- ment. Thus, it seemed that for many of the participants, music therapy aligned with a precious area in their life that they experienced as outside the realm of illness and treatment. To avoid intruding upon or damaging such a “musical sanctuary”, we need to be open to the idea that for some patients, and perhaps especially those with a particular interest in music, music therapy may not always be appropriate. The findings in this study, however, indicate that music therapy may align with and support the health-promoting use of music by “nurturing” such a freedom zone of engagement with music. Moreover, it seems that for many of our participants it was exactly within this paradox “opposite of treat- ment” that they found music therapy useful. However, for this to be possible, it is crucial to acknowledge the risks of “pathologizing” or “medicalizing” music if music therapy is framed within a clinical context of assessment or diagnosis- specific interventions (Rolvsjord, 2010). There is no consensus as to how music therapy processes should be under- stood in terms of what helps or what the “mechanisms of change” are (Gold et al., 2013). Outcome studies primarily adhere to a pathogenic paradigm, where mental health is understood as the absence of pathology (Provencher & Keyes, 2013). Thus, symptom reduction and functional improvement (Mössler et al., 2011, p. Discussion Hence, an understanding of music therapeutic processes as a matter of mechanisms changing something within the client may not be the most fruitful approach, partly because it ignores the patient’s own participation and contribu- tions (Rolvsjord, 2010, 2013; Stige, 2012b), and partly because it ignores the potentials of the freedom space so much appreciated by our participants. We argue that the notion of agency is a better point of departure for understanding why music therapy is found to be helpful for persons with severe mental illness. Agency can be understood as “the perceived ability to affect one’s own destiny and to engage meaningfully with others and reflects the dimensions of mastery and positive relationships with others” (Provencher & Keyes, 2013, p. 285). Theoretical perspectives in music therapy suggest that the musical interaction in music therapy may offer potentials for such experiences (Abrams, 2012; Ruud, 20 H.P. Solli and R. Rolvsjord 1997, 2010). Further, these elements of agency correspond to a high degree with our findings in this study, where participants reported that music therapy was an arena for engagement, mastery, and relationship. By playing music, writing songs, recording CDs, and performing music, music therapy became an arena for making sound, taking space, feeling alive, and being somebody – processes in which the participants regained experiences of ownership and authorship of their thoughts, feelings, and actions (Lysaker & Leonhardt, 2012). According to Davidson and Strauss (1992), entering the role of active agent in one’s own life and becoming a more social human being is interlinked with the process of discovering the possibilities of possessing a more positive and active sense of self. Thus, the recovery perspectives emphasize a radical level of user participa- tion related to service provision (Slade, 2009). Linked to such ideas of user participation, the possibilities to promote clients agency in music therapy have political implications regarding power relations and civil rights (Baines, 2013; Edwards, 2006; Solli, 2012; Stige, 2006). To enhance agency is empowering and regarded as a cornerstone of hope (Allen, Munich, & Rogan, 2004), which is, in turn, seen as a vital aspect of an ongoing recovery process (Slade, 2009). Discussion By maintaining a primary focus on the development of a positive sense of self and identity, and on promoting active and responsible roles in music therapy (and in life), music therapists will be able to support processes of personal and social recovery, something that also leads to symptom relief and better functioning (Davidson et al., 2009). As mental health care worldwide seems to be starting to adapt to the perspective of mental health recovery (Slade et al., 2012), and promotion and protection of mental health as a positive state is becoming a new goal (Fledderus et al., 2010; Herrman et al., 2005), so working within these rationales should make music therapy an attrac- tive approach to help people diagnosed with psychosis in years to come. This could make music therapy relevant in a range of settings, from acute wards, via diverse service centres, to non-clinical community settings. Funding This project has been financially supported by the Norwegian ExtraFoundation for Health and Rehabilitation through EXTRA funds, and by Lovisenberg Diakonale Hospital. Notes on contributors Hans Petter Solli is trained as a music therapist from the Norwegian Academy of Music, and holds a position as a music therapist at the Psychiatric unit of Lovisenberg Diakonale Hospital in Oslo. He is currently completing his PhD at GAMUT, The Grieg Academy – Department of music at the University of Bergen with a project about music therapy as recovery-oriented practice for people diagnosed with psychosis. aded by [Universitetsbiblioteket i Bergen] at 01:53 04 March 2014 Randi Rolvsjord is an Associate Professor in music therapy at the Grieg Academy – Institute of Music, University of Bergen, Norway. She is a music therapist with a Master in musicology from University of Oslo. She has practiced for many years as a music therapist in mental health care contexts, and published on topics of mental health and feminist perspectives. She holds a PhD from the Aalborg University with a dissertation on resource-oriented music therapy. Conclusion We have outlined four main themes of informants’ experiences of their participa- tion in music therapy. Our study confirmed many of the positive findings from outcome studies, but diverged as to how music therapy should be presented to best help patients in their current life situations. The perspective of mental health recovery was found to align to a substantial degree with the participants’ view of what helps and hinders processes of personal and social recovery. We have argued that mental health recovery, with its particular focus on personal and social agency, is a better framework for music therapy for patients with psychosis than a primary focus on symptom remission and elevation of functions. Based on the current findings, we argue for a shift in focus away from illness reduction toward promotion of positive mental health and wellness, away from a primary focus on methods, techniques, and interventions toward music as freedom to be 21 Nordic Journal of Music Therapy healthy, and away from standardized procedures and manuals toward a primary focus on personal and social agency. References Abrams, B. (2012). A relationship-based theory of music therapy: Understanding pro- cesses and goals as being-together-musically. In K. E. Bruscia (Ed.), Readings on music therapy theory (pp. 87–119). Gilsum, NH: Barcelona. Allen, J. G., Munich, R. L., & Rogan, A. (2004). Agency in illness and recovery. Unpublished manuscript. The Menninger Clinic and the Menninger Department of Psychiatry and Behavioral Science at the Baylor College of Medicine. Retrieved from http://www.menningerclinic.com. p g Alvesson, M., & Sköldberg, K. (2000). Reflexive methodology. 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P., Krüger, V., & Lie, S. A. (2009). Dose-response relationship in music therapy for people with serious mental disorders: Systematic review and metaanalysis. Clinical Psychology Review, 29, 193–207. doi:10.1016/j.cpr.2009.01.001 Grocke, D., Bloch, S., & Castle, D. (2008). Is there a role for music therapy in the care of the severely mentally ill? Australasian Psychiatry, 16, 442–445. doi:10.1080/ 10398560802366171 Grocke, D., Bloch, S., & Castle, D. (2009). The effect of group music therapy on quality of life for participants living with a severe and enduring mental illness. Journal of Music Therapy, 46(2), 90–104. doi:10.1093/jmt/46.2.90 py ( ) j Hammel-Gormley, A. (1995). Singing the songs: A qualitative study of music therapy with individuals having psychiatric illnesses as well as histories of childhood sexual abuse (Unpublished doctoral dissertation). New York University, New York, NY. Retrieved form http://steinhardt.nyu.edu Herrman, H., Saxena, S., & Moodie, R. (Eds.) (2005). 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A Case in Which Focal Convulsion Was the Initial Sign of Fatal Aortic Dissection
Aorta
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Published online: 2019-12-31 Published online: 2019-12-31 Published online: 2019-12-31 THIEME THIEME Case Report 144 144 Abstract Focal convulsion as an initial sign of aortic dissection is extremely rare. Type A aortic dissection involves the aortic arch, which may result in seizure either through the extension of the dissection into the common carotid arteries or through thromboem- bolism or cerebral hypoperfusion. Physicians should perform whole body computed tomography to determine whether or not dissection is present when treating patients with convulsion and a high level of fibrin degradation products. Keywords ►focal convulsion ►aortic dissection ►thromboembolism revealed no specific findings. A blood test revealed the following: white blood cell count, 10,000/μL; hemoglobin, 13.9 g/dL; platelet count, 12.7  104/mm3; total protein, 6.5 g/dL; glucose, 121 mg/dL; total bilirubin, 0.5 mg/dL; aspartate aminotransferase, 21 IU/L; alanine aminotrans- ferase, 16 IU/L; creatine phosphokinase, 77 IU/L; blood urea nitrogen, 17.2 mg/dL; creatinine, 0.70 mg/dL; sodium, 140 mEq/L; potassium, 4.1 mEq/L; chloride, 104 mEq/L; C-reactive protein, 0.3 mg/dL; activated partial thrombo- plastin time, 32.5 (26.2) s; international normalized ratio of prothrombin time, 0.98; fibrinogen, 217 mgL/dL; and fibrinogen degradation product (FDP), 377 μg/mL; tropo- nin T was not detected. Head computed tomography (CT) showed normal findings, head magnetic resonance imag- ing (MRI) showed only old lacunar infarctions, and MR angiography did not show any significant stenosis due to dissection. As her initial complaints subsided spontane- ously, the internal physician and neurologist allowed her to return home. However, the next morning, she was found in cardiac arrest by her family. She was transported to our hospital again. Her initial rhythm was asystole and advanced cardiac life support failed to obtain a return of spontaneous circulation. Autopsy imaging revealed Stan- ford’s Type A aortic dissection with cardiac tamponade (►Fig. 1). Her family did not permit a classical autopsy. Introduction Patients with aortic dissection (AD) present with various complaints and symptoms, with the major complaints being severe chest and back pain, which can shift with the progres- sion of AD. However, AD can be painless and lead to various symptoms, such as hoarseness, heart failure, syncope, stroke, paraplegia, anuria, or sudden death.1,2 We, herein, present the case of a patient with acute aortic dissectionType A whose initial complaint was focal convulsion. A Case in Which Focal Convulsion Was the Initial Sign of Fatal Aortic Dissection Youichi Yanagawa, MD, PhD1 Kouhei Ishikawa, MD1 Hiroki Nagasawa, MD1 Ikuto Takeuchi, MD1 Kei Jitsuiki, MD1 Shunsuke Madokoro, MD1 Akihiko Kondo, MD1 Hiromichi Ohsaka, MD, PhD1 Kazuhiko Omori, MD, PhD1 1Department of Acute Critical Care Medicine, Juntendo University, Shizuoka Hospital, Izunokuni City, Shizuoka, Japan Address for correspondence Youichi Yanagawa, MD, PhD, Department of Acute Critical Care Medicine, Juntendo University, Shizuoka Hospital, 1129 Nagaoka, Izunokuni City, Shizuoka, Japan 410-2295 (e-mail: yyanaga@juntendo.ac.jp). AORTA 2019;7:144–146. Copyright © 2019 by Thieme Medical Publishers, Inc., 333 Seventh Avenue, New York, NY 10001, USA. Tel: +1(212) 584-4662. Case Presentation A 74-year-old woman suddenly showed focal convulsion of the right upper extremity and right-side face with right conjugated deviation, following a loss of consciousness in front of her family. Her son called an ambulance. After a few minutes, she regained consciousness and complained of epigastralgia with cold perspiration. Her medical history included hypertension and hyperlipidemia. On arrival, she had clear consciousness, with a systolic blood pressure of 90 mm Hg, a heart rate of 66 beats per minute, and oxygen saturation of 95% under room air. A physical examination that included a neurological examination, chest roentgenography, and electrocardiography (ECG) received May 14, 2018 accepted after revision November 2, 2019 Copyright © 2019 by Thieme Medical Publishers, Inc., 333 Seventh Avenue, New York, NY 10001, USA. Tel: +1(212) 584-4662. DOI https://doi.org/ 10.1055/s-0039-3401023. ISSN 2325-4637. Focal Convulsion due to Aortic Dissection Yanagawa et al. 145 an aortic root dissection with possible compression of the left main coronary artery. The authors suggested that the sudden onset of symptoms heralded the beginning stages of aortic dissection, with left upper limb seizures resulting from dissection into the right carotid artery and the persistent loss of consciousness from global cerebral hypo- perfusion. In the third case, Chen et al5 reported a 61-year-old male who presented with a transient loss of consciousness accompanied by upward gaze and limb convulsion. Head CT revealed no specific findings. Chest X-ray revealed widening of the mediastinum. Subse- quently, chest CT demonstrated Stanford’s Type A aortic dissection. The patient experienced a loss of consciousness, accompanied by upward gaze and limb convulsion for approximately 10 seconds in the emergency room, and ECG at that time revealed transient cardiac asystole fol- lowed by a spontaneous recovery of the sinus rhythm. Accordingly, they concluded that cardiac asystole had been caused by a painless Type A aortic dissection that led to convulsive syncope because cerebral perfusion had been impeded. Fig. 1 Autopsy imaging. The imaging disclosed Stanford’s Type A aortic dissection with cardiac tamponade. Case Presentation Type A dissection involves the aortic arch, which may result in seizure either through the extension of the dissec- tion into the common carotid arteries or through throm- boembolism or cerebral hypoperfusion.6 Focal seizures may be induced by hypotension based on vulnerability of the previously compromised cerebral tissue or vessels due to changes in blood pressure.7 In the present case, the patient was in a state of shock on arrival and had old lacunar infarctions in her brain without fresh cerebral ischemia; thus, focal seizure with hypotension (cerebral hypoperfu- sion) due to Type A dissection was the most likely mecha- nism in the present case. Fig. 1 Autopsy imaging. The imaging disclosed Stanford’s Type A aortic dissection with cardiac tamponade. Discussion Focal convulsion as an initial sign of aortic dissection is extremely rare. This was the fourth case reported in the English literature. In the first case, Mo et al3 reported a 46-year-old man with Type A aortic dissection who expe- rienced a sudden loss of consciousness and right hemi- convulsive movements.3 On arrival, he had left hemiplegia. As MRI showed an area of abnormal hyperintensity in the right-middle cerebral artery territory on diffusion-weight- ed imaging, he was initially diagnosed with acute cerebral infarction with convulsion. However, routine chest radiog- raphy revealed a widened mediastinum. Reevaluation of the patient revealed significant blood pressure differentials in the patient’s arms. Chest CT revealed the Type A aortic dissection. The authors suggested that extension of dissec- tion into the common carotid arteries or through throm- boembolism or cerebral hypoperfusion due to Type A dissection might be a possible mechanism underlying seizure as the initial presentation of aortic dissection. In the second case, Oon et al4 reported a 66-year-old man with two brief periods of jerking movements involving the left upper limb which spontaneously ceased. Head CT showed no fresh lesions; thus, the initial diagnosis was status epilepticus secondary to scar epilepsy from a previous nonhemorrhagic infarct. However, he developed refractory severe hypotension, bradycardia, and hypoxia requiring mechanical ventilation and inotropic support. ECG showed new deep ST-segment depressions in the inferolateral leads and a coronary angiography revealed The patient showed a high level of FDP on arrival. As she did not have any signs of pulmonary embolism, whole body CT should have been performed to investigate the possibility of deep vein thrombosis, trauma, infection or disseminated intravascular coagulation, aortic dissection, or hematoma.8 Accordingly, physicians should perform whole body CT to determine whether or not aortic dissection is present when treating patients with convulsion and a high level of FDP. Focal Convulsion due to Aortic Dissection Yanagawa et al. 146 5 Chen CH, Liu KT. A case report of painless type A aortic dissection with intermittent convulsive syncope as initial presentation. Medicine (Baltimore) 2017;96(17):e6762 Funding This article received financial support from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT)-Supported Program for the Strategic Research Foundation at Private Universities, 2015 to 2019 concern- ing (The constitution of total researching system for comprehensive disaster, medical management, corre- sponding to wide-scale disaster). (No grant number) Conflict of Interest The authors declare no conflict of interest related to this article. Acknowledgments None. Acknowledgments None. AORTA Vol. 7 No. 5/2019 Focal Convulsion due to Aortic Dissection Yanagawa et al. References 1 Yanagawa Y, SakamotoT. Characteristics of patients thatexperience cardiopulmonary arrest following aortic dissection and aneurysm. J Emerg Trauma Shock 2013;6(03):159–163 6 Wright V, Horvath R, Baird AE. Aortic dissection presenting as acute ischemic stroke. Neurology 2003;61(04):581–582 2 Yanagawa Y, Omori K, Kando Y, Kitamura S. Acute type A aortic dissection mimicking hemorrhagic stroke. Sch J Med Case Rep 2017;5(05):324–326 7 Riley TL, Friedman JM. Stroke, orthostatic hypotension, and focal seizures. JAMA 1981;245(12):1243–1244 8 Riley RS, Gilbert AR, Dalton JB, Pai S, McPherson RA. Widely used types and clinical applications of D-Dimer assay. Lab Med 2016; 47(02):90–102 3 Mo HH, Chen SC, Lee CC. Seizure: an unusual primary presentation of typeAaorticdissection.AmJEmergMed2008;26(02):245.e1–245.e2 4 Oon JE, Kee AC, Toh HC. A case report of Stanford type A aortic dissection presenting with status epilepticus. Am J Emerg Med 2011;29(02):243.e5–243.e6 AORTA Vol. 7 No. 5/2019
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Unsupervised Approaches for the Segmentation of Dry ARMD Lesions in Eye Fundus cSLO Images
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Unsupervised Approaches for the Segmentation of Dry ARMD Lesions in Eye Fundus cSLO Images Clément Royer, Jérémie Sublime, Florence Rossant, Michel Paques To cite this version: Clément Royer, Jérémie Sublime, Florence Rossant, Michel Paques. Unsupervised Approaches for the Segmentation of Dry ARMD Lesions in Eye Fundus cSLO Images. Journal of Imaging, 2021, 7, ￿10.3390/jimaging7080143￿. ￿hal-03328443￿ To cite this version: Clément Royer, Jérémie Sublime, Florence Rossant, Michel Paques. Unsupervised Approaches for the Segmentation of Dry ARMD Lesions in Eye Fundus cSLO Images. Journal of Imaging, 2021, 7, ￿10.3390/jimaging7080143￿. ￿hal-03328443￿   Keywords: dry ARMD; unsupervised learning; automatic segmentation; clustering; W-net Citation: Royer, C.; Sublime, J.; Rossant, F.; Pâques, M. Unsupervised Approaches for the Segmentation of Dry ARMD Lesions in Eye Fundus cSLO Images. J. Imaging 2021, 7, 143. https://doi.org/10.3390/ jimaging7080143 Article Unsupervised Approaches for the Segmentation of Dry ARMD Lesions in Eye Fundus cSLO Images Clément Royer 1,*, Jérémie Sublime 1,2,* , Florence Rossant 1,* and Michel Paques 3 1 ISEP—School of Digital Engineers, 92130 Issy-Les-Moulineaux, France 1 ISEP—School of Digital Engineers, 92130 Issy-Les-Moulineaux, France g g , y , 2 LIPN—CNRS UMR 7030, LaMSN—Université Sorbonne Paris Nord, 93210 St Denis, France 3 Clinical Imaging Center 1423, Quinze-Vingts Hospital, INSERM-DGOS Clinical Investigation Center, 75012 Paris, France; mpaques@15-20.fr * Correspondence: clement.royer@ext.isep.fr (C.R.); jeremie.sublime@isep.fr or sublime@lipn.univ-paris13.fr (J.S.); florence.rossant@isep.fr (F.R.); Tel.: +33-1-4954-5262 (F.R.) 3 Clinical Imaging Center 1423, Quinze-Vingts Hospital, INSERM-DGOS Clinical Investigation Cen 75012 Paris, France; mpaques@15-20.fr * Correspondence: clement.royer@ext.isep.fr (C.R.); jeremie.sublime@isep.fr or sublime@lipn.univ-paris13.fr (J.S.); florence.rossant@isep.fr (F.R.); Tel.: +33-1-4954-5262 (F.R.) Abstract: Age-related macular degeneration (ARMD), a major cause of sight impairment for elderly people, is still not well understood despite intensive research. Measuring the size of the lesions in the fundus is the main biomarker of the severity of the disease and as such is widely used in clinical trials yet only relies on manual segmentation. Artificial intelligence, in particular automatic image analysis based on neural networks, has a major role to play in better understanding the disease, by analyzing the intrinsic optical properties of dry ARMD lesions from patient images. In this paper, we propose a comparison of automatic segmentation methods (classical computer vision method, machine learning method and deep learning method) in an unsupervised context applied on cSLO IR images. Among the methods compared, we propose an adaptation of a fully convolutional network, called W-net, as an efficient method for the segmentation of ARMD lesions. Unlike supervised segmentation methods, our algorithm does not require annotated data which are very difficult to obtain in this application. Our method was tested on a dataset of 328 images and has shown to reach higher quality results than other compared unsupervised methods with a F1 score of 0.87, while having a more stable model, even though in some specific cases, texture/edges-based methods can produce relevant results. HAL Id: hal-03328443 https://hal.science/hal-03328443v1 Submitted on 30 Aug 2021 L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. Journal of Imaging Journal of Imaging Journal of Imaging 1. Introduction Age-related macular degeneration (ARMD) is a degenerative disease that affects the retina, and a leading cause of visual loss. Received: 29 June 2021 Accepted: 10 August 2021 Published: 11 August 2021 In this paper, we focus on the dry form of this pathology which currently does not have any treatments. It is characterized by a progressive loss of pigment epithelium which engenders a lesion located in the macula, growing slowly and impeding more and more the patient central vision. The lesions, called geographic atrophy (GA), can be observed in eye fundus images. Figure 1 shows examples of confocal Scanning Laser Ophtalmoscopy (cSLO) images acquired in infrared (IR), a commonly used imaging technique for ARMD patients, where the GA appears as brighter areas. Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Despite intensive biological research, the factors involved in progression are poorly known. Therefore, clinical studies are needed to characterize the disease and its evolution. This can be done from eye fundus images, which are routinely acquired during the medical follow-up of patients. However, there are at present no efficient algorithms to automatically process large databases of images, even though it is very costly to process them manually: first, the manual delineation of the lesions is a very difficult and time-consuming task, given the complex structure of the GA. Secondly, the reliability of manual delineations is also an issue as even experts tends to disagree on their segmentations [1]. To solve this problem, in this work, we propose the first fully unsupervised application of automatic segmentation of GA using W-net [2] on cSLO IR acquired images (Section 2) and to assess Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). https://www.mdpi.com/journal/jimaging J. Imaging 2021, 7, 143. https://doi.org/10.3390/jimaging7080143 J. Imaging 2021, 7, 143 2 of 16 how well it performs compared with other state of the art unsupervised methods. Our contribution is therefore three-fold: how well it performs compared with other state of the art unsupervised methods. Our contribution is therefore three-fold: how well it performs compared with other state of the art unsupervised methods. Our contribution is therefore three-fold: • First, we propose a successful adaptation of the original developed by Xia et al. [2]. 1. Introduction We modified the architecture to adapt it to our images and their specifics. In ad- dition, furthermore, we fully trained our network and did not use any pre-trained model. • Second, we propose the first realistic unsupervised approach to the very difficult problem of ARMD lesion segmentation. Indeed, this problem is already difficult for humans, and has very little labelled data (hence why we cannot use supervised neural networks), thus making it quite a challenging problem for unsupervised algorithms. In this regard, we achieve very decent performance considering the nature of the problem and the challenges it presents. p g p • Third, we propose a fair and extensive comparison with other unsupervised methods (neural networks and others) used in other fields that we have also adapted to tackle the same problem. • Third, we propose a fair and extensive comparison with other unsupervised methods (neural networks and others) used in other fields that we have also adapted to tackle the same problem. Figure 1. Five pairs of images: (a) advanced case with blur, low contrast and very indented GA boundary; (b) less advanced case with lesions at the center and around the optic disk; (c) a new lesion appears in the second image (green arrow); (d) GA with complex structure and texture; (e) example of progression of a GA during 6 years. A third GA appeared (green arrow). Arrows point to the GA (red) and to the optic disk (blue). Figure 1. Five pairs of images: (a) advanced case with blur, low contrast and very indented GA boundary; (b) less advanced case with lesions at the center and around the optic disk; (c) a new lesion appears in the second image (green arrow); (d) GA with complex structure and texture; (e) example of progression of a GA during 6 years. A third GA appeared (green arrow). Arrows point to the GA (red) and to the optic disk (blue). The remainder of this paper is organized as follows: Our method is presented in Section 4.1 and the compared methods in Section 4.2, after the description of our dataset (Section 2) and the related works (Section 3). The experimental results are shown in Section 5. In addition, finally, conclusions and insights as to our future works are discussed in Section 6. 2. Materials We work on cSLO images acquired in IR. This modality is more robust and less invasive than fundus autofluorescence (FAF), and it has higher resolution and higher contrast between normal and diseased areas than color imaging, an older technology. Our database is composed of 18 series of images (328 images in total), showing the progression of the GA over several years for 13 patients (ARMD can affect both eyes). The time interval between two exams is about 6 months. All these images has been obtained from the Clinical J. Imaging 2021, 7, 143 3 of 16 Imaging Center of the Quinze-Vingts Hospital and all patients gave their informed consent for the use of images for clinical studies. Imaging Center of the Quinze-Vingts Hospital and all patients gave their informed consent for the use of images for clinical studies. All images are in gray-levels (1 channel). Black borders are present because of the spatial registration process. Moreover, the images present illumination artifacts, blur and a non-uniform illumination. We preprocess jointly the images of every series as follows: we crop the images to suppress the black borders and resize them to 256 × 256 pixels; then we apply a joint correction of the overall illumination [3] so that any two processed images have comparable gray-levels. This algorithm does not completely compensate for uneven illumination, but the remaining defect is the same in all processed images, helping the ophthalmologists in the visual comparison of any two exams. From the segmentation point of view, the algorithm homogenizes the luminosity and the contrast of the images applied to the W-net and thus reduces the radiometric variability. y The major challenge of the segmentation task is to adapt to the large and complex variability of GA structures and to cope with all kinds of image defects. Figure 1 illustrates the difficulty: variability in size, shape, texture, number of GA areas, with new lesions that may appear at any time or merge; low contrast, blur, high ambiguity in the actual position of the border even for the most contrasted images. Please note that 18 series of images may not be enough to fully represent the real variability of GAs, and can lead to a lack of generality for deep learning-based methods. In order to evaluate our algorithm, we asked ophthalmologists to delineate the GA areas. 2. Materials However, even with expert skills, the produced annotations may not be 100% reliable. Thus, the resulting pixel-wise annotations are only used to calculate classic segmentation quality measures (see Section 5.1). 3. Related Work Imaging 2021, 7, 143 4 of 16 Using deep learning, the authors of [26] applied a joint auto-encoder (initially applied on satellite images [27]) on the same dataset we are using in this paper (see Section 2), in order to perform automatic change detection in an unsupervised context learning. The algorithm outperformed the state-of-the-art; however, as this model aims to detect changes, it is not comparable with automatic segmentation algorithm. Kanezaki [28] combined clustering algorithm and CNN for a fully unsupervised model using a superpixel refinement method and achieving promising results for unsupervised automatic semantic segmentation. For a given image, the CNN first oversegments it (high number of cluster initially), then at each iteration, tries to reduce the number of cluster by merging them according to the result of the clustering algorithm. Table 1 summarizes the pros and cons for the related works. As we want to exploit the dataset provided by the Clinical Imaging Center of the Quinze-Vingts Hospital (Section 2), which represent a non-invasive modality acquisition adapted to the patient follow-up, other modality use (which can engender better results due to a better quality of imaging) will be considered as a drawback. Supervised training is also considered a weakness because of the annotations reliability. Table 1. Comparative summary of related works. Table 1. Comparative summary of related works. 3. Related Work A lot of research has been done to propose segmentation algorithms of the GA. Stan- dard algorithms have been applied, such as region growing [4,5] or active contour [6], region oriented variational methods with level set implementation [7,8], texture analy- sis [9] and watershed segmentation [10,11]. Most of the proposed methods are based on supervised machine learning approaches, with statistical models [12], random forests [13], random forests combined with Support Vector Machine [14] or k-nearest neighbor classi- fiers [15]. However, even in a supervised context, it is intricate to obtain a fully automatic algorithm reaching the required level of performance and some authors add human inter- action to guide their algorithm [16,17] Using deep learning, a reference model achieving impressive results for supervised segmentation is the U-net [18], and it has been implemented in many medical image segmentation problems (e.g., [19,20]). The U-net takes advantage of residual connections combined with a contracting and an expansive part. The authors of [21] proposed a supervised algorithm to follow-up the GA progression, using U-nets to first segment vessels and the optic disc, reducing the region of interest for the GA detection and then tracking it using intensity ratio between neighbor pixels. Other supervised deep learning- based methods were applied on ARMD as in [22] where they exploit transfer learning with deep neural networks to detect ARMD. Last but not least, a segmentation task has been investigated in a scene parsing context. The authors of [23,24] exploit spatial pyramid pooling architecture in order to perform semantic segmentation between multiples objects present in a scene. However, as the U-Net, both PSP-Net and APSP-Net are deep supervised methods and their training requires a large amount of annotated data, which is not suitable for our application, as mentioned previously. Thus, unsupervised methods can solve both the problem of data availability and the issue of the reliability of experts’ annotations. Unsupervised automatic segmentation is mainly handled in two steps: extracting features and then applying a clustering algorithm. The authors of [25] applied fuzzy CMeans clustering, which reached good performance for high-contrast FAF images, but performed less well for other modalities. J. 3. Related Work Method Pros Cons Region oriented [4,5] High performance on ARMD, semi-supervised (seeds) FAF/OCT images Conventionnal methods Active contour [5,6] High performance on retinal cases Segment optic discs Statistical [12] High performance on retinal cases Segment blood vessels and optic discs Random Forest [13] High performance on ARMD Color fundus images, supervised Random Forest + SVM [14] High performance on ARMD Screening and grading task, supervised Fuzzy C-means [25] Unsupervised, high performance on ARMD High contrast FAF images K-NN [15] High performance on ARMD FAF images, supervised Watershed [10,11] Semi supervised (seeds) OCT images U-net [18,21] High performance on ARMD Supervised, training on GPU Deep learning methods Transfert learning on ARMD [22] High performance Supervised, color fundus images Scene parsing [23,24] High performance Supervised, requires multiple objects in a scene, training on GPU Change detection [26] Unsupervised, applied on the same dataset Change detection task CNN + Superpixel refinement [28] Unsupervised, no training Produce a variable number of cluster in the segmentation W-net [2] Unsupervised, robust Training on GPU Our W-net Unsupervised, fast inference use, robust, high performance on ARMD Training on GPU Human interaction [16,17] High performance on ARMD Require human interaction Other methods In this paper, we focus on unsupervised algorithms to segment the GA in IR cSLO eye fundus images with dry-ARMD. We propose to adapt the W-net [2] as well as three other unsupervised methods and compare them in an experimental study. J. Imaging 2021, 7, 143 5 of 16 4. Methods 4.1. Our Method: W-Nets Adapted to ARMD Lesions Segmentation 4.1. Our Method: W-Nets Adapted to ARMD Lesions Segmentation 4.1. Our Method: W-Nets Adapted to ARMD Lesions Segmentation The W-net model is a fully convolutional autoencoder for which both encoder and decoder are U-net networks [18]. While U-nets are supervised neural networks commonly used for image segmentation, W-nets are the unsupervised equivalent. Unlike U-Nets, W-nets are trained using two loss functions. The first one is the usual reconstruction error used to train classic autoencoder, the second one is the soft-N-cut loss [2], a smooth version of the N-cut loss [29]. Minimizing the soft N-cut loss has the effect of enhancing the segmentation quality by maximizing the dissimilarity between the different clusters. The dissimilarity calculated is a function of the intensity pixel and the spatial position of the pixels. p During each training step, we have two successive optimization steps after each forward. First the full W-net is updated by back-propagating the self-reconstruction error (MSE = 1 n ∑n k=1(Yk −ˆYk)2, where n is the number of pixel in the image), then only the encoding part is updated based on the soft N-cut loss : Jso f t−Ncut(V, K) = K − K ∑ k=1 ∑u∈V,v∈V w(u, v)p(u = Ak)p(v = Ak) ∑u∈Ak,t∈V w(u, t)p(u = Ak) with p(u = Ak) the probability for the pixel u to belong to the class k, and w a function which compute a weight for each couple of pixel, based on their position in the image and their intensity [29]. The architecture of our W-net is presented in Figure 2. Hence, the entire training of the W-net is unsupervised: the MSE loss is computed with the W-net output and the image input, while the soft-N-cut loss is computed with the probability map produced by the encoder (after the softmax layer in Figure 2) and the weights (which only need the image input to be computed). Compared with the original one, an average-pooling layer has been added before the computation of the soft N-cut loss. This loss is based on graph calculation, and thus, is memory-consuming when using large size images and not applicable on 256 × 256 sized images. Hence, the value of the soft N-cut loss is approximated by the value of the loss applied on the 128 × 128 (average) pooled input. Figure 2. Our W-net architecture for ARMD lesions segmentation. 4.2.2. Active Contour Model without Edges Chan and Vese combined in [5] active contour methods, and Mumford-Shah functional and level set methods. Parametric active contour methods are based on a curve evolving technique: a parametrized curve C : [0, 1] −→R2 evolve and is stopped using an edge detector, which usually rely on the gradient |∇I| for a given image I. Such a method can then only detect objects with high gradient on their edges. Thus, the authors of [5] proposed a region oriented approach based on Mumford-Shah energy functional. p p g pp gy Let C be the evolving curve, I a given image, c1 and c2 the average value of I respec- tively inside C and outside C (case example with one object to detect from the background). The fitting energy function is defined as: F1(C) + F2(C) = Z inside(C) |I(x, y) −c1|2dxdy + Z outside(C) |I(x, y) −c2|2dxdy Thus, the solution of infC{F1(C) + F2(C)} gives the boundary of the object we want to detect. Thus, the solution of infC{F1(C) + F2(C)} gives the boundary of the object we want to detect. This algorithm is suitable for the GA segmentation as it can handle changes in topology with respect to the initialization, thanks to the level-set resolution method, as well as low contrast along the edges. 4. Methods Once it has been trained on a set of unlabeled images, our network can be used on any ARMD cSLO images acquired in IR that have a similar resolution: For each pixel, the network will provide the probability of belonging to each class. Then applying a simple argmax will produce a segmentation. In our case, the purpose is to obtain two classes corresponding to the GA and the retina background. Thus, when the W-net is set with K = 2, one segmentation class will represent the GA and the other one the retina background. However, when the W-net is set with K > 2, we have to map the extra classes Figure 2. Our W-net architecture for ARMD lesions segmentation. Figure 2. Our W-net architecture for ARMD lesions segmentation. Once it has been trained on a set of unlabeled images, our network can be used on any ARMD cSLO images acquired in IR that have a similar resolution: For each pixel, the network will provide the probability of belonging to each class. Then applying a simple argmax will produce a segmentation. In our case, the purpose is to obtain two classes corresponding to the GA and the retina background. Thus, when the W-net is set with K = 2, one segmentation class will represent the GA and the other one the retina background. However, when the W-net is set with K > 2, we have to map the extra classes J. Imaging 2021, 7, 143 6 of 16 to the GA class or the background class. Finally, once trained, our W-net will always produce the same semantic classes for every image it processes, thus requiring a manual mapping only once. to the GA class or the background class. Finally, once trained, our W-net will always produce the same semantic classes for every image it processes, thus requiring a manual mapping only once. 4.2. Compared Methods In this subsection, we present the three other compared algorithm: Gabor filters with KMeans [30], an active contour based model [5] and a model that combine CNN and clustering [28]. 4.2.1. Gabor + KMeans This algorithm is divided in three steps: creation of a set of Gabor filters, feature extraction using previous filters, pixels classification with KMeans on those features. For a given frequency u0, Gabor function in spatial domain is a Gaussian modulated with a sinusoïd: h(x, y) = 1 2πσxσy exp{−1 2[ x2 σ2x + y2 σ2y ]}.cos(2πu0x) with σx and σy variances in direction x and y. y To capture features in multiple direction, we can add a rotation θ to the filter. Thus, we chose a set of directions, which define the set of Gabor filters. Each filter output pass through a non-linear function (sigmoïd function). The texture features are completed with spatial information (pixel position). Finally, a KMeans clustering algorithm is applied on all the features, classifying each pixel and thus given us a pixel-wise segmentation. 4.2.3. CNN + Superpixel Refinement y yn Two steps are applied alternatively to train the network: n Two steps are applied alternatively to train the network: n Two steps are applied alternatively to train the network: • forward process: prediction of clusters cn with the network and refined cluster c′ n with the superpixel refinement process the superpixel refinement process • backward process: backpropagation of the signal error (cross-entropy loss) between the network response y ′ n and the refined cluster c′ n • backward process: backpropagation of the signal error (cross-entropy loss) between ′ • backward process: backpropagation of the signal e the network response y ′ n and the refined cluster c′ n the network response y ′ n and the refined cluster c′ n The training process of this model is different from the W-net one. One has to initialize and train the model for each individual image at contrary to the W-net which has to be trained only once. Indeed, the training process corresponds to the refinement of the model on a given image and can not be used to infer an other image. 4.2.3. CNN + Superpixel Refinement Kanezaki investigate the use of CNN for unsupervised segmentation. The algorithm is based on three assumptions: • “Pixels of similar features are desired to be assigned the same label” • “Spatially continuous pixels are desired to be assigned the same label” • “The number of unique cluster labels is desired to be large” For a given pixel vn of an RGB image (three channels) I = {vn ∈R3}N n=1 that we want to segment into q classes, we first extract p-dimensional features xn with p filters of size 3 × 3. Applying a linear classifier fc with weights Wc ∈Rp×q and bias bc ∈Rq gives us a J. Imaging 2021, 7, 143 7 of 16 response map for each pixel: {yn = Wcxn + bc}N n=1. Finally the cluster cn for each pixel is obtained by selecting the dimension with the greatest value. Thus, the output model is consistent with the features similarity constraint. To satisfy the spatial continuity constraint, K fine superpixels {Sk}K k=1 are extracted and all the pixels of a given superpixel is forced to have the same cluster (which will be the most frequent cluster in the superpixel). Slic algorithm (KMeans-based segmentation algorithm) is used to compute the superpixels. Hence, the K classes obtained with Slic algorithm applied on the image I will correspond to the K superpixels. The method in [28] aim to segment natural images (experiments on Berkeley Segmen- tation Dataset and Benchmark BSDS500) therefore, we do not have any prior knowledge of the number of unique clusters present in a given image. In this context, the algorithm must be able to output a variable number of clusters. Kanezaki’s strategy is to constraint the number q′ of output clusters with a maximum number of cluster q. One has 1 ≤q′ ≤q and to avoid the naive solution q′ = 1, he introduced the last constraint: q is preferred to be large. This is done by adding a whitening process, which transforms the response map yn into yn′ where each axis has zero mean and unit variance. 5.1. Experimental Setting 5.1. Experimental Setting 5.1. Experimental Setting In our experiments, we use 18 series of 5 to 52 images (328 images). Due to the relatively small number of series and their variable size, we could not use k-folds validation. However, we used 8 different random combinations of 12 series to train the model and 6 for the tests. Our W-net is compared with Gabor Filters for texture extraction [30] and KMeans algorithm for the segmentation, the CNN model with superpixel refinement [28] and finally an active contour model [5]. y As the lesions can only grow bigger, we also try to see if adding the segmentation from the previous image improves the results or not: we merge the segmentation provided by our W-net for the current Image It with the segmentation of the same W-net for the previous image It−1. This modification is supposed to reduce the risk of undersegmentation. Our network is set with a kernel size of 3, and each U-net produces 1024 features after the contracting part. Our model is trained on 250 epochs, using two Adam optimizers. The number of classes is set to 3 in the experiments: using two classes, the latent repre- sentation is too restrictive. Using three classes, the network learns extra classes for the background (healthy regions and blood vessels) or the ARMD lesions. Hyperparameters for Gabor filters methods, Chan and Vese’s method, and Kanezaki’s method have been tuned manually by referring to the visual output. Therefore, the fixed parameters are not the optimal ones, but a compromise to obtain the best average output. method have been tuned manually by referring to the visual output. Therefore, the fixed parameters are not the optimal ones, but a compromise to obtain the best average output. The evaluation is based on the pixels’ classification using true positive (TP), false positive (FP), and false negative (FN) to build dice metrics such as the F1-Score: The evaluation is based on the pixels’ classification using true positive (TP), false positive (FP), and false negative (FN) to build dice metrics such as the F1-Score: F1 = 2 × precision × recall precision + recall = TP TP + 0.5(FP + FN) precision = TP TP + FP with J. 5.1. Experimental Setting Imaging 2021, 7, 143 8 of 16 and and recall = TP TP + FN recall = TP TP + FN KMeans algorithm output directly the classification an not the probability to belong to each class. However, those probabilities are needed to compute the ROC curve. Hence we use fuzzy CMeans instead (which provides, with an argmax, the same output as Kmeans) KMeans algorithm output directly the classification an not the probability to belong to each class. However, those probabilities are needed to compute the ROC curve. Hence we use fuzzy CMeans instead (which provides, with an argmax, the same output as Kmeans) All the experiments have been done using a GEFORCE RTX 3090 GPU with 24Gb of RAM, Python 3.8.5, Pytorch 1.7.1 and Cuda 11.1. , p p use fuzzy CMeans instead (which provides, with an argmax, the same output as Kmeans) All the experiments have been done using a GEFORCE RTX 3090 GPU with 24Gb of RAM, Python 3.8.5, Pytorch 1.7.1 and Cuda 11.1. All the experiments have been done using a GEFORCE RTX 3090 GPU with 24Gb of RAM, Python 3.8.5, Pytorch 1.7.1 and Cuda 11.1. 5.2. Experimental Results As explained before, our W-net is set to three classes. With this configuration, we manually map the classes to the lesion or the background. Figure 3 shows an example of different classes obtained with our 3-class W-net: the class of interest corresponding to the GA is in green. The two other classes belong to the retina background. Please note that this mapping is arbitrary and may not be optimal in specific cases. The results are shown in Tables 2 and 3. Figure 3. Example of three classes W-net output. From left to right: original image, ground truth, 3-class W-net output. Figure 3. Example of three classes W-net output. From left to right: original image, ground truth, 3-class W-net output. Table 2. Average W-net dice scores on the training set. Method F1 Precision Recall W-net 0.83 ± 0.09 0.87 ± 0.08 0.81 ± 0.13 W-net + Segt−1 0.82 ± 0.07 0.82 ± 0.10 0.82 ± 0.11 Table 2. Average W-net dice scores on the training set. Table 2. Average W-net dice scores on the training set. Table 2 shows the average dice score (F1), precision and recall on the training set (W-net is the only model that need to be trained), while Table 3 focuses on the test set and features the comparison with the other algorithms introduced in Section 5.1. As one can see, W-net is the most relevant method. It has the best F1 score and achieves higher quality results with a better precision and recall. Moreover, our W-net has a smaller standard deviation for the F1 score and the precision, resulting in a more stable model. The bottom line (W-net + Segt−1) in both tables corresponds to the fusion of a given segmentation with the previous one (see Section 5.1). However, we can see that this modification does not lead to any significant increase in the result quality: while the Recall is indeed better (less under-segmentation), the F1 score is not significantly different from the one of our method on individual images. This can be explained by an accumulation of over-segmented areas propagating through the series, which is confirmed by a worst Precision that we observe. In any case, we can see that except for the recall—which can be explained by cases of under-segmentation—our W-net approaches outperform the Gabor filter and KMeans approach, Active contour method, and CNN model with superpixel refinement. J. Imaging 2021, 7, 143 9 of 16 Table 3. Average dice scores on the test set. Method F1 Precision Recall Active contour (Chan & Vese [5]) 0.73 ± 0.07 0.64 ± 0.13 0.86 ± 0.05 CNN + Superpixel Refinement (Kanezaki [28]) 0.65 ± 0.07 0.54 ± 0.10 0.85 ± 0.06 Gabor + KMeans [30] 0.77 ± 0.08 0.80 ± 0.12 0.75 ± 0.08 Our W-net 0.87 ± 0.07 0.90 ± 0.07 0.85 ± 0.11 W-net + Segt−1 0.85 ± 0.06 0.84 ± 0.07 0.87 ± 0.09 Table 3. Average dice scores on the test set. Our W-net superiority is also shown in Figure 4, where we can clearly see that the W-net is nearer to the perfect model compared to the Gabor filter with Fuzzy CMeans method. Please note that we compared the ROC curve for the two most relevant algorithm according to the results in Tables 2 and 3. Figure 4. Receiver Operating Characteristic curve of Gabor filter + fuzzy CMeans and W-net. Figure 4. Receiver Operating Characteristic curve of Gabor filter + fuzzy CMeans and W-net. Table 2. Average W-net dice scores on the training set. Table 4 shows detailed score on 6 series and we can see an example taken from each series in Figures 5–10. Figure 5. Patient id 117: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W- net segmentation, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figure 5. Patient id 117: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W- net segmentation, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. J. Imaging 2021, 7, 143 10 of 16 Table 4. Detailed dice scores on specific series. Patient Id Method F1 Precision Recall Nb. of Images Fig. 005 Active Contour 0.787 0.779 0.795 9 Figure 6 CNN + Superpixel refinement 0.690 0.623 0.787 Gabor + KMeans 0.791 0.760 0.828 Our W-net 0.785 0.806 0.765 W-net + Segt−1 0.799 0.805 0.792 010 Active Contour 0.644 0.504 0.892 6 Figure 8 CNN + Superpixel refinement 0.589 0.440 0.909 Gabor + KMeans 0.809 0.907 0.731 Our W-net 0.922 0.921 0.922 W-net + Segt−1 0.919 0.910 0.927 016 Active Contour 0.849 0.869 0.828 31 Figure 7 CNN + Superpixel refinement 0.790 0.752 0.840 Gabor + KMeans 0.678 0.596 0.786 Our W-net 0.676 0.880 0.924 W-net + Segt−1 0.706 0.817 0.622 020 Active Contour 0.654 0.516 0.901 50 Figure 9 CNN + Superpixel refinement 0.622 0.489 0.898 Gabor + KMeans 0.744 0.903 0.640 Our W-net 0.946 0.977 0.920 W-net + Segt−1 0.864 0.808 0.929 109 Active Contour 0.774 0.755 0.796 16 Figure 10 CNN + Superpixel refinement 0.717 0.695 0.767 Gabor + KMeans 0.700 0.685 0.718 Our W-net 0.782 0.936 0.672 W-net + Segt−1 0.799 0.903 0.717 117 Active Contour 0.658 0.512 0.920 6 Figure 5 CNN + Superpixel refinement 0.609 0.469 0.892 Gabor + KMeans 0.933 0.966 0.902 Our W-net 0.987 0.995 0.979 W-net + Segt−1 0.988 0.993 0.982 Table 4. Detailed dice scores on specific series. Figure 6. Patient id 005: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W- net segmentation, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figure 6. Patient id 005: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W- net segmentation, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. 11 of 16 J. Imaging 2021, 7, 143 Figure 7. Table 2. Average W-net dice scores on the training set. Patient id 016: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W-net clusters, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figure 7. Patient id 016: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W-net clusters, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figure 8. Patient id 010: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W- net segmentation, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figure 8. Patient id 010: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W- net segmentation, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figures 5 and 9 show examples from average cases (in terms of complexity of the lesion’s structures), where W-net outperforms other methods with a mean F1 score on the series of 0.98 for the first series, and 0.946 for the second one. This also highlights the capacity of W-net to correlate the different classes based on intensity values, while the other methods attempt (and fails) to do so based on textures rather than intensity. Figures 5 and 9 show examples from average cases (in terms of complexity of the lesion’s structures), where W-net outperforms other methods with a mean F1 score on the series of 0.98 for the first series, and 0.946 for the second one. This also highlights the capacity of W-net to correlate the different classes based on intensity values, while the other methods attempt (and fails) to do so based on textures rather than intensity. 12 of 16 12 of 16 J. Imaging 2021, 7, 143 Figure 9. Patient id 020: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W- net segmentation, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figure 9. Patient id 020: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W- net segmentation, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figure 10. Patient id 109: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W-net clusters, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. Figure 10. Patient id 109: (a) original image, (b) ground truth, (c) Gabor method segmentation, (d) W-net clusters, (e) CNN + superpixel refinement segmentation, (f) active contour segmentation. As said in the introduction, a lesion with blurred outlines will be difficult to segment. Table 2. Average W-net dice scores on the training set. This is illustrated in Figure 6 where the Gabor filter algorithm fails to segment the GA, while the W-net does better but with some undersegmentation. In this case, CNN with super-pixel refinement method and the active contour methods output a better result; however, the first one gives more classes than expected due to the algorithm’s setting [28]. Finally, Figures 7 and 10 show two cases where the lesion has different levels of contrast. These are good examples of cases in which it is useful to have three classes (which are represented in yellow/green/purple for example d): as one can see, most of the lesion class is contained within the green class, which is one of the two retina background classes, while the yellow class is the GA class (according to our mapping). In those cases and without the manual cluster/class mapping, both Gabor method and our W-net would fail Finally, Figures 7 and 10 show two cases where the lesion has different levels of contrast. These are good examples of cases in which it is useful to have three classes (which are represented in yellow/green/purple for example d): as one can see, most of the lesion class is contained within the green class, which is one of the two retina background classes, while the yellow class is the GA class (according to our mapping). In those cases and without the manual cluster/class mapping, both Gabor method and our W-net would fail J. Imaging 2021, 7, 143 13 of 16 to identify the GA. The W-net reliance on intensity creates this undersegmentation risk: a low-intensity region is more likely to belong to the background retina class. However, because of the extra class, in the case of our method, the segmentation can still easily be manually fixed. In this case, Kanezaki’s method and Chan and Vese’s method provide a better quality results. Nevertheless, it highlights the limits of unsupervised methods where user intervention is sometimes inevitable. to identify the GA. The W-net reliance on intensity creates this undersegmentation risk: a low-intensity region is more likely to belong to the background retina class. However, because of the extra class, in the case of our method, the segmentation can still easily be manually fixed. In this case, Kanezaki’s method and Chan and Vese’s method provide a better quality results. Nevertheless, it highlights the limits of unsupervised methods where user intervention is sometimes inevitable. Table 2. Average W-net dice scores on the training set. We can also mention that W-net outperfoms other compared algorithm on a long serie (Patient Id 020, fourth line of Table 4, Figure 9) which contain 50 images. This serie is an example of ARMD progression: as we can see in Figure 1e, the ARMD lesions progress from two tiny GA to three consequent GA in 6 years. Images from the beginning of the serie thus contain small GA which enhances risk of oversegmentation. This can also be seen in Figure 8 where despite a higher quality result provided by our W-net, it did not detect a small GA and oversegmented the top right region of the image. From these experiments, we can see that in most cases, our modified W-net produces a better quality segmentation than the other algorithms and has the advantage to be more stable. Furthermore, from cases such as Figure 6, we can see that because of its reliance on textures only, the Gabor filter based approach sometimes entirely fails to capture the GA and appears to detect only peripheral areas of textural transition. However, our proposed W-net -despite some mismatches between the clusters and the classes- manages to have a group of clusters that match the GA class. The CNN with superpixel refinement method provides relevant outputs but need a post-processing step to enhance the segmentation quality. In fact, the results are not smooth enough, and we have no guarantee to obtain two final clusters: the number of clusters in the outuput can vary from an image to another (even for two successive images from a given serie). This is due to the third criterion of Kanezaki’s system: the segmentation context is different from ours, we aim to segment a fixed number of classes. Last but not least, active contour methods can produce a better quality result in some specific cases as they can totally fail in an average case. That highlight the lack of generality of those methods compared to the high variability of both texture and structure of the GA regions. 6. Conclusions and Future Works The automatic segmentation of dry-ARMD lesion is a difficult problem with significant implications for patients afflicted by this disease, as it may allow for a better monitoring of the lesions progression. Despite the complexity of the task, we proposed a promising adaptation of W-nets to this problem. Our algorithm is fully unsupervised, which makes it possible to achieve good quality results without any need for labeled data that are difficult to come by, as even expert ophthalmologists often disagree on the proper segmentation of the lesions for difficult cases. Our proposed algorithm was tested on 328 images from 18 patients, and has proven to be very effective. However, we identified a weakness, which is the W-net’s tendency to undersegment the lesions. This can be explained by the intensity distribution in the images: a single-channel input model can only exploit pixel intensity and spatial information. Thus, high intensity regions will generally correspond to be a part of a lesion, while low intensity regions generally correspond to be a part of the background. However, there is a high variability in the contrast in the images and some cases can show a GA with an intensity barely lighter than the background, hence the interest of having three classes. Furthermore, the most difficult case for this task is when the lesion has a blurred outline (e.g., Figure 1(a.1)). Automatic unsupervised segmentation algorithms tend to fail in this specific case in two different ways: if the blurry lesion is too small, the result will be over-segmented. If the blurry lesion is too large, the result will be under-segmented. y g g On the other side, the three other algorithms have a lack of generality because of the restrictive settings. To better exploit their advantage, a proper fine tuning in each specific case should be needed, leading to a supervised process that requires medical expertise. J. Imaging 2021, 7, 143 14 of 16 14 of 16 Because of the reliability of the ground truths and the cost to produce them, the unsu- pervised context is the most appropriate to face this issue In our future work, we plan on improving our segmentation capabilities by combining our proposed algorithm with generative adversarial networks [31] that have been shown to produce higher quality outputs and to outperform traditional convolutional autoencoders. 6. Conclusions and Future Works Thus, a first improvement of the W-net is an adversial training, which could improve the reconstruction quality and therefore the segmentation map quality. q y g p q y Finally, deep learning performance depends a lot on the dataset training, thus en- rich the dataset with more series and with data augmentation can enhance robustness and performance. Author Contributions: M.P. is with the Clinical Imaging Center of Paris Quinze-Vingts hospital and provided the data after a first preprocessing step. M.P. also provided the medical knowledge necessary to interpret our algorithm’s results. F.R. and M.P. worked together to produce and validate ground truths as reliable as possible. F.R. worked on data curation and the preprocessing algorithm for lighting correction. Most of the software programming, investigation, and experiments, as well as the result visualization were done by C.R. during his internship and his 1st year of PhD thesis. J.S. and F.R. worked on the problem analysis and conceptualization, as well as the experiment design and validation. C.R., F.R. and J.S. all participated in the redaction and proof-reading of the manuscript. F.R., M.P. and J.S. conducted the project and are C.R. Ph.D. advisors. All authors have read and agreed to the published version of the manuscript. Funding: This research is partially funded by Sorbonne University, EDITE PhD scholarship. Informed Consent Statement: This study has been approved by a French ethical committee (Comité de Protection des Personnes) and all participants gave informed consent. Data Availability Statement: Sample images and the source code are available in https://github. com/clement-royer/Unsupervised-segmentation-of-dry-ARMD-lesions-in-cSLO-images-using-W- nets (accessed on 25 June 2021). Please note that since we are dealing with medical images, we are only allowed to disclose a limited number of them and not the full time series. Conflicts of Interest: The authors declare no conflict of interest. Abbreviations The following abbreviations are used in this manuscript: AE Autoencoder APSP Atrous Pyramid Spatial Pooling ARMD or AMD Age-Related Macular Degeneration CNN Convolutional Neural Networks cSLO confocal Scanning Laser Ophthalmoscopy FAF Fundus Autofluorescence GA Geographic Atrophy IR Infrared OCT Optical Coherence Tomography PSP Pyramid Spatial Pooling 5. Chan, T.; Vese, L. Active contours without edges. IEEE Trans. Image Process. 2001, 10, 266–277. [CrossRef] [PubMed] 6. Abdullah, A.S.; Rahebi, J.; Özok, Y.; Aljanabi, M. A new and effective method for human retina optic disc segmentation with fuzzy clustering method based on active contour model. Med. Biol. Eng. Comput. 2019, 58. [CrossRef] References 1. Platanios, E.A.; Al-Shedivat, M.; Xing, E.; Mitchell, T. Learning from Imperfect Annotations: An End-to-End Approach. 2020. 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https://openalex.org/W2174733190
https://figshare.com/articles/journal_contribution/Coral_record_of_southeast_Indian_Ocean_marine_heatwaves_with_intensified_Western_Pacific_temperature_gradient/10206092/1/files/18398108.pdf
English
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Coral record of southeast Indian Ocean marine heatwaves with intensified Western Pacific temperature gradient
Nature communications
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11,508
ARTICLE Received 27 Oct 2014 | Accepted 4 Sep 2015 | Published 23 Oct 2015 Coral record of southeast Indian Ocean marine heatwaves with intensified Western Pacific temperature gradient T Due to the remoteness of SEIO reefs and sparseness of historical data, it is hard to quantify the magnitude of temperature stress during past ‘Ningaloo Nin˜o’, La Nin˜a and WPG events. It is also not well known whether SEIO heatwaves always have a close association with ENSO on decadal or centennial timescales and whether they preferentially occur during a La Nin˜a-like mean state in the Pacific. g Here we aim to explore historical SST variability and occurrence of warm events in the SEIO and, for the first time, the role of the recently identified SST gradient between the Western and Central Pacific, the WPG11, as a large-scale driver in exacerbating heatwaves in the SEIO. To overcome the limitations of short-term instrumental observations, coral proxy records of SST were developed from ten long Porites spp. coral cores at three locations covering 11 of latitude (17–28 S) off the coast of Western Australia. Here we present a well-replicated 215-year reconstruction of annual SST for the SEIO based on coral Sr/Ca ratios and stable isotopes. The emergent long-term SST trends and interannual to multi-decadal variability highlight the key role of an increased WPG11–13, often in concert with strong La Nin˜a’s, in triggering extreme warm events in the SEIO. We trace the cause of historical heatwaves to large energy flux changes associated with an increased WPG11 as a result of the western Pacific warming faster than the central Pacific, illustrated by the second rotated empirical orthogonal function of tropical g g Hoell and Funk11 and Hoell et al.12,13 showed that during both El Nin˜o and La Nin˜a events the global impacts, including the SEIO, in terms of SST, atmospheric circulation and precipitation, were more severe when the SST anomalies in the western Pacific were strongly opposing those in the central Pacific SST than when the western Pacific SST anomalies were near neutral. Hoell and Funk11 described this gradient between the western and central Pacific as the Western Pacific Gradient (WPG)11. The WPG11 is defined as the standardized difference between the central Pacific 1 2 3 Latitude Longitude Year Normalised s.d. Coral record of southeast Indian Ocean marine heatwaves with intensified Western Pacific temperature gradient These studies11–13 show that the SST gradient between the central (Nin˜o4 region) and the western Pacific was an important measure of interannual to multi-decadal Pacific climate variability in addition to any previously derived metric of El Nin˜o-Southern Oscillation14 (ENSO) or combination of ENSO metrics (see Table 2 of Hoell and Funk11). (Nin˜o4 region14; 5 S–5 N, 160–210 E) and western Pacific SST (0–10 N, 130–150 E) between 1854 to 2010 from the 2  2 gridded extended reconstructed SST from NOAA version 3b15 (hereafter ERSST13; Fig. 1; Supplementary Fig. 1). These studies11–13 show that the SST gradient between the central (Nin˜o4 region) and the western Pacific was an important measure of interannual to multi-decadal Pacific climate variability in addition to any previously derived metric of El Nin˜o-Southern Oscillation14 (ENSO) or combination of ENSO metrics (see Table 2 of Hoell and Funk11). T he southeast Indian Ocean (SEIO) region that extends from the western shelf of the Australian continent marks the western boundary of the Indo-Pacific warm pool. It contains several uniquely biodiverse coastal fringing and offshore oceanic and atoll coral reefs (Fig. 1a). These reefs are strongly influenced by warm, poleward-flowing ocean boundary currents, the Holloway and Leeuwin Currents1–3. Historically, large-scale warming events resulting in coral bleaching have been relatively limited in the SEIO3–7, and occurred only locally in response to extreme austral summer sea surface temperatures (SST) during the 1998 El Nin˜o, the most widespread coral bleaching event yet recorded across the Indo-Pacific6,7. Consequently, the low levels of human development, infrequent coral bleaching, and high recovery potential of disturbed reefs6,7 suggest that this region may act as a coral refugia during climate warming. However, an extreme La Nin˜a during the austral summer of 2010/11 produced record-high SST leading to the first ever recorded large-scale coral bleaching along 12o of latitude of SEIO reefs3–5. This heat wave and similar historical events since 1960 have been dubbed the ‘Ningaloo Nin˜o’ and are thought to have been fuelled by an increased Indonesian Throughflow from the Pacific to the SEIO in response to the extreme La Nin˜a, warm Western Pacific SST, high sea-level, a strengthened Leeuwin Current and regional air-sea exchanges3,8–10. The large-scale drivers of individual heatwaves/‘Ningaloo Nin˜o’ that can lead to coral bleaching are still under investigation3,8,9. Coral record of southeast Indian Ocean marine heatwaves with intensified Western Pacific temperature gradient J. Zinke1,2,3,4,5, A. Hoell6,w, J.M. Lough3,7, M. Feng8, A.J. Kuret1,9, H. Clarke1,9, V. Ricca1,9, K. Rankenburg1,9 & M.T. McCulloch1,2,9 Increasing intensity of marine heatwaves has caused widespread mass coral bleaching events, threatening the integrity and functional diversity of coral reefs. Here we demonstrate the role of inter-ocean coupling in amplifying thermal stress on reefs in the poorly studied southeast Indian Ocean (SEIO), through a robust 215-year (1795–2010) geochemical coral proxy sea surface temperature (SST) record. We show that marine heatwaves affecting the SEIO are linked to the behaviour of the Western Pacific Warm Pool on decadal to centennial timescales, and are most pronounced when an anomalously strong zonal SST gradient between the western and central Pacific co-occurs with strong La Nin˜a’s. This SST gradient forces large-scale changes in heat flux that exacerbate SEIO heatwaves. Better understanding of the zonal SST gradient in the Western Pacific is expected to improve projections of the frequency of extreme SEIO heatwaves and their ecological impacts on the important coral reef ecosystems off Western Australia. 1 School of Earth and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia. 2 UWA Oceans Institute, 39 Fairway, Nedlands, Western Australia 6009, Australia. 3 Australian Institute of Marine Science, PMB 3, Townsville MC, Queensland 4810, Australia. 4 Department Environment and Agriculture, Curtin University of Technology, Kent Street, Bentley, Western Australia 6102, Australia. 5 School of Geography, Archaeology & Environmental Studies, University of the Witwatersrand, Wits 2050, South Africa. 6 Department of Geography, University of California Santa Barbara, Santa Barbara, California 93106, USA. 7 ARC Centre of Excellence for Coral Reef Studies, James Cook University, Queensland 4811, Australia. 8 Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Western Australia 6014, Australia. 9 ARC Centre of Excellence for Coral Reef Studies, The University of Western Australia, Crawley, Western Australia 6009, Australia. w Present address: NOAA/Earth System Research Laboratory, 325 Broadway, Boulder, Colorado, USA. Correspondence and requests for materials should be addressed to J.Z. (email: jens.zinke@gmail.com). NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications 1 & 2015 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9562 (Nin˜o4 region14; 5 S–5 N, 160–210 E) and western Pacific SST (0–10 N, 130–150 E) between 1854 to 2010 from the 2  2 gridded extended reconstructed SST from NOAA version 3b15 (hereafter ERSST13; Fig. 1; Supplementary Fig. 1). Coral record of southeast Indian Ocean marine heatwaves with intensified Western Pacific temperature gradient c WESTERN AUSTRALIA Perth Mermaid Houtman Abrolhos Bundegi Tantabiddi Imperieuse Clerke 112° 30° 20° 0 300 km NORTH a b 1 2 3 IWP06 Niño-4 WP –0.4 60E 30N 2nd Empirical orthogonal function 20N 10N 10S 20S 30S 0 80E 100E 120E 140E 160E 160W140W120W100W 80W 180 –0.3 3.0 2.0 1.0 0.0 –1.0 –2.0 –3.0 1960 1970 1980 1990 2000 2010 –0.2 –0.1 0 Covariance 0.1 0.2 0.3 0.4 Figure 1 | Southeast Indian Ocean reefs and tropical Indo-Pacific SST variability. (a) Locations of the three reef areas (1–3) sampled for long coral cores, (b) rotated empirical orthogonal function 2 (REOF2) covariance of ERSSTv3b15 anomalies, and (c) REOF2 time series, 1960–2013, which explains 21% of the variance. The WPG11 is defined as the standardized difference between average SSTover the Nin˜o4 domain14 (black box) and the Western Pacific (WP; blue box), while the Western Australian region is highlighted in grey with coral sampling locations indicated, 1, Houtman Abrolhos, 2, Ningaloo Reef and 3, Rowley Shoals. The black-dashed box marks the Indonesian warm pool region (IWP06 (ref. 26)). 1 2 3 Latitude Longitude Year Normalised s.d. c b IWP06 Niño-4 WP –0.4 60E 30N 2nd Empirical orthogonal function 20N 10N 10S 20S 30S 0 80E 100E 120E 140E 160E 160W140W120W100W 80W 180 –0.3 3.0 2.0 1.0 0.0 –1.0 –2.0 –3.0 1960 1970 1980 1990 2000 2010 –0.2 –0.1 0 Covariance 0.1 0.2 0.3 0.4 WESTERN AUSTRALIA Perth Mermaid Houtman Abrolhos Bundegi Tantabiddi Imperieuse Clerke 112° 30° 20° 0 300 km NORTH a 1 2 3 Normalised s.d. a Figure 1 | Southeast Indian Ocean reefs and tropical Indo-Pacific SST variability. (a) Locations of the three reef areas (1–3) sampled for long coral cores, (b) rotated empirical orthogonal function 2 (REOF2) covariance of ERSSTv3b15 anomalies, and (c) REOF2 time series, 1960–2013, which explains 21% of the variance. The WPG11 is defined as the standardized difference between average SSTover the Nin˜o4 domain14 (black box) and the Western Pacific (WP; blue box), while the Western Australian region is highlighted in grey with coral sampling locations indicated, 1, Houtman Abrolhos, 2, Ningaloo Reef and 3, Rowley Shoals. The black-dashed box marks the Indonesian warm pool region (IWP06 (ref. 26)). NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications acmillan Publishers Limited. All rights reserved. 2 Results Subsequently, a composite annual mean SST record for the SEIO including the three reefs was created by (i) normalizing (subtract mean and divide by standard deviation) each individual coral record to its variance using the time period 1961–1990 shared by all cores, (ii) averaging all records to form a composite chronology for the three reef areas, and (iii) averaging all three composite reef records to form a SEIO composite chronology. We converted our normalized SEIO coral composite proxy record to SST (hereafter WA coral SST) by scaling it to the standard deviation (over the period 1961–1990) of the 2  2 gridded ERSSTv3b15 and ground-truthed with the 1  1 gridded HadISST22 (1870–2010) from the UK Hadley Centre (Supplementary Tables 1–7) for the SEIO region 17–28 S, 113–119 E (Fig. 2; Supplementary Figs 3–5). Figure 2 | Southeast Indian Ocean coral SST anomaly reconstruction and Figure 2 | Southeast Indian Ocean coral SST anomaly reconstruction and Western Pacific SST anomalies. (a) Reconstructed annual WA coral SST anomaly (red) with 95% confidence interval (grey shaded) based on the spread of both coral and ERSST standard deviations between 1961 and 1990 compared with Indonesian warm pool26 (IWP06; blue) and WP SSTanomaly reconstructions15 (WP ERSST; black). SST anomalies are relative to 1961–1990 mean, (b) Number of coral cores through time, (c) Reconstruction skill statistics for WA coral SST against regional ERSST15 (17–28 S, 113–119 E) are calculated over the validation period (1920–1949) for each proxy nest, including the coefficient of determination (Rsq, magenta), the reduction of error (RE, orange), and the coefficient of efficiency (CE, black) and (d) Same as a, but detrended time series. confidence in the proxy record that would be lacking if based on a single coral core18,19. The excellent agreement between the coral core composite pre-1900 implies that SST coverage in SST reconstruction data sets based on ICOADS23 ship-of-opportunity (Supplementary Figs 3–5) suffers from poor sampling and interpolation from increasingly distant data points. g Least squares linear regression between WA coral SST and the modern SST reconstructions shows significant positive relation- ships that typically accounted for 20–40% of the SST variance over the entire record length (Supplementary Tables 1–7). Validation statistics show skill of the WA coral reconstruction for most of the record (Fig. 2c). The WA coral SST composite shows long-term warming (Fig. 2a; Supplementary Fig. 3) with strong multi-decadal variability superimposed before 1900 and after 1990. Results Coral geochemical proxy records of sea surface temperature. Porites coral cores were obtained from the Rowley Shoals (17 S, 119 E), Ningaloo Reef (21 S, 113 E) and the Houtman- Abrolhos Islands (HAI; 28 S, 114 E) between 2008 and 2010 (ref. 16; Fig. 1a). Coral d18O and Sr/Ca are widely used as robust proxies for SST17–19. While Sr/Ca is considered to be primarily controlled by SST, coral d18O can be influenced by both SST and d18Oseawater through precipitation minus evaporation (P  E) influencing surface ocean salinity19. However, interannual changes in P  E at the Rowley Shoals, Ningaloo Reef and HAI are too small to noticeably affect coral d18O. Therefore, the d18O record primarily reflects variations in SST. We combine two previously published bimonthly-resolved coral d18O records20,21 and two annually resolved Sr/Ca records from HAI8 with six new annually resolved Sr/Ca and d18O records to reconstruct a robust and well-replicated record of past SST variability in the SEIO (Fig. 2; Supplementary Figs 1–4). b 1800 1840 1880 1920 1960 2000 Year 2 4 6 8 10 Number of records b c CE 0 0.4 0.8 0 0.4 0.8 1800 1840 1880 1920 1960 2000 RE Rsq RE/CE Rsq Year c 95% CI STDV d –1 –0.5 0 0.5 1 –1 –0.5 0 0.5 1 1800 1840 1880 1920 1960 2000 WA coral SST IWP06 WP ERSST WA coral SST detrended (deg C) WP SST detrended (deg C) Year WP SST detrended (deg C) Coral proxy records of SST from three representative reefs of the SEIO were obtained for the period 1795–2010 (Fig. 2; Supplementary Figs 1–2). Least squares linear regressions between individual coral SST reconstructions from the three representative reefs of the SEIO were significant and positive over the record length, typically sharing between 35 to 41% of variance (Supplementary Tables 1–4). The longest records from HAI and Rowley Shoals shared 45% variance between 1798 and 1850 on decadal timescales (47 years), although the year-to-year variability was not always in phase. & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9562 ARTICLE b 1800 1840 1880 1920 1960 2000 Year 2 4 6 8 10 Number of records c CE 0 0.4 0.8 0 0.4 0.8 1800 1840 1880 1920 1960 2000 RE Rsq RE/CE Rsq Year –2 –1.5 –1 –0.5 0 0.5 1 –2 –1.5 –1 –0.5 0 0.5 1 1800 1840 1880 1920 1960 2000 95% CI STDV WA coral SST WP ERSST IWP06 WP SST (deg C) Year WA coral SST (deg C) a 95% CI STDV d –1 –0.5 0 0.5 1 –1 –0.5 0 0.5 1 1800 1840 1880 1920 1960 2000 WA coral SST IWP06 WP ERSST WA coral SST detrended (deg C) WP SST detrended (deg C) Year Figure 2 | Southeast Indian Ocean coral SST anomaly reconstruction and Western Pacific SST anomalies. (a) Reconstructed annual WA coral SST anomaly (red) with 95% confidence interval (grey shaded) based on the spread of both coral and ERSST standard deviations between 1961 and 1990 compared with Indonesian warm pool26 (IWP06; blue) and WP SSTanomaly reconstructions15 (WP ERSST; black). SST anomalies are relative to 1961–1990 mean, (b) Number of coral cores through time, (c) Reconstruction skill statistics for WA coral SST against regional ERSST15 (17–28 S, 113–119 E) are calculated over the validation period (1920–1949) for each proxy nest, including the coefficient of determination (Rsq, magenta), the reduction of error (RE, orange), and the coefficient of efficiency (CE, black) and (d) Same as a, but detrended time series. –2 –1.5 –1 –0.5 0 0.5 1 –2 –1.5 –1 –0.5 0 0.5 1 1800 1840 1880 1920 1960 2000 95% CI STDV WA coral SST WP ERSST IWP06 WP SST (deg C) Year WA coral SST (deg C) a Indo-Pacific SST11 (Fig. 1b,c; Supplementary Fig. 1). We show that the magnitude of the WPG varies independently between individual El Nin˜o and La Nin˜a events8–13 resulting in modification of the large-scale tropical circulation and precipitation fields11,13 affecting the energy and heat flux terms, warm water ocean advection through the coastal waveguide and sea-level pressure in the SEIO and ultimately the magnitude of SEIO marine heatwaves. a & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 M ill P bli h Li it d All i ht d Results However, our WA coral SST record indicates overall cooler mean SST during the nineteenth century up to the mid- twentieth century than any of the long-term instrumental SST data for the west Australian shelf (Fig. 2; Supplementary Figs 3 and 4). Although there are weaker long-term relationships with ship-based SST reconstructions, the multicore approach provides To assess if mean annual SST capture the major warm events in the SEIO during Ningaloo Nin˜o event years that are normally phase-locked to austral summer and autumn, we evaluated the occurrence of warm anomalies in mean annual versus monthly time scale ERSSTv.3b (ref. 15) since 1950 (Supplementary Table 8). This confirmed that mean annual SST did capture the vast majority (18 out of 26 events) of Ningaloo Nin˜o/Nin˜a event years defined in refs 3,9 (Supplementary Table 8). Our detrended mean annual WA coral SST is also significantly correlated 3 NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9562 ARTICLE 1800 1820 1840 1860 1880 1900 1920 1940 1960 1980 Correlation WA coral SST vs WPG and paleo-WPG 1795:2010 31-yr corr 95% conf –1 –0.8 –0.6 –0.4 –0.2 0 0.2 0.4 0.6 31-yr corr 95% conf 2000 Year d –2 –1 0 1 2 WPG (normalized s.d.) –0.5 0 0.5 WA coral SST (deg C) a WA coral SST vs WPG obs. –0.5 0 0.5 WA coral SST (deg C) Paleo-WPG (normalized s.d.) –4 –2 0 2 4 b c WA coral SST vs paleo-WPG WA coral SST vs Nino3.4 index –0.5 0 0.5 WA coral SST (deg C) La Niña W10 –2 –1 0 1 2 1800 1840 1880 1920 1960 2000 Nino3.4 (normalized s.d.) Year Figure 3 | Western Pacific Gradient—SEIO SST relationship. (a) WPG from observations (y axis inverted) compared to detrended WA coral SST, (b) paleo-WPG based on the difference between IWP06 (ref. 26) and Nin˜o3.4 reconstruction28, (c) Nin˜o3.4 instrumental index (blue ¼ La Nin˜a; red ¼ El Nin˜o) and La Nin˜a-like anomalies in the Nin˜o3.4 reconstruction28 superimposed (orange), and (d) 31-year running correlations between detrended WA coral SST and paleo-WPG (red solid line, red stippled 95% confidence interval based on a 1,000-sample Monte Carlo simulation58) and WPG from observations11 (purple solid line, purple stippled 95% confidence interval). Grey shaded areas indicates periods with statistically significant correlations (495%). Results 5 WA coral SST (deg C) Paleo-WPG (normalized s.d.) 5 WA coral SST (deg C) –2 –1 0 1 2 WPG (normalized s.d.) –0.5 0 0.5 WA coral SST (deg C) a WA coral SST vs WPG obs. –0.5 0 0.5 WA coral SST (deg C) Paleo-WPG (normalized s.d.) –4 –2 0 2 4 b c WA coral SST vs paleo-WPG WA coral SST vs Nino3.4 index –0.5 0 0.5 WA coral SST (deg C) La Niña W10 –2 –1 0 1 2 1800 1840 1880 1920 1960 2000 Nino3.4 (normalized s.d.) Year (r ¼ 0.59; P ¼ 0.0001; DF ¼ 59) with the Ningaloo Nin˜o index24,25 between 1948 and 2010, defined for January-February averages (Supplementary Table 9). a The role of the Western Pacific warm pool for SEIO SST. To assess the role of the Indo-Pacific warm pool on SEIO SST, we compared our WA coral SST reconstruction with SST proxy records from the Indonesian warm pool (detrended) derived from a multi-proxy reconstruction26 (hereafter IWP06) and the western Pacific from instrumental data15 (hereafter WP SST; Supplementary Table 5). IWP06 extends from 1782 to 1992 and is a composite from annual tree ring and coral records for the Indonesian Archipelago (Fig. 2). For the period 1795 to 1992, the IWP06 and WA coral SST were significantly correlated (r ¼ 0.48, Po0.001; DF ¼ 195) and this relationship remained statistically significant after detrending (Supplementary Table 5). WA coral SST indicates overall cooler mean SST during the nineteenth century up to the mid-twentieth century than IWP06. This is in agreement with a recent compilation of tropical coral SST reconstructions27 that also showed cooler SST in the Indian Ocean than in the Western Pacific for the entire nineteenth and early twentieth century. Both WA coral SST and IWP06 co-vary on multi-decadal timescales with highest amplitudes between 1795 and 1850 and post 1980 (Fig. 2). The higher amplitude variations in WA coral SST between 1795 and 1850 are solely based on HAI and RS data sets (four cores). The coral records agree best on decadal timescales in this time interval, and show less agreement for year to year events. Our reconstruction skill statistics also revealed lowest skill for the period 1800–1840 with the coefficient of efficiency (CE) just above zero (Fig. 2c). Thus, the absolute magnitude of SST anomalies between 1795 and 1850 in our reconstruction should be interpreted with caution. Results 1800 1820 1840 1860 1880 1900 1920 1940 1960 1980 Correlation WA coral SST vs WPG and paleo-WPG 1795:2010 31-yr corr 95% conf –1 –0.8 –0.6 –0.4 –0.2 0 0.2 0.4 0.6 31-yr corr 95% conf 2000 Year d WA coral SST vs WPG and paleo-WPG 1795:2010 p WA coral SST was also significantly correlated with WP SST (r ¼ 0.55; Po0.001; DF ¼ 154), and this relationship was statistically significant after detrending (Supplementary Table 5). The highest correlation between WA coral SST and WP SST was found after 1980 (r ¼ 0.68; Po0.001; DF ¼ 28). The same holds for the correlation between WA coral SST and the Nin˜o4 index14 (r ¼  0.68; Po0.001; DF ¼ 28). Post-1980, WA coral SST was also significantly correlated with the WPG11 (r ¼  0.69; P ¼ 0.002; DF ¼ 28; Fig. 3a). These results indicate that post 1980, SST in the SEIO was most strongly connected with the western Pacific rather than the Indian Ocean, especially the warm pool and Nin˜o4 region, and the WPG11 (Supplementary Tables 5–7; Supplementary Figs 7–9). Year Figure 3 | Western Pacific Gradient—SEIO SST relationship. (a) WPG from observations (y axis inverted) compared to detrended WA coral SST, (b) paleo-WPG based on the difference between IWP06 (ref. 26) and Nin˜o3.4 reconstruction28, (c) Nin˜o3.4 instrumental index (blue ¼ La Nin˜a; red ¼ El Nin˜o) and La Nin˜a-like anomalies in the Nin˜o3.4 reconstruction28 superimposed (orange), and (d) 31-year running correlations between detrended WA coral SST and paleo-WPG (red solid line, red stippled 95% confidence interval based on a 1,000-sample Monte Carlo simulation58) and WPG from observations11 (purple solid line, purple stippled 95% confidence interval). Grey shaded areas indicates periods with statistically significant correlations (495%). Figure 3 | Western Pacific Gradient—SEIO SST relationship. (a) WPG Figure 3 | Western Pacific Gradient—SEIO SST relationship. (a) WPG from observations (y axis inverted) compared to detrended WA coral SST, (b) paleo-WPG based on the difference between IWP06 (ref. 26) and Nin˜o3.4 reconstruction28, (c) Nin˜o3.4 instrumental index (blue ¼ La Nin˜a; red ¼ El Nin˜o) and La Nin˜a-like anomalies in the Nin˜o3.4 reconstruction28 superimposed (orange), and (d) 31-year running correlations between detrended WA coral SST and paleo-WPG (red solid line, red stippled 95% confidence interval based on a 1,000-sample Monte Carlo simulation58) and WPG from observations11 (purple solid line, purple stippled 95% confidence interval). NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications Results La Nin˜a years (based on the instrumental data Nin˜o3.4 index14 post-1854 and a combination of paleo-Nin˜o3.4 indices pre-1854 (refs 28,29)) were grouped into strong (41 s.d.), moderate (40.5 s.d.) and weak events (o0.5 s.d.) for mean annual values. We also classified weak El Nin˜o years. Years in bold indicate events recorded in the WA coral SST. Table 1 | Occurrence of positive SEIO SST anomalies and the strength of WPG and Nino3.4 events. SEIO, southeast Indian Ocean; SST, sea surface temperature; WPG, Western Pacific Gradient The negative WPG years were grouped into strong (41 standard deviation (s.d.) of annual mean values) and moderate (o1 s.d.) years, and neutral/positive WPG years (based on the paleo-WPG cross- validated with the instrumental WPG11). La Nin˜a years (based on the instrumental data Nin˜o3.4 index14 post-1854 and a combination of paleo-Nin˜o3.4 indices pre-1854 (refs 28,29)) were grouped into strong (41 s.d.), moderate (40.5 s.d.) and weak events (o0.5 s.d.) for mean annual values. We also classified weak El Nin˜o years. Years in bold indicate events recorded in the WA coral SST. propagate along the west Australian coast as coastal Kelvin waves8,24 to the SEIO generating warm SST anomalies (Supplementary Fig. 6) and (3) generating positive SLP anomalies over the Western Pacific that induce negative SLP and cyclonic meridional wind anomalies in the SEIO3,8–10. Thus, for strong SEIO warm events a strongly negative WPG intensifies the atmospheric and oceanic processes typically associated with La Nin˜a11. The opposite holds for El Nin˜o events and positive WPG11. We tested our hypothesis that the WPG is also remotely driving changes in the lower troposphere over the northwestern coast of Australia which have been shown to be of paramount importance to enhance the magnitude of SEIO marine heatwaves3,8–10,24. We computed composites for negative and positive WPG from objectively analysed air-sea fluxes (OAFlux)32 and NCEP–NCAR Reanalysis I (ref. 33) for the global oceans available from 1958 to 2012. Figure 4 shows that the atmospheric circulation during strong negative WPG (and La Nin˜a) is moistening the lower troposphere in the western part of the Indonesian warm pool and the northwest Australian shelf, which reduces the latent heat flux from the surface (Fig. 4b) and reduces the amount of energy drawn from the sea surface thereby causing an increase in SSTs. The opposite is true for strong positive WPG episodes (El Nin˜o events). Results The vertically integrated moisture flux drawn from NCEP–NCAR Reanalysis I (ref. 33) for 1958 to 2012 indicates a cyclonic circulation in the Indian Ocean off the west coast of Australia (Fig. 4d), which increases the flux of moisture into the region (one effect of this is enhanced rainfall9). The cyclonic atmospheric circulation and low SLP were found to be one of the key drivers of the 2011 marine heat wave3,9. Furthermore, there are significant reductions in evaporation and latent heat flux (Fig. 4a,b), which cause increases in SST accompanied by very small changes in the sensible heat flux (Fig. 4c). These changes in heat and energy flux terms are also associated with reduced wind speeds as suggested in Marshall et al.25. throughout the record, being highest between 1800 to 1850, 1900 to 1950 and post 1980. Both observed and paleo-WPG agree on the strengthening relationship with WA coral SST since 1980 (Fig. 3e). However, the paleoreconstruction reveals that the recent strong relationship is not unprecedented and mostly likely part of natural multi-decadal oscillations in the WPG. In contrast, the correlation between WA coral SST and WA ERSST with the Nin˜o-4 (ref. 14) index and a Nino3.4 reconstruction28 was stable for most of the twentieth century, yet weaker for most of the nineteenth century (Supplementary Figs 7–9). Thus, we conclude that the paleo-WPG showed stronger connectivity with the SEIO for both the nineteenth and twentieth century than the paleo- Nin˜o3.4 (ref. 14) index. However, the change in ENSO connectivity centred around 1820 could also be related to larger uncertainty in our WA coral SST and/or the paleo-Nin˜o3.4 (ref. 14) index (Supplementary Fig. 9). Nin˜o3.4 (refs 14,29) paleoclimate reconstructions slightly differ in the early 1800’s in the number of La Nin˜a years and that might have affected our analysis. y Nevertheless, the WA coral SST anomalies after 1990 are significantly warmer than any event in the past with 1989, 1996, 1999 and 2008 being the hottest years. The WA coral SST (Fig. 2) identified the hottest year on record in 1999/2000, which corresponds to one of the strongest La Nin˜a and the most extreme negative WPG11 events up to the year 2010 (Fig. 1). These recent warm anomalies were also exacerbated by the long- term warming trend of the WP11 and the SEIO8,30 (Fig. 2a). Results The years following 2008 have seen continuously high SST in both regions24,30 marked by a strongly persistent negative WPG11 (Fig. 3a) and resulting in several coral bleaching events off WA between 2011 and 2013 (ref. 24). Sea surface height31 (SSH) is a dynamic measure of connectivity between the Western Pacific and the SEIO through oceanic waveguides3,8,24. Our WA coral SST was significantly correlated with SSH in the WP, including the WPG region, between 1958 and 2010 (r ¼ 0.59; Po0.001; DF ¼ 45) and from the Indonesian Throughflow region to the southwest Australian coast (Supplementary Fig. 6). The correlation between the WPG and SSH mirrors the results from WA coral SST with even higher correlations (r ¼  0.80; Po0.001; DF ¼ 45). The connection is largely due to the existence of the equatorial and coastal waveguides along the coast of west Australia3 on decadal time scale driven by the WPG11 and ENSO3,9,24. Results Grey shaded areas indicates periods with statistically significant correlations (495%). The role of the west pacific gradient for SEIO SST. To assess the importance of western Pacific forcing of SEIO warm events we used the WPG11 defined as the standardized difference between the central Pacific (Nin˜o4 region14; 5 S–5 N, 160–210E) and western Pacific SST (0–10 N, 130–150 E) between 1854 and 2010 from ERSST15 (Fig. 1). We assessed the long-term stability of the relationship between WA coral SST and the WPG and La Nin˜a events using detrended data (Fig. 3). We also computed a paleo-WPG between 1795 and 1992 from the difference between IWP06 (ref. 26) and a proxy reconstruction of the Nin˜o3.4 index28 and extracted La Nin˜a events from both the instrumental Nin˜o3.4 (ref. 14) index and a paleoreconstruction28 (Fig. 3). The paleo-WPG reconstruction was shown to be insensitive to the choice of independent Nino3.4 reconstructions28,29 (detrended) based on paleoclimate data (Supplementary Fig. 10). anomalies in the SEIO during the nineteenth century, although set against a cooler mean state of the tropical oceans (Fig. 1; Table 1). Post-1980, we observed an increase in positive SEIO SST anomalies. The majority of warm years over the entire record length correspond to past La Nin˜a events28,29 of varying strength and a moderate to strong negative WPG (Fig. 3a-d; Table 1). From Table 1 we can conclude that 51 out of 58 years with positive WA coral SST anomalies occurred during strong or moderate negative WPG years (WPG index is negative indicating a warm Western Pacific and cool central Pacific). To assess the multi-decadal relationship between WA coral SST, ENSO and the WPG we computed 31-year running correlations (Fig. 3e; Supplementary Figs 7–9). We found the highest correlation with the observed WPG and Nin˜o-4 after 1980 at levels unprecedented since at least 1854 (Supplementary Figs 7–9). However, the correlations with the paleo-WPG indicate significantly higher correlations than with the observed WPG WA coral SST (detrended) showed frequent positive anomalies between 1795 and 1900 with highest magnitudes between 1800 and 1850 (Fig. 3a,b). Thus, the co-occurrence of a strongly negative WPG and La Nin˜a appeared to drive warm SST 4 NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. & 2015 Macmillan Publishers Limited. All rights reserved. & 2015 Macmillan Publishers Limited. & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. Results All rights reserved ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9562 Table 1 | Occurrence of positive SEIO SST anomalies and the strength of WPG and Nino3.4 events. Strong WPG Moderate WPG Neutral/positive WPG Strong La Nin˜a 1826, 1829, 1893, 1910, 1917, 1934, 1943, 1950, 1974, 1989, 1999, 2000, 2008 1849, 1863, 1873, 1874, 1890, 1894 1971 Moderate La Nin˜a 1806, 1870, 1944, 1945, 1955, 1975, 2001 1797, 1802, 1823, 1824, 1828, 1835, 1857, 1861, 1871, 1880, 1909, 1939, 1976, 1996 1796, 1840, 1876, 1911, 1984 Weak La Nin˜a 1805, 1833, 1879, 1898, 1933, 1949, 1962 1825, 1830, 1832, 1847, 1852, 1872, 1882, 1916, 1932 1798, 1799, 1809, 1810, 1851, 1925 Weak El Nin˜o 1844, 1845, 1846 1850 SEIO, southeast Indian Ocean; SST, sea surface temperature; WPG, Western Pacific Gradient The negative WPG years were grouped into strong (41 standard deviation (s.d.) of annual mean values) and moderate (o1 s.d.) years, and neutral/positive WPG years (based on the paleo-WPG cross- validated with the instrumental WPG11). La Nin˜a years (based on the instrumental data Nin˜o3.4 index14 post-1854 and a combination of paleo-Nin˜o3.4 indices pre-1854 (refs 28,29)) were grouped into strong (41 s.d.), moderate (40.5 s.d.) and weak events (o0.5 s.d.) for mean annual values. We also classified weak El Nin˜o years. Years in bold indicate events recorded in the WA coral SST. Table 1 | Occurrence of positive SEIO SST anomalies and the strength of WPG and Nino3.4 events. Strong WPG Moderate WPG Neutral/positive WPG Strong La Nin˜a 1826, 1829, 1893, 1910, 1917, 1934, 1943, 1950, 1974, 1989, 1999, 2000, 2008 1849, 1863, 1873, 1874, 1890, 1894 1971 Moderate La Nin˜a 1806, 1870, 1944, 1945, 1955, 1975, 2001 1797, 1802, 1823, 1824, 1828, 1835, 1857, 1861, 1871, 1880, 1909, 1939, 1976, 1996 1796, 1840, 1876, 1911, 1984 Weak La Nin˜a 1805, 1833, 1879, 1898, 1933, 1949, 1962 1825, 1830, 1832, 1847, 1852, 1872, 1882, 1916, 1932 1798, 1799, 1809, 1810, 1851, 1925 Weak El Nin˜o 1844, 1845, 1846 1850 SEIO, southeast Indian Ocean; SST, sea surface temperature; WPG, Western Pacific Gradient The negative WPG years were grouped into strong (41 standard deviation (s.d.) of annual mean values) and moderate (o1 s.d.) years, and neutral/positive WPG years (based on the paleo-WPG cross- validated with the instrumental WPG11). NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited All rights reserved Discussion l Our results imply that over the past 215 years the WPG11 was a key player in Indo-Pacific climate connectivity in addition to ENSO-driven SST anomalies. Recent changes in the WPG, combined with strong WP warming after the Indo-Pacific climate regime shift of the late 1990s (refs 24,34), are driving significant thermal anomalies impacting coral reef ecosystems over several thousands of kilometres from the Indonesian seas to the southern coast of Western Australia and along the southwest Pacific. The abrupt rise in western Pacific SST in the late 1990s was also addressed by recent studies8,11,24,35,36. Hoell and Funk11 showed that the abrupt warming of the west Pacific has resulted in a more The question arises how the WPG can force heatwaves in remote coral reefs of the SEIO over large spatial scales. Foremost, the WPG, during and independently from ENSO, remotely influences SEIO warm events by (1) enhancing easterly equatorial wind stress in the western Pacific11, (2) inducing equatorial downwelling Rossby waves in the western Pacific which then 5 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9562 60° E –20 –15 –10 –5 0 5 10 15 20 80° E 100° E 120° E 140° E 160° E 180˚E 20° N Evaporation (cm per year) 10° N 10° S 20° S 30° S 40° S 0 a 60° E –20 –15 –10 –5 0 5 10 15 20 –20 –15 –10 –5 0 5 10 15 20 –20 –1.5 –1 –0.5 0 0.5 1 1.5 –15 –10 –5 0 5 10 15 20 80° E 100° E 120° E 140° E 160° E 180˚E 60° E 80° E 100° E 120° E 140° E 160° E 180˚E 60° E 80° E 100° E 120° E 140° E 160° E 180˚E 60° E 80° E 100° E 120° E 140° E 160° E 180˚E 20° N Evaporation (cm per year) Latent heating (W m–2) Sensible heating (W m–2) Moisture flux and moisture flux divergence 30 Reference vector 10° N 10° S 20° S 30° S 40° S 0 20° N 10° N 10° S 20° S 30° S 40° S 0 20° N d 10° N 10° S 20° S 30° S 40° S 20° N 10° N 0 10° S 20° S 30° S 40° S 0 c a b Figure 4 | Heat and energy flux terms related to changes in the West Pacific gradient. Discussion l (a) Surface ocean evaporation32, (b) latent heat flux32, (c) sensible heat flux32 and (d) vertically integrated moisture flux (kg m  1 s  1) and moisture flux divergence (coloured) related to the change in the WPG between 1958 and 2012 (ref. 33). (a–d) show the flux relationship as composites between negative and positive WPG gradient occurrences. The number of positive and negative occurrences are 8 (16 in total), which correspond to 33% of the 58-year record. Positive flux in a to c means the ocean is gaining heat. All shadings in (a–d) are significant to Po0.05 using a two-tailed Monte Carlo test. –20 –15 –10 –5 0 5 10 15 20 E 60° E 80° E 100° E 120° E 140° E 160° E 180˚E Latent heating (W m–2) 20° N 10° N 10° S 20° S 30° S 40° S 0 b b b a –20 –15 –10 –5 0 5 10 15 20 60° E 80° E 100° E 120° E 140° E 160° E 180˚E Sensible heating (W m–2) 20° N 10° N 0 10° S 20° S 30° S 40° S c –1.5 –1 –0.5 0 0.5 1 1.5 E 60° E 80° E 100° E 120° E 140° E 160° E 180˚E Moisture flux and moisture flux divergence 30 Reference vector 20° N d 10° N 10° S 20° S 30° S 40° S 0 d Figure 4 | Heat and energy flux terms related to changes in the West Pacific gradient. (a) Surface ocean evaporation32, (b) latent heat flux32, (c) sensible heat flux32 and (d) vertically integrated moisture flux (kg m  1 s  1) and moisture flux divergence (coloured) related to the change in the WPG between 1958 and 2012 (ref. 33). (a–d) show the flux relationship as composites between negative and positive WPG gradient occurrences. The number of positive and negative occurrences are 8 (16 in total), which correspond to 33% of the 58-year record. Positive flux in a to c means the ocean is gaining heat. All shadings in (a–d) are significant to Po0.05 using a two-tailed Monte Carlo test. negative WPG, which in turn has forced strong drought-inducing teleconnections across the Northern Hemisphere and the circum-Indian Ocean. Discussion l However, the period since the late 1990s is also characterized by marked oscillations in WP and SEIO SST associated with the Interdecadal Pacific Oscillation coupled with more frequent La Nin˜a and Ningaloo Nin˜o events3–10,24. The increased magnitude of thermal stress anomalies in the SEIO since the late 1990s revealed by our WA coral SST and similar events in the SW Pacific are supported by recent work on the 2011–2013 Ningaloo Nin˜o’s3,8,9,24,25, by the severity of warming following the 2011 La Nin˜a along the Western Australian coast3–10,24 and observed mass coral bleaching in Papua New Guinea and the southwest Pacific Islands (Fiji, Solomon)37 during the 1999/2000 protracted La Nin˜a. These findings point to an uncertain future for WP and SEIO coral reef ecosystems, despite their not being exposed to many of the local pressures degrading other reefs around the world (for example, pollution, overfishing), because they are living close to their upper thermal threshold. will dominate over that of the WP. At times, for instance between 1800 and 1850, both the Nin˜o3.4 index and the WPG showed large amplitude variations on multi-decadal timescales that are mirrored by WA coral SST. Similar large amplitude variations in the early 19th century were also observed in coral records from the Western Pacific Warm Pool27,40,41. This multi-decadal variability in the nineteenth century was most probably related to internal variability of the climate system and appears to be a prominent signal across the Indo-Pacific warm pool. Part of the multi-decadal ups and downs is related to large volcanic eruptions in the period 1800–1850 (ref. 42). Thus, the independent variability of the WPG from ENSO is of pivotal importance for Indo-Pacific climate connectivity and their impacts on the environment and human society. Recently, Cai et al.43 showed, for a subset of CMIP5 models, a high likelihood for a more intense WPG between the Maritime continent and the central Pacific and intensified La Nin˜a events in twenty-first century climate projections, further highlighting the importance of the coral records presented here. Our work provides an historical perspective on marine heatwaves in the SEIO and shows that recent thermal stress events are likely the result of strong anthropogenic warming that made it easier for natural climate variability to exceed the critical threshold for mass coral bleaching to occur in this previously thought coral refugia region. Discussion l Improved SST reconstructions and sustained long-term monitoring are keys to our ability to predict the ecological consequences of continued warming for the unique WP and SEIO coral reef socioecological systems. The temporal evolution of the WPG with future ocean warming combined with decadal climate variability discussed here will determine the thermal stress level that coral reefs in the teleconnected regions experience. The western pole of the WPG index has been warming strongly in the past two decades and, together with Indian Ocean SST, closely tracks radiative anthropogenic forcing38,39. This western Pacific warming is at the heart of the recent strengthening of the Pacific Walker Circulation that ultimately strengthened the climate connectivity between the WP and the SEIO presented here35,36,38. Our results also reveal that, at times, the WP and central Pacific warm or cool at similar rates, resulting in small changes to the WPG. Consequently, during such periods of low WPG variability we find weaker relationships with our SEIO SST reconstruction. For these periods, ENSO forcing from the Nin˜o4 or Nin˜o3.4 regions NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9562 Samples were analysed for trace element concentration on a Thermo Scientific XSERIES 2 quadrupole inductively coupled plasma mass spectrometer. The standard reference material for calibration is the JCp-1 Porites sp. standard prepared by the Geological Survey of Japan52. All Sr/Ca data are normalized to JCp-1 with Sr/Ca ¼ 8.838 mmol mol  1. External reproducibility has been checked by repeated analysis (N ¼ 150) of our in-house coral (Porites sp.) standard Davies Reef (DR) which gives Sr/Ca ¼ 8.953±0.34% (2s). southernmost reef of the Rowley Shoals, and are part of an ongoing study into the climatological history of Australia’s coral reefs conducted by AIMS16. Each of the 90 mm diameter cores (IMP05A, 175196 S, 118969 E; 8-m water depth, 3.43-m long) and IMP03A (175369 S, 118974 E, 14-m water depth, 3.11-m long) were taken from bommies of Porites genus B2-km apart. Two 70-mm diameter cores CLE09 (1.5-m long, 10-m water depth) and MER09 (1.5-m long, 17-m water depth) were obtained from Clerke (northernmost atoll) and Mermaid (halfway between Imperieuse and Clerke) reefs during research cruises of AIMS and the University of Western Australia (UWA), respectively, in 2009. southernmost reef of the Rowley Shoals, and are part of an ongoing study into the climatological history of Australia’s coral reefs conducted by AIMS16. Each of the 90 mm diameter cores (IMP05A, 175196 S, 118969 E; 8-m water depth, 3.43-m long) and IMP03A (175369 S, 118974 E, 14-m water depth, 3.11-m long) were taken from bommies of Porites genus B2-km apart. Two 70-mm diameter cores CLE09 (1.5-m long, 10-m water depth) and MER09 (1.5-m long, 17-m water depth) were obtained from Clerke (northernmost atoll) and Mermaid (halfway between Imperieuse and Clerke) reefs during research cruises of AIMS and the University of Western Australia (UWA), respectively, in 2009. g The stable oxygen isotope (d18O) ratios in Kuhnert et al.20,21 were analysed on a Finnigan MAT 251 mass spectrometer calibrated against NBS-19. They are reported in per mil versus Vienna Pee Dee Belemnite isotope scale (% VPDB). Analytical errors of replicate measurements of an internal laboratory standard (Solnhofen limestone) are less than ±0.07 for d18O. The d18O analyses of the new HAB10A coral record was undertaken at the West Australian Biogeochemistry Centre (WABC) at UWA following the protocol of Paul and Skrzypek53. ARTICLE For Ningaloo and Rowley Shoals, no adjustment was needed. Annual band counting for all cores was based on annually sampled records only and all agreed with the number of years in the geochemical records. A composite SST record was created by (i) normalizing (subtract mean and divide by s.d.) each individual coral geochemical record to its variance using the time period 1961–1990 shared by all cores, (ii) averaging all records to form a composite chronology for the three reef areas and (iii) averaging all three composite reef records to form a SEIO composite chronology (hereafter WA coral SST). We converted our normalized SEIO coral composite proxy record to SST by scaling it to the s.d. of ERSSTv3b (ref. 15; over the period 1961–1990), the longest and most reliable continuous SST dataset for the SEIO region, over the region 17–28 S, 113–119 E. To determine the accuracy of the long-term composite record, we calculated the 95% confidence interval in the spread of the SST s.d. (grey shading in Fig. 2a,d) for 1961–1990 in both WA coral SST and ERSSTv3b (ref. 15) and subsequently estimated the spread in the scaling coefficient. We used the maximum spread in the scaling coefficient as uncertainty bounds on our final coral record for both WA coral SST with trend (grey shading in Fig. 2a) and for detrended data (grey shading in Fig. 2d). To allow for the number of coral records decreasing backwards in time, reconstruction skill statistics55 for each nest of SST reconstructions starting with 2 records and ending with the composite record of all 10 proxy time series were calculated over the validation period 1920–1949, including the coefficient of determination (Rsq), the reduction of error (RE), and CE (Fig. 2c). Values of RE (CE) above zero indicate some statistical skill in that the reconstructed values over the validation period are better estimates of SST than the mean of the calibration (validation) period. The calibration period was 1950–2008 and comprised two-thirds of the years that the proxy and instrumental SST time series with best data coverage shared in common, with the validation period (1920–1949) comprising the remaining one-third. The choice of the validation period was largely based on the HadSST3 (ref. 56) data sets for the West Australia region (17–28 S, 113-19 E) which showed large data gaps between 1870 and 1920. ARTICLE d18O was analysed using GasBench II coupled with Delta XL Isotope Ratio Mass Spectrometer (Thermo-Fisher Scientific, Bremen, Germany). All results were expressed using the standard d-notation (d18O) and reported in per mil (%) after normalization to the Vienna Pee Dee Belemnite isotope scale (% VPDB). The multi-point normalization was based on three international standards NBS18, NBS19 and L-SVEC, each replicated twice54. The analytical uncertainty was lower than ±0.10% (1s) for d18O. The proxy SST data from this study will be made available through NOAA paleoclimate database (www.ncdc.noaa.gov/paleo/). Ningaloo Reef extends over 300 km and includes the only example in the world of an extensive fringing coral reef on the west coast of a continent. Ningaloo Marine Park (NMP) was listed as a World Heritage site in 2013 (ref. 45). Tantabiddi Reef lies in the northwestern section of NMP and forms a narrow lagoon which provides rapid exchange with the open ocean and the Leeuwin Current (LC). Bundegi Reef lies in the northeastern section of the NMP, an area that extends into the shallow Exmouth Gulf. Coral cores (Porites spp.) from Tantabiddi (TNT07C; 2191 0S,11397 0E; 2.5-m water depth, 1.55 m long) and Bundegi (BUN05C; 2187 0S,11417 0E; 2-m water depth; 1.78-m long) were drilled in October 2008 by AIMS16. Both corals sampled were from inner reef environments located within 200–300 m of the shoreline. Growth rates for the corals were determined from the X-ray photographs and were between 1–1.6 cm per year for Tantabiddi and 1.2–1.9 cm per year Bundegi. The published stable isotope record from Tantabiddi Reef extends from 1878 to 1994 (ref. 20). A core of 2.8 m in length from 3-m water depth was recovered in May 1995 (growth rate ranged between 1.04 and 1.36 cm per year). Age models and reconstructions. We developed all chronologies based on annual density banding assisted by luminescence banding. For the Abrolhos corals, we adopted a second step to assess the agreement between geochemical records where we had additional information based on a long higher resolution sampling (Kuhnert et al.20). The new cores HAB05B and HAB10A had some horizons where annual banding was not very clear in the X-rays. Therefore, we used the COFECHA tool to cross-date the individual geochemical records with the annualized high-resolution record from Kuhnert et al.20 (see Methods in Zinke et al.8). This indicated the critical time intervals in need of optimization in the Abrolhos records. ARTICLE Coral cores from the Houtman Abrolhos Islands (HAI; cores HAB10A and HAB05B) are described in detail in refs 8,21. The HAI are a group of carbonate platforms lying approximately 50–60 km offshore of the western coast of Western Australia (WA), and is the southernmost true coral reef formation SouthEast Indian Ocean46 (SEIO). The HAI lie within the path of the LC, and support an astonishing diversity of corals for such a high latitude reef (28.5 S, 113 E). Given their latitude, the HAI are subject to relatively low seasonal SST variation of B4 C, largely attributable to the LC47. The intra-annual variation in salinity of B0.4 p.s.u. is also low47. However, interannual variability of mean annual HAI SST is high, with La Nin˜a years being significantly warmer (annual mean temperature in 2011 was 1.5 C above twentieth century average SST) than El Nin˜o years47. The cored colonies were all Z1.5 m in height and on the leeward side of the reef. Cores were extracted using a hydraulic drill, and the hole was then sealed with a concrete plug to prevent microbial infection, colonization of the bore hole and to allow recolonization by the living tissue layer. The use of replicate cores from the same area allowed smoothing of any inconsistencies and minimizing the presence of false signals from localized environmental factors48. Following initial sectioning and preparation by AIMS and UWA, core slices were cut into sections B500-mm long using a Buehler IsoMet 1000 precision sectioning saw. Joints between subsections were cut on an interlocking angle to ensure appropriate sampling overlap, thus preserving the chronology. Slices were visually inspected aided by densitometry measurements16 for diagenesis along the growth axis, which may impart an artificial cooling/warming signal48,49 The segments were then cut as needed to allow router access to the principal growth axis and exposing a ledge for milling. Using a Zenbot CNC controlled Hitachi router with a 4-mm routing bit, the ledge was milled 2.5 mm inwards from the growth axis for each consecutive high and low-density band comprising one coral growth year. This excess material was removed to ensure that any surface contaminants from handling could not contaminate the next sample. Each slab was then cleaned with a reagent-grade solution of sodium hypochlorite (NaOCl) and milli-Q water at a 1:1 ratio for 24 h. ARTICLE This process removes excess organic material, particularly in the tissue layer, whilst preserving the trace element composition of the sample50 Excess NaOCl and particulate matter were then removed from the slab by ultrasonic cleaning in deionized water for thirty minutes, with the water replaced at 10-min intervals. Finally, the sections were dried in a Contherm Thermotec 2000 drying oven. Skeletal density banding was prominent in all cores (visible in X-rays) and were the dominant control for determining age relationships and the orientations of the growth axes given their established use as coral chronometers51 (Supplementary Figs 11–16). Luminescence banding was used to confirm the position/orientation of the growth axes where density banding was difficult to interpret in small sections of the cores. Density and luminescence banding on the whole cores showed excellent agreement and thus their combined use enabled the most accurate interpretation of the orientation of the growth axis. Instrumental data. The reconstructed annual SST was verified against four SST data sets: (1) the NOAA 0.25  0.25 gridded Advanced Very High-Resolution Radiometer Optimally Interpolated SST57 (AVHRR OISSTv2 1981 to 2010); (2) the 2  2 gridded extended reconstructed SST from NOAA version 3b (ref. 15); (3) the 1  1 gridded HadISST22 (1870–2010); and (4) 5  5 gridded HadSST3 (ref. 56), the latter two from the UK Hadley Centre (Supplementary Tables 1–4). We use the Western Pacific SST gradient11 (WPG) defined as the standardized difference between the central Pacific (Nin˜o4 region14; 5 S–5 N, 160–210 E) and western Pacific SST (0–10 N, 130–150 E) between 1854 and 2010. All data sets were accessed via the Royal Netherlands Meteorological Institute (KNMI) online climate explorer58. Sr/Ca and stable isotope analysis. Following the method of Zinke et al.8, annual samples of B50 mg (mean 52.28 mg; s.d.±1.03 mg) of finely powdered core dust were homogenized and then weighed into thoroughly cleaned 5-ml Eppendorf tubes, then dissolved in 2.1 ml of 0.562 N HNO3. The dissolved samples were first diluted to a calcium concentration of 100 p.p.m. by taking an aliquot of 30 ml from the primary dissolution and adding 2.7 ml of 2% HNO3. The final trace element aliquots were prepared at 10 p.p.m. by using a 30 ml aliquot of the first dilution and adding 2.7 ml of 2% HNO3 spiked with trace concentrations of scandium, bismuth, praseodymium and yttrium so that the sensitivity of the instruments could be scaled. Methods C l i Core locations and sampling. The Rowley Shoals are located in the eastern tropical Indian Ocean, on the edge of the northwest Australian shelf, forming an extended shelf region of tertiary carbonate composition bounded by shelf edge atolls44. Two cores were obtained in 2009 from Imperieuse Reef (Fig. 1), the NATURE COMMUNICATIONS | 6:8562 NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. 6 NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. References Kataoka, T., Tozuka, T., Behera, S. & Yamagata, T. On the Ningaloo Nin˜o/ Nin˜a. Clim. Dyn. 43, 1463–1482 (2013). y 10. Tozuka et al. Locally and remotely forced atmospheric circulation anomalies of Ningaloo Nino/Nina. Clim. Dyn. 43, 2197–2205 (2014). 41. Linsley, B. K., Wu, H. C., Dassie´, E. P. & Schrag, D. P. Decadal changes in South Pacific sea surface temperatures and the relationship to the Pacific decadal oscillation and upper ocean heat content. Geophys. Res. Lett. 42, 2358–2366 (2015). 11. Hoell, A. & Funk, C. The ENSO-related West Pacific sea surface temperature gradient. J. Clim. 26, 9545–9562 (2013). 12. Hoell, A., Funk, C. & Barlow, M. La Nin˜a Diversity and Northwest Indian Ocean Rim Teleconnections. Clim. Dyn. 43, 2707–2724 (2014). 42. Schmidt, G. A. et al. Climate forcing reconstructions for use in PMIP i l i f h l ill i ( 1 0) G i M d l D 4 33 45 ( 42. Schmidt, G. A. et al. Climate forcing reconstructions for use in PMIP simulations of the last millennium (v1.0). Geosci. Model Dev. 4, 33–45 ( 13. Hoell, A., Funk, C. & Barlow, M. The forcing of southwest Asia teleconnections by low frequency sea surface temperature variability during boreal winter. J. Clim. 28, 1511–1526 (2015). 43. Cai, W. et al. Increased frequency of extreme La Nin˜a events under greenhouse warming. Nat. Clim. Change 5, 132–137 (2015). g g 44. Babcock, R. C., Willis, B. L. & Simpson, C. Mass spawning of corals on a high latitude coral reef. Coral Reefs 13, 161–169 (1994). 14. Kaplan, A. et al. Analyses of global sea surface temperature 1856-1991. J. Geophys. Res. 103, 18567–18589 (1998). 45. Depczynski, M. et al. Bleaching coral mortality and subsequent survivorship on a West Australian fringing reef. Coral Reefs 32, 233–238 (2013). 15. Smith, T. M., Reynolds, R. W., Peterson, T. C. & Lawrimore, J. Improvements to NOAA’s historical merged land–ocean surface temperature analysis (1880–2006). J. Clim. 21, 2283 (2008). g g f 46. Veron, J. E. N. & Marsh, L. M. Hermatypic corals of Western Australia: records and annotated species list. Rec. West. Aust. Mus. 29, 1–136 (1988). 16. Cooper, T. F., O’Leary, R. A. & Lough, J. M. Growth of Western Australian Corals in the Anthropocene. Science 335, 593–596 (2012). 47. Abdo, D. A., Bellchambers, L. & Evans, S. N. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9562 Wilson et al.28 Nin˜o 3.4 reconstruction we selected the negative anomalies that correspond with weak to extreme La Nin˜a events. We computed a paleo-WPG between 1795 and 1992 from the difference between annual mean IWP06 (ref. 23) and a reconstruction of the annual mean Nin˜o 3.4 index28. This differs from the observational WPG defined as the standardized difference between the central Pacific (Nin˜o4 region14; 5S–5 N, 160–210E) and western Pacific SST15 (0–10 N, 130–150 E). The IWP06 record does include the western Pacific region (0–10 N, 130–150 E), yet is of larger extent. Currently, no paleoclimatic reconstruction is available for the Nin˜o4 region, so we relied on the Nin˜o3.4 index of Wilson et al.28 which is significantly correlated with the Nin˜o4 index (r ¼ 0.82 (r ¼ 0.76–0.87, 95% confidence interval), Po0.001, N ¼ 138). The Nin˜o3.4 region also represents the central tropical Pacific and shares a large amount of variance with the Nin˜o4 region (r ¼ 0.92, Po0.001, N ¼ 138) and is therefore considered the best available record to calculate a paleo-WPG. We note that the standard deviation of IWP06 and the Nin˜o3.4 reconstruction are of different magnitude than the observational indices for the WP SST and Nin˜o3.4. Nevertheless, we verified our approach by directly comparing the observed WPG with our paleo-WPG to ensure that the timing and relative magnitudes of anomalies were well matched with the observational record. The correlation between the (detrended) observed WPG and paleo-WPG was significant (r ¼ 0.67 (r ¼ 0.57–0.75, 95% confidence interval), Po0.001, N ¼ 138). Considering only data after 1880, where SST observations are considered more reliable, resulted in a higher correlation between WPG and paleo-WPG (r ¼ 0.77 (r ¼ 0.69–0.82, 95% confidence interval), Po0.001, N ¼ 112). 23. Woodruff, S. D. et al. ICOADS Release 2.5: Extensions and enhancements to the surface marine meteorological archive. Int. J. Climatol. 31, 951–967 (2011). 24. Feng, M. et al. Decadal increase in Ningaloo Nino since the late 1990s. Geophys. Res. Lett. 41, 104–112 (2015). 25. Marshall, A. G., Hendon, H. H., Feng, M. & Schiller, A. Initiation and amplification of the Ningaloo Nin˜o. Clim. Dyn. doi:10.1007/s00382-015-2477-5 (2015). 26. D’Arrigo, R. et al. The reconstructed Indonesian warm pool sea surface temperatures from tree rings and corals: Linkages to Asian monsoon drought and El Nin˜o–Southern Oscillation. Paleoceanography 21, PA3005 (2006). g p y 27. Tierney, J. E. References 1. Condie, S. A. & Andrewartha, J. R. Circulation and connectivity on the Australian North West Shelf. Cont. Shelf Res. 28, 1724 (2008). 34. Lyon et al. Tropical pacific forcing of a 1998–1999 climate shift: observational analysis and climate model results for the boreal spring season. Clim. Dyn. 43, 893–909 (2014). 2. D’Adamo, N., Fandry, C., Buchan, S. & Domingues, C. Northern Sources of the Leeuwin Current and the ‘Holloway Current’ on the North West Shelf. J. Roy. Soc. WA 92, 53 (2009). 35. Solomon, A. & Newman, M. Reconciling disparate twentieth-century Indo- Pacific ocean temperature trends in the instrumental record. Nat. Clim. Change 2, 691–699 (2012). 3. Feng, M., McPhaden, M. J., Xie, S. P. & Hafner, J. La Nin˜a forces unprecedented Leeuwin Current warming in 2011. Sci. Rep. 3, 1277 (2013). 36. Compo, g. P. & Sardeshmukh, P. D. Removing ENSO-related variations from the climate record. J. of Climate 23, 1957–1978 (2010). 4. Moore, J. A. et al. Unprecedented Mass Bleaching and Loss of Coral across 12 of Latitude in Western Australia in 2010–11. PLoS ONE 7, e51807 (2012). 37. Wilkinson, C. R. (ed.) Status of Coral Reefs, GCRMN Report 141–159 (Australian Institute of Marine Science, 2012). 5. Wernberg, T. et al. An extreme climate event alters marine ecosystem structure in a global biodiversity hotspot. Nat. Clim. Change 3, 78–82 (2012). 38. Funk, C & Hoell, A. The leading mode of observed and CMIP5 ENSO-residual sea surface temperatures and associated changes in Indo-Pacific climate. J. Clim. 28, 4309–4329 (2015). 6. Halford, A. R. & Caley, M. J. Towards an understanding of resilience in isolated coral reefs. Glob. Change Biol. 15, 3031–3045 (2009). 7. Gilmour, J. P., Smith, L. D., Heyward, A. J., Baird, A. H. & Pratchett, M. S. Recovery of an isolated coral reef system following severe disturbance. Science 340, 69–71 (2013). 39. Sandeep, S., Stordal, F., Sardeshmukh, P. D. & Compo, G. P. Pacific Walker Circulation variability in coupled and uncoupled climate models. J. Clim. 43, 103–117 (2014). 8. Zinke, J. et al. Corals record long-term Leeuwin Current variability during Ningaloo Nin˜o/Nin˜a since 1795. Nat. Commun. 5, 3607 (2014). 40. Osborne, M. C., Dunbar, R. B., Mucciarone, D. A., Druffel, E. & Sanchez- Cabeza, J.-A. 215-yr coral Þ¢18O time series from Palau records dynamics of the West Pacific Warm Pool following the end of the Little Ice Age. Coral Reefs 33, 719–731 (2014). 9. ARTICLE et al. Tropical sea-surface temperatures for the past four centuries reconstructed from coral archives. Paleocenography 30, 226–252 (2015). 28. Wilson, R. et al. Reconstructing ENSO: the influence of method, proxy data, climate forcing and teleconnections. J. Quaternary Sci. 25, 62–78 (2010). g y 29. Emile-Geay, J., Cobb, K. M., Mann, M. E. & Wittenberg, A. T. Estimating 29. Emile-Geay, J., Cobb, K. M., Mann, M. E. & Wittenberg, A. T. Estimating Central Equatorial Pacific SST Variability over the Past Millennium. Part II: Reconstructions and Implications. J. Clim. 26, 2329–2352 (2013). 30. Lewis, S. C. & Karoly, D. J. Anthropogenic contributions to Australia’s record summer temperatures of 2013. Geophys. Res. Lett. 40, 3705–3709 (2013). p p y ( ) 31. Carton, J. A. & Giese, B. S. A reanalysis of ocean climate using simple ocean data assimilation (SODA). Mon. Weather Rev. 136, 2999–3017 (2008). reliable, resulted in a higher correlation between WPG and paleo-WPG (r ¼ 0.77 (r ¼ 0.69–0.82, 95% confidence interval), Po0.001, N ¼ 112). 32. Yu, L. & Weller, R. A. Objectively analyzed air-sea heat fluxes for the global ice-free oceans (1981–2005). Bull. Am. Meteor. Soc. 88, 527–539 (2007). 33. Kalnay et al. The NCEP/NCAR 40-Year Reanalysis Project. Bull. Am. Meteor. Soc. 77, 437–471 (1996). ARTICLE Paleo-WPG from paleoclimate data. We extracted the mean annual Nin˜o3.4 reconstructions from www.ncdc.noaa.gov/paleo/28,29. The Indonesian warm pool SST reconstruction (IWP06 (ref. 26)) was kindly provided by Rosanne D’Arrigo. We extracted La Nin˜a events from two Nin˜o 3.4 paleoreconstructions28,29. For the 7 NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. & 2015 Macmillan Publishers Limited. All rights reserved. References Turning up the heat: Increasing temperature and coral bleaching at the high latitude coral reefs of the Houtman Abrolhos Islands. PLoS ONE 7, e43878 (2012). 17. Corre`ge, T. Sea surface temperature and salinity reconstructions from coral geochemical tracers. Palaeogeogr. Palaeoclimatol. Palaeoecol. 232, 408–428 (2006). 48. DeLong, K. L., Flannery, J. A., Maupin, C. R., Poore, R. Z. & Quinn, T. M. A coral Sr/Ca calibration and replication study of two massive corals from the Gulf of Mexico. Palaeogeogr. Palaeoclimatol. Palaeoecol. 307, 117–128 (2011). 18. Pfeiffer, M., Dullo, W.-Chr., Zinke, J. & Garbe-Scho¨nberg, D. Three monthly coral Sr/Ca records from the Chagos Archipelago covering the period of 1950 to 1995 A.D.: Reproducibility and implications for quantitative reconstructions of sea surface temperature variations. Int. J. Earth Sci. 98, 53–66 (2009). 49. DeLong, K. L., Quinn, T. M., Taylor, F. W., Shen, C.-C. & Lin, K. Improved coral-base paleoclimate reconstructions by replicating 350-years of coral Sr/Ca variations. Palaeogeogr. Palaeoclimatol. Palaeoecol. 373, 6–24 (2013). 19. Lough, J. M. A strategy to improve the contribution of coral data to high- resolution paleoclimatology. Palaeogeogr. Palaeoclimatol. Palaeoecol. 204, 115–143 (2004). 50. Nagtegaal, R. et al. Spectral luminescence and geochemistry of coral aragonite: effects of whole-core chemical treatments. Chem. Geol. 318–319, 6–15 (2012). 51. Lough, J. M. & Cooper, T. F. New insights from coral growth band studies in an era of rapid environmental change. Earth Sci. Rev. 108, 170–184 (2011). 20. Kuhnert, H. et al. A 200-year coral stable oxygen isotope record from a high- latitude reef off Western Australia. Coral Reefs 18, 1–12 (1999). 52. Okai, T., Suzuki, A., Kawahata, H., Terashima, S. & Imai, N Preparation of a new Geological Survey of Japan geochemical reference material: Coral JCp-1. Geostandard. Newslett. 26, 95–99 (2002). 21. Kuhnert, H., Paetzold, J., Wyrwoll, K. H. & Wefer, G. Monitoring climate variability over the past 116 years in coral oxygen isotopes from Ningaloo Reef, Western Australia. Int. J. Earth Sci. 88, 725–732 (2000). 53. Paul, D. & Skrzypek, G. Flushing time and storage effects on the accuracy and precision of carbon and oxygen isotope ratios of sample using the GasBench II technique. Rapid Commun. Mass Spectrom. 20, 2033–2040 (2006). 22. Rayner, N. A. Global analyses of sea surface temperature, sea ice, and night marine air temperature since the late nineteenth century. J. Geophys. Res. 108, 4407 (2003). NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9562 Tim McClanahan (Wildlife Conservation Society) for discussions on the paper. Kirsty Brooks from UWA helped mill the samples. Eric Matson (AIMS) provided skilled technical support for coral core collection and sample preparation. 54. Paul, D., Skrzypek, G. & Forizs, I Normalization of measured stable isotope composition to isotope reference scale – a review. Mass Spectrom 21, 3006–3014 (2007). 55. Cook, E. R., Meko, D. M., Stahle, D. W. & Cleaveland, M. K. Drought reconstructions for the continental United States. J. Clim. 12, 1145–1162 (1999). Acknowledgements We acknowledge the Australian Institute of Marine Science coral core sampling campaign conducted using the RV Solander under the leadership of Dr Tim Cooper. J.Z. was supported by an Indian Ocean Marine Research Centre UWA/AIMS/CSIRO collaborative assistant professorial fellowship and a Honorary Fellowship with the University of the Witwatersrand (South Africa). M.F. is supported by the CSIRO Oceans and Atmosphere Flagship and also partly by the Australian Climate Change Science Program (ACCSP) and Western Australia Marine Science Institute (WAMSI). This research is partly funded by the Gorgon Barrow Island Net Conservation Benefits Fund, which is administered by the WA Department of Parks and Wildlife. M.T.M. and J.M.L. activities are conducted under the auspices of the ARC Centre of Excellence for Coral Reef Studies. J.M.L. was supported by AIMS. M.T.M. was a recipient of a Western Australian Premiers Fellowship kindly provided by the WA Premiers Department and an ARC Laureate Fellowship. Laboratory facilities were constructed using funds provided by an ARC LIEF grant 100100203, UWA and partner institutions. We thank the West Australian Biogeochemistry Centre, in particular G. Skrzypek and P. Grierson, for stable isotope measurements. We thank Andrew Heyward and James Gilmour (AIMS), and Competing financial interests: The authors declare no competing financial interests. Author contributions 56. Kennedy et al. Reassessing biases and other uncertainties in sea-surface temperature observations since 1850 part 2: biases and homogenisation. J. Geophys. Res. 116, D14104 (2011). J.Z., A.H., J.L.M. and M.F. designed the data analysis and interpretation. J.Z., A.K., H.C., V.R., K.R. and M.T.M. analysed the coral samples and contributed to the reconstruction methods. J.Z., A.H., J.L.M., M.F. wrote the manuscript. All authors discussed the results and contributed in writing the paper. 57. Reynolds, R. W. et al. Daily High-resolution Blended Analyses for sea surface temperature. J. Clim. 20, 5473–5496 (2007). 58. Trouet, V. & van Oldenborgh, G. J. KNMI Climate Explorer: a web-based research tool for high-resolution paleoclimatology. Tree Ring Res. 69, 3–13 (2013). Competing financial interests: The authors declare no competing financial interests. Reprints and permission information is available online at http://npg.nature.com/ reprintsandpermissions/ Additional information Supplementary Information accompanies this paper at http://www.nature.com/ naturecommunications Supplementary Information accompanies this paper at http://www.nature.com/ naturecommunications References NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications 8 NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.c & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. Reprints and permission information is available online at http://npg.nature.com/ reprintsandpermissions/ How to cite this article: Zinke, J. et al. Coral record of southeast Indian Ocean marine heatwaves with intensified Western Pacific temperature gradient. Nat. Commun. 6:8562 doi: 10.1038/ncomms9562 (2015). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ NATURE COMMUNICATIONS | 6:8562 | DOI: 10.1038/ncomms9562 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved.
https://openalex.org/W4390539465
https://microbialcellfactories.biomedcentral.com/counter/pdf/10.1186/s12934-023-02283-z
English
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Methanol bioconversion into C3, C4, and C5 platform chemicals by the yeast Ogataea polymorpha
Microbial cell factories
2,024
cc-by
13,805
Abstract Background  One carbon (C1) molecules such as methanol have the potential to become sustainable feedstocks for biotechnological processes, as they can be derived from CO2 and green hydrogen, without the need for arable land. Therefore, we investigated the suitability of the methylotrophic yeast Ogataea polymorpha as a potential production organism for platform chemicals derived from methanol. We selected acetone, malate, and isoprene as industrially relevant products to demonstrate the production of compounds with 3, 4, or 5 carbon atoms, respectively. Results  We successfully engineered O. polymorpha for the production of all three molecules and demonstrated their production using methanol as carbon source. We showed that the metabolism of O. polymorpha is well suited to produce malate as a product and demonstrated that the introduction of an efficient malate transporter is essential for malate production from methanol. Through optimization of the cultivation conditions in shake flasks, which included pH regulation and constant substrate feeding, we were able to achieve a maximum titer of 13 g/L malate with a production rate of 3.3 g/L/d using methanol as carbon source. We further demonstrated the production of acetone and isoprene as additional heterologous products in O. polymorpha, with maximum titers of 13.6 mg/L and 4.4 mg/L, respectively. Conclusion  These findings highlight how O. polymorpha has the potential to be applied as a versatile cell factory and contribute to the limited knowledge on how methylotrophic yeasts can be used for the production of low molecular weight biochemicals from methanol. Thus, this study can serve as a point of reference for future metabolic engineering in O. polymorpha and process optimization efforts to boost the production of platform chemicals from renewable C1 carbon sources. *Correspondence: Lars Mathias Blank lars.blank@rwth-aachen.de 1iAMB - Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany *Correspondence: Lars Mathias Blank lars.blank@rwth-aachen.de 1iAMB - Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany *Correspondence: Lars Mathias Blank lars.blank@rwth-aachen.de 1iAMB - Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany © The Author(s) 2023. RESEARCH Open Access Microbial Cell Factories Microbial Cell Factories (2024) 23:8 Wefelmeier et al. Microbial Cell Factories (2024) 23:8 https://doi.org/10.1186/s12934-023-02283-z Methanol bioconversion into C3, C4, and C5 platform chemicals by the yeast Ogataea polymorpha Katrin Wefelmeier1, Simone Schmitz1, Benjamin Jonas Kösters1, Ulf Winfried Liebal1 and Lars Mathias Blank1* Abstract Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Background One of the key challenges for society in this century is to mitigate anthropogenic global warming and to establish a sustainable economy within the planetary boundar­ ies [1]. To achieve this, essential platform chemicals and materials must be produced independently of dwindling fossil fuel resources and with minimized greenhouse gas emissions [2]. A bioeconomy, in which fossil feed­ stocks are replaced with biological substrates could play an essential role in achieving this goal [3]. It has been estimated that producing bulk chemicals using indus­ trial biotechnology rather than petrochemical processes could save 500–1000 million tons of CO2 per year glob­ ally [4]. Microorganisms, in particular, possess unique properties that enable the production of complex multi- carbon compounds with high efficiency under mild reac­ tion conditions. However, most microbial production processes currently rely on glucose as a carbon source, which requires arable land and thus potentially competes with the food sector [5]. This is particularly problematic if increasing quantities of sugars were to be used for pro­ ducing large quantities of bulk chemicals. An alternative to glucose feedstocks could be the use of one carbon (C1) molecules, (e.g., methane, methanol, or formic acid). In the future, these molecules could be derived from the hydrogenation of CO2 with green hydrogen, providing a means to produce important platform chemicals in a car­ bon-neutral manner [6, 7]. In this study, we further want to evaluate the poten­ tial of O. polymorpha to become a versatile cell factory for the production of low molecular weight biochemi­ cals. We modified O. polymorpha to produce acetone, isoprene, and malate, as examples of C3-C5 molecules derived from methanol (Fig. 1). The dicarboxylic acid malic acid (C4H6O5) is a main flavor component of many l Fig. 1  Metabolic modifications introduced into O. polymorpha for producing malate, acetone, or isoprene from methanol as carbon source. Used ab­ breviations: Pyc(P): pyruvate carboxylase, OAA: oxaloacetate Mdh(p): malate dehydrogenase, Mae1(p): malic acid transporter, ThlA(p): acetyl-CoA acet­ yltransferase, AcetoACoA: acetoacetyl-CoA, CtfAB(p): butyrate-acetoacetate CoA-transferase, YbgC(p): thioesterase, Adc(p): acetoacetate decarboxylase, tHmgr(p): truncated 3-hydroxy-3-methylglutaryl-CoA reductase, Isps(p): isoprene synthase, HMG-CoA: 3-hydroxy-3-methylglutaryl coenzyme A, DMAPP: dimethylallyl pyrophosphate Fig. 1  Metabolic modifications introduced into O. polymorpha for producing malate, acetone, or isoprene from methanol as carbon source. Wefelmeier et al. Microbial Cell Factories (2024) 23:8 Wefelmeier et al. Microbial Cell Factories (2024) 23:8 Page 2 of 15 Page 2 of 15 (2024) 23:8 Wefelmeier et al. Microbial Cell Factories Several microbes are natively able to use C1 com­ pounds as their sole carbon and energy source, e.g., methylotrophic yeasts. This group of yeasts can assimi­ late methanol (MeOH) into formaldehyde via the metha­ nol oxidase (MOX) [8]. The produced formaldehyde can then either be oxidized to CO2 for energy generation or assimilated to form biomass constituents via the xylulose monophosphate (XuMP) pathway [9]. Using methanol as a carbon source has the advantage that it can be easily stored in its liquid form, which circumvents mass trans­ fer problems that occur during gas fermentations based on CO2 or methane [10]. A promising methylotrophic yeast is Ogataea polymorpha. It is known for its high protein secretion rates [11, 12] and thus has been used to produce heterologous proteins on an industrial scale [13]. Apart from that, its thermotolerance and strong methanol-inducible promoters also make it a promising host organism for producing platform chemicals derived from C1 molecules [14, 15]. There are several recent studies, in which industrially relevant chemicals, such as free fatty acids [16], hyaluronic acid [17], and the terpe­ noid β-elemene [18] were produced in O. polymorpha. Background Used ab­ breviations: Pyc(P): pyruvate carboxylase, OAA: oxaloacetate Mdh(p): malate dehydrogenase, Mae1(p): malic acid transporter, ThlA(p): acetyl-CoA acet­ yltransferase, AcetoACoA: acetoacetyl-CoA, CtfAB(p): butyrate-acetoacetate CoA-transferase, YbgC(p): thioesterase, Adc(p): acetoacetate decarboxylase, tHmgr(p): truncated 3-hydroxy-3-methylglutaryl-CoA reductase, Isps(p): isoprene synthase, HMG-CoA: 3-hydroxy-3-methylglutaryl coenzyme A, DMAPP: dimethylallyl pyrophosphate Wefelmeier et al. Microbial Cell Factories (2024) 23:8 Page 3 of 15 Wefelmeier et al. Microbial Cell Factories fruits and is thus widely used as a flavor enhancer and acidulant in the food industry [19, 20]. Additionally, it has a broad range of applications in the cosmetics and pharmaceutical industry, but it can also be applied for metal or textile finishing [21, 22]. Further, its polymer poly(malic acid) has many interesting properties, such as its high water solubility, biodegradability, and biocom­ patibility, which make it an interesting molecule, e.g., for drug delivery systems [23]. Acetone (C3H6O) is used as a solvent and as an intermediate for polymethyl methac­ rylate plastics [24]. At the beginning of the 20th century, acetone was already being produced biotechnologically with the bacterium Clostridium acetobutylicum in the famous acetone-butanol-ethanol (ABE) fermentation [25]. Today, acetone is produced almost exclusively from fossil resources. The same applies to isoprene (C5H8), whose main application is in its polymerized form as a rubber material [26, 27]. Also, for isoprene, an alternative microbial production is possible, since there are a large number of isoprene-emitting plants whose isoprene syn­ thases can be used for heterologous expression in micro­ organisms [28]. importance for the growth metabolism and suggests that growth rate reduction or two-phase production are suit­ able optimization strategies. It can further be seen that the metabolic pathway for malate production seems to be the most efficient of the three selected products, as with minimal growth almost all the carbon can be directed to product generation, which corresponds to the maximum theoretical yield of 0.25 molMalate/molMeOH.l We tested how rerouting of carbon fluxes to distinct pathways affects the simulated production rates. Besides the unconstraint reference flux (Ref), we investigated the pathway scenarios (I) Blocked TCA (TCA-) with muta­ tions to impair TCA flux (see Methods), (II) Forced TCA activity (TCA+), (III) Forced glyoxylate cycle (GlxStd), and (IV) Forced impaired glyoxylate shunt (GlxVar) with deactivated mitochondrial malate dehydrogenase. The optimal target production route via the Ref-flux is similar to the inactive TCA scenario, because of the comparable yields (Table 1). Background The yields drop if fluxes are forced via glyoxylate shunt, but this decrease is weaker for acetone and isoprene than for malate. A principal component analysis (PCA) of the flux distributions visualizes the similarity among the solutions (Fig. 2B, Supplementary Excel Sheet 1). Overall, there are three distinct clusters that represent different pathway modes (I) Ref and TCA-, (II) TCA+, and (III) glyoxylate shunt fluxes. The fluxes for the different products are similar within the pathway clusters. Particularly clustered are fluxes of the reference solution (Ref) and inactive TCA (TCA-) and reflect their similarity. Acetone and isoprene (circle/diamond) have a high flux similarity in the different scenarios. As all of these chemicals are needed in large quanti­ ties, manufacturing these bulk chemicals using renew­ able resources, such as C1 molecules, has the potential to considerably reduce the environmental impact of their production. Therefore, this study aims to evaluate the suitability of O. polymorpha as a production organism for malate, acetone, and isoprene as proof-of-concept plat­ form chemicals. Metabolic modellingh While the absolute position in the plot is irrelevant, the relative distance of points reflects the degree of similarity between flux distributions. Details about the reactions constrained for each scenario can be found in the SI: Figure S1 Fig. 2  (A) Production envelope of the yield for malate, acetone, and isoprene in response to growth rate. A higher slope of malate indicates stronger consumption with growth. (B) Principal component analysis of simulated flux distributions of five different metabolic scenarios while optimizing for target production: unconstraint reference flux (Ref: black), inhibition of TCA cycle (TCA-: red), enforcing high TCA cycle (TCA+: blue), enforcing glyoxylate shunt (GlxStd: green) and glyoxylate shunt without malate dehydrogenase (GlxVar: magenta). While the absolute position in the plot is irrelevant, the relative distance of points reflects the degree of similarity between flux distributions. Details about the reactions constrained for each scenario can be found in the SI: Figure S1 from Schizosaccharomyces pombe was introduced as the transportation of malic acid across the plasma mem­ brane has often been described to be a limiting factor in malate production [32, 33]. Mae1(p) was characterized as a voltage-dependent anion channel, and in a comparison of 7 different carboxylic acid transporters, it showed the highest activity toward malate and the least detrimental effects on growth when overexpressed in Saccharomyces cerevisiae [34]. All three genes were codon-optimized for O. polymorpha and expressed using methanol-inducible promoters (Details on genetic constructs in Supple­ mentary Information (SI): Table S1). To determine the impact of the individual genes on production, strains were engineered that had only the MAE1 transporter gene (T-strain) or the MDH and PYC gene (PM-strain) integrated into their genome, in addition to the strain with all three heterologous genes (PMT-strain). The con­ structed strains were then analyzed for malate produc­ tion using methanol as the sole carbon source. To this end, pre-cultures were first grown on YPD-medium with glucose (cf. Methods section), in order to obtain a certain amount of biomass. Since all introduced heterologous genes are under the control of methanol-inducible pro­ moters, no malate production takes place during this pre­ culture phase. To induce production, the cells were then washed and transferred to mineral Verduyn medium (cf. SI: Table S2-4) containing only methanol as a carbon source. Figure 3A & B show the malate production and growth behavior on methanol of the engineered strains and the unmodified WT strain. Metabolic modellingh As less flux through the TCA cycle seems to be beneficial for malate production from methanol in O. polymorpha (cp. Figure 2; Table 1), the reductive TCA cycle (rTCA) as an alternative production pathway was overexpressed in the cytosol of O. polymorpha (Fig. 1). The pyruvate carboxylase (Pyc(p), EC:6.4.1.1.) and malate dehydroge­ nase (Mdh(p), EC:1.1.1.37) from Rhizopus oryzae were selected as they have already been successfully used in a number of studies for malate production in yeasts [30, 31]. Additionally, the malic acid transporter Mae1(p) The genome scale model (GSMM) of O. polymorpha can describe metabolic conditions of malate, acetone, and isoprene production. We used the existing genome scale model iUL909 [29] and added reactions for acetone and isoprene production to generate the updated GSMM iOpol23. The added reactions are isoprene synthase, acetoacetyl-CoA hydrolase, acetoacetate decarboxyl­ ase as well as transport reactions. The production enve­ lope in Fig. 2 shows the yield benefits with lower growth rates. Malate has the highest slope, which signifies the Table 1  Simulated yields of optimal target production for different scenarios of metabolic activity. The yield is calculated as the production rate of the respective product divided by the methanol uptake uptake rate (both mmol/gDW/h). ‘Ref’ refers to a simulation without special constraints, ‘TCA-’ was constrained to inhibit circular TCA cycle flux, in ‘TCA+’ flux was forced to enter circular TCA cycle, ‘GlxStd’ represents a flux distribution forced into the standard glyoxylate shunt, and ‘GlxVar’ represents a flux distribution with forced fluxes without malate dehydrogenase activity. The identity of the reactions within the reaction network ist sketched in the SI the Figure S1 Scenario Ref TCA- TCA+ GlxStd GlxVar Yield, molMalate/molMeOH 0.25 0.25 0 0.02 0 Yield, molAceton/molMeOH 0.2 0.19 0 0.02 0 Yield, molIsoprene/molMeOH 0.11 0.10 0 0.01 0 Wefelmeier et al. Microbial Cell Factories Page 4 of 15 Fig. 2  (A) Production envelope of the yield for malate, acetone, and isoprene in response to growth rate. A higher slope of malate indicates stronger consumption with growth. (B) Principal component analysis of simulated flux distributions of five different metabolic scenarios while optimizing for target production: unconstraint reference flux (Ref: black), inhibition of TCA cycle (TCA-: red), enforcing high TCA cycle (TCA+: blue), enforcing glyoxylate shunt (GlxStd: green) and glyoxylate shunt without malate dehydrogenase (GlxVar: magenta). Metabolic modellingh When a highly efficient exporter such as Mae1(p) trans­ ports this malate from the cytosol into the extracellular space, this would prevent the transport of electrons into the mitochondria and thus limit ATP generation via the respiratory chain. Hence, this could be a possible cause for the growth defect observed after the introduction of the transporter into O. polymorpha, and it could at the same time explain why overexpression of the trans­ porter gene alone already leads to an increase in malate production. consume malate, when methanol was used as an addi­ tional carbon source, but instead consumed the metha­ nol (Fig. 4A&B). Here, it can be observed again that the used PMT-strain takes up methanol as a substrate but does not channel this assimilated carbon into biomass formation as there is no growth on methanol observed (Fig. 4C). This experiment shows how methanol seems to be a preferred carbon source compared to malate and highlights how in future experiments it will be essen­ tial to make methanol available at all time points of the cultivation to avoid the uptake of malate by the yeast. Consequently, different methanol feeding strategies were tested. It has to be considered that the expression of all heterologous genes in the malate-producing strain is controlled through methanol-inducible promoters. Therefore, different inducing methanol concentrations of 0.5% (4 g/L) and 2% (16 g/L) were tested. Once these ini­ tial methanol concentrations were nearly depleted, addi­ tional methanol pulses between 1% and 4% were added to the cells. With these varied cultivation modes, the experi­ ments were carried out for 7 days (Fig. 5). Evaluating these results, it can be concluded that feed­ ing the strain frequently with low methanol concentra­ tions is beneficial for production. The highest malate titer of 8.9 ± 0.4  g/L was achieved, when the strain was supplied with an initial methanol concentration of 0.5% methanol and was then fed with a fresh pulse of 1% methanol every day (Fig. 5). In contrast to that, feeding the strain with pulses of 4% methanol led to a comparably low maximal titer of 5.7 ± 0.3 g/L, which is likely related to the toxicity of methanol at higher concentrations. As the PMT-strain showed promising results over­ all, this strain was further characterized. It was evalu­ ated whether the PMT-strain could take up malate from the medium. Metabolic modellingh The initial methanol con­ centration in the Verduyn medium was 4 g/L (0.5%(v/v)) and during cultivation the cells were provided with two additional pulses of 16 g/L (2%) methanol once the meth­ anol concentration was depleted (methanol consumption data in SI: Figure S2). This cultivation method was cho­ sen because our previous studies showed that even low concentrations of methanol are toxic to carboxylic acid- producing O. polymorpha strains. The addition of metha­ nol in multiple pulses to the shake flasks was shown to be an effective strategy for reducing methanol toxicity to the cells [35]. While for the WT- and PM-strain no malate was detected over the whole course of the experiment, both the T-strain as well as the PMT-strain produced signifi­ cant amounts of malate. After 72 h the PMT- and T-strain still produced comparable amounts of 4.1 ± 0.2  g/L and 3.4 ± 0.1 g/L malate, respectively (Fig. 3A). However, after that, production stopped in the T-strain and a final titer of only 3.6 ± 0.0 g/L malate was reached at the end of the cultivation. Production in the PMT-strain still contin­ ued and reached a malate concentration of 7.7 ± 0.4 g/L after 144 h. These results highlight that the transporter enabling malate export out of the cells is essential to enable high-level malate production. It is also striking that the PMT-strain, although showing high malate pro­ duction, showed nearly no growth when cultured with Page 5 of 15 Wefelmeier et al. Microbial Cell Factories Fig. 3  Production of malate (A) from methanol and development of optical density (B) in O. polymorpha cultures. Comparison of the unmodified wild­ type (WT) strain, a strain overexpressing the PYC and MDH gene of Rhizopus oryzae (PM), a strain overexpressing the malate transporter gene MAE1 of Schizosaccharomyces pombe (T) and a strain overexpressing all three of these heterologous genes (PMT). Cultivations were performed on Verduyn medium in 250 mL shake flasks. Error bars represent the standard deviation of biological triplicates. (C) Illustration of the malate-aspartate shuttle, Used abbreviations: Glutamate (Glu), α-ketoglutarate (α-KG) Fig. 3  Production of malate (A) from methanol and development of optical density (B) in O. polymorpha cultures. Metabolic modellingh Comparison of the unmodified wild­ type (WT) strain, a strain overexpressing the PYC and MDH gene of Rhizopus oryzae (PM), a strain overexpressing the malate transporter gene MAE1 of Schizosaccharomyces pombe (T) and a strain overexpressing all three of these heterologous genes (PMT). Cultivations were performed on Verduyn medium in 250 mL shake flasks. Error bars represent the standard deviation of biological triplicates. (C) Illustration of the malate-aspartate shuttle, Used abbreviations: Glutamate (Glu), α-ketoglutarate (α-KG) methanol as carbon source (Fig. 3B). A possible explana­ tion could be the high activity of NADH shuttle systems, such as the malate-aspartate shuttle, under these growth conditions. The malate-aspartate shuttle translocates electrons across the mitochondrial membrane to make them available for energy generation via the respiratory chain [36] (Fig. 3C). For the methylotrophic yeast Kom­ agataella phaffii (Pichia pastoris), it has been reported that the malate-aspartate shuttle is highly active when methanol is present in the medium [37], which reflects the high maintenance energy associated with growth on methanol compared to growth on glucose [38, 39]. Consequently, it can be expected that in O. polymorpha growth on methanol triggers a high flux towards malate. When a highly efficient exporter such as Mae1(p) trans­ ports this malate from the cytosol into the extracellular space, this would prevent the transport of electrons into the mitochondria and thus limit ATP generation via the respiratory chain. Hence, this could be a possible cause for the growth defect observed after the introduction of the transporter into O. polymorpha, and it could at the same time explain why overexpression of the trans­ porter gene alone already leads to an increase in malate production. methanol as carbon source (Fig. 3B). A possible explana­ tion could be the high activity of NADH shuttle systems, such as the malate-aspartate shuttle, under these growth conditions. The malate-aspartate shuttle translocates electrons across the mitochondrial membrane to make them available for energy generation via the respiratory chain [36] (Fig. 3C). For the methylotrophic yeast Kom­ agataella phaffii (Pichia pastoris), it has been reported that the malate-aspartate shuttle is highly active when methanol is present in the medium [37], which reflects the high maintenance energy associated with growth on methanol compared to growth on glucose [38, 39]. Consequently, it can be expected that in O. polymorpha growth on methanol triggers a high flux towards malate. Metabolic modellingh polymorpha PMT-strain. Cultivation in Verduyn medium with either 6.7 g/L malate (green circles) or 6.7 g/L malate and 4 g/L methanol (yellow squares) as carbon source. Measurement of malate (A) and methanol (B) concentration and optical density (C). Cultivation was per­ formed in System Duetz microtiter plates. Error bars represent the standard deviation of three biological replicates Fig. 4  Malate uptake of O. polymorpha PMT-strain. Cultivation in Verduyn medium with either 6.7 g/L malate (green circles) or 6.7 g/L malate and 4 g/L methanol (yellow squares) as carbon source. Measurement of malate (A) and methanol (B) concentration and optical density (C). Cultivation was per­ formed in System Duetz microtiter plates. Error bars represent the standard deviation of three biological replicates Fig. 4  Malate uptake of O. polymorpha PMT-strain. Cultivation in Verduyn medium with either 6.7 g/L malate (green circles) or 6.7 g/L malate and 4 g/L methanol (yellow squares) as carbon source. Measurement of malate (A) and methanol (B) concentration and optical density (C). Cultivation was per­ formed in System Duetz microtiter plates. Error bars represent the standard deviation of three biological replicates Fig. 5  Analyzing the effect of different feeding patterns on malate production. ((A))Measurement of malate concentration throughout the experiment. (B)Optical density at the end of the experiment and amount of malate produced per amount of consumed methanol after 6 days (in molMalate/molMeOH). The experiment was performed in 250 mL shake flasks on Verduyn medium with either 0.5% or 2% of initial methanol concentration and then feeding pulses of 1%, 2%, or 4% once the methanol concentration was depleted. Error bars represent the standard deviation of the biological replicates formed in System Duetz microtiter plates. Error bars represent the standard deviation of three biological replicates Fig. 5  Analyzing the effect of different feeding patterns on malate production. ((A))Measurement of malate concentration throughout the experiment. (B)Optical density at the end of the experiment and amount of malate produced per amount of consumed methanol after 6 days (in molMalate/molMeOH). The experiment was performed in 250 mL shake flasks on Verduyn medium with either 0.5% or 2% of initial methanol concentration and then feeding pulses of 1%, 2%, or 4% once the methanol concentration was depleted. Error bars represent the standard deviation of the biological replicates a yield of around 0.056 molMalate/molMeOH, the cells that were fed with 4% only achieved a 45% lower yield of 0.025 molMalate/molMeOH. Metabolic modellingh Hence, the PMT-strain was cultivated in medium with 6.7  g/L (50 mM) of externally supplied malate as well as a mixture of 6.7 g/L malate and 4 g/L methanol (Fig. 4). When malate was supplied to the medium as the sole available carbon source, the cells were able to take up the malate and grow to an optical density of 10.7 ± 0.7 within five days (Fig. 4C). In contrast to that, the cells did not Also, when considering malate production in relation to the amount of methanol consumed, higher yields were achieved by feeding low concentrations of methanol to the medium. While feeding pulses of 1% methanol led to (2024) 23:8 (2024) 23:8 Page 6 of 15 Wefelmeier et al. Microbial Cell Factories Page 6 of 15 Wefelmeier et al. Microbial Cell Factories (2024) 23:8 a yield of around 0.056 molMalate/molMeOH, the cells that were fed with 4% only achieved a 45% lower yield of 0.025 molMalate/molMeOH. Therefore, lower methanol concen­ trations of 1% were used for feeding the cultures in the following experiments. To get a more accurate idea of when and under what week. Each day, the malate and methanol concentrations and the pH in the medium were measured (Fig. 6A-C). It was observed that the rate of malate production was highest during the first three days of cultivation. Dur­ ing this time the cells produced 9.7 ± 0.8  g/L of malate (Fig. 6A). After that, production slowed down consider­ Fig. 5  Analyzing the effect of different feeding patterns on malate production. ((A))Measurement of malate concentration throughout the experiment. (B)Optical density at the end of the experiment and amount of malate produced per amount of consumed methanol after 6 days (in molMalate/molMeOH). The experiment was performed in 250 mL shake flasks on Verduyn medium with either 0.5% or 2% of initial methanol concentration and then feeding pulses of 1%, 2%, or 4% once the methanol concentration was depleted. Error bars represent the standard deviation of the biological replicates Fig. 4  Malate uptake of O. polymorpha PMT-strain. Cultivation in Verduyn medium with either 6.7 g/L malate (green circles) or 6.7 g/L malate and 4 g/L methanol (yellow squares) as carbon source. Measurement of malate (A) and methanol (B) concentration and optical density (C). Cultivation was per­ formed in System Duetz microtiter plates. Error bars represent the standard deviation of three biological replicates Fig. 4  Malate uptake of O. Metabolic modellingh Therefore, lower methanol concen­ trations of 1% were used for feeding the cultures in the following experiments. week. Each day, the malate and methanol concentrations and the pH in the medium were measured (Fig. 6A-C). It was observed that the rate of malate production was highest during the first three days of cultivation. Dur­ ing this time the cells produced 9.7 ± 0.8  g/L of malate (Fig. 6A). After that, production slowed down consider­ ably and a maximum titer of 10.4 ± 0.5 g/L was obtained on day 5 of the cultivation. After that, the malate titers To get a more accurate idea of when and under what conditions malate is produced in O. polymorpha, the PMT-strain was fed with 1% methanol daily for one (2024) 23:8 Page 7 of 15 Page 7 of 15 Wefelmeier et al. Microbial Cell Factories Fig. 6  Malate production of O. polymorpha PMT-strain in methanol fed-batch experiment in shake flasks. Malate production (A, D, green squares), opti­ cal density (A, D, blue circles), methanol concentration (B, E, red triangles), and pH (C, F, grey diamonds) in shake flasks that were fed with 8 g/L (1%) of methanol every 24 h. Comparison of Verduyn medium with 100 mM of KH-phthalate (A, B, C) and 200 mM KH-phthalate (D, E, F) as buffer. Panels(G, H & I) represent an experiment where shake flasks were fed with a constant methanol feed using the LIS system. (G: OD (blue circles), Malate concentration (green squares), H: Methanol concentration, I: pH) Fig. 6  Malate production of O. polymorpha PMT-strain in methanol fed-batch experiment in shake flasks. Malate production (A, D, green squares), opti­ cal density (A, D, blue circles), methanol concentration (B, E, red triangles), and pH (C, F, grey diamonds) in shake flasks that were fed with 8 g/L (1%) of methanol every 24 h. Comparison of Verduyn medium with 100 mM of KH-phthalate (A, B, C) and 200 mM KH-phthalate (D, E, F) as buffer. Panels(G, H & I) represent an experiment where shake flasks were fed with a constant methanol feed using the LIS system. (G: OD (blue circles), Malate concentration (green squares), H: Methanol concentration, I: pH) decreased slightly. Some byproducts were observed as well during this cultivation. Succinate was the main byproduct, which can be explained by the fact that the transporter Mae1(p) can also transport other dicar­ boxylic acids apart from malate [34]. Metabolic modellingh (2001), the transporter Mae1(p) is reliant on the pH difference between the cytoplasm and extracellular space [40]. In heterologous expression studies of MAE1 in Saccharomyces cerevisiae it was observed that malic acid import is restricted and export is encouraged at the pH level of the medium above 4. In comparison, a lower pH enables the cell to import malic acid [40]. This corresponds well to the observed phenomenon in this experiment, where the malate titer decreases as soon as the pH drops below a level of 4 (Fig. 6A&C). Further, it has to be considered that with a decrease in pH, a higher percentage of the acid will be present in its protonated form (pKa1 Malic acid: 3.4). The protonated acid can thus diffuse more easily through the cell membrane and lead to an acidification of the cytoplasm [41]. This might be an additional reason, why malate production stops after day 3. Consequently, controlling the pH of the cultiva­ tion medium will be a critical factor for improving malate production. As a first step to do so, the amount of buf­ fer used in the cultivation medium was doubled from a concentration of 100 mM KH-phthalate (Fig. 6A-C) to 200 mM (Fig. 6D-F). Increasing the buffer concentration led to a slower drop in the pH and during the whole cul­ tivation, the pH remained at a level above 4.0 (Fig. 6F). In comparison with using 100 mM of buffer, malate production also improved. The malate titer in the cul­ ture increased over the whole course of the experiment and reached a final value of 12.7 ± 1.2 g/L (Fig. 6D) after 7 days. At the same time, methanol accumulation hap­ pened more slowly in this cultivation with a final metha­ nol titer of only 9.8 ± 1.8 g/L at the end of the cultivation. This experiment highlights that control of pH is a criti­ cal parameter for malate production in this strain and that a pH value above 4 seems to be advantageous for production. Further optimizing this cultivation in a more controlled setting, e.g., in a bioreactor that allows both pH control and constant methanol feeding will be of critical impor­ tance to further improve malate production in O. poly­ morpha. As bioreactor cultivations further allow for the optimization of oxygen supply, it will also be an interest­ ing option to exploit O. Metabolic modellingh This corresponds well to the observed phenomenon in this experiment, where the malate titer decreases as soon as the pH drops below a level of 4 (Fig. 6A&C). Further, it has to be considered that with a decrease in pH, a higher percentage of the acid will be present in its protonated form (pKa1 Malic acid: 3.4). The protonated acid can thus diffuse more easily through the cell membrane and lead to an acidification of the cytoplasm [41]. This might be an additional reason, why malate production stops after day 3. Consequently, controlling the pH of the cultiva­ tion medium will be a critical factor for improving malate production. As a first step to do so, the amount of buf­ fer used in the cultivation medium was doubled from a concentration of 100 mM KH-phthalate (Fig. 6A-C) to 200 mM (Fig. 6D-F). Increasing the buffer concentration led to a slower drop in the pH and during the whole cul­ tivation, the pH remained at a level above 4.0 (Fig. 6F). In comparison with using 100 mM of buffer, malate production also improved. The malate titer in the cul­ ture increased over the whole course of the experiment and reached a final value of 12.7 ± 1.2 g/L (Fig. 6D) after 7 days. At the same time, methanol accumulation hap­ pened more slowly in this cultivation with a final metha­ nol titer of only 9.8 ± 1.8 g/L at the end of the cultivation. This experiment highlights that control of pH is a criti­ cal parameter for malate production in this strain and that a pH value above 4 seems to be advantageous for production. Moreover, it was assumed that keeping the metha­ nol concentration during the cultivation constant could which allows constant substrate feeding to shake flasks. With this system, a total daily concentration of 1% of methanol was supplied in a constant feed to the cultures (Fig. 6G-I). Like this, the methanol concentration in the cultures was successfully kept constant (Fig. 6H), which also improved malate production. After 4 days a titer of 13.2 ± 2.5 g/L malate was obtained (Fig. 6G). In the pre­ vious experiment, without constant methanol feeding (Fig. 6D-F), a similar maximum titer of 12.7 ± 1.2 g/L was achieved, but it took seven days to reach this titer. The constant methanol feeding thus considerably decreased the necessary cultivation time. Metabolic modellingh At the time when the highest malate titer was measured (day 5), the cor­ responding succinate titer reached 0.5 ± 0.0  g/L (SI: Figure S3). As the malate titer decreased in the follow­ ing days, the succinate titer continued to increase. In decreased slightly. Some byproducts were observed as well during this cultivation. Succinate was the main byproduct, which can be explained by the fact that the transporter Mae1(p) can also transport other dicar­ boxylic acids apart from malate [34]. At the time when the highest malate titer was measured (day 5), the cor­ responding succinate titer reached 0.5 ± 0.0  g/L (SI: Figure S3). As the malate titer decreased in the follow­ ing days, the succinate titer continued to increase. In addition to succinate, minor amounts of pyruvate (max. titer 38  mg/L) and fumarate (max. titer 7  mg/L) were also detected during this cultivation. It is noticeable that the by-products are initially produced at a low rate and then the production rate increases when malate pro­ duction stops after day 3. Consequently, we expected that with the optimization of malate production in this strain, the production of byproducts will decrease. Dur­ ing the first two days of the cultivation, the supplied Wefelmeier et al. Microbial Cell Factories (2024) 23:8 (2024) 23:8 Page 8 of 15 Wefelmeier et al. Microbial Cell Factories methanol pulses of 1% are still completely consumed from the medium within one day. However, over time an accumulation of methanol in the culture occurs. At the end of the cultivation, the final methanol titer reached 375 ± 63 mM (Fig. 6B). At the same time, it was observed that the pH dropped from an initial value of 5.0 to a value of 3.8 (Fig. 6C). This was assumed to be a major reason, why the production of malate stopped at one point dur­ ing the experiment. According to a study by Camarasa et al. (2001), the transporter Mae1(p) is reliant on the pH difference between the cytoplasm and extracellular space [40]. In heterologous expression studies of MAE1 in Saccharomyces cerevisiae it was observed that malic acid import is restricted and export is encouraged at the pH level of the medium above 4. In comparison, a lower pH enables the cell to import malic acid [40]. Metabolic modellingh polymorpha’s suitability for high cell density fermentations, which could push malate pro­ duction even further. Moreover, it was assumed that keeping the metha­ nol concentration during the cultivation constant could improve production. The chosen method of manual addi­ tion of methanol pulses in shake flasks, although techni­ cally simple and straightforward, does not allow accurate feeding and leads to fluctuating methanol concentrations in the culture (Fig. 6B&E). This could stress the cells by alternating between carbon starvation and methanol tox­ icity. Therefore, the Liquid Injection System (LIS, SBI Sci­ entific Bioprocessing, Baesweiler, Germany) was tested, Metabolic modellingh During the first 4 days of the cultivation malate is thus produced at a rate of 3.4  g/L/d Additionally, the production of byproducts decreased during this cultivation. At the timepoint where the highest malate titer was measured 0.1 ± 0.0 g/L succi­ nate was detected (SI: Figure S3). This is only 20% of what has been observed under the same conditions with only 100 mM buffer and manual methanol feeding. Again, it can clearly be seen that as soon as the pH reaches a value around 4.0 production stops and malate is even taken up. This emphasizes how it will also be essential to further optimize pH levels to improve malate production in this strain. Still, the methanol titers and yields that are already achieved with the non-optimized cultivation strategy in this study are highly promising. So far, the only reported instance in which malate was produced using methanol as a substrate is in Pichia pastoris, another methylotro­ phic yeast. Guo et al. reported the production of 2.8 g/L of malic acid from methanol with an engineered P. pasto­ ris strain [30]. Additionally, it should be considered that the malate titers obtained in this study were achieved without the addition of neutralizing agents such as CaCO3, which are often added during production pro­ cesses of organic acids to avoid acid stress and thus boost production. Although the addition of CaCO3 for neutral­ ization may have the potential to further increase malate production in O. polymorpha, it also makes purification of the acid produced more laborious [42], so the costs and benefits of this approach should be carefully assessed in subsequent experiments. Further optimizing this cultivation in a more controlled setting e g in a bioreactor that allows both pH control methanol pulses of 1% are still completely consumed from the medium within one day. However, over time an accumulation of methanol in the culture occurs. At the end of the cultivation, the final methanol titer reached 375 ± 63 mM (Fig. 6B). At the same time, it was observed that the pH dropped from an initial value of 5.0 to a value of 3.8 (Fig. 6C). This was assumed to be a major reason, why the production of malate stopped at one point dur­ ing the experiment. According to a study by Camarasa et al. Acetone production To enable acetone synthesis in O. polymorpha the precur­ sor acetyl-CoA has to be converted in three enzymatic steps Wefelmeier et al. Microbial Cell Factories (2024) 23:8 Page 9 of 15 Wefelmeier et al. Microbial Cell Factories (2024) 23:8 (2024) 23:8 Wefelmeier et al. Microbial Cell Factories to acetone via aceto-acetyl-CoA and acetoacetone as inter­ mediates. In Clostridium acetobutylicum these reactions are catalyzed by an acetyl-CoA acetyltransferase (thiolase, ThlA(p), EC 2.3.1.9), a butyrate-acetoacetate CoA-transfer­ ase (CtfAB(p), EC 2.8.3.9) and subsequently by an acetoac­ etate decarboxylase (Adc(p), EC 4.1.1.4) (Fig. 1). Therefore, this study aimed to introduce variants of all these three enzymes into O. polymorpha to enable acetone synthesis. For the first enzymatic step catalyzed by the acetyl-CoA acetyltransferase, the THLA gene from Clostridium aceto­ butylicum was chosen. For the intermediate reaction step, there was also a clostridial gene variant (CTFAB) selected. However, CtfAB(p) requires acetate as a cofactor and at the same time has a high Km value for acetate (1200 mM). This is often considered to be the limiting factor in heterologous acetone production [43]. As an alternative to CtfAB(p) the YbgC(p) enzyme from Haemophilus influenzae was also introduced into O. polymorpha. YbgC(p) is a thioesterase (EC:3.1.2.-) that allows acetate-independent hydrolysis of acetoacetyl-CoA to form acetoacetate and has already been applied in Escherichia coli for heterologous acetone produc­ tion [44]. For the last reaction step instead of the clostridial variant (Adc(p)), an alternative enzyme from Paenibacillus polymyxa (PpAdc(p)) was introduced into O. polymorpha. This enzyme is reported to have a comparable turnover number and a more favorable Km value for acetoacetone than the clostridial variant (Specific activity: 269 µmol/min/ mg; Km 0.94 mM [45]). Consequently, two O.polymorpha strains were engineered that overproduced either PpAdc(p), CtfAB(p) and ThlA(p) (ACT-strain) or PpAdc(p), YbgC(p) and ThlA(p) (AYT-strain). All of the heterologous genes were codon-optimized for O. polymorpha expressed using either the strong methanol-inducible MOX or CAT pro­ moter (SI Table S1). To allow the detection of the volatile product acetone, the two created strains were cultivated in 250 mL air-tight serum bottles using 0.5% methanol as carbon source. Additionally, a supplementation of 25 mM ammonium acetate to the medium was tested for the ACT- strain, as the CtfAB(p) requires acetate as a cofactor. After 5 days of cultivation, the cultures were sampled. Acetone production The final optical density as well as the concentration of acetone and leftover methanol in the cultivation medium were deter­ mined (Fig. 7A). For both the ACT and AYT strain, acetone produc­ tion was demonstrated successfully. These strains pro­ duced 3.2 ± 1.0  mg/L (ACT) and 2.2 ± 0.1  mg/L acetone (AYT), respectively (Fig. 7A). Adding acetate to the medium of the ACT strain did not increase acetone production. For all strains, the 0.5% methanol supplied in the medium were not consumed completely. For the AYT strain 91.2 ± 8.8 mM of methanol remained in the culture broth, which corresponds to 73% of the initially supplied methanol concentration. As the used serum bottles are completely air-tight to avoid evaporation of the produced acetone the only oxygen available for the cells to grow is the headspace in the culture. As growth Fig. 7  Acetone titer, final optical density, and methanol concentration for O. polymorpha strains overexpressing heterologous genes for acetone synthe­ sis. O. polymorpha strains either overproducing PpAdc(p), CtfAB(p), and ThlA(p) (ACT) or PpAdc(p), YbgC(p), and ThlA(p) (AYT). Strains were cultivated in 250 mL air-tight serum bottles with 25 mL Verduyn medium + 4 g/L (0.5% (v/v)) methanol. For the ACT strain, an additional condition was analyzed where 1.5 g/L acetate were added to the medium (+ Acetate). The headspace consisted either of 100% air (A) or of 50% air and 50% pure oxygen (B). Error bars represent the standard deviation of biological triplicates Fig. 7  Acetone titer, final optical density, and methanol concentration for O. polymorpha strains overexpressing heterologous genes for acetone synthe­ sis. O. polymorpha strains either overproducing PpAdc(p), CtfAB(p), and ThlA(p) (ACT) or PpAdc(p), YbgC(p), and ThlA(p) (AYT). Strains were cultivated in 250 mL air-tight serum bottles with 25 mL Verduyn medium + 4 g/L (0.5% (v/v)) methanol. For the ACT strain, an additional condition was analyzed where 1.5 g/L acetate were added to the medium (+ Acetate). The headspace consisted either of 100% air (A) or of 50% air and 50% pure oxygen (B). Error bars represent the standard deviation of biological triplicates Fig. 7  Acetone titer, final optical density, and methanol concentration for O. polymorpha strains overexpressing heterologous genes for acetone synthe­ sis. O. polymorpha strains either overproducing PpAdc(p), CtfAB(p), and ThlA(p) (ACT) or PpAdc(p), YbgC(p), and ThlA(p) (AYT). Acetone production However, there was no acetone detected in any of these created strains (data not shown). Consequently, of the tested strains the ACT strain with supplemented acetate in the medium and oxygen- enriched headspace produced the highest acetone titer in this study. These acetone titers are far from what can be achieved in an ABE fermentation with Clostridium acetobutylicum as a native acetone producer [46]. How­ ever, to our knowledge, this is the first time that a heter­ ologous production pathway for acetone was successfully introduced in a yeast as a heterologous host. Even though titers are still low these results provide a proof-of-princi­ ple that acetone production from methanol as a substrate is possible. The created O. polymorpha strains were subsequently transferred to closed serum bottles on Verduyn medium containing 0.5% MeOH as the sole carbon source and cultivated at 37 °C. Consistent with the experiments with the acetone-producing strains, 50% of the headspace of the culture was replaced with pure oxygen. As isoprene has a boiling point of 34 °C, isoprene was quantified from the headspace of the culture. As a control the unmodified O. polymorpha wildtype (WT) strain was included in the experiment. Figure 8 shows the amount of produced iso­ prene in these experiments. While the unmodified WT strain did not produce any isoprene, all other strains showed isoprene production. The strain expressing a single copy of the Populus alba ISPS gene showed the highest isoprene production of 4.4 ± 0.7 mg per L of culture medium. The strain express­ ing the single copy of the Pueraria montana ISPS gene produced considerably less isoprene compared to the Populus alba strain (0.7 ± 0.1 mg/L). It was also observed that the strain overexpressing the Populus alba isoprene synthase gene grew to a higher biomass density than the WT strain. This might be linked to the expression of the isoprene synthase gene pulling more carbon flux into the mevalonate pathway, which also provides the precursors for ergosterol synthesis, that are essential for growth [56]. It was further assessed whether an increased gene copy number could further enhance isoprene pro­ duction, by introducing a second copy of the respec­ tive isoprene synthase gene into these strains. However, introducing another copy of the Pueraria montana ISPS gene only led to a slightly increased isoprene titer of 1.0 ± 0.2 mg/L. Acetone production Strains were cultivated in 250 mL air-tight serum bottles with 25 mL Verduyn medium + 4 g/L (0.5% (v/v)) methanol. For the ACT strain, an additional condition was analyzed where 1.5 g/L acetate were added to the medium (+ Acetate). The headspace consisted either of 100% air (A) or of 50% air and 50% pure oxygen (B). Error bars represent the standard deviation of biological triplicates Wefelmeier et al. Microbial Cell Factories (2024) 23:8 (2024) 23:8 Page 10 of 15 Wefelmeier et al. Microbial Cell Factories on methanol is strictly aerobic in O. polymorpha, it was assumed that the yeast cells could not consume the entire methanol due to oxygen being limiting. Therefore, the experiment was repeated, but this time 50% of the head­ space was replaced with pure oxygen (Fig. 7B). With these experimental conditions, all cultures completely consumed methanol from the cultivation medium, which also led to an increase in the final optical density. At the same time, acetone titers increased. The AYT strain pro­ duced 3.5 ± 0.4 mg/L acetone, while the ACT strain even reached a titer of 8.6 ± 2.1  mg/L. Adding acetate to the medium even pushed acetone production further in the ACT strain to 13.6 ± 2.9 mg/L. The precursors for acetone are also part of O. polymorpha’s native metabolism. There is, e.g., a native isozyme of the acetyl-CoA acetyltransfer­ ase (EC.2.3.1.9; ERG10) as part of the mevalonate path­ way (MVA pathway) in O. polymorpha. The mevalonate pathway is essential for ergosterol synthesis and thus for growth. We can therefore assume that there will be production of acetoacetyl-CoA under a variety of differ­ ent culture conditions. Therefore, it was tested whether the introduction of PpAdc(p) alone or PpAdc(p) in com­ bination with CtfAB(p) or YbgC(p) already resulted in acetone production. However, there was no acetone detected in any of these created strains (data not shown). Consequently, of the tested strains the ACT strain with supplemented acetate in the medium and oxygen- enriched headspace produced the highest acetone titer in this study. These acetone titers are far from what can be achieved in an ABE fermentation with Clostridium acetobutylicum as a native acetone producer [46]. How­ ever, to our knowledge, this is the first time that a heter­ ologous production pathway for acetone was successfully introduced in a yeast as a heterologous host. Acetone production Surprisingly, the introduction of a second copy of the Populus alba isoprene synthase even led to a decreased titer compared to the single copy integration Acetone production Even though titers are still low these results provide a proof-of-princi­ ple that acetone production from methanol as a substrate is possible. we also created O. polymorpha strains with a double integration of the respective isoprene synthase cassette. Further, we aimed at increasing the supply of the precur­ sor DMAPP as it has been described extensively, how to increase the flux through the mevalonate pathway in yeast species [18, 51, 52]. The irreversible conversion of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonate, catalyzed by the enzyme 3-hydroxy-3-meth­ ylglutaryl-CoA reductase (Hmgr(p)) is regarded as the initial rate-limiting step of the mevalonate pathway [53, 54]. In yeasts, this enzyme has an N-terminal signal pep­ tide that anchors it to the endoplasmic reticulum mem­ brane. Deleting this anchor and thus making the enzyme available in the cytosol, has been described as one of the key strategies to enable a higher flux through the meval­ onate pathway [55]. Thus, a truncated copy of the HMGR gene (tHMGR) from Saccharomyces cerevisiae was addi­ tionally introduced into the genome of O. polymorpha and overexpressed using the strong methanol-inducible MOX promoter. on methanol is strictly aerobic in O. polymorpha, it was assumed that the yeast cells could not consume the entire methanol due to oxygen being limiting. Therefore, the experiment was repeated, but this time 50% of the head­ space was replaced with pure oxygen (Fig. 7B). With these experimental conditions, all cultures completely consumed methanol from the cultivation medium, which also led to an increase in the final optical density. At the same time, acetone titers increased. The AYT strain pro­ duced 3.5 ± 0.4 mg/L acetone, while the ACT strain even reached a titer of 8.6 ± 2.1  mg/L. Adding acetate to the medium even pushed acetone production further in the ACT strain to 13.6 ± 2.9 mg/L. The precursors for acetone are also part of O. polymorpha’s native metabolism. There is, e.g., a native isozyme of the acetyl-CoA acetyltransfer­ ase (EC.2.3.1.9; ERG10) as part of the mevalonate path­ way (MVA pathway) in O. polymorpha. The mevalonate pathway is essential for ergosterol synthesis and thus for growth. We can therefore assume that there will be production of acetoacetyl-CoA under a variety of differ­ ent culture conditions. Therefore, it was tested whether the introduction of PpAdc(p) alone or PpAdc(p) in com­ bination with CtfAB(p) or YbgC(p) already resulted in acetone production. Production of isoprene To enable isoprene synthesis in O. polymorpha an iso­ prene synthase (Isps(p), EC:4.2.3.27) has to be intro­ duced, that can catalyze the formation of isoprene from dimethylallyl diphosphate (DMAPP) as a substrate. DMAPP is a native intermediate of the mevalonate path­ way in yeast species. In this study, two different variants of the isoprene synthase were tested, one from Pueraria montana (kudzu vine) and the other one from Populus alba (white poplar). Both of these genes have already been applied successfully for the heterologous produc­ tion of isoprene in different microbial species [28, 47, 48]. As isoprene synthase genes typically have low turnover numbers and high Km values [49], it has been reported, that increasing the number of copies of isoprene synthase genes enhances the isoprene production [50]. Therefore, (2024) 23:8 Page 11 of 15 Wefelmeier et al. Microbial Cell Factories Fig. 8  Production of isoprene from methanol in O. polymorpha strains overproducing isoprene synthases (Isps(p)) from either Pueraria montana or Populus alba. In strains marked with “(2x)”, the respective isoprene syn­ thase gene was integrated twice. The unmodified wildtype (WT) strain was included as a negative control. Error bars represent standard devia­ tions of the biological replicates however, isoprene production stayed at the same level (4.59 ± 0.09 mg/L) as with the original medium, indicat­ ing that the availability of magnesium is not a limiting factor in the cultivation (SI: Figure S4). The highest isoprene titer obtained in this study (4.4 mg/L) is already substantially higher than the titers that were achieved with similarly modified strains of Saccharomyces cerevisiae (0.5  mg/L, [50]) and Yar­ rowia lipolytica (0.53 mg/L, [47]) cultivated on glucose. This highlights the potential of O. polymorpha as a pos­ sible isoprene production organism. Compared to other yeasts, O. polymorpha as a thermotolerant organism fur­ ther has the advantage that it can be cultivated at a tem­ perature above the boiling point of isoprene. In addition to avoiding product inhibition and potentially facilitat­ ing product purification, this has the advantage that the cultivation temperature is closer to the temperature opti­ mum of the isoprene synthases, potentially allowing the enzymes to function more efficiently than in mesophilic organisms. In the model organism S. cerevisiae, iso­ prene production from glucose has already been further advanced by extensive genetic modifications and optimi­ zation of cultivation conditions, which ultimately enabled isoprene production at a gram-per-liter scale. Production of isoprene This would also be reflected in the fact that the strain expressing a second copy of the isoprene synthase of Populus alba no longer showed improved biomass formation compared to the unmodi­ fied WT strain. Since the single integration strain of the Populus alba ispS produced most isoprene, further cul­ tivation conditions were tested for this strain. As the Populus alba isoprene synthase has its optimal reaction temperature synthase at 40 °C [57], isoprene production of the Populus alba strain was analyzed at an elevated cultivation temperature. However, this elevated tem­ perature led both to a decrease in growth and isoprene production (SI: Figure S4). This could be related to the increased volatility of the substrate methanol at higher temperatures, whereby less methanol is available in the cultivation medium and growth and product forma­ tion are correspondingly impeded. Further, as isoprene synthases require magnesium as a cofactor, we assessed whether an increased magnesium content in the medium might improve production. The magnesium titer in the medium was increased to 20 mM a concentration at which the Populus alba isoprene synthase was reported to be activated [57]. With this medium adaptation Production of isoprene These opti­ mization strategies include targeting an additional copy of the isoprene production pathway to the mitochondria [58], directed evolution of the isoprene synthase [59], and performing fed-batch cultivations at high cell densi­ ties [60]. These strategies indicate potential ways to also increase isoprene production from methanol in O. poly­ morpha in the future. Fig. 8  Production of isoprene from methanol in O. polymorpha strains overproducing isoprene synthases (Isps(p)) from either Pueraria montana or Populus alba. In strains marked with “(2x)”, the respective isoprene syn­ thase gene was integrated twice. The unmodified wildtype (WT) strain was included as a negative control. Error bars represent standard devia­ tions of the biological replicates strain (2.7 ± 0.2 mg/L). As the isoprene synthase genes are under the control of strong methanol-inducible promot­ ers (SI: Table S1), this decreased production might sug­ gest an increased metabolic burden resulting from the elevated gene expression. This would also be reflected in the fact that the strain expressing a second copy of the isoprene synthase of Populus alba no longer showed improved biomass formation compared to the unmodi­ fied WT strain. Since the single integration strain of the Populus alba ispS produced most isoprene, further cul­ tivation conditions were tested for this strain. As the Populus alba isoprene synthase has its optimal reaction temperature synthase at 40 °C [57], isoprene production of the Populus alba strain was analyzed at an elevated cultivation temperature. However, this elevated tem­ perature led both to a decrease in growth and isoprene production (SI: Figure S4). This could be related to the increased volatility of the substrate methanol at higher temperatures, whereby less methanol is available in the cultivation medium and growth and product forma­ tion are correspondingly impeded. Further, as isoprene synthases require magnesium as a cofactor, we assessed whether an increased magnesium content in the medium might improve production. The magnesium titer in the medium was increased to 20 mM a concentration at which the Populus alba isoprene synthase was reported to be activated [57]. With this medium adaptation strain (2.7 ± 0.2 mg/L). As the isoprene synthase genes are under the control of strong methanol-inducible promot­ ers (SI: Table S1), this decreased production might sug­ gest an increased metabolic burden resulting from the elevated gene expression. Strain construction Th d The overexpressed genes in this study were codon- optimized for O. polymorpha and ordered as synthetic DNA fragments via the GeneArt gene synthesis service (Thermo Fisher Scientific, Waltham, MA, USA). As an exception, the truncated 3-hydroxy-3-methylglutaryl- CoA reductase gene (tHMGR) was directly amplified from the genome of Saccharomyces cerevisiae. All over­ expressed genes were integrated into the genome of O. polymorpha using the pHIP expression vectors [67]. The created pHIP expression plasmids are listed in the Sup­ plementary Information (SI: Table S1). For the expression of the CtfAB(p) enzyme from Clostridium acetobuty­ licum, the genes for both the A and B subunit were co- expressed in O. polymorpha using the ERBV-1 (Equine rhinitis B virus) 2 A peptide [69]. Apart from optimizing the precursor supply, develop­ ing strategies to efficiently avoid methanol toxicity will be essential for successfully establishing the production of platform chemicals from methanol. In this study, utiliza­ tion of the LIS system allowed constant methanol feed­ ing to shake flasks and was demonstrated to be a simple solution to circumvent substrate toxicity already during the early characterization phase of newly constructed strains, a technology that can be used beyond methanol and yeast. For integration, the pHIP vectors were linearized at unique restriction sites in the promoter region of the vec­ tor and then transformed as linear cassettes into O. poly­ morpha through LiAc/single-stranded carrier DNA/PEG transformation [70]. For selection after transformation, the cells were spread on YPD agar plates supplemented with either 200 µg/mL hygromycin, 100 µg/L zeocin, or 100 mg/L nourseothricin. Conclusionh This study successfully demonstrates the production of three different industrially relevant chemicals in the yeast Ogataea polymorpha using methanol as a substrate. It high­ lights how the yeast’s metabolism is not equally well suited for the production of all of these molecules and thus also emphasizes the necessity for further engineering of the methanol metabolism of methylotrophic yeast. These find­ ings serve as a point of reference for future metabolic engi­ neering efforts of O. polymorpha to boost the production of low molecular weight compounds from methanol. Perspectives for producing methanol-derived chemicals in O. polymorpha y In this study, we successfully demonstrated the produc­ tion of malate, acetone, and isoprene using methanol as carbon source for the yeast O. polymorpha. Malate could be produced with highly promising titers of 13.2 g/L and productivities of 3.4  g/L/d. This reflects that O. poly­ morpha appears to be an excellent organism for malate production, possibly due to the high activity of the malate-aspartate shuttle when methanol is used as a car­ bon source. These results, therefore, also underline the suitability of methylotrophic yeasts for producing car­ boxylic acids from C1 molecules, as similar titers can nei­ ther be achieved with photoautotrophic bacteria growing on CO2 nor with methylotrophic bacteria at the moment [61–63]. Still, studies reporting the production of low molecular weight biochemicals in methylotrophic yeasts using methanol as substrate are currently rare in the lit­ erature. This might be related to the intrinsic properties of methanol metabolism in yeast. The majority of the assimilated carbon is oxidized to CO2 in the dissimilatory branch of methanol metabolism. When methanol is used Wefelmeier et al. Microbial Cell Factories (2024) 23:8 Wefelmeier et al. Microbial Cell Factories (2024) 23:8 Page 12 of 15 Page 12 of 15 Wefelmeier et al. Microbial Cell Factories as a carbon source, 50–70% of the total carbon flux in the methylotrophic yeast P. pastoris passes through this dissimilatory branch [64]. As a result, metabolism dur­ ing growth on methanol is characterized by low carbon flux to pyruvate and even lower flux to acetyl-CoA (33% and 13% of the methanol uptake flux, respectively) [65]. While this means that there are few overflow metabo­ lites produced during growth on methanol, it makes the production of chemicals derived from these precursors challenging. This is also reflected in the fact that the pro­ duction of acetone and isoprene with O. polymorpha in this study only occurs at comparatively low levels and that the yield of malate on methanol only reaches 0.099 mol/ mol, which corresponds to 40% of the theortical maxi­ mum yield. To enable the synthesis of larger amounts of methanol-derived chemicals in yeasts, it will be crucial to reroute the carbon flux towards precursors such as pyru­ vate and acetyl-CoA in addition to optimizing the respec­ tive biosynthesis pathways. Strains and mediah The strains engineered in this study are based on the strain Ogataea polymorpha NCYC495 leu1.1 ∆yku80 [67]. Pre-cultures of O. polymorpha were grown at 37 °C in YPD medium (10  g/L yeast extract, 20  g/L peptone, 20 g/L glucose). If not otherwise stated, the defined min­ eral Verduyn medium [68] buffered with 100 mM KH- Phthalate and variable concentrations of methanol as carbon source, was used for all cultivations. In addition, the medium was supplemented with 0.5 g/L leucine, as the constructed strains are leucine-auxotrophic, and with 1 g/L yeast extract as an additional nitrogen source and auxiliary substrate, which reportedly improves methanol utilization [30]. A detailed description of the medium composition can be found in the supplementary information (SI: Table S2-4). For plasmid propagation, competent Escherichia coli cells (NEB® 10-beta, High Efficiency) were used. E. coli cells were grown at 37 °C in LB medium, supplemented as required with 100 µg/L ampicillin. Perspectives for producing methanol-derived chemicals in O. polymorpha Potential strategies that have been suggested for this include the overexpression of the dihydroxyacetone synthase (DHAS) to increase the assimilation of formaldehyde [66], knocking out the glucose-6-phosphate isomerase to reduce flux through the pentose phosphate pathway [30] or downregulation of the dissimilatory branch of methanol assimilation [38, 65]. All these strategies bear the risk of disturbing the delicate balance in methanol metabolism and leading to an accumulation of toxic intermediates such as formalde­ hyde and thus have to be carefully tested. Analytical methods High-performance liquid chromatography (HPLC-UV- RI) was used to monitor methanol consumption and malate production. To this end, 1 mL of yeast culture was centrifuged at maximum speed and the supernatant was filtered through Rotilabo syringe filters (Carl Roth, pore size 0.2 m). The filtered supernatants were then analyzed using a DIONEX UltiMate 3000 HPLC System (Thermo Fisher Scientific) equipped with a Metab-AAC column (300 × 7.8 mm, ISERA, Düren, Germany). 5 mM H2SO4 was used as running buffer at a flow rate of 0.6 mL/min and a temperature of 30 °C. A SHODEX RI-101 detector (Showa Denko Europe GmbH, München, Germany) and a DIONEX UltiMate 3000 Variable Wavelength Detector (Thermo Fisher Scientific) set to 210 nm were used for detection. Analytes were identified by comparison of the retention time and UV/RI quotient to standards.i equipped with a Pora BOND Q column (50  m, Inner diameter: 0.32 mm, film thickness: 5 μm, Agilent Tech­ nologies Inc.). Helium was used as carrier gas at a flow rate of 1.8 mL/min, and the following temperature profile was applied: 50 °C constant for 5 min, an increase of 8 °C/ min to 250 °C, 250 °C constant for 15 min. Cultivation conditionsh The malate-producing O. polymorpha strains were cul­ tivated in 250 mL shake flasks or 24-well System Duetz microtiter plates, filled with 25 mL or 3 mL Verduyn medium, respectively. Cultivations were performed at 37 °C with 250 rpm shaking. For the constant methanol feeding experiment, the Liquid Injection System (LIS, SBI Wefelmeier et al. Microbial Cell Factories (2024) 23:8 Page 13 of 15 Wefelmeier et al. Microbial Cell Factories Table 2  Settings of the GSMM iOpol23 to simulate five different pathway scenarios. The setting of the ‘Unconstraint Reference’ is also the basis for the remaining four scenarios Table 2  Settings of the GSMM iOpol23 to simulate five different pathway scenarios. The setting of the ‘Unconstraint Reference’ is also the basis for the remaining four scenarios Scenario Model Adaptation Unconstraint Reference (Ref) MeOH rate: 10 mmol/gDW/h Objective: malate/acetone/isoprene Blocked TCA (TCA-) = Ref and: Upper bound = 0 for: (PDHa1, PDHcm, ACLSm, AKGDH1 + 2, CITtam, CITtap, CSp + m) Forced TCA (TCA+) = Ref and: Lower bound = 7.8 for: AKGDam Forced Glyoxylate shunt (Glx + Std) = Ref and: Lower bound = 10 for: ICL Forced, Impaired Glyoxylate shunt (Glx + Mut) = Glx + Std and: Lower/Upper bound = -10/2.85 for: MDHm Scientific Bioprocessing, Baesweiler, Germany) was used, which allows automated feeding of liquids into shake flask cultures. During cultivation, the shake flasks were weighed daily to determine the evaporation rate of the medium. The measured product titers and optical densi­ ties were then corrected for this evaporation. The strains producing acetone or isoprene were culti­ vated in 250 mL serum bottles which were sealed with air-tight rubber stoppers, to prevent evaporation of the volatile products during cultivation. The bottles were filled with 25 mL cultivation medium. To avoid oxygen limitation of the cells, 50% of the headspace was removed from the flask and replaced with pure oxygen. Simulations d d We adapted the existing genome scale metabolic model of O. polymorpha (iUL909) to arrive at the new model iOpol23 (https://github.com/iAMB-RWTH-Aachen/ Opol-GSMM). The new model contains reactions for iso­ prene synthase (EC: 4.2.3.27), acetoacetyl-CoA hydrolase (EC: 3.1.2.11), acetoacetate decarboxylase (EC: 4.1.1.4) and transport reactions for acetone and isoprene. The yield simulations were performed with methanol as sole carbon source with an uptake rate of 10 mmol/gDW/h. Different scenarios of metabolic fluxes were tested for their capacity to generate the products and Table 2 shows the respective settings of the genome scale model. The boundaries for AKGDam, ICL, and MDHm were manu­ ally identified as the minimum/maximum fluxes that still supported feasible solutions. There are in total 15 combi­ nations of simulations (3 target metabolites in 5 pathway scenarios) and all flux solutions are provided as supple­ mentary material. The flux balance analysis simulations were performed with cobrapy (v0.17.1) in Python (v3.9.7) with the standard optimization function [71]. The prin­ cipal component analysis (PCA) was conducted with scikitlearn (v1.0.2). A Jupyter Notebook with a workflow of the whole analysis is available on GitHub (https:// github.com/iAMB-RWTH-Aachen/Opol-GSMM). For acetone quantification, the serum bottles used for cultivation were cooled to 4 °C, after which samples were taken from the culture broth, filtered through Rotilabo syringe filters (Carl Roth, pore size 0.2  μm) and then directly stored in screw-cap GC-vials at 4  °C. A Trace GC Ultra GC (Thermo Fisher Scientific) equipped with a flame ionization detector (FID) was used for the determi­ nation of acetone titers. Analytes were separated with a Zebron ZB-WAX column (length: 30 m, film thickness: 0.25 μm, inner diameter: 0.25 mm, Zebron, Phenomenex, UK). The measurement was performed with helium as carrier gas with a flow rate of 2 mL/min, an injection volume of 1 µL, a split ratio of 1:40, an inlet temperature of 220  °C, and the following temperature profile: 40  °C constant for 2.5 min, an increase of 35 °C/min to 150 °C, an increase of 40 °C/min to 250 °C, 250 °C constant for 3 min. For isoprene analytics, 1 mL of culture headspace was taken from the culture with a Hamilton 1001 gas-tight syringe (Hamilton Bonaduz AG, Bonaduz, Switzerland). The headspace samples were analyzed with an Agilent 8890 gas chromatograph with a flame ionization detector (FID) (Agilent Technologies Inc., Santa Clara, CA, USA), Supplementary Information Data Availability The data produced in this study are presented in the article or additional material. 16. Li Y, Zhai X, Yu W, Feng D, Shah AA, Gao J, et al. Production of free fatty acids from various carbon sources by Ogataea polymorpha. Bioresour Bioprocess. 2022;9(1):78. More accessible and interactive data is available at: https://github.com/ iAMB-RWTH-Aachen/Opol-GSMM. This repository contains an Excel-file with the experimental data for Figs. 3, 4, 5, 6, 7 and 8, the adapted genome scale metabolic model of O. polymorpha (iOpol23), and a Jupyter Notebook with a workflow of the simulation. 17. Manfrão-Netto JHC, Queiroz EB, Rodrigues KA, Coelho CM, Paes HC, Rech EL, et al. Evaluation of Ogataea (Hansenula) polymorpha for hyaluronic acid production. Microorganisms. 2021;9(2):312. 18. Ye M, Gao J, Zhou YJ. Global metabolic rewiring of the nonconventional yeast Ogataea polymorpha for biosynthesis of the sesquiterpenoid β-elemene. Metab Eng. 2023;76:225–31. Acknowledgements We acknowledge Hannelore Eschmann and Björn Johnen from the Institute of Technical and Macromolecular Chemistry (ITMC) of RWTH Aachen University for their support with the isoprene analytics. We thank Valentina Vidal Tagle for her assistance in setting up the Liquid Injection System. We also thank our students Marlene Maria Menke, Mara Dauber, and Adlen Ergin Adil for their support in the METAFOR project and all METAFOR members for numerous discussions throughout the entire project time. 7. Alper E, Yuksel Orhan O. CO2 utilization: developments in conversion pro­ cesses. Petroleum. 2017;3(1):109–26. 8. Ledeboer AM, Edens L, Maat J, Visser C, Bos JW, Verrips CT, et al. Molecular cloning and characterization of a gene coding for methanol oxidase in Hansenula polymorpha. Nucleic Acids Res. 1985;13(9):3062–82. 9. Yurimoto H, Kato N, Sakai Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabo­ lism. Chem Record. 2005;5(6):367–75. Declarations 19. Pérez-Díaz IM, McFeeters RF. Microbiological preservation of cucumbers for bulk storage using acetic acid and food preservatives. J Food Sci. 2008;73(6):M287–91. Supplementary Information h l l pp y The online version contains supplementary material available at https://doi. org/10.1186/s12934-023-02283-z. Page 14 of 15 Wefelmeier et al. Microbial Cell Factories (2024) 23:8 (2024) 23:8 Wefelmeier et al. Microbial Cell Factories 5. Lindner JP, Beck T, Bos U, Albrecht S. Assessing land use and biodiversity impacts of industrial biotechnology. In: Fröhling M, Hiete M, editors. Sustain­ ability and life cycle assessment in industrial biotechnology. 1st ed. Cham: Springer; 2019. pp. 233–54. Supplementary Material 1 Supplementary Material 2 6. Bushuyev OS, De Luna P, Dinh CT, Tao L, Saur G, van de Lagemaat J, et al. What should we make with CO2 and how can we make it? Joule. 2018;2(5):825–32. Funding 13. Manfrão-Netto JHC, Gomes AMV, Parachin NS. Advances in using Hansenula polymorpha as chassis for recombinant protein production. Front Bioeng Biotechnol. 2019;7. This work was funded by the German Federal Ministry of Education and Research (BMBF) as part of the METAFOR project (Grant no. FKZ 031B0850A). The laboratory of Lars M. Blank is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – Exzellenzcluster 2186 “The Fuel Science Center” ID: 390919832. 14. Yan C, Yu W, Zhai X, Yao L, Guo X, Gao J, et al. Characterizing and engineering promoters for metabolic engineering of Ogataea polymorpha. Synth Syst Biotechnol. 2022;7(1):498–505. 15. Reinders A, Romano I, Wiemken A, De Virgilio C. The thermophilic yeast Han­ senula polymorpha does not require trehalose synthesis for growth at high temperatures but does for normal acquisition of thermotolerance. J Bacteriol. 1999;181(15):4665–8. Open Access funding enabled and organized by Projekt DEAL. Author contributions 10. Munasinghe PC, Khanal SK. Biomass-derived syngas fermentation into biofu­ els: opportunities and challenges. Bioresour Technol. 2010;101(13):5013–22. KW: Conceptualization, Methodology, Investigation, Formal analysis, Project Administration, Writing—original draft, Writing—review & editing. SS: Conceptualization, Methodology, Investigation, Formal analysis, Writing – review & editing. BJK: Methodology, Investigation. UWL: For Metabolic Modelling section: Conceptualization, Methodology, Writing—original draft, Writing—review & editing. LMB: Conceptualization, Project administration, Funding acquisition, Supervision, Writing—review & editing. All authors read and approved the final manuscript. 11. Mayer AF, Hellmuth K, Schlieker H, Lopez-Ulibarri R, Oertel S, Dahlems U, et al. An expression system matures: a highly efficient and cost-effective process for phytase production by recombinant strains of Hansenula polymorpha. Biotechnol Bioeng. 1999;63(3):373–81. 12. Gellissen G, Kunze G, Gaillardin C, Cregg J, Berardi E, Veenhuis M et al. New yeast expression platforms based on methylotrophic Hansenula polymorpha and Pichia pastoris and on dimorphic Arxula adeninivorans and Yarrowia lipolytica – A comparison. FEMS Yeast Res. 2005;5(11):1079–96. lipolytica – A comparison. FEMS Yeast Res. 2005;5(11):1079–96. Consent for publication Not applicable. 21. Saito F, Kishimoto K, Nobira Y, Kobayakawa K, Sato Y. Nickel electroplat­ ing bath using malic acid as a substitute agent for boric acid. Met Finish. 2007;105(10):192–204. 21. Saito F, Kishimoto K, Nobira Y, Kobayakawa K, Sato Y. Nickel electroplat­ ing bath using malic acid as a substitute agent for boric acid. Met Finish. 2007;105(10):192–204. Competing interests 22. Kim BH, Jang J, Ko SW. Durable press finish of cotton fabric using malic acid as a crosslinker. Fibers Polym. 2000;1(2):116–21. The authors declare no competing interests. 23. Loyer P, Cammas-Marion S. Natural and synthetic poly(malic acid)-based deri­ vates: a family of versatile biopolymers for the design of drug nanocarriers. J Drug Target. 2014;22(7):556–75. Received: 23 September 2023 / Accepted: 19 December 2023 Received: 23 September 2023 / Accepted: 19 December 2023 24. Veith C, Diot-Néant F, Miller SA, Allais F. Synthesis and polymerization of bio- based acrylates: a review. Polym Chem. 2020;11(47):7452–70. 25. William Bunch A. 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Significance of CYCLOOXYGENASE-2(COX-2), PERIOSTIN (POSTN) and INTERLEUKIN-4(IL-4) gene expression in the pathogenesis of chronic rhinosinusitis with nasal polyps
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Eur Arch Otorhinolaryngol (2015) 272:3715–3720 DOI 10.1007/s00405-014-3481-9 RHINOLOGY Jarosław Miłon´ski • Hanna Zielin´ska-Bliz´niewska • Karolina Przybyłowska • Piotr Pietkiewicz • Barbara Korzycka-Zaborowska • Ireneusz Majsterek • Jurek Olszewski Jarosław Miłon´ski • Hanna Zielin´ska-Bliz´niewska • Karolina Przybyłowska • Piotr Pietkiewicz • Barbara Korzycka-Zaborowska • Ireneusz Majsterek • Jurek Olszewski Received: 12 November 2014 / Accepted: 25 December 2014 / Published online: 9 January 2015  The Author(s) 2015. This article is published with open access at Springerlink.com Abstract The purpose of this paper was to evaluate the level of Cyclooxygenase-2 (COX-2), Periostin (POSTN) and Interleukin-4(IL-4) gene expression in patients with chronic rhinosinusitis with nasal polyps, without polyps and with a nasal septum deviation. The tests were performed on 63 patients (24 women and 39 men) with chronic rhinosi- nusitis and polyps (CRSwP—study group I), with deter- mination of the COX-2, POSTN and IL-4 gene expression; an allergy was diagnosed in 38 cases. The reference groups were patients with chronic rhinosinusitis without polyps–– CRS (n = 23, including 14 women and 9 men) and patients with nasal septum deviation––DSN (n = 18, including 9 women and 9 men). The expression level was determined in the polyp tissue and the mucosa of paranasal sinus collected during an FESS. The expression level of studied genes was also evaluated in the material. Immediately after being collected, the tissue fragments were placed in test tubes with 1 ml of RNAlater (Qiagen, Hilden, Germany) preventing the degradation of RNA and frozen at -70 C. The studies revealed an increased level of POSTN, IL-4 gene expression and a decreased level of COX-2 gene expression that may be associated with the development of chronic rhinosinusitis with nasal polyps. An analysis of the expression level indicates the participation of POSTN and IL-4 in the development of chronic rhinosinusitis with nasal polyps in patients with atopy. Keywords Gene expression  Chronic rhinosinusitis with nasal polyps Introduction For a very long time, nasal polyps were considered to be adenomas, and their development was associated with desmoplasia. There are numerous hypotheses on the for- mation of polyps [1–5]. In 1896, Hayek assumed that polyps formed as a consequence of an exudate which pushes the mucosa out, leading to local congestion, oedema and blood retention in the vessels. In 1907, Yonge described another reason, cystic distension of the mucosal glands (caused by their excessive activity and ongoing chronic inflammation) which, supposedly, pressed mechanically against local blood vessels and the glands themselves, leading to the oedema and congestion. More recent hypotheses emphasise the significance of isolated damage to the epithelium and its basement mem- brane, related to the inflammation process as a sign to start polypogenesis, e.g., a 1991 hypothesis by Larsen and Tos [6]. In 1997, Bernstein [7] presented an interesting concept of disorders in the function of ion channels in the epithelial cellular membrane, including excessive absorption of Na? and increased transmission of CL-. He claimed that by increasing the transport of water into interstitial spaces, the increased transepithelial ion transport induced oedema and the formation of nasal polyps. K. Przybyłowska  I. Majsterek Department of Chemistry and Clinical Biochemistry, Medical University of Lodz, Lodz, Poland Currently, the following factors are listed as pathogenic for chronic rhinosinusitis with/without nasal polyps: 12 3 3 Eur Arch Otorhinolaryngol (2015) 272:3715–3720 3716 – exogenous factors: viruses, bacteria, fungi, drugs, injuries, toxic substances, or environmental pollution; – exogenous factors: viruses, bacteria, fungi, drugs, injuries, toxic substances, or environmental pollution; paranasal sinuses, a total of 63 patients with chronic rhi- nosinusitis with polyps (CRS with P) were randomly selected for study group I, for which the level of COX-2 and POSTN gene expression was to be determined. This group included 24 women and 39 men (mean age 48.7 ± 13.3 years) with a diagnosed allergy in 38 cases (60 %). The reference groups were: patients with CRS without P––CRS (n = 23, including 14 women and 9 men, mean age 46.4 ± 13.2 years) and patients with nasal sep- tum deviation—DSN (n = 18, including 9 women and 9 men, mean age 42.8 ± 13.9 years—Table 1). Introduction – general endogenous factors: allergy, oversensitivity to acetylsalicylic acid and its derivatives, hormonal dis- orders, laryngopharyngeal reflux, diseases with the formation of granulation tissue, immunity disorders, genetic syndromes of ciliary disorders (Kartagener syndrome, cystic fibrosis), or oedemal causes; – local endogenous factors: anatomic abnormalities (enlarged ethmoid bulla, aerated and distended middle nasal concha, and nasal septum deviation), tumours, or acquired syndromes of ciliary disorders in the respira- tory epithelium [8–11]. The expression level was determined in the polyp tissue and the mucosa of paranasal sinus collected during an endoscopic FESS. Fragments of the mucosa from paranasal sinuses with CRS without Ps and a fragment of the mucosa from the lower nasal concha in patients with nasal septum deviation were collected during the planned endoscopic procedures. The expression level of the genes was also evaluated in the material. Polyps, as part of the course of chronic rhinosinusitis, are considered primarily to be the consequences of advanced inflammatory processes [12–15]. However, the actual processes responsible for their development remain unclear. Current studies focus on explaining the role of mucosal epithelium in the nose and sinuses; its lesions (similarly as in asthma) may start and then sustain the pathophysiolog- ical processes [14]. The significance of the epithelium in the development of respiratory diseases results from its immunoregulative function and biological activity, as well as the possibility of releasing numerous mediators. Cur- rently, it is assumed that the development of nasal polyps consists of: Immediately after being collected, the tissue fragments were placed in test tubes with 1 ml of RNAlater (Qiagen, Hilden, Germany) to prevent the degradation of RNA, and frozen at -70 C. The studies were approved by the Bio- ethics Commission at the Medical University of Lodz (Decision no. RNN/40/09/KB of 6th January 2009), and consent of each patient was obtained. Qualitative and quantitative assessment of mRNA The concentration of RNA and clarity of obtained samples were assessed spectrophotometrically. The obtained RNA samples were diluted 50 times in H2O-DEPC. The reading was performed with three wavelengths: 260 nm—maxi- mum absorption for RNA and 280 nm—maximum absorption for proteins against the reference solution (in this case, 100 ll of DEPC water). Isolation of RNA – disorder of the epithelial cell function, – eosinophilic inflammation of the mucosa. – eosinophilic inflammation of the mucosa. The total RNA from the collected tissue fragments was isolated with TriPure Isolation Reagent (Roche Diagnostics GmbH, Mannheim, Germany) according to the manufac- turer’s recommendations. The purpose of this paper was to evaluate the level of CYCLOOXYGENASE-2 (COX-2), PERIOSTIN (POSTN), INTERLEUKIN-4 (IL-4) gene expression in patients with chronic rhinosinusitis: with nasal polyps, without polyps and with nasal septum deviation. Table 1 Characteristics of study group (gender) Materials and methods Out of 300 patients (140 women and 160 men) hospitalised in the Department of Otolaryngology and Laryngological Oncology, Medical University of Lodz in 2010–2012 qualified for surgical endoscopic treatment of the nose and Table 1 Characteristics of study group (gender) Gender Groups Summary I Study (CRSwP) II Control 1 (CRS) II Control 2 (DNS) n % n % n % Man 39 61.9 9 39.1 9 50.0 57 Woman 24 38.1 14 60.9 9 50.0 47 Summary 63 100.0 23 100.0 18 100.0 104 123 Gender Groups Summary I Study (CRSwP) II Control 1 (CRS) II Control 2 (DNS) n % n % n % Man 39 61.9 9 39.1 9 50.0 57 Woman 24 38.1 14 60.9 9 50.0 47 Summary 63 100.0 23 100.0 18 100.0 104 Table 1 Characteristics of study group (gender) 12 123 Eur Arch Otorhinolaryngol (2015) 272:3715–3720 3717 Reverse transcription reaction and without polyps, with the expression level in tissues from the control group (DSN), a significantly higher level in the tissues with chronic rhinosinusitis was shown. It has been observed that the COX-2 expression level was higher in a statistically significant manner in the mucosa of patients with CRS without Ps as compared to the expres- sion level in the mucosa and polyp tissue in patients with CRS with P. Moreover, in the polyp tissue the COX-2 expression level was significantly lower than in the mucosa with CRS with P (Table 2). No relationship between the differences in the COX-2 expression level and presence of atopy in patients with CRS and P was shown, neither in the polyp tissue nor in the mucosa (Table 3). The synthesis of cDNA on the matrix of isolated RNA was performed with the use of a commercial RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific, Waltham, MA, USA) with the use of reverse transcriptase M-MuLV (Moloney murine leukaemia virus). The results of a gel densitometry were used to specify the relative amount of mRNA of the COX-2, POSTN and IL-4 genes. The level of analysed genes was standardised against the reference gene, GAPDH. Statistic methods The analysis of POSTN gene expression indicated a significantly higher level of mRNA in polyps and nasal mucosa of those patients with CRS with Ps (CRSwP) and patients with CRS without Ps (CRS), as compared to the level in the nasal mucosa from the control group (DSN). Moreover, it was observed that the POSTN mRNA level was significantly higher in polyps compared to the mucosa of patients with CRS with Ps (CRSwP) and without Ps (CRS), whereas no differences in the POSTN expression were observed in comparisons of the mucosa of these two groups of patients (Table 4). The high expression of the POSTN gene in patients with ChRS with Ps was related to the presence of an allergy (Table 5). The collected data were compiled using descriptive meth- ods and statistical conclusion methods. Spearman’s rank correlation coefficient was used to examine whether there is a relationship between the studied features and the level of gene expression. The differences between mean values (or frequencies) and the relations between characteristics for which the calculated value of the test was equal or greater than the critical value, based on appropriate tables, were considered statistically significant, with the correct number of degrees of freedom and an error probability of p \ 0.05. The analysis of IL-4 gene expression indicated a sig- nificantly higher level of this cytokine in the polyp tissue and nasal mucosa of the patients with CRS with Ps (CRSwP), as compared to the level in the nasal mucosa from those patients with CRS without Ps (CRS) and from Results Comparing the level of COX-2 expression between the tissues from those patients with chronic rhinosinusitis, with Table 2 The level of COX-2 gene expression in patients with chronic rhinosinusitis with nasal polyps (CRSwP), without nasal polyps (CRS) and in patients with nasal septum deviation (DNS) CRSwP (n = 63) CRS (n = 23) mucosa mediana (25 %; 75 %) DNS (n = 18) mucosa mediana (25 %; 75 %) Polyp mediana (25 %; 75 %) Mucosa mediana (25 %; 75 %) 0.697 (0.561; 0.816) 0.770 (0.727; 0.897) vs polyp p < 0.007 1.236 (1.022; 1.386) vs polyp CRSw P p < 0.001 vs mucosa CRSwP p < 0.001 0.400 (0.315, 0.470) vs polyp CRSwP p < 0.001 vs mucosa CRSwP P < 0.001 vs mucosa CRS p < 0.001 Table 3 The level of COX-2 gene expression in patients with ChRS with Ps, considering the presence of atopy CRSwP CRSwP with atopy (n = 38) CRSwP without atopy (n = 25) P Polyp Mucosa 0.697 (0.548; 0.786) 0.767 (0.724; 0.808) 0.697 (0.540; 0.837) 0.797 (0.729; 1.268) 0.354 0.124 1 3 expression in patients with chronic rhinosinusitis with nasal polyps (CRSwP), without nasal polyps (CRS) and tion (DNS) Table 3 The level of COX-2 gene expression in patients with ChRS with Ps, considering the presence of atopy CRSwP CRSwP with atopy (n = 38) CRSwP without atopy (n = 25) P Polyp Mucosa 0.697 (0.548; 0.786) 0.767 (0.724; 0.808) 0.697 (0.540; 0.837) 0.797 (0.729; 1.268) 0.354 0.124 3718 Eur Arch Otorhinolaryngol (2015) 272:3715–3720 Table 4 The level of POSTN gene expression in patients with chronic rhinosinusitis with nasal polyps (CRSwP), without nasal polyps (CRS) and in patients with nasal septum deviation (DNS) CRSwP (n = 63) CRS (n = 23) mucosa mediana (25 %; 75 %) DNS (n = 18) mucosa mediana (25 %; 75 %) Polyp mediana (25 %; 75 %) Mucosa mediana (25 %; 75 %) 2.480 (2.395; 2.743) 0.520 (0.460; 0.590) vs polyp p \ 0.001 0.524 (0.454; 0.626) vs polyp CRSwP p \ 0.001 vs mucosa CRSwP p = 0.178 0.425 (0.355; 0.503) vs polyp CRSwP p \ 0.001 vs mucosa CRSwP P = 0.019 vs mucosa CRS p = 0.031 TN gene expression in patients with chronic rhinosinusitis with nasal polyps (CRSwP), without nasal polyps (CRS) eptum deviation (DNS) Table 4 The level of POSTN gene expression in patients with chronic rhinosinusitis with nasal polyps (CRSw and in patients with nasal septum deviation (DNS) Table 5 The level of POSTN gene expression in patients with ChRS with Ps, considering the presence of atopy POSTN mediana (25 %; 75 %) CRSwP with atopy (n = 38) CRSwP without atopy (n = 25) P Polyp 2.590 (2.450; 3.000) 2.420 (2.190; 2.550) <0.001 Mucosa 0.520 (0.430; 0.590) 0.525 (0.470; 0.620) 0.456 Table 6 The level of IL-4 gene expression in patients with chronic rhinosinusitis with nasal polyps (CRSwP), without nasal polyps (CRS) and in patients with nasal septum deviation (DNS) CRSwP (n = 63) CRS (n = 23) mucosa mediana (25 %; 75 %) DNS (n = 18) mucosa mediana (25 %; 75 %) Polyp mediana (25 %; 75 %) Mucosa mediana (25 %; 75 %) 0.821 (0.747; 1.117) 0.818 (0.732; 1.039) vs polyp p = 0.189 0.747 (0.529; 0.977) vs polyp CRSwP p < 0.001 vs mucosa CRSwP p 5 0.014 0.116 (0.106; 0.161) vs polyp CRSwP p < 0.001 vs mucosa CRSwP P < 0.001 vs mucosa CRS p < 0.001 Table 7 The level of IL-4 gene expression in patients with ChRS with Ps, considering the presence of atopy CRSwP CRSwP with atopy (n = 38) CRSwP without atopy (n = 25) P Polyp Mucosa 1.056 (0.797; 1.272) 0.916 (0.816; 1.119) 0.777 (0.719; 0.816) 0.736 (0.679; 0.760) <0.001 <0.001 the control group (DSN). Results No statistically significant dif- ferences in the level of IL-4 between the polyp tissue and mucosa of those patients with CRS with Ps (CRSwP) were found. A statistically significant increase of expression in the nasal mucosa of those patients with CRS without Ps (CRS) as compared to the control group was observed (Table 6). The high expression of IL-4 gene in patients with CRS with Ps (CRSwP) was related to the presence of an allergy (Table 7). Discussion Thus, these data suggest that the disorders of the (COX-1) and (COX-2) cyclooxygenase path apply to the entire mucosa of patients with the aspirin triad, instead of being associated only with nasal polyps and the mucosa of the upper respiratory tract in patients diagnosed with the aspirin triad, and they cannot be associated with the healthy mucosa of patients without the triad [17]. Ishida et al. [28] confirmed the enhanced expression of PERIOSTIN in the mucosal tissues of patients with allergic rhinitis, and in the mucosal tissues from the sinuses of patients with CRS and nasal polyps, as compared to the control group. Moreover, the POSTN expression was sig- nificantly higher in those patients with CRS and nasal polyps than in those patients with allergic rhinitis. Studies by Ishida et al. suggest that PERIOSTIN plays an important role in the remodelling of mucosa in allergic rhinitis and the formation of the polyp in the course of chronic rhi- nosinusitis and aspirin-induced asthma (AIA) [28, 29]. The results of the authors’ own studies indicated a sig- nificantly higher level of POSTN expression in polyps and nasal mucosa of those patients with CRS with Ps (study group) and those patients with CRS without Ps (control group I), as compared to the level in the nasal mucosa from control group II (DSN). Moreover, it was observed that the POSTN mRNA level was significantly higher in polyps as compared to the mucosa of patients with CRS with/without Ps, whereas no differences in the POSTN expression were observed while comparing the mucosa of these two groups of patients. The high expression of the POSTN gene in patients with ChRS with Ps was related to the presence of atopy as observed in the polyp tissues, whereas no similar dependence was found in the mucosa of these patients. In the authors’ own studies, comparing the level of COX-2 expression between the tissues from the patients with ChRS, with and without nasal polyps, with the expression level in tissues from the control group (DSN), a significantly higher level in the tissues with chronic rhi- nosinusitis was shown. It has been observed that the COX-2 expression level was higher in a statistically significant manner in the mucosa of patients with ChRS without Ps as compared to the expression level in the mucosa and polyp tissue in patients with ChRS with Ps. Discussion The COX-2 gene is one of the best researched genes with regard to expression and related mechanisms. Based on numerous experimental studies, it has been proven that an increase in COX-2 expression is observed in many diseases and types of cancer in people. The disorders in the regu- lation of cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) have been described by numerous researchers in 12 123 Eur Arch Otorhinolaryngol (2015) 272:3715–3720 3719 the nasal polyps of patients with AIA (Aspirin-Induced Asthma). However, it is unclear whether these disorders are characteristic only of nasal polyps or the entire mucosa of the upper respiratory tract in patients with the aspirin triad (nasal polyps ? intolerance of salicylates ? asthma). The studies undertaken so far have proved ambiguous, and many indicate an increased COX expression in the tissues of nasal polyps [16–20]. with nasal polyps shares a pathogenetic background with asthma, while subepithelial fibrosis plays an important role in both. Jia et al. [25] also confirmed the role of periostin as a biomarker in chronic eosinophilic respiratory track inflammation in patients with asthma. Norris et al. [26] showed that POSTN is expressed in normal mucosa. However, its overexpression may be a significant factor contributing to the pathogenesis of nasal polyps [27]. Moreover, the results of tests with the use of micromatrix comparing the gene expression levels in the tissue of nasal polyps from patients with chronic rhinosi- nusitis and bronchial asthma showed a characteristic increase in the POSTN gene expression for the studied group of patients, differing from the control group. Recent studies by Roca-Ferrer et al. [21] present the differences in COX-2 expression between the polyp tissue and control mucosa. Using three methods of expression analysis (ELISA, Western blot and immunofluorescence), no significant increase of COX-2 expression was observed in those patients with Aspirin-Induced Asthma (AIA). It was observed that IL-1b significantly stimulates the pro- duction of PGE2 prostaglandin in fibroblasts from the control of mucosa, but there was no significant effect on fibroblasts obtained from the mucosa of patients with AIA. The stimulation of IL-1b activated the increased expression of COX-1 and COX-2 in fibroblasts obtained from the control (of nasal mucosa from patients without AIA), but not in fibroblasts from the mucosa of patients with AIA. Discussion Moreover, in the polyp tissue, the COX-2 expression level was significantly lower than in the mucosa with ChRS with Ps. A relation- ship between the decreased COX-2 expression level and oversensitivity to ASA and NSAIDs in the polyp tissue and mucosa with ChRS with Ps was observed. They were studied to assess the significance of fibro- blasts in the formation of polyps in the course of chronic rhinosinusitis and the role of IL-4 in the activation of fibroblasts. It was observed that IL-4 influences the regu- lation of leukotriene receptor expression, and the prolifer- ation of fibroblasts and their secretion of proinflammatory cytokines participating in the formation of polyps. The next studied gene is PERIOSTIN (POSTN), whose excessive expression has recently been shown in other types of tissues, including cerebral tissue, sperm or T lymphocytes, and myocardium, taking part in the remod- elling following a myocardial infarction. 1. An increased level of POSTN, IL-4 gene expression and a decreased level of COX-2 gene expression may References 18. Krzeski A, Gromek I (2007) Przewlekłe zapalenie zatok przyn- osowych w zespole nadwra_zliwos´ci na niesteroidowe leki prze- ciwzapalne. Terapia 11:5–13 1. Bachert C, Gevaert P, Van Cauwenberge P (1999) Nasal polyp- osis—a new concept on the formation of polyps. ACI Int 11:130–135 19. Van Zele T, Claeys S, Gevaert P et al (2006) Differentiation of chronic sinus diseases by measurement of inflammatory media- tors. Allergy 61:1280–1289 2. Berger G, Kattan A, Bernheim J et al (2002) Polypoid mucosa with eosinophilia and glandular hyperplasia in chronic rhinosi- nusitis: a histopathological and immunohistochemical study. Laryngoscope 112:738–745 20. Walgama E, Thanasumpun T, Gander R, Batra PS (2013) Com- parison of endoscopically-guided swab vs. aspirate culture tech- niques in post-endoscopic sinus surgery patients: blinded, prospective analysis. Int Forum Allergy Rhinol 27:170–177 3. Bernstein JM (1997) The immunohistopathology and patho- physiology of nasal polyps. The differential diagnosis of nasal polyps. W: Settipane GA, Lund VJ, Berstein JM, Tos M (red) Nasal polyps. Epidemiology, pathogenesis and treatment. OceanSide Publications Inc, Providence, 85–95 21. Roca-Ferrer J, Pujols L, Gartner S et al (2006) Upregulation of COX-1 and COX-2 in nasal polyps in cystic fibrosis. Thorax 61(7):552–563 22. Takayama G, Arima K, Kanaji T et al (2006) Periostin: a novel component of subepithelial fibrosis of bronchial asthma down- stream of Il-4 and Il-13 signals. J Allergy Clin Immunol 118:98–104 4. Tos M, Sasaki Y, Ohnishi M, Larsen P, Drake-Lee AB (1992) Pathogenesis of nasal polyps. Rhinol Suppl 14:181–185 5. Tos M, Larsen PL, Larsen K, Caye-Thomasen P (2010) Patho- genesis and pathophysiology of nasal polyps. W: Onerci TM, Ferguson BJ (red) Nasal polyposis. Springer-Verlag Berlin, 53–64 23. Compalati E, Ridolo E, Passalacqua G et al (2010) The link between allergic rhinitis and asthma: the united airways disease. Expert Rev Clin Immunol 6:413–423 6. Larsen PL, Tos M (1991) Origin of nasal polyps. Laryngoscope 101(3):305–312 24. Pawankar R, Nonaka M (2007) Inflammatory mechanisms and remodeling in chronic rhinosinusitis and nasal polyps. Curr Allergy Asthma Reports 7:202–208 7. Bernstein JM, Kansal R (2005) Superantigen hypothesis for the early development of chronic hyperplastic rhinosinusitis with massive nasal polyposis. Curr Opin Otolaryngol Head Neck Surg 13:39–44 25. Jia G, Erickson RW, Choy DF et al (2012) Asthma and lower airways disease: periostin is a systemic biomarker of eosinophilic airway inflammation in asthmatic patients. J Allergy Clin Immunol 130(3):647–654 8. Conclusions Takayama et al. [22] showed that PERIOSTIN secreted by pulmonary fibroblasts in response to IL-4 and IL-13 is a new component of the subepithelial fibrosis in asthma. Many authors [23, 24] believe that chronic rhinosinusitis 1. An increased level of POSTN, IL-4 gene expression and a decreased level of COX-2 gene expression may 3 12 3 3720 Eur Arch Otorhinolaryngol (2015) 272:3715–3720 be related to the development of chronic rhinosinusitis with nasal polyps. 12. Arcimowicz M, Balcerzak J, Samolin´ski BK (2005) Polipy nosa—niejednorodna patologia. Pol Merkur Lek 19(111):276–279 be related to the development of chronic rhinosinusitis with nasal polyps. 2. An analysis of the expression level indicates the participation of POSTN and IL-4 in the development of chronic rhinosinusitis with nasal polyps in patients with atopy. 13. Arcimowicz M, Balcerzak J (2007) Wspo´łczesne spojrzenie na polipy nosa. Terapia 11:14–23 14. Bernstein JM (2005) Update of the molecular biology of nasal polyposis. Otolaryngol Clin N Am 38:1243–1255 15. Pawliczak R, Lewandowska-Polak A, Kowalski ML (2005) Pathogenesis of nasal polyps: an update. Curr Allergy Asthma Rep 5:463–471 Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, dis- tribution, and reproduction in any medium, provided the original author(s) and the source are credited. 16. Forer B, Kivity S, Sade J, Landsberg R (2011) Aspirin desensi- tization for ASA triad patients––prospective study of the rhi- nologist’s perspective. Rhinology 49(1):95–99 17. Kiefer JR, Pawlitz JL, Moreland KT, Stegeman RA et al (2000) Structural insights into the stereochemistry of the cyclooxygenase reaction. Nature 405:97–101 References Barnes KC (2006) Genetic epidemiology of health disparities in allergy and clinical immunology. J Allergy Clin Immunol 117(2):243–254 26. Norris RA, Damon B, Mironov V et al (2007) Periostin regulates collagen fibrillogenesis and the biomechanical properties of connective tissues. J Cell Biochem 101:695–711 9. Benninger MS, Ferguson BJ, Hadley JA et al (2003) Adult chronic rhinosinusitis definitions, diagnosis, epidemiology, and pathophysiology. Otolaryngol Head Neck Surg 129(Suppl 3):1–32 27. Nishioka GJ, Cook PR, Davis WE, McKinsey JP (1994) Immu- notherapy in patients undergoing functional endoscopic sinus surgery. Otolaryngol Head Neck Surg 110(4):406–412 10. Meltzer EO, Hamilos DL, Hadley JA et al (2004) Rhinosinusitis: establishing definitions for clinical research and patient care. Otolaryngol Head Neck Surg 131:1–62 28. Ishida A, Ohta N, Suzuki Y et al (2012) Expression of pendrin and periostin in allergic rhinitis and chronic rhinosinusitis. Al- lergol Int 61(4):589–595 y g g 11. Pietruszewska W, Kuna P (2011) Leczenie przewlekłego za- palenia zatok u chorych ze wspo´łistnieja˛ca˛ choroba˛ alergiczna˛. Terapia 9(2):77–84 29. Pietruszewska W, Olejniczak I, Jo´zefowicz-Korczyn´ska M, Gryczyn´ski M (2006) Badania nad etiopatogeneza˛ polipo´w nosa. Otolaryng Pol 60(4):551–556 12 123
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Immune Repertoire Profiling Reveals that Clonally Expanded B and T Cells Infiltrating Diseased Human Kidneys Can Also Be Tracked in Blood
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RESEARCH ARTICLE OPEN ACCESS Citation: Weinberger J, Jimenez-Heredia R, Schaller S, Suessner S, Sunzenauer J, Reindl-Schwaighofer R, et al. (2015) Immune Repertoire Profiling Reveals that Clonally Expanded B and T Cells Infiltrating Diseased Human Kidneys Can Also Be Tracked in Blood. PLoS ONE 10(11): e0143125. doi:10.1371/ journal.pone.0143125 Immune Repertoire Profiling Reveals that Clonally Expanded B and T Cells Infiltrating Diseased Human Kidneys Can Also Be Tracked in Blood Johannes Weinberger1,2☯, Raul Jimenez-Heredia1,2☯, Susanne Schaller3, Susanne Suessner1,2, Judith Sunzenauer4,5, Roman Reindl-Schwaighofer4,5, Richard Weiss6, Stephan Winkler3, Christian Gabriel1,2, Martin Danzer1,2*, Rainer Oberbauer4,5* 1 Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria, 2 Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria, 3 Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria, 4 Department of Internal Medicine III, KH Elisabethinen, Linz, Austria, 5 Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria, 6 Department of Molecular Biology, University of Salzburg, Salzburg, Austria ☯These authors contributed equally to this work. * martin.danzer@o.roteskreuz.at (MD); rainer.oberbauer@meduniwien.ac.at (RO) ☯These authors contributed equally to this work. * martin.danzer@o.roteskreuz.at (MD); rainer.oberbauer@meduniwien.ac.at (RO) Abstract Recent advances in high-throughput sequencing allow for the competitive analysis of the human B and T cell immune repertoire. In this study we compared Immunoglobulin and T cell receptor repertoires of lymphocytes found in kidney and blood samples of 10 patients with various renal diseases based on next-generation sequencing data. We used Biomed-2 primer panels and ImmunExplorer software to sequence, analyze and compare comple- mentarity determining regions and V-(D)-J elements. While generally an individual’s renal receptor repertoire is different from the repertoire present in blood, 94% (30/32) of the lym- phocytes with clonal expansion in kidney can also be traced in blood however, not all of these clonotypes are equally abundant. Summarizing the data of all analyzed patients, 68% of highly expanded T cell clonotypes and 30% of the highly expanded B cell clonotypes that have infiltrated the kidney can be found amongst the five most abundant clonotypes in blood. In addition, complementarity determining region 3 sequences of the immunoglobulin heavy chains are on average more diverse than T cell receptor beta chains. Immune reper- toire analysis of tissue infiltrating B and T cells adds new approaches to the assessment of adaptive immune response in kidney diseases. Our data suggest that expanded clonotypes in the tissues might be traceable in blood samples in the course of treatment or the natural history of the disease. Introduction Competing Interests: The authors have declared that no competing interests exist. The adaptive immune system shields the human body from a large variety of potential patho- gens. This protection is mediated by B and T lymphocytes and their receptors that bind patho- gen derived antigens as well as major histocompatibility complex (MHC) bound peptides. The adaptive immune system shields the human body from a large variety of potential patho- gens. This protection is mediated by B and T lymphocytes and their receptors that bind patho- gen derived antigens as well as major histocompatibility complex (MHC) bound peptides. During the development of B and T cells, the variable antigen receptor gene segments are rear- ranged through targeted DNA recombination events. Additional sequence complexity is intro- duced by the addition or removal of nucleotides at the junctions of these segments. Especially the gene sequences in complementarity determining regions (CDR), notably CDR3, contribute most to Immunoglobulin (IG) and T cell receptor (TR) diversity [1, 2]. Apart from receptor specificity, B and T cells can differentiate into several cell subtypes cov- ering a wide range of different tasks. Besides their potential to differentiate into antibody secreting plasma cells, B cells can function as antigen-presenting or immune-regulatory cells [3]. They are also involved in the formation of local lymphoid tissue [4]. T helper cells (CD4+) conduct the immunological response via cytokine release and cytotoxic T cells (CD8+) directly attack cells presenting foreign antigens via MHC-I.[5, 6] According to the clonal theory of adaptive immunity, antigen recognition through specific B or T cell receptors results in the clonal expansion of all antigen specific lymphocyte subtypes thereby explaining the highly dynamic nature of B and T cell diversity. In recent years, next-generation sequencing has become part of the study of the immune repertoire. The technology enables in-depth analysis of rearranged IG and TR loci that is incomparable with regards to sensitivity. The rearranged V-(D)-J regions are short enough (around 500bp, including CDR 1, 2 and 3) to be a perfect target for high-throughput sequenc- ing methods.[7–9] The technology was recently applied to several studies that contributed greatly to extend the community’s knowledge of the nature of IG and TR clonality and diversity [10]. Heather Morris and her group, for example, recently published a study which revealed that donor-reactive T cells are reduced in tolerant kidney transplant patients, while this is not the case in non-tolerant patients [11]. Immune Repertoire in Kidney Diseases Editor: Grant Lythe, University of Leeds, UNITED KINGDOM Editor: Grant Lythe, University of Leeds, UNITED KINGDOM Accepted: October 30, 2015 Published: November 23, 2015 Published: November 23, 2015 Copyright: © 2015 Weinberger et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits Copyright: © 2015 Weinberger et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: The authors confirm that all data underlying the findings are fully available without restriction. The raw sequencing data have been uploaded to Zenodo (10.5281/zenodo.27483). Funding: This work was supported by Austrian Science Funds P25726 (https://www.fwf.ac.at/en/) and European Regional Development Funds DAABAA_00720 (http://ec.europa.eu/regional_policy/ en/funding/erdf/). 1 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Introduction As there is high prevalence of B and T cell expansion and due to the fact that diversity plays an important role after organ transplantation, a number of studies have been conducted to investigate lymphocyte repertoires related to kidney diseases. Referring to most important findings of recent studies it can be assumed that lymphocytes that are infiltrating the site of inflammation, undergo local clonal expansion and have a major impact on disease progression [4, 12–14]. The clearly shown connection of organ health and B and T cell diversity and clonality is a tremendous encouragement for the use of this technology as a potential biomarker. Combining comprehensive FACS sorting with IG and TR repertoire sequencing could even allow us to determine the cell subtype of specific highly expanded B or T cells and open doors for personal- ized treatment. However, one has to deal with a practical issue for this analysis as it would require a tissue sample for every assay. By comparing the lymphocyte repertoire in blood and kidney samples, we evaluated if an analysis of blood derived immune repertoire reflects tissue specific immuno- logical activity in renal disease including kidney transplantation. For an initial proof of concept, we analyzed the lymphocyte repertoire in large pieces of kidney tissue following nephrectomy to reduce sampling bias in small volume needle biopsies. Contrasting most studies in the field we decided not to focus on B or T cells but to analyze both cell types simultaneously instead. We believe that scientific output can be significantly increased by combining B and T cell data due to the mutual dependency of B and T cells in immunological responses. 2 / 20 Immune Repertoire in Kidney Diseases Immunomagnetic Isolation MNCs derived from one patient with acute allograft rejection (patient 10) were sequentially sorted using EasySep™(Stemcell Technologies, Vancouver, Canada) in different subpopula- tions: CD4+, CD8+ and a combination of CD19+, CD20+ and CD138+, according to manufac- turer’s instructions. Flow cytometry For flow cytometry (FCM) analyses, 50μl of twice-washed cells from MNC fractions (starting material blood or kidney tissue samples) were stained for 20 minutes with 5μl of each antibody followed by 3μl of conjugated antibodies at room temperature using concentrations recom- mended by the suppliers (BD Biosciences, BD Pharmingen and eBioscience). For the gating strategy and a detailed list of antibodies used see S2 Table and S1–S3 Figs. Paired two-tailed t- tests were performed to compare different cell types and compartment (blood vs. kidney) val- ues with a level of significance of 0.05. Sample processing Surgical wedge biopsies (size approx. 1x1x2cm), 9ml EDTA-blood and 40 ml of urine were obtained from every patient. We incised the tissues with a scalpel and rinsed them in PBS with a sterile syringe and needle. The resulting cell suspension was filtered with a 40μm nylon cell strainer (BD Biosciences, Franklin Lakes, NJ). Mononuclear cells (MNCs) were isolated from the tissue cell suspension and from the EDTA-blood by Ficoll density gradient (GE Healthcare, Little Chalfond, U.K.) according to manufacturer’s protocol. IG and TR amplification from urine samples with standard protocols were unsuccessful. Materials and Methods Patient cohort The study population consisted of 10 patients who underwent nephrectomy at the Elisabethi- nen Hospital (Linz, Austria) (age range 24 to 81 years). Basic characteristics and individual dis- eases are shown in S1 Table. Informed written consent was obtained from all participating patients according to the Declaration of Helsinki. Ethical approval for the sample collection with the number E-9-12 was obtained from the Ethical Committee of Upper Austria on 2013- 01-21. PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Sequencing: From DNA extraction to MiSEQ sequencing Genomic DNA was extracted from MNCs using MagNAPure Compact (Roche Diagnostics, Basel, Switzerland) according to the supplier’s instructions. First amplification of rearranged V-(D)-J elements was performed in a final volume of 100μl as follows: 95°C for 10 min, 35 cycles of 95°C for 30 s, 58°C for 45 s and 72°C for 45 s, and 72°C for 10 min. The PCR mixture contained 5U of AmpliTaq Gold polymerase (Applied Biosystems, Foster City, CA), 0.2 mM of each dNTP, 1x Buffer II (Applied Biosystems, Foster City, CA), 3.25 mM and 1.25 mM of MgCl2 for T and B cells, respectively, and equimolar pooled primers based on Biomed-2 primer panels (see S1 File) (Metabion, Planegg, Germany).[15] Template input concentration is dependent on the B/T cell ratio of DNA extracted from MNCs and therefore varied in between samples (up to 0.8μg of DNA for IGH respectively up to 1μg of DNA for TRB). A second amplification (adaptor ligation step) was performed to integrate the indices and the P5 and P7 tails for Illumina sequencing using the Nextera DNA library preparation kit (Illumina, San Diego, CA). Final volume of the 2nd PCR was 50μl and amplification conditions PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 3 / 20 Immune Repertoire in Kidney Diseases were as follows: 95°C for 10 min, 10 cycles of 95°C for 15 s, 63°C for 30 s and 72°C for 30 s, and 72°C for 5 min. The PCR mixture contained 2.5U of AmpliTaq Gold polymerase, 0.2mM of each dNTP, 1x Buffer II, 2mM of MgCl2, 5μl of the first PCR product, and 5μl of each index primer as recommended by Illumina. Final PCR products were purified using Agencourt AMPureXP beads (Beckman Coulter, Brea, CA) in a 1 to 0.95 DNA per bead ratio. The purified amplicons were analyzed by Agilent DNA 1000 (Agilent Technologies, Santa Clara, CA) and normalized using Kapa Library Quantification (KapaBiosystems, Wilmington, MA) as described in the manufacturer’s instructions. Samples were pooled with TE buffer in a final pool concentration of 4nM and diluted to a final concentration of 15pM. The sequencing run was performed in a MiSeq sequencer (Illumina) using the MiSeq Reagent Kit v3 2x300 cycles (Illumina).[7, 9] Due to the fact that next-generation sequencing is a very sensitive technique it is important to take provisional steps against contamination. Sample preparations for kidney and blood samples were done independently. Data analysis Illumina Miseq output files (paired-end fastq files without Nextera adaptors) were imported into the CLC Genomics Workbench (CLC Bio, version 7, Aarhus, Denmark). Base calls with low quality were trimmed and overlapping paired-end sequences were merged using the NGS core tools of CLC Bio. The forward and reverse reads proofed to be highly overlapping in all 5 primer sets (~200bp for IGH Primer Set 1, ~250 Primer Set 2, a full overlap for Primer Set 3 and ~250bp for TRB Primer Set 1 and 2) minimizing the chance of inaccurate merging. Fasta files were exported from CLC software and uploaded to the HighV-QUEST program at the IMGT webpage (http://www.imgt.org/HighV-QUEST) for the analysis of rearranged immuno- globulin and T cell receptor sequences and so as to assign specific V-(D)-J elements to the sequences [16]. IMEX [17] was used to analyze V-(D)-J usage and sequence functionality, to visualize and summarize the number of productive, unproductive and unknown sequences as well as to study clonality through CDR3 sequences and/or V-(D)-J combination. B and T cells and clones of individual B and T cells (clonotypes) are defined due to their unique CDR3 sequence on nucleotide level. In order to increase readability the nucleotide sequence of the CDR3s was translated to amino acid sequences. It is important to note that clonotypes can also be defined according to other sequence based information, i.e. according to the entire receptor sequence or the V-(D)-J element combination. Sequencing: From DNA extraction to MiSEQ sequencing We also used double indexing for every sample with an index combination that always differed for blood and kidney of the same patient. In addition, we regularly performed wipe tests to confirm DNA free conditions. PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Definition of expansion As characterization of all analyzed clonotypes would go beyond the scope of this essay we were forced to set limitations which define clonotypes as expanded or as normally abundant. We derived cut off values to define clonal expansion based on data derived from four blood sam- ples of healthy individuals. We took five times the average of the clonotypes with the highest abundance (top clonotypes) based on data from the healthy control group. We also addressed the issue of increasing uncertainty at decreasing percent values. This uncertainty is strongly related to the amount of DNA/cell input into PCRs, so low DNA input results in loss of preci- sion for measuring low percent values. Related to our cell input range we defined 1% as the lower limit. We applied these thresholds for both the kidney and blood compartment due to the fact that we had no access to healthy renal tissue. The minimum abundances for clonotypes to be marked as expanded were defined as follows: 5.46% for amplification with IGH Primer 4 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Immune Repertoire in Kidney Diseases Set 1, 1.15% for IGH Primer Set 2, 1% for IGH Primer Set 3, 6.82% for TRB Primer Set 1and 10.73% for TRB Primer Set 2 (see S3 Table). The selected B cell clonotypes shown in the manu- script have been collapsed, choosing always those with the highest percentage among all three IGH primer sets (see S4 Table). Regarding T cells, all expanded clonotypes were selected, since the information given by the two TRB primer sets should be considered additive, not redun- dant [15]. Set 1, 1.15% for IGH Primer Set 2, 1% for IGH Primer Set 3, 6.82% for TRB Primer Set 1and 10.73% for TRB Primer Set 2 (see S3 Table). The selected B cell clonotypes shown in the manu- script have been collapsed, choosing always those with the highest percentage among all three IGH primer sets (see S4 Table). Regarding T cells, all expanded clonotypes were selected, since the information given by the two TRB primer sets should be considered additive, not redun- dant [15]. Diversity calculation In order to calculate the diversity we used a specific workflow that comprises several consecu- tive steps. First we calculated the number of unique clonotypes per sample (a) as previously described by our group [17] and then we used these (a) values for the calculation of the inverse Simpson’s diversity index, defining R as total number of reads of all unique clonotypes and ri as the number of reads of each unique clonotype. The inverse Simpson’s diversity index was calculated in the following: DS ¼ 1= Xa i¼1riðri  1Þ RðR  1Þ DS ¼ 1= Xa i¼1riðri  1Þ RðR  1Þ The algorithm to calculate the (a) value allows a mathematical estimation for each individ- ual sample concerning the number of reads that include sequencing errors in the CDR3 region. If the raw data included 1000 different CDR3 sequences (clonotypes) and the mathematical model estimated 200 reads to be artificial clonotypes created by sequencing errors, we reduced the number of clonotypes found in a sample down to 800. The values “R” and “r" for the for- mula are, therefore, affected by this error correction, as the 200 clonotypes with the lowest read amounts are discarded. It is important to note that we do not define specific reads as erroneous; we rather define a number of erroneous reads per raw reads of an individual sample and dis- card a number of reads based on this information. Paired two-tailed t-tests were used to compare the unique number of clonotypes of B vs. T cells with a level of significance of 0.05. Independent two-tailed t-tests were performed to com- pare Simpson’s index values with a level of significance of 0.05. In addition, we performed sta- tistical tests to confirm that our diversity values were not biased by varying numbers of reads of the individual samples (S4 Fig). Similarity calculation Similarities between blood and kidney compartments were calculated with Morisita-Horn (MH) similarity index, comparing all unique numbers of clonotypes (explanation given above) of one compartment with the repertoire of the other for each individual sample. MH was calcu- lated in the following: CMH ¼ 2 Xn i¼1xijxik Xn i¼1x2 ij=N2 j   þ Xn i¼1x2 ik=N2 k     NjNk xij and xik are the numbers of reads of a specific clonotype i in samples j (blood) and k (kidney), Nj (Sn i¼1xij) is the total number of reads in sample j; and Nk (Sn i¼1xik) is the total number of reads in sample k. Independent two-tailed t-tests were performed to compare MH index values with a level of significance of 0.05. xij and xik are the numbers of reads of a specific clonotype i in samples j (blood) and k (kidney), Nj (Sn i¼1xij) is the total number of reads in sample j; and Nk (Sn i¼1xik) is the total number of reads in sample k. Independent two-tailed t-tests were performed to compare MH index values with a level of significance of 0.05. 5 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Immune Repertoire in Kidney Diseases Results After isolating B and T lymphocytes from renal tissue samples and peripheral blood, we applied high-throughput sequencing on the rearranged V-(D)-J regions to assess IG and TR clonality and diversity of the B and T cell repertoire in both compartments. The study com- prised blood and tissue samples from 10 patients that were nephrectomized for various medical reasons (S1 Table). Within all patients, we identified a total of 613 036 different clonotypes in blood samples (252 443 B cell clonotypes and 360 593 T cell clonotypes) as well as 261 280 dis- tinct clonotypes in the tissue samples (154 670 and 106 610 for B and T cell clonotypes, respec- tively). Detailed information on each individual measurement can be found in S5 Table. In order to assess similarity of the B and T cell repertoire between both compartments, we calculated the Morisita-Horn (MH) similarity index (Fig 1A). Contrasting the presence/ absence similarity coefficients (e.g. Jaccard or Sorensen), MH also considers the relative fre- quencies of the compared clonotypes between samples. Overall, the results show a significantly Fig 1. Comparison of Morisita-Horn (MH) similarity index. (A) Comparison of all B and T cell clonotypes after sequencing error correction between compartments in both directions, comparing the clonotypes from the kidney found also in the blood, and those from the blood found also in the kidney. The numbers of clonotypes per compartment that have been included in the analysis are defined by the a values calculated as described in the section diversity calculation (a values from every dataset are listed in S5 Table). In the M-H formula the “n” corresponds to the a value. (B) Comparison of high abundant clonotypes between compartments and comparison of low abundant clonotypes between compartments. High abundant clonotypes are defined as the top 20 and low abundant clonotypes are defined as those in positions from 21 to 1 000. The repertoire comparison was also performed in both directions, from blood to kidney and vice versa. MH can range from 0 (no similarity) to 1 (absolute similarity). Error bars represent the standard deviation between samples of the same group. doi:10 1371/journal pone 0143125 g001 Fig 1. Comparison of Morisita-Horn (MH) similarity index. Results (A) Comparison of all B and T cell clonotypes after sequencing error correction between compartments in both directions, comparing the clonotypes from the kidney found also in the blood, and those from the blood found also in the kidney. The numbers of clonotypes per compartment that have been included in the analysis are defined by the a values calculated as described in the section diversity calculation (a values from every dataset are listed in S5 Table). In the M-H formula the “n” corresponds to the a value. (B) Comparison of high abundant clonotypes between compartments and comparison of low abundant clonotypes between compartments. High abundant clonotypes are defined as the top 20 and low abundant clonotypes are defined as those in positions from 21 to 1 000 The repertoire comparison was also performed in both directions from Fig 1. Comparison of Morisita-Horn (MH) similarity index. (A) Comparison of all B and T cell clonotypes after sequencing error correction between compartments in both directions, comparing the clonotypes from the kidney found also in the blood, and those from the blood found also in the kidney. The numbers of clonotypes per compartment that have been included in the analysis are defined by the a values calculated as described in the section diversity calculation (a values from every dataset are listed in S5 Table). In the M-H formula the “n” corresponds to the a value. (B) Comparison of high abundant clonotypes between compartments and comparison of low abundant clonotypes between compartments. High abundant clonotypes are defined as the top 20 and low abundant clonotypes are defined as those in positions from 21 to 1 000. The repertoire comparison was also performed in both directions, from blood to kidney and vice versa. MH can range from 0 (no similarity) to 1 (absolute similarity). Error bars represent the standard deviation between samples of the same group. doi:10.1371/journal.pone.0143125.g001 6 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Immune Repertoire in Kidney Diseases lower similarity of B cells compared to T cells in both compartments (p<0.05). In depth analy- sis of the repertoires showed that high abundant clonotypes (top 20) correlate better within compartments compared to low abundant clonotypes (clonotypes from position 21 to 1 000) (Fig 1B). CDR3-based comparisons in both directions differed significantly between high and low abundant clonotypes for B cells (p<0.01) and T cells (p<0.01). Expanded B and T cell clonotypes in kidney and blood compartment In kidney tissue samples expanded B and T cell clonotypes were found in 8 of 10 patients. Overall, we identified 32 expanded clonotypes in kidney samples (12 T cell clonotypes and 20 B cell clonotypes). In blood samples, expanded clonotypes were found in 6 of 10 patients. We identified a total of 12 expanded clonotypes in blood samples (6 B cell clonotypes and 6 T cell clonotypes). For detailed information on all expanded clonotypes see Table 1 and S4 Table. According to our data clonal expansion of B and T cells is linked. In 8 out of 9 patients (patient 6 was excluded from this analysis because B cell data was discarded) clonal expansion appeared either in both cell types or in none. All, except two clonotypes that were expanded in the kidney (93.8%) were also found in the blood samples (12 of 12 T cell clonotypes and 18 of 20 B cell clonotypes). However, not all of these clonotypes showed equally high abundance in systemic circulation. Only 6 T cell clonotypes and 6 B cell clonotypes fulfilled the defined crite- ria for clonal expansion in the blood samples. Similarly, all expanded clonotypes in the blood could also be traced in the kidneys. Overall, 3 B cell clonotypes and 3 T cell clonotypes that were expanded in the blood also showed clonal expansion in the kidney. Results The average of MH similar- ity for clonotypes in blood found in kidney was 0.41 (SD = 0.23) for B cells and 0.56 (SD = 0.15) for T cells in the top 20 clonotypes, while for low abundant clonotypes the average similarity was 0.03 (SD = 0.02) for B cells and 0.11 (SD = 0.09) for T cells. The average of MH similarity for clonotypes in kidney found in blood was 0.46 (SD = 0.31) for B cells and 0.76 (SD = 0.28) for T cells in the top 20 clonotypes, while for low abundant clonotypes the average similarity was 0.05 (SD = 0.05) for B cells and 0.23 (SD = 0.11) for T cells. Individual values for MH similarities are provided in S6 Table. PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 CDR3 sequences, V-(D)-J elements and functionality of highly expanded clonotypes in kidney and blood of all patients. ID Indication Cell Type Primer set CDR3 VDJ Functionality % Kidney % Blood Top 5 in Blood Patient 1 Tumor B cells VH-FR2+JH ARGGGSGSSEVSPGEFDP IGHV4-34/IGHJ5/IGHD3-10 P 12,72% 7,28% ✔ VH-FR1+JH ARDLGYCSSTSCYCSGGSC*F IGHV3-30/IGHJ4/IGHD2-2 UP 10,04% 4,85% ✔ VH-FR3+JH TFVRLEFKLWQTGGRRRTGRNPSAKSSPRRGSGNAWPGQTVL*L IGHV4-39/IGHJ4/IGHD1/ OR15-1a UP 7,49% 0,15% ✖ VH-FR3+JH ATSTVTTSAEYFQH IGHV3-11/IGHJ1/IGHD4-17 P 2,62% 7,01% ✔ VH-FR3+JH ARGLLGGDYGY IGHV4-34/IGHJ4/IGHD4-17 P 2,42% 0,47% ✔ VH-FR3+JH VRVQV**KCLPP IGHV4-34/IGHJ4/IGHD6-25 UP 1,35% 0,05% ✖ T cells Vß+Jß Set2 ASSYPGMGPQF TRBV6-2/TRBJ2-1/TRBD1 P 14,38% 28,95% ✔ Vß+Jß Set2 ASKVGLADSYNEQF TRBV6-5/TRBJ2-1/TRBD2 P 11,36% 0,06% ✖ Vß+Jß Set1 ASEGQDNSPLH TRBV6-1/TRBJ1-6/TRBD1 P 6,02% 13,34% - Patient 2 Tumor B cells VH-FR3+JH ARGKSSYGMDV IGHV3-11/IGHJ6/IGHD6-19 P 1,05% n.d. ✖ VH-FR3+JH ARARQQLNA IGHV4-30-2/IGHJ5/IGHD6- 13 P 0,42% 1,39% - T cells Vß+Jß Set1 ASSYSIFGSQPQH TRBV6-5/TRBJ1-5/TRBD2 P 28,04% 22,06% ✔ Vß+Jß Set1 ASMGGWLH TRBV6-5/TRBJ1-2/TRBD2 UP 7,23% 6,62% ✔ Patient 3 Tumor B cells VH-FR3+JH ARLVDYGDYIDY IGHV4-30-2/IGHJ4/IGHD4- 17 P 1,13% <0.01% ✖ T cells No expansion Table 1. CDR3 sequences, V-(D)-J elements and functionality of highly expanded clonotypes in kidney and blood of all patients. ID Indication Cell Type Primer set CDR3 VDJ Functionality % Kidney % Blood Top 5 in Blood Patient 1 Tumor B cells VH-FR2+JH ARGGGSGSSEVSPGEFDP IGHV4-34/IGHJ5/IGHD3-10 P 12,72% 7,28% ✔ VH-FR1+JH ARDLGYCSSTSCYCSGGSC*F IGHV3-30/IGHJ4/IGHD2-2 UP 10,04% 4,85% ✔ VH-FR3+JH TFVRLEFKLWQTGGRRRTGRNPSAKSSPRRGSGNAWPGQTVL*L IGHV4-39/IGHJ4/IGHD1/ OR15-1a UP 7,49% 0,15% ✖ VH-FR3+JH ATSTVTTSAEYFQH IGHV3-11/IGHJ1/IGHD4-17 P 2,62% 7,01% ✔ VH-FR3+JH ARGLLGGDYGY IGHV4-34/IGHJ4/IGHD4-17 P 2,42% 0,47% ✔ VH-FR3+JH VRVQV**KCLPP IGHV4-34/IGHJ4/IGHD6-25 UP 1,35% 0,05% ✖ T cells Vß+Jß Set2 ASSYPGMGPQF TRBV6-2/TRBJ2-1/TRBD1 P 14,38% 28,95% ✔ Vß+Jß Set2 ASKVGLADSYNEQF TRBV6-5/TRBJ2-1/TRBD2 P 11,36% 0,06% ✖ Vß+Jß Set1 ASEGQDNSPLH TRBV6-1/TRBJ1-6/TRBD1 P 6,02% 13,34% - Patient 2 Tumor B cells VH-FR3+JH ARGKSSYGMDV IGHV3-11/IGHJ6/IGHD6-19 P 1,05% n.d. ✖ VH-FR3+JH ARARQQLNA IGHV4-30-2/IGHJ5/IGHD6- 13 P 0,42% 1,39% - T cells Vß+Jß Set1 ASSYSIFGSQPQH TRBV6-5/TRBJ1-5/TRBD2 P 28,04% 22,06% ✔ Vß+Jß Set1 ASMGGWLH TRBV6-5/TRBJ1-2/TRBD2 UP 7,23% 6,62% ✔ Patient 3 Tumor B cells VH-FR3+JH ARLVDYGDYIDY IGHV4-30-2/IGHJ4/IGHD4- 17 P 1,13% <0.01% ✖ T cells No expansion Table 1. CDR3 sequences, V-(D)-J elements and functionality of highly expanded clonotypes in kidney and blood of all patients. Immune Repertoire in Kidney Diseases Table 1. CDR3 sequences, V-(D)-J elements and functionality of highly expanded clonotypes in kidney and blood of all patients. ID Indication Cell Type Primer set CDR3 VDJ Functionality % Kidney % Blood Top 5 in Blood Patient 1 Tumor B cells VH-FR2+JH ARGGGSGSSEVSPGEFDP IGHV4-34/IGHJ5/IGHD3-10 P 12,72% 7,28% ✔ VH-FR1+JH ARDLGYCSSTSCYCSGGSC*F IGHV3-30/IGHJ4/IGHD2-2 UP 10,04% 4,85% ✔ VH-FR3+JH TFVRLEFKLWQTGGRRRTGRNPSAKSSPRRGSGNAWPGQTVL*L IGHV4-39/IGHJ4/IGHD1/ OR15-1a UP 7,49% 0,15% ✖ VH-FR3+JH ATSTVTTSAEYFQH IGHV3-11/IGHJ1/IGHD4-17 P 2,62% 7,01% ✔ VH-FR3+JH ARGLLGGDYGY IGHV4-34/IGHJ4/IGHD4-17 P 2,42% 0,47% ✔ VH-FR3+JH VRVQV**KCLPP IGHV4-34/IGHJ4/IGHD6-25 UP 1,35% 0,05% ✖ T cells Vß+Jß Set2 ASSYPGMGPQF TRBV6-2/TRBJ2-1/TRBD1 P 14,38% 28,95% ✔ Vß+Jß Set2 ASKVGLADSYNEQF TRBV6-5/TRBJ2-1/TRBD2 P 11,36% 0,06% ✖ Vß+Jß Set1 ASEGQDNSPLH TRBV6-1/TRBJ1-6/TRBD1 P 6,02% 13,34% - Patient 2 Tumor B cells VH-FR3+JH ARGKSSYGMDV IGHV3-11/IGHJ6/IGHD6-19 P 1,05% n.d. ✖ VH-FR3+JH ARARQQLNA IGHV4-30-2/IGHJ5/IGHD6- 13 P 0,42% 1,39% - T cells Vß+Jß Set1 ASSYSIFGSQPQH TRBV6-5/TRBJ1-5/TRBD2 P 28,04% 22,06% ✔ Vß+Jß Set1 ASMGGWLH TRBV6-5/TRBJ1-2/TRBD2 UP 7,23% 6,62% ✔ Patient 3 Tumor B cells VH-FR3+JH ARLVDYGDYIDY IGHV4-30-2/IGHJ4/IGHD4- 17 P 1,13% <0.01% ✖ T cells - No expansion - - - - - Patient 4 Tumor B cells - No expansion - - - - - T cells - No expansion - - - - - Patient 5 Contracted B cells - No expansion - - - - - T cells - No expansion - - - - - Patient 6 Contracted B cells - Discarded data - - - - - T cells Vß+Jß Set2 ASSSVAATSTDTQY TRBV27/TRBJ2-3/TRBD2 P 16,69% 9,80% ✔ Vß+Jß Set2 ASSLRGPGQAGNEQF TRBV5-4/TRBJ2-1/TRBD1 P 13,51% 11,21% ✔ Patient 7 Hydronephrotic B cells VH-FR1+JH ASVMGPLLWFGKSQHRYYFDY IGHV4-34/IGHJ4/IGHD3-10 P 35,43% 6,70% ✔ T cells Vß+Jß Set1 ASSPYTTGRKLF TRBV12-3/TRBJ1-4/TRBD1 P 18,62% 4,47% ✔ Vß+Jß Set1 ASSKEYRGAGGYT TRBV6-5/TRBJ1-2/TRBD1 P 14,52% 4,80% ✔ Vß+Jß Set1 ASSPDRGGNQPQH TRBV18/TRBJ1-5/TRBD1 P 9,62% 0,66% ✖ Patient 8 Hydronephrotic B cells VH-FR2+JH ALAVSWSRGGDY IGHV1-69/IGHJ4/IGHD6-6 P 2,39% <0.01% ✖ VH-FR2+JH ARRVSSSAADWFDP IGHV4-30-4/IGHJ5/IGHD6- 13 P 2,12% <0.01% ✖ T cells Vß+Jß Set1 ASGLSVNQPQH TRBV12-5/TRBJ1-5/TRBD2 P 11,11% 1,46% ✔ Patient 9 Hydronephrotic B cells VH-FR3+JH VRERPDGWGNGMDV IGHV3-53/IGHJ6/IGHD3-10 P 0,76% 13,71% - VH-FR2+JH ARGDSTYNWFDP IGHV1-2/IGHJ5/IGHD5-24 P 0,05% 3,98% - VH-FR3+JH ARDFRKRCFDI IGHV3-48/IGHJ3/IGHD4-11 P 1,11% 0,15% ✔ T cells Vß+Jß Set1 AALARGF TRBV19/TRBJ1-1/TRBD2 UP 13,13% 0,01% ✖ Patient 10 Acute rejection B cells VH-FR3+JH ARSPDCGGDCYSGMDV IGHV4-34/IGHJ6/IGHD2-21 P 26,57% 0,01% ✖ VH-FR3+JH ARDIAAAGSWGYYYYYGMDV IGHV3-33/IGHJ6/IGHD6-13 P 20,35% 0,01% ✖ VH-FR3+JH ARGAIRDGYKPNGTSI IGHV4-34/IGHJ2/IGHD5-24 UP 13,40% 0,01% ✖ VH-FR1+JH AETSDTVGVTDAMGWTTGST IGHV1-24/IGHJ5/IGHD2-2 UP 5,70% <0.01% ✖ VH-FR3+JH ATEKWGSFGV IGHV1-24/IGHJ3/IGHD3-16 P 3,61% <0.01% ✖ Table 1. V-(D)-J element distribution of expanded B and T cell clonotypes An analysis of V-(D)-J element distribution of the immunoglobulin heavy chain (IGH) in highly expanded B cell clonotypes reveals a predominance of certain elements: IGHV4-34 (26.1%), IGHD3-10 (17.4%), IGHD4-17 (13.0%), IGHD6-13 (13.0%), IGHJ4 (39.1%) and IGHJ5 (21.7%) (Fig 2a). For T cells the distribution is similar: TRBV6-5 (26.7%), TRBD1 (46.7%), TRBD2 (53.3%), TRBJ2-1 (33.3%) and TRBJ1-5a (20.0%) (Fig 2b). Our data showed predominance of specific elements, irrespective of the underlying disease. Contrasted with our healthy population element distribution (See S5 and S6 Figs), the above mentioned predomi- nant V, D and J elements in highly expanded B cell clonotypes always appear within the top-10 most common elements in healthy individuals. Moreover, all IGHJ elements were found in at least one expanded clonotype. For T cells, TRBV6-5 was found in healthy individuals repre- senting an 8.9% of the complete repertoire, being the highest represented element on the healthy population. TRBJ element frequencies of expanded clonotypes cannot be compared directly with the data obtained from healthy individuals due to the limitations given by the BIOMED-2 primer settings, where different J elements are targeted in different PCR reactions and, therefore, final percentages do not represent the entire repertoire. In order to determine potential predominance of specific V, D and J elements in the course of certain diseases large cohorts of both, healthy and diseased individuals, should be analyzed and compared. In this study the identified expanded clonotypes showed the same element usage as healthy probands PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 7 / 20 Immune Repertoire in Kidney Diseases ID Indication Cell Type Primer set CDR3 VDJ Functionality % Kidney % Blood Top 5 in Blood VH-FR2+JH ARVNGLVRGARGFDY IGHV3-21/IGHJ4/IGHD3-10 P 2,49% <0.01% ✖ VH-FR2+JH **YLLLLC IGHV7-81/IGHJ4/IGHD3-22 UP 1,78% n.d. ✖ VH-FR2+JH FGYYDSSGYYYGEAFDI IGHV3-7/IGHJ3/IGHD3-22 P 1,50% <0.01% ✖ CD8+ - T cells Vß+Jß Set2 ASSWTSGSGNEQF TRBV27/TRBJ2-1/TRBD2 P 35,63% 0.30% ✖ Vß+Jß Set1 ASSTVGDKDNS TRBV11-3/TRBJ2-7/TRBD1 UP 2,02% 9.47% - Vß+Jß Set2 AISDPTLAGGPEQF TRBV10-3/TRBJ2-1/TRBD2 P 1.95% 18.03% - Percent values for expanded clonotypes in kidney and blood samples are highlighted in bold. Expanded clonotypes that could not be detected in the other compartment were marked as not detected, n.d. Clonotypes are also categorized according to primer sets regarding Biomed-2 primer panel [15]. B cell results from patient 6 were discarded due to low amount of DNA input leading to inaccurate clonotype proportions. T cell results from blood sample of patient 10 were sorted in CD4+/CD8- and CD4-/CD8+ subpopulations. The T helper cell subpopulation showed no expansions and is therefore not listed (we found a very low abundance of the expanded clonotype in the kidney in this sample and we assume that these are traces from the CD4-/CD8+ population and therefore this sample was discarded). Functionality of the rearranged chain is marked P for productive and UP for unproductive. ( ) ID Indication Cell Type Primer set CDR3 VDJ Functionality % Kidney % Blood Top 5 in Blood VH-FR2+JH ARVNGLVRGARGFDY IGHV3-21/IGHJ4/IGHD3-10 P 2,49% <0.01% ✖ VH-FR2+JH **YLLLLC IGHV7-81/IGHJ4/IGHD3-22 UP 1,78% n.d. ✖ VH-FR2+JH FGYYDSSGYYYGEAFDI IGHV3-7/IGHJ3/IGHD3-22 P 1,50% <0.01% ✖ CD8+ - T cells Vß+Jß Set2 ASSWTSGSGNEQF TRBV27/TRBJ2-1/TRBD2 P 35,63% 0.30% ✖ Vß+Jß Set1 ASSTVGDKDNS TRBV11-3/TRBJ2-7/TRBD1 UP 2,02% 9.47% - Vß+Jß Set2 AISDPTLAGGPEQF TRBV10-3/TRBJ2-1/TRBD2 P 1.95% 18.03% - Percent values for expanded clonotypes in kidney and blood samples are highlighted in bold. Expanded clonotypes that could not be detected in the other compartment were marked as not detected, n.d. Clonotypes are also categorized according to primer sets regarding Biomed-2 primer panel [15]. B cell results from patient 6 were discarded due to low amount of DNA input leading to inaccurate clonotype proportions. T cell results from blood sample of patient 10 were sorted in CD4+/CD8- and CD4-/CD8+ subpopulations. ID Indication Cell Type Primer set CDR3 VDJ Functionality % Kidney % Blood Top 5 in Blood Patient 1 Tumor B cells VH-FR2+JH ARGGGSGSSEVSPGEFDP IGHV4-34/IGHJ5/IGHD3-10 P 12,72% 7,28% ✔ VH-FR1+JH ARDLGYCSSTSCYCSGGSC*F IGHV3-30/IGHJ4/IGHD2-2 UP 10,04% 4,85% ✔ VH-FR3+JH TFVRLEFKLWQTGGRRRTGRNPSAKSSPRRGSGNAWPGQTVL*L IGHV4-39/IGHJ4/IGHD1/ OR15-1a UP 7,49% 0,15% ✖ VH-FR3+JH ATSTVTTSAEYFQH IGHV3-11/IGHJ1/IGHD4-17 P 2,62% 7,01% ✔ VH-FR3+JH ARGLLGGDYGY IGHV4-34/IGHJ4/IGHD4-17 P 2,42% 0,47% ✔ VH-FR3+JH VRVQV**KCLPP IGHV4-34/IGHJ4/IGHD6-25 UP 1,35% 0,05% ✖ T cells Vß+Jß Set2 ASSYPGMGPQF TRBV6-2/TRBJ2-1/TRBD1 P 14,38% 28,95% ✔ Vß+Jß Set2 ASKVGLADSYNEQF TRBV6-5/TRBJ2-1/TRBD2 P 11,36% 0,06% ✖ Vß+Jß Set1 ASEGQDNSPLH TRBV6-1/TRBJ1-6/TRBD1 P 6,02% 13,34% - Patient 2 Tumor B cells VH-FR3+JH ARGKSSYGMDV IGHV3-11/IGHJ6/IGHD6-19 P 1,05% n.d. ✖ VH-FR3+JH ARARQQLNA IGHV4-30-2/IGHJ5/IGHD6- 13 P 0,42% 1,39% - T cells Vß+Jß Set1 ASSYSIFGSQPQH TRBV6-5/TRBJ1-5/TRBD2 P 28,04% 22,06% ✔ Vß+Jß Set1 ASMGGWLH TRBV6-5/TRBJ1-2/TRBD2 UP 7,23% 6,62% ✔ Patient 3 Tumor B cells VH-FR3+JH ARLVDYGDYIDY IGHV4-30-2/IGHJ4/IGHD4- 17 P 1,13% <0.01% ✖ T cells - No expansion - - - - - Patient 4 Tumor B cells - No expansion - - - - - T cells - No expansion - - - - - Patient 5 Contracted B cells - No expansion - - - - - T cells - No expansion - - - - - Patient 6 Contracted B cells - Discarded data - - - - - T cells Vß+Jß Set2 ASSSVAATSTDTQY TRBV27/TRBJ2-3/TRBD2 P 16,69% 9,80% ✔ Vß+Jß Set2 ASSLRGPGQAGNEQF TRBV5-4/TRBJ2-1/TRBD1 P 13,51% 11,21% ✔ Patient 7 Hydronephrotic B cells VH-FR1+JH ASVMGPLLWFGKSQHRYYFDY IGHV4-34/IGHJ4/IGHD3-10 P 35,43% 6,70% ✔ T cells Vß+Jß Set1 ASSPYTTGRKLF TRBV12-3/TRBJ1-4/TRBD1 P 18,62% 4,47% ✔ Vß+Jß Set1 ASSKEYRGAGGYT TRBV6-5/TRBJ1-2/TRBD1 P 14,52% 4,80% ✔ Vß+Jß Set1 ASSPDRGGNQPQH TRBV18/TRBJ1-5/TRBD1 P 9,62% 0,66% ✖ Patient 8 Hydronephrotic B cells VH-FR2+JH ALAVSWSRGGDY IGHV1-69/IGHJ4/IGHD6-6 P 2,39% <0.01% ✖ VH-FR2+JH ARRVSSSAADWFDP IGHV4-30-4/IGHJ5/IGHD6- 13 P 2,12% <0.01% ✖ T cells Vß+Jß Set1 ASGLSVNQPQH TRBV12-5/TRBJ1-5/TRBD2 P 11,11% 1,46% ✔ Patient 9 Hydronephrotic B cells VH-FR3+JH VRERPDGWGNGMDV IGHV3-53/IGHJ6/IGHD3-10 P 0,76% 13,71% - VH-FR2+JH ARGDSTYNWFDP IGHV1-2/IGHJ5/IGHD5-24 P 0,05% 3,98% - VH-FR3+JH ARDFRKRCFDI IGHV3-48/IGHJ3/IGHD4-11 P 1,11% 0,15% ✔ T cells Vß+Jß Set1 AALARGF TRBV19/TRBJ1-1/TRBD2 UP 13,13% 0,01% ✖ Patient 10 Acute rejection B cells VH-FR3+JH ARSPDCGGDCYSGMDV IGHV4-34/IGHJ6/IGHD2-21 P 26,57% 0,01% ✖ VH-FR3+JH ARDIAAAGSWGYYYYYGMDV IGHV3-33/IGHJ6/IGHD6-13 P 20,35% 0,01% ✖ VH-FR3+JH ARGAIRDGYKPNGTSI IGHV4-34/IGHJ2/IGHD5-24 UP 13,40% 0,01% ✖ VH-FR1+JH AETSDTVGVTDAMGWTTGST IGHV1-24/IGHJ5/IGHD2-2 UP 5,70% <0.01% ✖ VH-FR3+JH ATEKWGSFGV IGHV1-24/IGHJ3/IGHD3-16 P 3,61% <0.01% ✖ (Continued) unctionality of highly expanded clonotypes in kidney and blood of all patients. PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 8 / 20 Immune Repertoire in Kidney Diseases Fig 2. Quantification of element frequency (%) in highly expanded clonotypes. (A) VH, DH and JH element distribution of expanded B cell clonotypes and (B) Vß, Dß and Jß element distribution of expanded T cell clonotypes. We would appreciate the creation of a publicly available database with common V- (D)-J element frequency distribution in human populations to identify potential shifts in the course of diseases as to our knowledge this has not been provided to the community until this date. Fig 2. Quantification of element frequency (%) in highly expanded clonotypes. (A) VH, DH and JH element distribution of expanded B cell clonotypes and (B) Vß, Dß and Jß element distribution of expanded T cell clonotypes. We would appreciate the creation of a publicly available database with common V- (D)-J element frequency distribution in human populations to identify potential shifts in the course of diseases as to our knowledge this has not been provided to the community until this date. doi:10.1371/journal.pone.0143125.g002 which allows us to assume that no disease specific preferential selection of certain elements occurred. Concluding, our data confirms the findings of previous studies that the frequencies of V, D and J element usage in human populations are not equally distributed but rather spe- cific. [18, 19] The T helper cell subpopulation showed no expansions and is therefore not listed (we found a very low abundance of the expanded clonotype in the kidney in this sample and we assume that these are traces from the CD4-/CD8+ population and therefore this sample was discarded). Functionality of the rearranged chain is marked P for productive and UP for unproductive Table 1. (Continued) ID 9 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Immune Repertoire in Kidney Diseases Fig 3. Average percentage of blood and kidney lymphocyte subpopulations in all patients. T cells were separately analyzed for CD4+ and CD8+ subpopulations. NKT cells were gated using CD3+/CD56+ and NK cells, by CD3-/CD56+. Cells presenting CD19+ and/or CD20+ surface markers were categorized as B cells. Significant differences were marked by a connecting line and the corresponding P-value (paired two-sided t-test). Fig 3. Average percentage of blood and kidney lymphocyte subpopulations in all patients. T cells were separately analyzed for CD4+ and CD8+ subpopulations. NKT cells were gated using CD3+/CD56+ and NK cells, by CD3-/CD56+. Cells presenting CD19+ and/or CD20+ surface markers were categorized as B cells. Significant differences were marked by a connecting line and the corresponding P-value (paired two-sided t-test). doi:10.1371/journal.pone.0143125.g003 population in blood and in renal tissue showed significantly lower percentages in the kidney samples (p = 0.002, 48.8% in blood and 31.1% in kidney) (Fig 3). NK and NKT cells were added to the FACS analyses to attain a holistic picture of the lymphocytes subpopulations. In addition recent studies pointed out that the field of kidney transplantation could profit from including NK cells to immune monitoring analyses.[21] Details are shown in S7 Table. Lymphocyte subpopulations in kidney and peripheral blood In the blood compartment, T cells accounted for 74.7% (SD = 10.5) of all lymphocytes, with a significant predominance of CD4+ clones (48.8%, SD = 12.6)) compared to CD8+ (22.2%, SD = 9.4) (p<0.01). The overall B cell proportion of lymphocytes was 11.6% (SD = 5.9) and in Natural killer (NK) cells represented 11.5% (SD = 7.0) in blood, while natural killer T cells (NKT) comprised 5.1% (SD = 4.5). Therefore, the lymphocyte subpopulations are consistent with common values for peripheral blood lymphocyte subpopulations [20]. In kidney samples, the average for T cells was 65.5% (SD = 13.7) (31.7% for CD8+, SD = 18.0, and 31.1% for CD4+, SD = 10.1, with no significant differences; p = 0.94), which is significantly different from the T cells in the blood (p = 0.04). B cell proportions represented a 12.8% (SD = 6.8). NKT cells accounted for 6.6% (SD = 5.2) and NK cells for 16.3% (SD = 12.0). A comparison of CD4+ PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 10 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Diversity B and T cell repertoire diversities of the tested samples were significantly dissimilar. The mean diversity values of all B cells in blood (1/Ds = 5 069.8, SD = 4 633.1) was significantly higher (p = 0.002) than the mean diversity values of T cells in blood (1/Ds = 2 624.7, SD = 2 834.8). B and T cells derived from kidneys showed an even greater difference in diversity with a 6.5-fold higher diversity value for B cells compared to T cells (kidney derived T cells 1/Ds = 441.6, SD = 352.8, kidney derived B cells 1/Ds = 2 876.4, SD = 4 188.2; p = 0.016). Comparing the two compartments, T cell diversity is significantly lower in the kidney than in the blood (p = 0.025) (Fig 4a). Contrasting the latter, healthy volunteers displayed a diversity of 1/Ds = 6 445.4 for blood derived B cells (SD = 3 095.8) and of 1/Ds = 1 628.3 for blood derived T cells (SD = 1 741.0). There were no significant differences between the healthy volunteers’ blood diversity and the patient’s blood diversity in both, B cells (p = 0.32) and T cells (p = 0.65). However, sig- nificant differences between the B cells (p = 0.03) and the T cells (p = 0.048) of the diseased PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 11 / 20 Immune Repertoire in Kidney Diseases Fig 4. Inverse Simpson’s diversity index and cell input. (a) IGH and TRB diversity of the average of all patients and healthy volunteers based on the inverse Simpson’s diversity index. Independent two-sided t test were performed with a level of significance of 0.05. (b) Average cell input of all patients and healthy volunteers for B and T cells. Paired two-sided t test were performed with a level of significance of 0.05. Error bars represent the standard deviation between samples of the same group. Fig 4. Inverse Simpson’s diversity index and cell input. (a) IGH and TRB diversity of the average of all patients and healthy volunteers based on the inverse Simpson’s diversity index. Independent two-sided t test were performed with a level of significance of 0.05. (b) Average cell input of all patients and healthy volunteers for B and T cells. Paired two-sided t test were performed with a level of significance of 0.05. Error bars represent the standard deviation between samples of the same group. doi:10.1371/journal.pone.0143125.g004 Fig 4. Discussion Our next-generation sequencing (NGS) data of IG and TR repertoires from patients with vari- ous kidney diseases confirmed that clonal expansion of renal infiltrating T and B cells is a com- mon phenomenon [4]. Most of these expanded clonotypes can also be traced in peripheral blood samples of these patients, albeit not all of them showed an equally high abundance in both compartments. To a certain degree these findings contradict former studies were it was not possible to find the same clonotypes in blood and kidney [4] or other diseased tissue [22–24]. In addition, our data suggest that clonal expansions of T and B cells are correlating (in 8 out of 9 patients), a fact not described in previous studies. Once locally highly abundant B and T cell clonotypes have been identified, immune repertoire analysis of lymphocytes from periph- eral blood samples may facilitate monitoring disease progression or response to therapy.[25] In the absence of lymphoma, highly expanded B and T cells indicate the presence of a locally expressed antigen that drives proliferation and clonal expansion. The highly expanded clono- types in our samples represented up to 30% of all B and T cells in the respective sample suggest- ing a strong antigenic stimulus for proliferation. Interestingly some of the high abundant clonotypes shown in Table 1 appear to have unproductive IGH or TRB chains which seems impossible at the first glance. There are several explanations for that phenomenon, however. One option is that certain highly expanded B or T cell clonotypes are biallelic clonotypes and are, therefore, carriers of an unsuccessful rearrangement on the first allele, followed by a suc- cessful one at the second [26]. This automatically leads to a parallel abundance of a productive and unproductive chain on gDNA level. Another source for highly abundant unproductive chains can be PCR crossover products [27] or alignment errors from the IMGT database. We also sequenced blood samples from healthy individuals that did not show any signs of clonal expansions in order to have a baseline for definition of expansion. The definition of thresholds allows to condense the amount of clonotypes and to facilitate the tracking of the predominant clonotypes in both compartments. Since there are no previous definitions of expansion in literature [8, 28], we applied 5 times the average of the highest clonotype of differ- ent healthy donors for each independent primer set (S3 Table). Diversity On average, the healthy volun- teers’ cell input was significantly different (141 432 for T cells, SD = 78 651.3, and 60 613 for B PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 12 / 20 Immune Repertoire in Kidney Diseases cells, SD = 33 707.5; p = 0.037). A comparison of cells derived from healthy individuals’ blood with cells derived from patients’ blood and kidney showed significant differences only in the T cell input between healthy individuals’ blood and patients’ blood, although this could be explained as a result of the small healthy cohort (healthy individuals’ blood vs. patients’ blood B cells input p = 0.29; healthy individuals’ blood vs. patients’ kidney B cells input p = 0.20; healthy individuals’ blood vs. patients’ blood T cells input p = 0.02; and healthy individuals’ blood vs. patients’ kidney T cells input p = 0.82). We found higher diversity values for B cells even if our analysis contained significantly more T cells. Diversity Inverse Simpson’s diversity index and cell input. (a) IGH and TRB diversity of the average of all patients and healthy volunteers based on the inverse Simpson’s diversity index. Independent two-sided t test were performed with a level of significance of 0.05. (b) Average cell input of all patients and healthy volunteers for B and T cells. Paired two-sided t test were performed with a level of significance of 0.05. Error bars represent the standard deviation between samples of the same group. doi:10.1371/journal.pone.0143125.g004 renal tissue compared to blood from healthy volunteers could be found. Our results show that, the comparison between B and T cells for all healthy volunteers also showed significant differ- ences (p = 0.001). Further details on diversity calculation are given in S8 Table. In order to confirm whether the differences in the observed diversity values were influenced by the cell input we calculated the average cell input of all patients and healthy volunteers for B and T cells in blood and kidney (S9 Table). Results proof, that, as expected, in blood and kidney T cells were significantly more abundant than B cells (T cells in blood = 287 816, SD = 84 402.3; B cells in blood = 38 081, SD = 21 475, p = 0.00002; T cells in kidney = 153 648, SD = 105 538, B cells in kidney = 35 226, SD = 32 031, p = 0.001). Similarly, T cells showed sig- nificant differences between compartments (p = 0.006) (Fig 4b). On average, the healthy volun- teers’ cell input was significantly different (141 432 for T cells, SD = 78 651.3, and 60 613 for B p y SD = 105 538, B cells in kidney = 35 226, SD = 32 031, p = 0.001). Similarly, T cells showed sig- nificant differences between compartments (p = 0.006) (Fig 4b). On average, the healthy volun- teers’ cell input was significantly different (141 432 for T cells, SD = 78 651.3, and 60 613 for B SD = 105 538, B cells in kidney = 35 226, SD = 32 031, p = 0.001). Similarly, T cells showed sig- nificant differences between compartments (p = 0.006) (Fig 4b). PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Discussion Despite the low sam- ple size, we found some idiosyncrasies in the different patient groups that have to be confirmed in larger cohorts. For tumor and contracted kidneys B and T cell expansions varied and com- piled a heterogeneous picture. The patient group suffering from hydronephrotic kidneys showed high T cell clonality in all kidney samples. We could also find B cell expansions in all three patients including patient 9, who had higher expansions in blood than in kidney samples. In addition to the small sample size, heterogeneity of biopsy areas is also likely to contribute to inconsistencies in the results. Finally, we analyzed data of one patient with the diagnosis of acute renal allograft rejection. The blood derived T cells of this patient were split into cytotoxic T cells and T helper cells for gaining additional information about the specificities of the expanded clonotypes in the kidney. Overall 59.7% of MNCs derived from kidney counted for T cells in this patient, compared to an average of 37.1% in diseased kidneys in general. Also a much higher percentage of cytotoxic T cells (49.5% in the patient compared to 17.9% on average) was found. Based on our criteria we found 3 highly abundant T cell clonotypes in this patient, 2 in the blood and 1 in the kidney. All three clonotypes could be identified as CD8+ T cells. As we did not sort the kidney derived T cells we had to identify the specificity of the kidney derived expanded T cell clonotype indi- rectly by checking the specificity of this clonotype in blood. In this patient we found very low B cell diversity values that are most probably present due to low proportions of B cells in the kid- ney (0.85%). Nevertheless abundance frequencies of high abundant clonotypes are not affected by low cell input next to a potentially higher observational error [33]. However, the three inde- pendent IGH amplifications showed comparable values and therefore proved that the increase of observational error is negligible in this case. (Clonotype frequencies of the three independent IGH amplifications are shown in S4 Table) It should be noted that even though immune repertoire profiling was revolutionized by NGS. Existing restrictions such as sequencing errors (related to the technology) and PCR bias and limitations by sensitivity can only be partly overcome and depend heavily on the used approach [10, 34, 35]. Discussion This was a very conservative definition of expansion so we are confident that a clonotype, that we marked as expanded, is indeed exceeding frequencies which can appear in healthy individuals (S7 Fig). Nevertheless, the definition of thresholds might benefit from large cohorts and less heterogeneous samples. Even so, the definition of natural occurring fluctuations of clonotype frequencies, which fre- quencies can still be considered as healthy and where pathological abundances start is still chal- lenging and must be addressed in future work. A general limitation of immune repertoire profiling is the incapability to define the antigen specificity of an expanded clonotype by analyzing the receptor sequence. Even by the help of state of the art technology it is impossible to confirm that the expansion of tissue infiltrating lymphocytes is caused by the interaction of a kidney disease related antigen with specific IG and TR, as no antigen specificity can be attributed to an individual sequence. However, it 13 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Immune Repertoire in Kidney Diseases seems plausible that clonotypes that are highly expanded in the kidney and have lower abun- dances in the blood derive from clonal expansions stimulated by local antigens. Indeed this was the case for the majority of expanded clonotypes. Nevertheless, we also found 8 expanded clo- notypes with higher relative abundances in blood than in kidney. In this case the possibility that the driving force for clonal expansion might not be related to local antigen stimulus in the kidney cannot be dismissed. [29, 30] By applying Morisita-Horn similarity index on both compartments for high and low abundant clonotypes the data indicates that there is significantly higher similarity in-between compartments for high abundant clonotypes than for low abundant clonotypes. On the one hand this could be explained due to an increase of observational errors in the course of decreasing abundances but on the other hand this could also be a specific phenomenon related to different homing and migration behavior between activated and non- activated cells [31, 32]. Additional investigation using NGS based immune repertoire analysis focusing on homing and migration of expanded B and T cells including B and T cell subgroups could be beneficial to achieve sufficient insights. Patients included in our study were nephrectomized due to four different renal diseases (tumor, contracted kidney, hydronephrosis and acute allograft rejection). PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Discussion For this study we decided to utilize a genomic DNA-based amplification design, combined with high sample input to facilitate estimation of the clonality of a given TRB or IGH sequence by applying a well-established multiplex primer approach [9]. Using genomic DNA in contrast to mRNA as a starting template has the advantage of superior sensitivity [36] including the drawback that recently developed strategies to reduce the multiplex PCR bias are only available for cDNA approaches [34, 37]. As shown in this study, harvesting B and T cells from a large biopsy of the kidney in accordance with a highly sensitive genomic DNA PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 14 / 20 Immune Repertoire in Kidney Diseases amplification enables the detection of expanded clones in tissue. Surprisingly, these clonotypes can be confirmed in peripheral blood. The used set-up is possibly the reason why our data can- not be easily compared to the work already undertaken. Cheng and coworkers [4] demon- strated that expanded clones in the kidney are detectable but they were unable to track these CDR3 sequences in the blood most probably due to a reduced sensitivity based on small cylin- der biopsies or cDNA amplification. Moreover, additional studies using other diseased tissues [22–24] have also failed to provide an orienting contiguity. In recent years several reports focusing on genomic DNA based immune repertoire profil- ing [9, 36, 38, 39] have confirmed the usability of next generation sequencing; however method reproducibility, as shown in S8 Fig, is a fundamental requirement to produce reliable data and should always be examined individually. Moreover, concordance of the three independent IGH amplifications of all predominant B cell clonotypes was tested to provide additional validation of the data (S3 Table). It is particularly challenging to determine diversity values, i.e. the broadness of the immune repertoire as it requires extrapolation from a small sample size to bigger ones, e.g., from a 10ml blood tube to the whole individual.[40, 41] In order to simplify the diversity analysis, we decided to define the diversity only for the sample and not for the patient. Although our analy- sis contained significantly more T cells, we still found higher diversity values for B cells. Taking into account these differences in cell numbers we can assume that the results for diversity are underrepresenting B cell diversity in relation to T cells. Discussion This reflects our expectations as the additional diversification process of somatic hypermutation and affinity maturation is restricted to B cells. Moreover, we could observe higher diversity in the blood than in the kid- ney for T cells as well as for B cells. This was not surprising either, as cells that infiltrate the kid- ney tissue should be only a small fraction of the whole repertoire that specifically interacts with renal tissue related antigens. The human immune system permanently interacts with pathogens, and some pathogens might trigger detectable clonal proliferation even if the person can be considered healthy. Therefore, defining a repertoire as healthy or diseased requires the definition of reliable cut- offs that further require analysis of huge cohorts of healthy volunteers. In summary, with this study we were able to demonstrate that B and T cells that show clonal expansion in kidneys can also be traced in blood. We encourage the community to expand investigations in this field by using less heterogeneous and larger sample sizes as the results are very promising with regard to the application of Immune repertoire profiling in combination with FACS as a potential blood based biomarker. Supporting Information In order to confirm that the number of unique clonotypes (a) of each patient was not biased by the number of reads, we calculated the Pearson’s sample correlation coefficient (r) between reads and unique clonotypes for each independent primer set. The results showed no correla- tion. Also, a paired two-tailed T test comparison between blood and kidney confirmed that sig- nificant differences in unique numbers of clonotypes are independent from read counts. (DOCX) S5 Fig. Vh, Dh and Jh element distribution (%) in healthy individuals. V, D and J gene ele- ments appear at similar frequencies in the four healthy volunteers (see correlation tables). Only Jh element distribution was dissimilar for healthy 1. Vh elements that were not present in any of the healthy volunteers: V7-NL1, V7-77, V7-56, V7-40D, V7-27, V4-80, V4-30-1, V3-79, V3- 76, V3-75, V3-65, V3-60, V3-6, V3-57, V3-50, V3-42D, V3-42, V3-41, V3-37, V3-36, V3-30-5, V1-67, V1-17, V1-14 and V1-12. Dh elements not present: D5-5 and D4-4. Correlation between healthy individuals for V, D and J element distribution was calculated using Pearson’s sample correlation coefficient (r). (DOCX) S5 Fig. Vh, Dh and Jh element distribution (%) in healthy individuals. V, D and J gene ele- ments appear at similar frequencies in the four healthy volunteers (see correlation tables). Only Jh element distribution was dissimilar for healthy 1. Vh elements that were not present in any of the healthy volunteers: V7-NL1, V7-77, V7-56, V7-40D, V7-27, V4-80, V4-30-1, V3-79, V3- 76, V3-75, V3-65, V3-60, V3-6, V3-57, V3-50, V3-42D, V3-42, V3-41, V3-37, V3-36, V3-30-5, V1-67, V1-17, V1-14 and V1-12. Dh elements not present: D5-5 and D4-4. Correlation between healthy individuals for V, D and J element distribution was calculated using Pearson’s sample correlation coefficient (r). (DOCX) S6 Fig. Vβ, Dβ and Jβ element distribution (%) in healthy individuals. V, D and J segments appear at similar frequencies in the four healthy volunteers (see correlation tables). There are no correlation data from Dβ elements because the number of elements is too low (only two). Jβ elements are separated in Vβ-Jβ Set 1 and Vβ-Jβ Set 2 because the BIOMED-2 reverse primers for T cell receptors are additive and therefore it is not possible to sum up frequencies to a single value. Supporting Information S1 Fig. Gating strategy for T cell subpopulations. CD45+CD3+ T cells were gated using Horizon V500-A and PE-A antibodies after standard lymphocyte FSC vs. SSC (or volume vs. internal complexity) sorting. CD8+ and CD4+ were sorted using FITC-A and APC-A, respec- tively. This strategy was used for MNCs derived from blood and kidney. (DOCX) S2 Fig. Gating strategy for analysis of NK and NKT cells. CD45+CD3+ T cells were gated using Horizon V500-A and APC-A antibodies after standard lymphocyte FSC vs. SSC (or vol- ume vs. internal complexity) sorting. CD3-CD56+ (NK) and CD3+CD56+ (NKT) were sorted using PE-A for CD56+ vs. APC-A for CD3+. This strategy was used for MNCs derived from blood and kidney. B cells (CD19+CD3-CD56-) were additionally gated to corroborate the results from the CD3 vs. CD56 comparison. (DOCX) 15 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Immune Repertoire in Kidney Diseases S3 Fig. Gating strategy for the analysis of B cells (CD19+ and/or CD20+). CD45+ lympho- cytes were gated using Horizon V500-A after standard lymphocyte FSC vs. SSC (or volume vs. internal complexity) sorting. CD19+ and CD20+ were sorted using APC-A and FITC-A, respectively. We considered the condition CD19+ and/or CD20+ to count all possible B cells subtypes (CD19+/CD20-, CD19-/CD20+ and CD19+/CD20+). This strategy was used for MNCs derived from blood and kidney. (DOCX) S3 Fig. Gating strategy for the analysis of B cells (CD19+ and/or CD20+). CD45+ lympho- cytes were gated using Horizon V500-A after standard lymphocyte FSC vs. SSC (or volume vs. internal complexity) sorting. CD19+ and CD20+ were sorted using APC-A and FITC-A, respectively. We considered the condition CD19+ and/or CD20+ to count all possible B cells subtypes (CD19+/CD20-, CD19-/CD20+ and CD19+/CD20+). This strategy was used for MNCs derived from blood and kidney. (DOCX) S3 Fig. Gating strategy for the analysis of B cells (CD19+ and/or CD20+). CD45+ lympho- cytes were gated using Horizon V500-A after standard lymphocyte FSC vs. SSC (or volume vs. internal complexity) sorting. CD19+ and CD20+ were sorted using APC-A and FITC-A, respectively. We considered the condition CD19+ and/or CD20+ to count all possible B cells subtypes (CD19+/CD20-, CD19-/CD20+ and CD19+/CD20+). This strategy was used for MNCs derived from blood and kidney. (DOCX) S4 Fig. Effects of read counts on the diversity “a” value (number of unique clonotypes). Supporting Information Small percentages that correspond to primers not present in the primer set can occur due to element assignment error or cross-contamination (J2-1, J2-5, J2-3 and J2-4 for Vβ-Jβ Set 1, and J2-7. J2-2, J1-3, J2-6, J1-1, J1-2, J1-5, J1-4 and J1-6 for Vβ-Jβ Set 2). Vβ elements not present in any of the healthy volunteers: V8-2, V8-1, V7-5, V5-2, V22-1, V17, V1, V23, V21, V16 and V12-2. Correlation between healthy individuals for V, D and J element distribution was calculated using Pearson’s sample correlation coefficient (r). (DOCX) S7 Fig. Top 20 highest expanded clonotypes for blood and kidney in all patients and for blood in healthy individuals. The histograms represent the abundance (in %, Y-axis) of each clonotype (CDR3-based, X-axis) and the red line represents the assigned thresholds for IGH primer sets 1, 2 and 3 and TRB primer sets 1 and 2. (DOCX) PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 S7 Fig. Top 20 highest expanded clonotypes for blood and kidney in all patients and for blood in healthy individuals. The histograms represent the abundance (in %, Y-axis) of each clonotype (CDR3-based, X-axis) and the red line represents the assigned thresholds for IGH primer sets 1, 2 and 3 and TRB primer sets 1 and 2. S8 Fig. Technical replicates. In the experiment design for three replicates with B and T cell expansions, we compared not only if there is a difference between replicates due to PCR or hands-on errors, but also if the sequencing run can bias the reproducibility of the protocol. Pearson’s sample correlation coefficient for each primer set displays high correlation values between replicates in both, B and T cells, with no remarkable differences between sequencing runs. Only T cell primer set 1 correlation shows lower values for replicate 1 compared to PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 16 / 20 Immune Repertoire in Kidney Diseases replicates 2 or 3 due to a specific clone dropout in replicate 1 (ASSWSPGGNTIY). The top 10 highest abundant clonotype comparison for each primer set shows the variability of the same CDR3-based clonotype percentage among replicates. Each clonotype is highlighted in one dif- ferent color for each primer set to compare the concordance in rank position between repli- cates. (DOCX) S1 File. Biomed-2 primer panel. The list of nucleotide sequences is provided for each forward and reverse primer for all IGH and TRB primer sets. Also the concentration for each primer in the first amplification is given. The information includes the target sequence in 5’-3’ and the Nextera adaptor sequence in 5’-3’. S1 Table. Clinical data of patients. The 10 patients included in the study are grouped by age range (using 10-year block groups) and by cause of nephrectomy. The sampled material used for each individual patient is listed for the peripheral blood (ml), kidney tissue (cm x cm) and urine (ml). A histological description of each piece of tissue is also provided. (DOCX) S2 Table. Antibodies used for FACS. The reaction of lymphocyte subpopulations was evalu- ated with monoclonal antibodies (mAb) by 4 to 5 color FCM analysis on a FACSAria III (Bec- ton Dickinson). Three FCM tubes were used for each patient and material (Tube 1: CD8-FITC, CD3-PE, CD4-APC, CD45-HorizonV500; Tube 2: CD19-FITC, CD56-PE, CD3-APC-A, CD45-HorizonV500; and Tube 3: CD20-FITC, CD19-APC-A, CD45-HorizonV500). Data was analyzed using FACSDiva software Version 7.0 (BD Biosciences). (DOCX) S3 Table. Most frequent clonotype from healthy probands. For expansion threshold calcula- tion, we considered the percent values of the most frequent clonotypes in blood of healthy pro- bands for B cell primer sets 1, 2 and 3, and for T cell primer sets 1 and 2. Acknowledgments We would like to thank Susanne Pramendorfer for the improvements on the use of English in the manuscript. S7 Fig. Top 20 highest expanded clonotypes for blood and kidney in all patients and for blood in healthy individuals. The histograms represent the abundance (in %, Y-axis) of each clonotype (CDR3-based, X-axis) and the red line represents the assigned thresholds for IGH primer sets 1, 2 and 3 and TRB primer sets 1 and 2. Frequencies of lymphocyte subpopulations (T cells, cytotoxic T cells, helper T cells, NKT cells, NK cells and B cells) are given for every patient in blood and kidney as well as P-values for pairwise comparisons (paired two-sided t-test). (DOCX) S8 Table. Inverse Simpson’s diversity index. High values represent broader diversity. In order to remove sequencing error derived clonotypes we used the diversity calculation feature of S8 Table. Inverse Simpson’s diversity index. High values represent broader diversity. In order to remove sequencing error derived clonotypes we used the diversity calculation feature of IMEX [17]. Diversity was then calculated for patients’ blood and kidney and for healthy indi- viduals’ blood using the inverse Simpson’s diversity formula described in the material and methods section. (DOCX) S8 Table. Inverse Simpson’s diversity index. High values represent broader diversity. In order to remove sequencing error derived clonotypes we used the diversity calculation feature of IMEX [17]. Diversity was then calculated for patients’ blood and kidney and for healthy indi- viduals’ blood using the inverse Simpson’s diversity formula described in the material and methods section. q g yp y IMEX [17]. Diversity was then calculated for patients’ blood and kidney and for healthy indi- viduals’ blood using the inverse Simpson’s diversity formula described in the material and methods section. S9 Table. Cell input. (1) divided in T cells (CD4+ and CD8+) and B cells. B cells in patient 6 were discarded due to low input. The cell input was calculated using FACS results percentages (2) Cell input of healthy probands using cell proportions from literature (70% T cells and 30% B cells). (3) P-values for comparisons between cell types and compartments using paired two- sided T-test. The calculation was performed using the following formula: Cell input = [X]μg/ mlFACS(1000pg/μg)/(6.6pg/cell)30μl. [X]μg/ml is the O.D. concentration of the extracted DNA from the isolated MNCs. FACS is the percentage of cells from each cell type. 6.6pg/cell is the standard amount of DNA in pg per cell. 30μl is the input volume for 1st PCR amplification. (DOCX) Author Contributions Conceived and designed the experiments: JW RJ CG MD SW RW RO. Performed the experi- ments: JW RJ S. Suessner JS. Analyzed the data: JW RJ MD S. Schaller RR RW SW. Contributed reagents/materials/analysis tools: CG RO. Wrote the paper: JW RJ MD S. Schaller RR SW RO. Critical revision of article for intellectual content: MD RW SW CG RO. S7 Fig. Top 20 highest expanded clonotypes for blood and kidney in all patients and for blood in healthy individuals. The histograms represent the abundance (in %, Y-axis) of each clonotype (CDR3-based, X-axis) and the red line represents the assigned thresholds for IGH primer sets 1, 2 and 3 and TRB primer sets 1 and 2. In order to determine representative thresholds, the averages of all healthy probands’ highest clonotypes were calcu- lated for each B and T cell primer set and the resulting value was multiplied by 5. All values above these thresholds were considered expanded in our study. We considered 1% as the lower limit to feel confident about the value, so for B cell primer set 3 we increased the threshold from 0.69% to 1%. The same values were used for blood and kidney (we had no access to healthy renal tissue). (DOCX) S4 Table. B cell comparison of all primer sets. Comparison of abundance (in %) and rank position of the clonotypes (rank refers to position depending on abundant frequencies) was considered to be expanded in our study for the three B cell primer sets. Collapse of the data for Table 1 was done selecting the highest percentage between primer sets and the same primer set in the other compartment. Expanded clonotypes that could not be detected in the other com- partment or primer set were marked as not detected, n.d. (DOCX) S5 Table. Reads, clonotypes and diversity correction. Individual information is given for all primer sets in blood and kidney on the number of reads, the number of clonotypes from sequencing (CDR3-based), the corrected number of unique clonotypes [17] and the percentage of corrected clonotypes selected from the sequencing output after excluding sequencing errors. 1 stands for CD4+ sorted cells and 2 stands for CD8+ sorted cells. (DOCX) 17 / 20 PLOS ONE | DOI:10.1371/journal.pone.0143125 November 23, 2015 Immune Repertoire in Kidney Diseases S6 Table. Morisita-Horn similarity index calculation. Individual calculations for all patients (min. = 0; max. = 1) for all versus all CDR3-based clonotype comparisons, high abundant clones (top 20) comparison and low abundant clones (from position 21 to 1000) comparison. Patient 10 displays two values on the TR because the blood sample was sorted in CD4+ and CD8+ subpopulations; IG values for patient 6 were discarded due to low DNA concentration. 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Plant functional diversity and nutrient availability can improve restoration of floating fens via facilitation, complementarity and selection effects
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Royal Netherlands Academy of Arts and Sciences (KNAW) Plant functional diversity and nutrient availability can improve restoration of floating fens via facilitation, complementarity and selection effects van Zuidam, Jeroen P.; van Leeuwen, Casper; Bakker, Elisabeth S.; Verhoeven, Jos T.A.; Ijff, Stéphanie; Peeters, Edwin T.H.M.; van Zuidam, Bastiaan G.; Soons, Merel B. Plant functional diversity and nutrient availability can improve restoration of floating fens via facilitation, complementarity and selection effects van Zuidam, Jeroen P.; van Leeuwen, Casper; Bakker, Elisabeth S.; Verhoeven, Jos T.A.; Ijff, Stéphanie; Peeters, Edwin T.H.M.; van Zuidam, Bastiaan G.; Soons, Merel B. published in Journal of Applied Ecology 2019 DOI (link to publisher) 10.1111/1365-2664.13256 document version Publisher's PDF, also known as Version of record document license CC BY Li k bli i i KNAW R h P l published in Journal of Applied Ecology 2019 DOI (link to publisher) 10.1111/1365-2664.13256 document version Publisher's PDF, also known as Version of record document license CC BY Link to publication in KNAW Research Portal Link to publication in KNAW Research Portal citation for published version (APA) van Zuidam, J. P., van Leeuwen, C., Bakker, E. S., Verhoeven, J. T. A., Ijff, S., Peeters, E. T. H. M., van Zuidam, B. G., & Soons, M. B. (2019). Plant functional diversity and nutrient availability can improve restoration of floating fens via facilitation, complementarity and selection effects. Journal of Applied Ecology, 56(1), 235- 245. https://doi.org/10.1111/1365-2664.13256 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. General rights C i ht d ghts for the publications made accessible in the public portal are retained by the authors and/or other copyright owners accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the KNAW public portal for the purpose of pr research s may download and print one copy of any publication from the KNAW public portal for the purpose of private study or search. • You may not further distribute the material or use it for any profit-making activity or commercial gain. • You may freely distribute the URL identifying the publication in the KNAW public portal. You may not further distribute the material or use it for any profit making activity or commercial ga • You may freely distribute the URL identifying the publication in the KNAW public portal. Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. y this document breaches copyright please contact us providing details, and we will remove access to the work immediate ur claim down policy believe that this document breaches copyright please contact us providing details, and we will remove access to the wo vestigate your claim. Jeroen P. van Zuidam1,2* | Casper H. A. van Leeuwen1,3*  | Elisabeth S. Bakker3  |  Jos T. A. Verhoeven1 | Stéphanie Ijff4 | Edwin T. H. M. Peeters5  |  Bastiaan G. van Zuidam5 | Merel B. Soons1 1Ecology & Biodiversity Group, Department of Biology, Utrecht University, Utrecht, The Netherlands 2Dutch Botanical Research Foundation (FLORON), Nijmegen, The Netherlands 3Department of Aquatic Ecology,  Netherlands Institute of Ecology (NIOO- KNAW), Wageningen, The Netherlands 4Deltares, Marine and Coastal Systems, Delft, The Netherlands 5Aquatic Ecology and Water Quality Management Group, Wageningen University, Wageningen, The Netherlands Correspondence Merel B. Soons Email: m.b.soons@uu.nl Funding information NWO-TTW Handling Editor: David Moreno Mateos 1Ecology & Biodiversity Group, Department of Biology, Utrecht University, Utrecht, The Netherlands 2Dutch Botanical Research Foundation (FLORON), Nijmegen, The Netherlands 3Department of Aquatic Ecology,  Netherlands Institute of Ecology (NIOO- KNAW), Wageningen, The Netherlands 4Deltares, Marine and Coastal Systems, Delft, The Netherlands 5Aquatic Ecology and Water Quality Management Group, Wageningen University, Wageningen, The Netherlands Correspondence Merel B. Soons Email: m.b.soons@uu.nl Funding information NWO-TTW Handling Editor: David Moreno Mateos 1Ecology & Biodiversity Group, Department of Biology, Utrecht University, Utrecht, The Netherlands 1Ecology & Biodiversity Group, Department of Biology, Utrecht University, Utrecht, The Netherlands 2Dutch Botanical Research Foundation (FLORON), Nijmegen, The Netherlands 3Department of Aquatic Ecology,  Netherlands Institute of Ecology (NIOO- KNAW), Wageningen, The Netherlands 4Deltares, Marine and Coastal Systems, Delft, The Netherlands 5Aquatic Ecology and Water Quality Management Group, Wageningen University, Wageningen, The Netherlands Correspondence Merel B. Soons Email: m.b.soons@uu.nl Funding information NWO-TTW Handling Editor: David Moreno Mateos Abstract 1. Peat-forming wetlands, particularly floating fens that form the initial stages of these ecosystems, are declining globally due to excavation, dehydration and eu- trophication. Restoration typically involves reestablishment of early-successional open-water stages, with oligotrophic conditions that are characteristic for these systems. However, restoration success is notoriously limited. A potential improve- ment may be to initiate succession by reintroducing of target plant species. Knowledge is therefore needed on (a) which plant functional groups should be re- introduced to stimulate fen formation; and (b) how to manage nutrient levels during restoration, considering that plant growth may be slow in oligotrophic conditions. 1. Peat-forming wetlands, particularly floating fens that form the initial stages of these ecosystems, are declining globally due to excavation, dehydration and eu- trophication. Restoration typically involves reestablishment of early-successional open-water stages, with oligotrophic conditions that are characteristic for these systems. However, restoration success is notoriously limited. A potential improve- ment may be to initiate succession by reintroducing of target plant species. Knowledge is therefore needed on (a) which plant functional groups should be re- introduced to stimulate fen formation; and (b) how to manage nutrient levels during restoration, considering that plant growth may be slow in oligotrophic conditions. 2Dutch Botanical Research Foundation (FLORON), Nijmegen, The Netherlands 2. We hypothesized that increasing functional diversity of introduced species would stimulate the formation of peat-forming target communities, their biomass accu- mulation and expansion onto open water. We also hypothesized that nutrient availability would mediate the relative contribution of specific functional groups to these effects. We investigated this in 36 artificial outdoor ponds by manipulat- ing plant functional diversity (clonal dominants, clonal stress-tolerators and inter- stitials) on constructed rafts with fen-forming communities, and subjected these to a range of nutrient loadings over 2 years. 2. We hypothesized that increasing functional diversity of introduced species would stimulate the formation of peat-forming target communities, their biomass accu- mulation and expansion onto open water. We also hypothesized that nutrient availability would mediate the relative contribution of specific functional groups to these effects. We investigated this in 36 artificial outdoor ponds by manipulat- ing plant functional diversity (clonal dominants, clonal stress-tolerators and inter- stitials) on constructed rafts with fen-forming communities, and subjected these to a range of nutrient loadings over 2 years. 3. Increasing functional diversity as well as increasing nutrient loadings had stimulating effects on plant biomass accumulation, cover formation and rhizome growth onto open water. *Both authors contributed equally. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2018 The Authors. Journal of Applied Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society R E S E A R C H A R T I C L E J Appl Ecol. 2019;56:235–245. E-mail address: pure@knaw.nl E-mail address: pure@knaw.nl E-mail address: pure@knaw.nl Download date: 24. Oct. 2024 Received: 31 January 2018  |  Accepted: 10 July 2018 DOI: 10.1111/1365-2664.13256 1 | INTRODUCTION because of positive species interactions (i.e. facilitation) (Cardinale et al., 2012; Hooper et al., 2005; Loreau & Hector, 2001). Second, productivity can increase due to a selection effect: at higher diver- sity the chance increases that a highly productive species or func- tional group is present (Loreau & Hector, 2001; Wardle, 1999). 1 Peat-­forming wetlands provide a multitude of services, including car- bon storage, water purification, water retention and habitat provi- sioning for typical and endangered species; and are of great cultural value to humans (Chimner, Cooper, Wurster, & Rochefort, 2017; Lamers et al., 2015; Mitsch, Bernal, & Nahlik, 2013; Verhoeven, 1992). However, these ecosystems have severely declined on a global scale due to excavation, dehydration and eutrophication (Dahl, 2011; Zedler & Kercher, 2005). This applies particularly to the species-­rich communities typical for the onset of peat formation by the colonization of open water, such as floating fens (Hajkova, Hajek, & Kintrova, 2009; Soomers, Karssenberg, Verhoeven, Verweij, & Wassen, 2013), which have become very rare and are difficult to re- store (Chimner et al., 2017). Past restoration projects have shown that species-­rich, peat-­forming communities seldom return naturally after reestablishment of their typical abiotic conditions (Lamers et al., 2015). This may be due to dispersal limitation, slow coloni- zation or low recruitment of arriving diaspores in the reestablished abiotic conditions (Brederveld, Jähnig, Lorenz, Brunzel, & Soons, 2011; Fraaije, ter Braak, Verduyn, Verhoeven, & Soons, 2015b; Fraaije et al., 2015a; Sarneel, Soons, Geurts, Beltman, & Verhoeven, 2011; Van Leeuwen, Sarneel, van Paassen, Rip, & Bakker, 2014). Consequently, restoration projects may greatly benefit from species reintroductions (Chimner et al., 2017; Rochefort et al., 2016). Overyielding is well-­documented for terrestrial ecosystems (Hooper et al., 2005), in which its strength can depend on abi- otic conditions including nutrient availability (del Río, Schütze, & Pretzsch, 2014; Schmid, 2002). In wetland ecosystems, plant functional diversity has been shown to increase plant biomass (Engelhardt & Ritchie, 2001), decrease methane effluxes (Bouchard, Frey, Gilbert, & Reed, 2007; Schultz, Andrews, O’Reilly, Bouchard, & Frey, 2011) and change nitrogen cycling (Schultz, Bouchard, & Frey, 2012). However, for wetland ecosystems, current knowledge on the diversity–productivity framework and potential mediating effects of nutrients on relations within this framework is still limited (Giller et al., 2004). Which keystone plant functional groups should be in- troduced, and at which nutrient levels, is largely unclear. K E Y W O R D S assisted colonization, floating fen, functional diversity, peat formation, restoration, rhizome formation, terrestrialization, wetlands assisted colonization, floating fen, functional diversity, peat formation, restoration, rhizome formation, terrestrialization, wetlands Abstract Both complementarity (due to niche partitioning or facilitation) and se- lection effects were mechanisms underlying the diversity effect, with a constant rela- tive importance over the entire range of nutrient availabilities. Different functional groups were important for biomass production at different nutrient availabilities. Rhizome formation by clonal stress-tolerators contributed disproportionately to open water colonization, identifying this functional group as key across all nutrient levels. 3. Increasing functional diversity as well as increasing nutrient loadings had stimulating effects on plant biomass accumulation, cover formation and rhizome growth onto open water. Both complementarity (due to niche partitioning or facilitation) and se- lection effects were mechanisms underlying the diversity effect, with a constant rela- tive importance over the entire range of nutrient availabilities. Different functional groups were important for biomass production at different nutrient availabilities. Rhizome formation by clonal stress-tolerators contributed disproportionately to open water colonization, identifying this functional group as key across all nutrient levels. wileyonlinelibrary.com/journal/jpe  |  235 wileyonlinelibrary.com/journal/jpe J Appl Ecol. 2019;56:235–245. Journal of Applied Ecology 236 van ZUIDAM et al. 4. Synthesis and applications. Restoration of floating fen communities can be stimu- lated during the first 2 years by introducing a high functional diversity of plant species. These include fast-growing clonal species, clonal stress-tolerators and in- terstitials, which facilitate each other. Restoration is dependent on the presence of clonal stress-tolerators such as Calla palustris, Comarum palustre and Menyanthes trifoliata for expansion onto the open water. Furthermore, restoration can start under a wide range of water nutrient levels, including eutrophic conditions. 1 | INTRODUCTION Especially for nutrient levels, the question remains whether it is better to restore oligotrophic conditions typical for peat-­forming wetland systems (Verhoeven, 1986) and the associated (red-­listed) plant species (Rydin, Jeglum, & Jeglum, 2013); or to stimulate plant bio- mass production by providing more nutrients to initiate succession and peat formation (Lawlor, Schulze, Beck, & Müller-­Hohenstein, 2010). Nutrients change many processes within plants and interac- tions among plants (Kraiser, Gras, Gutiérrez, González, & Gutiérrez, 2011), and may therefore also affect mechanisms such as comple- mentarity and selection effects. Introducing a wide selection of plant species typically stimulates development of target communities during ecosystem restoration, especially if this includes keystone species with important ecosys- tem functions (Geist & Hawkins, 2016; Lunt et al., 2013). At a given nutrient availability, species-­rich plant communities are generally more productive than species-­poor communities, which is known as a positive diversity–productivity relationship or overyielding (Balvanera et al., 2006; Cardinale, 2011; Hooper et al., 2005; Spehn et al., 2005). Overyielding can be caused by two primary mecha- nisms. First, species complementarity can increase productivity if intraspecific competition in monocultures exceeds interspecific competition in mixed communities; either because species or func- tional groups partition available resources (niche partitioning) or Here, we aim to provide recommendations for the restoration of peat-­forming, floating fen wetland communities by evaluating the effectiveness of manipulated functional diversity of intro- duced plants during the initial phase of restoration across a gra- dient of nutrient availability. We hypothesized that (a) increasing functional diversity of introduced species would stimulate the formation of peat-­forming target communities, their biomass accumulation and expansion onto open water; and that (b) nu- trient availability would affect the underlying mechanisms and mediate the relative contribution of specific functional groups Journal of Applied Ecology van ZUIDAM et al. 237 to the bottom of the ponds to prevent plant interactions between mats. to these effects. We expected most biomass accumulation in the vegetation at very high nutrient levels (mediated by rapid bio- mass production of fast-­growing, competitive helophytes such as Phragmites australis), but most expansion of the communities onto open water at low-­to-­intermediate nutrient levels (medi- ated by rapid clonal expansion of rhizomatous helophytes such as Comarum palustre). Furthermore, we anticipated that a third functional group, nonclonal helophytes, would be facilitated by the floating fen formation by either of the two other groups. 2.1 | Experimental design We experimentally studied the influence of functional plant diver- sity on biomass accumulation, cover and rhizome formation by wet- land plant species over a nutrient gradient in 36 artificial outdoor ponds in Loenderveen, the Netherlands (52°12′41″N, 5°2′18″E). The ponds were square, 1.5 m deep, 5.0 × 5.0 m wide at the top and 3.0 × 3.0 m wide at the bottom and lined with waterproof foil. Each pond was filled with a 0.3 m layer of sand–clay mixture (10:1), and a 0.7 m water column from a nearby lake (“Waterleidingplas”). This lake water was used to initially fill the ponds, and subsequently used to control the water level via an overflow mechanism. This water was oligotrophic due to phosphate removal for drinking water (measured monthly during the 2-­year experimental period (n = 24): mean total N = 2.71 ± 0.42SD mg/L, mean total P = 0.008 ± 0.005SD mg/L; Waternet, unpubl. data). No fish were present in the ponds. To pre- vent variation among ponds in possible nutrient uptake, submerged vegetation was removed each July from ponds with a submerged plant cover >60%. The artificially created ponds enabled us to exper- imentally manipulate nutrient availability and the functional diver- sity of introduced plants without interference of existing vegetation and/or environmental conditions. To investigate interactions among the three functional groups, mats received plants from either only one, two or all three of the functional groups—resulting in seven combinations of functional groups (Figure 1). Each functional group was always represented by all three species from that group. If multiple functional groups were present, the number of individual plants was the same for each functional group (Figure 1, Table S2). Planting densities on the mats resembled realistic and cost-­effective planting schemes as applied locally in restoration projects in the Netherlands. To investigate possible effects of nutrient availability on the developing plant communities, we manipulated nutrient loadings in the ponds throughout the experiment. Nine different loadings of both nitrogen and phosphorus were applied by weekly additions of NO3NH4 and KH2PO4 to the water column in the ponds (range 0–5.0 mg N and 0–0.5 mg P/L, details in Table S3) from April until October in both study years. Loadings mimicked a full range from oligotrophic to hypertrophic waters. To avoid stoichiometric effects, KH2PO4 and NO3NH4 were added in a ratio of 1:12.6 to obtain a N:P ratio of 10:1 g/g throughout all treatments. 1 | INTRODUCTION We investigated this by manipulating functional diversity of experi- mental wetland plant communities for 2 years, after which we measured the accumulation of biomass as a proxy for vegetation carbon storage, and the formation of plant cover and rhizomes as proxies for colonization of open water. At the start of the experiment, 24 young plants were inserted into small holes cut into the coconut fibre top of each mat. Each mat received 24 individual plants belonging to one, two or three functional groups based on the classification method as initially proposed by Boutin and Keddy (1993) (Figure 1). These three functional groups differ in their functional morphology: clonal dominants (represented by Typha latifolia, P. australis and Phalaris arundinacea), clonal stress-­tolerators (Calla palustris, C. palustre and Menyanthes trifoliata) and interstitials (Alisma plantago-aquat- ica, Iris pseudacorus and Acorus calamus). All species (except A. plantago-aquatica) are rhizomatous to some extent, but the tall clonal dominants typically have much longer creeping rhizomes than the shorter interstitials, while the much shorter clonal stress-­ tolerators proliferate via rhizomes and creeping stems extensively. The optimal habitat of the clonal stress-­tolerators is more oligotro- phic than that of the other two groups (species traits presented in Table S1). We manipulated functional diversity by regulating func- tional richness (i.e. the number of functional groups) instead of species diversity to make our results more widely applicable, and avoid the implicit assumption that all species are equally different from each other (Hooper et al., 2005). Our selection of three dif- ferent species within each functional group makes the results per group more representative for species with that same functional role. 2.1 | Experimental design All combinations of func- tional groups were exposed to the whole nutrient gradient, with two replicates per combination in every nutrient treatment (Figure S2). Few species other than those selected for the functional groups spontaneously colonized on the mats. In total these were <5 species, dominated by Mimulus guttatus and Bidens frondosa, with a combined fresh weight always <10% of the total vegetation fresh weight. These species were removed in May, June, August and October 2013 and April, May, June and July 2014. We studied growth of nine typical wetland plant species in these ponds from September 2012 to September 2014. Seedlings of all species were grown from seeds in potting soil. When their above-­ ground parts measured ~0.05 m in height, the seedlings were di- vided over 126 artificial mats or rafts (“Röhrichtmatten,” Bestmann Green Systems, Tangstedt, Germany) that were randomly distributed across all the ponds. Each pond received either three or five mats to ensure complete randomization of the experimental treatments. The mats (1.0 × 1.0 m) were made of a base layer of floating polyethylene strings with a coconut fibre mat fixed on top (Figure S1). The poly- ethylene strings were tied together, creating a floating mat with an open structure through which roots could grow into the water. The mats did not contain any nutrients, and were kept apart by a fixation 238 Journal of Applied Ecology van ZUIDAM et al. FI G U R E 1 Schematic overview of the seven different possible planting combinations (indicated by encircled numbers) for the 126 experimental mats. Each mat (large squares) was planted with 24 individual plants (filled coloured squares) from nine different species belonging to three different functional groups FI G U R E 1 Schematic overview of the seven different possible planting combinations (indicated by encircled numbers) for the 126 experimental mats. 2.1 | Experimental design Each mat (large squares) was planted with 24 individual plants (filled coloured squares) from nine different species belonging to three different functional groups 0.0 to 532.0 g dry weight per individual plant with a mean of 41.5 g; (b) percentage cover on the mats, hereafter “cover,” after two sea- sons ranging from 0% to 25.3% formed by individual plants with a mean of 4.3%; (c) presence of rhizomes growing onto the open water from the sides of the floating mats, hereafter “rhizome presence,” modelled as binomial variable (present on 79 of the 126 mats after two seasons); (d) length of rhizomes formed by individual plants, hereafter “rhizome length” (ranging from 0 to 9.63 m, with a mean of 0.45 m). 2.2 | Data collection Data were collected per plant species per mat at the end of the ex- periment. First, we estimated the percentage of cover on each mat. Second, we recorded the presence (yes/no) and length (total in m) of rhizomes growing onto the open water surface (measured starting from the edges of the mats). Third, as an indicator of fen formation and ultimately vegetation carbon storage, all above-­ground biomass per plant species that formed on the mats (so excluding rhizome biomass) was destructively harvested by collecting all plant mate- rial growing above the mats. All plant material was dried for at least 48 hr at 70°C, and weighed on a scale (d = 0.1 g). Most roots had grown into the polyethylene of the mat, which made it impossible to harvest root biomass representatively. The mixed-­effects models were fitted with one of four possi- ble dependent variables: (a) biomass, (b) cover, (c) rhizome presence and (d) rhizome length. Residuals were normalized by natural log-­ transformations of biomass, cover and rhizome length, and analysed using package “nlme” (Pinheiro, Bates, DebRoy, & Sarkar, 2015). The presence of rhizomes was analysed as a binomial dependent vari- able using package “lme4” (Bates, Mächler, Bolker, & Walker, 2015). Nutrient loading into the ponds (ranging from 0 to 5.0 mg N/L and 0 to 0.5 mg P/L) was included as continuous predictor variable numer- ically ranging from 0 to 5, hence, estimated effect sizes in the models are presented on the scale of nitrogen loadings. Nutrient loading was centred by subtracting the mean from all values to improve inter- pretability (Raudenbush & Bryk, 2002). Intercepts in all models were allowed to vary by pond by including individual pond (36 levels) as random factor. 2.3 | Data analysis We analysed how the development of vegetation on the mats was af- fected by the functional groups, combinations of functional groups, functional diversity and nutrient availability in multiple general(ized) linear mixed-­effects models in r for statistics (R-­Development-­Core-­ Team, 2017). Four dependent variables were used in all statistical analyses, calculated per mat (Model I) or per individual plant per functional group (Model II, III and IV): (a) above-­ground living plant biomass, hereafter “biomass,” which after two growing seasons ranged from In Model I we tested whether cumulative values per mat cal- culated for either one of the four vegetation variables responded Journal of Applied Ecology van ZUIDAM et al. 239 to diversity (modelled as continuous predictor variable, ranging from one to three functional groups per mat), nutrient availability and their interaction. In Models II, III and IV we evaluated effects of treatments on vegetation variables calculated per individual plant. Model II analysed possible effects on vegetation variables of clonal dominants, Model III for clonal stress-­tolerators and Model IV for the interstitials. Models II, III and IV tested whether particu- lar functional groups responded to the presence of particular other functional groups, and hence examined possible complementarity effects in more detail. The presence of the other two functional groups was modelled as binomial fixed factors: either present (1) or not (0). For example, in Model II the biomass of clonal dominants was the dependent variable, therefore the presence of clonal stress-­ tolerators (1/0) and presence of interstitials (1/0) were included as fixed factors. Details on model selection are provided in Supporting Information Methods. that were present (Figure 2a–c, Model Ia, b and c in Table 1, ­respectively). Rhizome length did not increase due to functional diversity (Figure 2d, Model Id in Table 1). Nutrient addition had a much stronger effect than functional diversity on final plant biomass (Figure 2a–c, see also Figure S1). Mean biomass of all mats was 40 g when no nutrients were added, which increased 26-­fold to 1,048 g at the highest nutrient loading. Nutrients affected coverage less than biomass, but again had a stronger effect on coverage than functional diversity. Mean cover ranged from 15% at the lowest nutrient level to 72% cover at the highest nutrient level (a fourfold increase). 2.3 | Data analysis At the lowest nutrient level, rhizomes formed on 7 of 14 mats (50%), and at the highest nutrient level on 11 of 14 mats (79%); a relative increase by 58%. Furthermore, nutrient loading increased rhizome length >19-­fold, from 0.90 m ± 0.45SD at the lowest, to 17.9 m ± 17.0SD at the highest nutrient level (Figure 2d). In addition to the mixed models, we applied randomization tests to quantify the effects of functional groups expressed in standard deviation units on three variables: total plant biomass, total plant cover and total rhizome length per mat (Gotelli, Ulrich, & Maestre, 2011). Our working hypothesis was that the presence or absence of a particular functional group significantly affected all three of these variables. The null hypothesis was that mats with and without a particular functional group would not differ more than expected by chance. This method has been developed for species, but we here applied it analogously to functional groups. More details can be found in Supporting Information Methods. 3.1 | Effects of functional diversity and nutrient loading Mean biomass (dry weight in g), cover (in %) and the probability of rhizome formation on the mats increased with functional richness and nutrient loading (Table 1, Figure 2, Table S4). The positive ef- fects of increasing functional diversity were consistent across dif- ferent levels of nutrient loading. The vegetation transgressively overyielded, that is, the maximum biomass and cover produced by the best mixed community (1,894 g dry weight and 100% cover per mat for mats with all three functional groups) exceeded the maximum biomass and cover produced by the best monoculture (1,288 g for the monoculture with interstitials and 90.5% cover per mat for the monoculture with clonal stress-­tolerators). Biomass production, cover formation and the probability of rhizome forma- tion on the mats increased with the number of functional groups 3.2 | Relative contributions of the three functional groups The three functional groups differed in their relative contributions to the vegetation that had formed on the mats after 2 years, and this relative importance depended on nutrient loading (Figure 3). Summed over all nutrient levels, biomass formed by clonal domi- nants was 11.7% of all formed biomass, which was less than the biomass formed by the clonal stress-­tolerators (35.2%) or the in- terstitials (53.1%). At low nutrient loadings clonal stress-­tolerators contributed most to biomass, while at high nutrient loadings the interstitials contributed more (significantly so if a functional groups standardize effect size exceeds 2.0, Figure 3a). Cover on the mats, summed over all nutrient levels, was mostly formed by the clonal stress-­tolerators and interstitials (Figure 3b). Clonal dominants contributed 19.2% of the cover, clonal stress-­tolerators 42.7% and interstitials 38.1%. Clonal stress-­tolerators formed rhi- zomes on 64 of the 72 mats (89%) on which they were present, the clonal dominants on 29 of the 72 (40%) of the mats on which they were present, and the interstitials did not form rhizomes. The clonal stress-­tolerators contributed most to the presence of rhizomes on the mats at all nutrient levels, while the relative contribution of clonal dominants to rhizome presence increased with increasing nutrient availability (Figure 3c). Clonal stress-­ tolerators also formed the longest rhizomes at all nutrient levels (Figure 3d): the rhizomes of clonal stress-­tolerators grew farther onto the open water (mean distance from mats: 1.48 m ± 2.18SD, maximum: 9.63) than rhizomes of clonal dominants (mean distance from mats: 0.09 m ± 0.13SD, maximum: 0.52). To disentangle possible complementarity and selection effects as underlying mechanisms explaining observed net diversity–pro- ductivity effects, we used the additive partitioning technique as described by Loreau and Hector (2001). For every mixture and for every nutrient level we calculated the net effect, the complemen- tarity effect and the selection effect. More details can be found in Supporting Information Methods. 3.3 | Complementarity and selection effects among the functional groups The positive effect of functional richness on biomass accumula- tion and cover formation could almost entirely be attributed to a species complementarity effect (Figure 4a,b). The positive Journal of Applied Ecology 240 van ZUIDAM et al. 3.3 | Complementarity and selection effects among the functional groups TA B LE 1 Final model-­averaged parameter estimates (β), their standard errors (SE), 95% confidence intervals and p-­values for significant terms remaining in the models after model selection (for details on model selection see Table S4) Model Dependent variable Predictor variablea βb SE 95% CI p-­value Back-­transformed effect sizesc Ia Biomass per mat Intercept 4.45 0.23 4.00–4.90 <0.001 Nutrient 0.56 0.14 0.28–0.84 <0.001 Min: 40 g Max: 1,048 g 26-­fold increase Richness 0.26 0.11 0.037–0.49 0.02 Min: 251 g Max: 367 g 1.46-­fold increase Ib Cover per mat Intercept 2.70 0.12 2.47–2.93 <0.001 Nutrient 0.29 0.05 0.18–0.40 <0.001 Min: 15% Max: 72% 4-­fold increase Richness 0.30 0.06 0.18–0.42 <0.001 Min: 25% Max: 36% 1.48-­fold increase Ic Rhizome presence per mat Intercept 0.22 0.12 0.089–0.52 0.06 Nutrient 0.061 0.027 0.006–0.12 0.03 Min: 7/14 50% of mats Max: 11/14 79% of mats 1.29-­fold increase Richness 0.19 0.06 0.071–0.30 0.002 Min: 27/54 50% of mats Max: 16/18 89% of mats 1.39-­fold increase Id Rhizome length per mat Intercept 0.27 0.33 −0.40 to 0.93 0.43 Nutrient 0.53 0.11 0.31–0.75 <0.001 Min: 0.90 m Max: 17.9 m 19-­fold increase Clonal dominants IIb Cover per plant Intercept 0.82 0.08 0.67–0.98 <0.001 Presence clonal stress-­ tolerators 0.40 0.07 0.26–0.55 <0.001 Absent: 1.60% Present: 3.34% 2-­fold increase Presence interstitials 0.23 0.08 0.08–0.38 <0.01 Absent: 1.96% Present: 2.98% 1.5-­fold increase IIc Rhizome presence per plant Intercept 0.52 0.08 0.37–0.69 <0.001 Presence interstitials −0.25 0.11 −0.46 to −0.03 0.02 Absent: 19/36 mats rhizomes Present: 10/36 mats rhizomes 2-­fold lower chance with interstitials present Clonal stress-tolerators IIIa Biomass per plant Intercept 3.27 0.09 3.08–3.51 <0.001 Nutrient 0.52 0.07 0.38–0.66 <0.001 Min: 9.3 g Max: 144.1 g 16-­fold increase IIIb Cover per plant Intercept 1.62 0.08 1.46–1.78 <0.001 Nutrient 0.30 0.05 0.20–0.40 <0.001 Min: 1.98% Max: 15.12% 7-­fold increase IIIc Rhizome presence per plant Intercept 0.90 0.04 0.81–0.98 <0.001 Nutrient 0.047 0.023 2.8 × 10−5 to 0.094 0.05 Min: 6/8 mats Max: 8/8 mats Minor effect IIId Rhizome length per plant Intercept −0.54 0.12 −0.84 to −0.23 <0.001 Nutrient 0.69 0.08 0.54–0.85 <0.001 Min: 0.13 m Max: 5.0 m 38-­fold longer Interstitials IVa Biomass per plant Intercept 2.99 0.13 2.67–3.25 <0.001 Nutrient 0.88 0.08 0.71–1.00 <0.001 Min: 2.72 Max: 271.00 100-­fold more IVb Cover per plant Intercept 1.35 0.07 1.21–1.49 <0.001 Nutrient 0.30 0.026 0.25–0.36 <0.001 Min: 2.03 g Max: 12.78 g 6-­fold increase Presence clonal dominants 0.21 0.09 0.03–0.39 0.02 Absent: 4.49% Present: 5.30% 1.18-­fold increase Presence clonal stress-­ tolerators 0.29 0.09 0.10–0.47 <0.01 Absent: 4.21% Present: 5.58% 1.33-­fold increase Notes. Notes. aFor binomial factors of functional group presence, the absence of functional groups was always the intercept. bFor nutrients, effect sizes are presented on the scale for nitrogen concentrations (ranging from 0 to 5.0 mg N/L). cEffect sizes on back-­transformed scales are indicated with minimal and maximal values. 3.3 | Complementarity and selection effects among the functional groups The vertical axis depicts the number of standard deviations that a functional group deviates from a random expected mean of equal contribution by every functional group, which is expressed in units of standardized effect size (SES). SES-­values deviating more than the thresholds of 2.0 (dashed lines) from zero indicate that a functional group contributes significantly more (>2.0) or less (<−2.0) to a vegetation parameter than expected. SES-­values are indicated for different nutrient loadings, and as mean values per functional group (±SE) –2 –1 0 1 2 3 4 Standardized effect size biomass Clonal dominants Clonal stress tolerators Interstitials (a) –2 –1 0 1 2 3 4 Standardized effect size cover (b) –2 –1 0 1 2 3 4 Standardized effect size rhizome presence (c) –2 –1 0 1 2 3 4 Standardized effect size rhizome length 0 N + 0 P 0.15 N + 0.015 P 0.3 N + 0.03 P 0.6 N + 0.06 P 0.9 N + 0.09 P 1.2 N + 0.12 P 1.5 N + 0.15 P 3.0 N + 0.30 P 5.0 N + 0.50 P (d) Mean values Nutrient loadings relation between richness and the probability of rhizome forma- FI G U R E 2 Biomass as gram dry weight per mat (a), coverage in percentage per mat (b), rhizome presence (1/0) (c) and rhizome length (d) in response to functional diversity (one, two or three functional groups) and nutrient loadings of nitrogen (N) and phosphorus (P). The vertical axes are log-­scaled in panels a, b and d. (c) Overlapping points are staggered on the horizontal axis 10 100 1,000 1 2 3 Biomass (g dry weight per mat) 0 N + 0 P 0.15 N + 0.015 P 0.3 N + 0.03 P 0.6 N + 0.06 P 0.9 N + 0.09 P 1.2 N + 0.12 P 1.5 N + 0.15 P 3.0 N + 0.3 P 5.0 N + 0.5 P 10 100 1 2 3 Cover (% per mat) 0.0 0.5 1.0 1 2 3 Rhizome presence (binomial) 0.1 1.0 10.0 1 2 3 Number of functional groups Rhizome length (m from mats) (a) (b) (c) (d) FI G U R E 3 The relative contributions of the three different functional groups to (a) biomass, (b) cover, (c) rhizome presence and (d) rhizome length per mat at the different levels of nutrient loadings in mg/L. 3.3 | Complementarity and selection effects among the functional groups The vertical axis depicts the number of standard deviations that a functional group deviates from a random expected mean of equal contribution by every functional group, which is expressed in units of standardized effect size (SES). SES-­values deviating more than the thresholds of 2.0 (dashed lines) from zero indicate that a functional group contributes significantly more (>2.0) or less (<−2.0) to a vegetation parameter than expected. 3.3 | Complementarity and selection effects among the functional groups SES-­values are indicated for different nutrient loadings, and as mean values per functional group (±SE) –2 –1 0 1 2 3 4 Standardized effect size biomass Clonal dominants Clonal stress tolerators Interstitials (a) –2 –1 0 1 2 3 4 Standardized effect size cover (b) –2 –1 0 1 2 3 4 Standardized effect size rhizome presence (c) –2 –1 0 1 2 3 4 Standardized effect size rhizome length 0 N + 0 P 0.15 N + 0.015 P 0.3 N + 0.03 P 0.6 N + 0.06 P 0.9 N + 0.09 P 1.2 N + 0.12 P 1.5 N + 0.15 P 3.0 N + 0.30 P 5.0 N + 0.50 P (d) Mean values Nutrient loadings 10 100 1,000 Biomass (g dry weight per mat) 0 N + 0 P 0.15 N + 0.015 P 0.3 N + 0.03 P 0.6 N + 0.06 P 0.9 N + 0.09 P 1.2 N + 0.12 P 1.5 N + 0.15 P 3.0 N + 0.3 P 5.0 N + 0.5 P (a) –2 –1 0 1 2 3 4 Standardized effect size biomass Clonal dominants Clonal stress tolerators Interstitials (a) –2 –1 0 1 2 3 4 Standardized effect size cover (b) 1 2 3 10 100 1 2 3 Cover (% per mat) (b) (b) –2 –1 0 1 2 3 4 Standardized effect size rhizome presence (c) 0.0 0.5 1.0 1 2 3 Rhizome presence (binomial) 0.1 1.0 10.0 1 2 3 Number of functional groups Rhizome length (m from mats) (c) (d) (c) –2 –1 0 1 2 3 4 Standardized effect size rhizome length 0 N + 0 P 0.15 N + 0.015 P 0.3 N + 0.03 P 0.6 N + 0.06 P 0.9 N + 0.09 P 1.2 N + 0.12 P 1.5 N + 0.15 P 3.0 N + 0.30 P 5.0 N + 0.50 P (d) Mean values Nutrient loadings FI G U R E 3 The relative contributions of the three different FI G U R E 3 The relative contributions of the three different functional groups to (a) biomass, (b) cover, (c) rhizome presence and (d) rhizome length per mat at the different levels of nutrient loadings in mg/L. 3.3 | Complementarity and selection effects among the functional groups aFor binomial factors of functional group presence, the absence of functional groups was always the intercept. bFor nutrients, effect sizes are d h l f i i ( i f 0 5 0 N/L) cEff i b k f d l i di d i h i i l TA B LE 1 Final model-­averaged parameter estimates (β), their standard errors (SE), 95% confidence intervals and p-­values for significant terms remaining in the models after model selection (for details on model selection see Table S4) TA B LE 1 Final model-­averaged parameter estimates (β), their standard errors (SE), 95% confidence intervals and p-­values for significant terms remaining in the models after model selection (for details on model selection see Table S4) TA B LE 1 Final model-­averaged parameter estimates (β), their standard errors (SE), 95% confidence intervals and p-­values for significant terms remaining in the models after model selection (for details on model selection see Table S4) van ZUIDAM et al. Journal of Applied Ecology 241 | FI G U R E 2 Biomass as gram dry weight per mat (a), coverage in percentage per mat (b), rhizome presence (1/0) (c) and rhizome length (d) in response to functional diversity (one, two or three functional groups) and nutrient loadings of nitrogen (N) and phosphorus (P). The vertical axes are log-­scaled in panels a, b and d. (c) Overlapping points are staggered on the horizontal axis 10 100 1,000 1 2 3 Biomass (g dry weight per mat) 0 N + 0 P 0.15 N + 0.015 P 0.3 N + 0.03 P 0.6 N + 0.06 P 0.9 N + 0.09 P 1.2 N + 0.12 P 1.5 N + 0.15 P 3.0 N + 0.3 P 5.0 N + 0.5 P 10 100 1 2 3 Cover (% per mat) 0.0 0.5 1.0 1 2 3 Rhizome presence (binomial) 0.1 1.0 10.0 1 2 3 Number of functional groups Rhizome length (m from mats) (a) (b) (c) (d) FI G U R E 3 The relative contributions of the three different functional groups to (a) biomass, (b) cover, (c) rhizome presence and (d) rhizome length per mat at the different levels of nutrient loadings in mg/L. 3.3 | Complementarity and selection effects among the functional groups The vertical axis depicts the number of standard deviations that a functional group deviates from a random expected mean of equal contribution by every functional group, which is expressed in units of standardized effect size (SES). SES-­values deviating more than the thresholds of 2.0 (dashed lines) from zero indicate that a functional group contributes significantly more (>2.0) or less (<−2.0) to a vegetation parameter than expected. SES-­values are indicated for different nutrient loadings, and as mean values per functional group (±SE) 3 Number of functional groups FI G U R E 2 Biomass as gram dry weight per mat (a), coverage in percentage per mat (b), rhizome presence (1/0) (c) and rhizome length (d) in response to functional diversity (one, two or three functional groups) and nutrient loadings of nitrogen (N) and phosphorus (P). The vertical axes are log-­scaled in panels a, b and d. (c) Overlapping points are staggered on the horizontal axis FI G U R E 2 Biomass as gram dry weight per mat (a), coverage in percentage per mat (b), rhizome presence (1/0) (c) and rhizome length (d) in response to functional diversity (one, two or three functional groups) and nutrient loadings of nitrogen (N) and phosphorus (P). The vertical axes are log-­scaled in panels a, b and d. (c) Overlapping points are staggered on the horizontal axis relation between richness and the probability of rhizome forma- tion was mostly due to a selection effect (Figure 4c), related to the increased probability to have clonal stress-­tolerators present relation between richness and the probability of rhizome forma- tion was mostly due to a selection effect (Figure 4c), related to the increased probability to have clonal stress-­tolerators present on mats with higher diversity. The same mechanisms remained im- portant across the gradient of nutrient loadings, although the ef- fect sizes increased proportionally to the increases of biomass and van ZUIDAM et al. 3.3 | Complementarity and selection effects among the functional groups 242 Journal of Applied Ecology 0.0 4.0 8.0 12.0 Diversity effects on biomass (g dry weight per mat) Two functional groups Three functional groups Net effect Selection effect Complementarity effect 0.0 2.0 4.0 6.0 Diversity effects on cover (% per mat) –0.5 0.0 0.5 1.0 1.5 0 N + 0 P 0.15 N + 0.015 P 0.3 N + 0.03 P 0.6 N + 0.06 P 0.9 N + 0.09 P 1.2 N + 0.12 P 1.5 N + 0.15 P 3.0 N + 0.30 P 5.0 N + 0.50 P Nutrient loadings Diversity effects on rhizome presence (binomial) (a) (b) (c) cover formation caused by higher nutrient availability (Figure 4, Table S5). Effects were in most cases stronger on mats with three functional groups than on mats with two functional groups (Table S5). For biomass production, the mean proportion of the net effect that was explained by the complementarity effect was 1.00 ± 0.07SD, the selection effect was close to zero, and this pat- tern was largely consistent over the different nutrient loadings (Table S5). For cover formation, the proportion explained by the complementarity effect was 0.99 ± 0.04SD and the selection ef- fect was again close to zero. For the presence of rhizomes, the se- lection effect did explain a large proportion of the net effect: the net effect consisted of 0.25 ± 0.24SD selection, and 0.15 ± 0.50SD complementarity effect across all nutrient loadings and diversity levels (details in Table S5). Net effect Selection effect Complementarity effect A more detailed investigation of possible positive interactions among functional groups underlying the complementarity effect indicated both facilitation and competition (Models II, III and IV in Table 1 and Table S4). Cover formation by interstitials increased by 18% if clonal dominants were present. Clonal stress-­tolerators facil- itated cover formation by clonal dominants (+109%) and interstitials (+29%). The presence of interstitials increased cover formation by clonal dominants (+52%), but decreased the chance that this func- tional group formed rhizomes (−50%). –0.5 0.0 0.5 1.0 1.5 0 N + 0 P 0.15 N + 0.015 P 0.3 N + 0.03 P 0.6 N + 0.06 P 0.9 N + 0.09 P 1.2 N + 0.12 P 1.5 N + 0.15 P 3.0 N + 0.30 P 5.0 N + 0.50 P Nutrient loadings Diversity effects on rhizome presence (binomial) (c) 4 | DISCUSSION Our results show that restoration of peat-­forming ecosystems may benefit from increasing plant functional richness and nutrient avail- ability for the developing communities, because this stimulates plant growth and the colonization of open water by floating vegetation in the initial years after species reintroduction. In our experimen- tal setup, the most functionally diverse communities formed more biomass and cover due to complementarity and facilitation among introduced functional groups. Additionally, the presence of the functional group of clonal stress-­tolerators strongly enhanced rhi- zome growth and thereby colonization of open water, indicating a strong positive selection effect. Together, these results support our hypothesis that increasing functional diversity can stimulate initial growth and expansion of plant species typical for peat-­forming com- munities. This knowledge can help to increase the success of wet- land restoration projects. Nutrient loadings FI G U R E 4 This figure visualizes the net, complementarity and selection effects of functional diversity on (a) biomass production in grams per mat, (b) percentages of mats covered by vegetation and (c) the presence of rhizomes per mat (1 = rhizomes, 0 = no rhizomes), and how they change over the gradient of experimental nutrient loadings (in mg/L). In general, an increase of diversity to three functional groups (grey lines) affected the vegetation parameters stronger than an increase to two functional groups (black lines); and the strength of the effects increased with nutrient loadings. For biomass and cover formation, the net effect could almost completely be explained by the complementarity effect— over the entire gradient of nutrient loadings. For rhizome presence, the selection effect was the most important mechanism. The vertical axis is natural log-­scaled for biomass and cover (a and b), and a binomial scale for rhizome presence (c). Statistical details are available in Table S5 Our observation of overyielding in mixed wetland communi- ties is in line with the general diversity–productivity framework in terrestrial ecosystems (Balvanera et al., 2006; Cardinale, 2011; Hooper et al., 2005; Spehn et al., 2005) and confirms previ- ous studies in wetland ecosystems (Engelhardt & Ritchie, 2001; Schultz et al., 2011, 2012). Our study expands the available knowledge for wetland systems by using different species and a different approach, and—most importantly—specifically tests the mediating role of nutrient availability in the diversity–productivity Journal of Applied Ecology van ZUIDAM et al. 243 framework. In contrast to our expectation that clonal dominant species such as P. 4 | DISCUSSION australis would thrive at high nutrient conditions and form the most rhizomes on the open water, rhizome forma- tion could be attributed almost entirely to clonal stress-­tolerators at all nutrient conditions. Rapid growth and rhizome formation by the clonal stress-­tolerators probably explains why this functional group facilitated cover formation of the interstitials and clonal dominants. However, this effect was smaller than anticipated. No interstitials were found outside the mats, and clonal dominants only formed few rhizomes in comparison to the clonal stress-­ tolerators. Hence, the strong selection effect for the presence of the clonal stress-­tolerators makes them crucial for the expansion of vegetation onto the open water. representing the initial phase of species establishment in which competition may not yet have played a dominant role; (b) the use of artificial floating mats, on which facilitation may have oc- curred because plant and rhizome growth seemed to stabilize the mats—suggesting our results are particularly applicable to situa- tions in which floating vegetation reaches far onto the open water and is subjected to wind and water flow; and (c) spatial effects: in contrast to terrestrial ecosystems (Tilman, 1994) competition for space may be lower in range expanding ecosystems such as vegetation expanding onto open water. The complementarity ef- fect remained the dominant mechanism across all levels of nutri- ent availability. Overall, our results therefore suggest that under range-­expanding conditions such as the colonization of open water, facilitation among wetland functional groups may increase resource use efficiency and biomass accumulation over a broad gradient of nutrient availabilities. Nutrient loading affected the relative importance of the different functional groups for biomass accumulation, and hence the potential of the vegetation to form peat during later developmental stages. In line with our second hypothesis, the clonal stress-­tolerators were the most important for biomass accumulation under low and in- termediate nutrient conditions. However, with increasing nutrient availability the interstitials became more important. We expected a hump-­shaped relation between nutrient loadings and biomass accu- mulation, with low plant growth at low nutrient availability and high nutrient levels hampering the expansion of fringe (edge) vegetation, such as observed in the field (e.g. Lamers et al., 2015). However, both biomass and cover formation increased consistently with increasing nutrient loading, suggesting that nutrient additions can have posi- tive effects on biomass accumulation and plant expansion during the first years of wetland restoration. 4.2 | Floating fen restoration Difficulties with restoration of floating fens are a problem because of the rapid losses of this important ecosystem type world-­wide (Chimner et al., 2017; Lamers et al., 2015). Even after abiotic condi- tions have been restored in degraded systems, propagules of target plants need to arrive (Soomers, Karssenberg, Soons, et al., 2013) and establish (Sarneel & Soons, 2012) at suitable shallow shorelines for rhizomatous growth to expand onto open water (Sarneel, Huig, Veen, Rip, & Bakker, 2014; Sarneel et al., 2011). Our study shows the added value of introducing multiple, carefully selected target species during restoration, and the relevance of nutrient availability for these plants during the initial years of restoration projects. This knowledge can be applied when selecting plant species for introduction and when determining whether or not to manipulate nutrient levels during wetland restoration practises. For example, the process of nutrient reduction need not necessarily be finished before species are reintro- duced at a site, as the availability of nutrients appears not to be a lim- iting factor for restoration success during the establishment phase. After this phase, nutrient levels should be more tightly managed to ensure development and persistence of target species known to re- spond negatively to nutrient-­rich conditions (e.g. Lamers et al., 2015). 4 | DISCUSSION This experiment therefore shows that increasing functional diversity can enhance initial restoration success of peat-­forming communities, and that this phase does not necessarily require oligotrophic conditions. 4.3 | Conclusions and implications for wetland restoration Balvanera, P., Pfisterer, A. B., Buchmann, N., He, J. S., Nakashizuka, T., Raffaelli, D., & Schmid, B. (2006). Quantifying the evidence for biodi- versity effects on ecosystem functioning and services. Ecology Letters, 9, 1146–1156. https://doi.org/10.1111/j.1461-0248.2006.00963.x This study implies that for restoration of the initial succession stages of peat-­forming ecosystems, increasing plant functional diversity in peat-­forming ecosystems can accelerate community development during restoration of the initial stages, both as es- tablishment of new ecosystems or expansion of existing systems. Community biomass accumulation, cover and rhizome formation all increased with functional group richness. Peat-­forming com- munities can benefit from facilitation among different functional groups, and initially develop under a surprisingly wide range of nutrient availabilities. The observed facilitation effects suggest that increasing functional diversity can stimulate terrestrialization and peat formation. However, apart from facilitation we also ob- served a positive selection effect. In our experiment, the impact of adding clonal stress-­tolerators to mats was very large. Clonal stress-­tolerators acted as a keystone functional group for the colo- nization of open water, and importantly contributed to the early phase of fen restoration. Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015). Fitting linear mixed-­ effects models using lme4. Journal of Statistical Software, 67, 1–48. Bouchard, V., Frey, S. D., Gilbert, J. M., & Reed, S. E. (2007). Effects of mac- rophyte functional group richness on emergent freshwater wetland functions. Ecology, 88, 2903–2914. https://doi.org/10.1890/06-1144.1 Boutin, C., & Keddy, P. A. (1993). A functional classification of wet- land plants. Journal of Vegetation Science, 4, 591–600. https://doi. org/10.2307/3236124 Brederveld, R. J., Jähnig, S. C., Lorenz, A. W., Brunzel, S., & Soons, M. B. (2011). Dispersal as a limiting factor in the colonization of restored mountain streams by plants and macroinvertebrates. Journal of Applied Ecology, 48, 1241–1250. https://doi.org/10.1111/j.1365-2664.2011.02026.x Cardinale, B. J. (2011). Biodiversity improves water quality through niche partitioning. Nature, 472, 86–89. https://doi.org/10.1038/nature09904 Cardinale, B. J., Duffy, J. E., Gonzalez, A., Hooper, D. U., Perrings, C., Venail, P., … Naeem, S. (2012). Biodiversity loss and its impact on humanity. Nature, 486, 59–67. https://doi.org/10.1038/nature11148 Chimner, R. A., Cooper, D. J., Wurster, F. C., & Rochefort, L. (2017). An overview of peatland restoration in North America: Where are we after 25 years? Restoration Ecology, 25, 283–292. https://doi.org/10.1111/rec.12434 Restoration Ecology, 25, 283–292. https://doi.org/10.1111/rec.1 Dahl, T. E. (2011). Status and trends of wetlands in the conterminous United States 2004 to 2009 (p. 108). Washington, DC: U.S. ACKNOWLEDGEMENTS This project was funded by NWO-­TTW (The Netherlands Organisation for Scientific Research—Applied and Engineering Sciences). The authors thank Jenneke Visser and two anonymous referees for helpful comments, Koos Swart for maintenance of the pond system, Waternet for hosting the experimental pond facil- ity in Loenderveen, Ariane Scholman, Dieuwertje Boonstra and Kristel van Zuijlen for help with fieldwork, and Yann Hautier for discussions on the data analysis. del Río, M., Schütze, G., & Pretzsch, H. (2014). Temporal variation of com- petition and facilitation in mixed species forests in Central Europe. Plant Biology, 16, 166–176. https://doi.org/10.1111/plb.12029 Dingemans, B. J., Bakker, E. S., & Bodelier, P. L. (2011). Aquatic herbi- vores facilitate the emission of methane from wetlands. Ecology, 92, 1166–1173. https://doi.org/10.1890/10-1297.1 Doherty, J. M., & Zedler, J. B. (2014). Dominant graminoids support restoration of productivity but not diversity in urban wetlands. Ecological Engineering, 65, 101–111. https://doi.org/10.1016/j. ecoleng.2013.07.056 Engelhardt, K. A. M., & Ritchie, M. E. (2001). Effects of macrophyte spe- cies richness on wetland ecosystem functioning and services. Nature, 411, 687–689. https://doi.org/10.1038/35079573 4.3 | Conclusions and implications for wetland restoration Department of the Interior; Fish and Wildlife Service. AUTHORS’ CONTRIBUTIONS J.V.Z., J.V. and M.B.S. conceived the ideas and designed the ex- periment; J.V.Z. and S.I.J. collected the data; C.V.L., M.B.S. and E.S.B. analysed the data; E.P. and B.V.Z. contributed to the data analysis; C.V.L. led the writing of the manuscript. All authors contributed critically to the drafts and gave final approval for publication. Ervin, G. N. (2009). An experimental study on the facilitative effects of tussock structure among wetland plants. Wetlands, 27, 620–630. Fraaije, R. G. A., ter Braak, C. J. F., Verduyn, B., Breeman, L. B. S., Verhoeven, J. T. A., & Soons, M. B. (2015a). Early plant recruitment stages set the template for the development of vegetation pat- terns along a hydrological gradient. Functional Ecology, 29, 971–980. https://doi.org/10.1111/1365-2435.12441 Fraaije, R. G. A., ter Braak, C. J. F., Verduyn, B., Verhoeven, J. T. A., & Soons, M. B. (2015b). Dispersal versus environmental filtering in a dynamic system: Drivers of vegetation patterns and diversity along stream riparian gradients. Journal of Ecology, 103, 1634–1646. https://doi.org/10.1111/1365-2745.12460 4.1 | Complementarity and selection effects among the functional groups Productivity in our experimental wetlands increased with func- tional diversity due to both complementarity and selection effects. Complementarity was the dominant mechanism causing overyield- ing for biomass accumulation and cover formation in the mixed communities, and the selection effect for the presence of clonal stress-­tolerators was the most important for rhizome formation. Observing a complementarity effect suggests that there was inter- specific resource partitioning among the three functional groups, or that the groups facilitated each other (Hooper et al., 2005). Because positive interactions (facilitation) were much more common than negative interactions (competition), facilitation provides a likely ex- planation for the observed complementarity effect. Our experiment did not fully resemble the natural field situa- tions. Two important differences between our experiments and field situations are (a) the absence of herbivores such as waterbirds, which can severely reduce expanding vegetation in fen systems (Dingemans, Bakker, & Bodelier, 2011; Sarneel et al., 2014), so that the effect of any species reintroductions is likely to be strongly re- duced; and (b) a lack of water flow around the mats. In most field situations, debris, sediments and plant seeds will become trapped in expanding rhizomes analogous to the way described in tussocks (Ervin, 2009). This could provide a suitable substrate for new seed- lings or other species to establish and expand, thereby contributing to the developing community. Addressing these additional aspects in long-­term field evaluations could further improve wetland resto- ration practises. Observing facilitation is in line with some previous studies (Le Bagousse-­Pinguet, Liancourt, Gross, & Straile, 2012), but deviates from most studies describing competition among wetland plants (Doherty & Zedler, 2014; Engelhardt & Ritchie, 2001; Valiente-­ Banuet & Verdú, 2008; Weis, Cardinale, Forshay, & Ives, 2007). This may be explained by (a) the short duration of our experiment, 244 Journal of Applied Ecology van ZUIDAM et al. 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M., & Soons, M. B. (2012). Post-­dispersal probability of germi- nation and establishment on the shorelines of slow-­flowing or stag- nant water bodies. Journal of Vegetation Science, 23, 517–525. https:// doi.org/10.1111/j.1654-1103.2011.01367.x Supporting Information section at the end of the article. How to cite this article: van Zuidam JP, van Leeuwen CHA, Bakker ES, et al. Plant functional diversity and nutrient availability can improve restoration of floating fens via facilitation, complementarity and selection effects. J Appl Ecol. 2019;56:235–245. https://doi.org/10.1111/1365-2664.13256 Sarneel, J. M., Soons, M. B., Geurts, J. J. M., Beltman, B., & Verhoeven, J. T. A. (2011). Multiple effects of land-­use changes impede the coloni- zation of open water in fen ponds. Journal of Vegetation Science, 22, 551–563. https://doi.org/10.1111/j.1654-1103.2011.01281.x Schmid, B. (2002). The species richness–productivity controversy. 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Aedes aegypti post-emergence transcriptome: Unveiling the molecular basis for the hematophagic and gonotrophic capacitation
PLoS neglected tropical diseases
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OPEN ACCESS Citation: de Carvalho SS, Rodovalho CM, Gaviraghi A, Mota MBS, Jablonka W, Rocha-Santos C, et al. (2021) Aedes aegypti post-emergence transcriptome: Unveiling the molecular basis for the hematophagic and gonotrophic capacitation. PLoS Negl Trop Dis 15(1): e0008915. https://doi. org/10.1371/journal.pntd.0008915 PLOS NEGLECTED TROPICAL DISEASES PLOS NEGLECTED TROPICAL DISEASES RESEARCH ARTICLE Aedes aegypti post-emergence transcriptome: Unveiling the molecular basis for the hematophagic and gonotrophic capacitation Stephanie S. de CarvalhoID1,2, Cynara M. RodovalhoID3, Alessandro GaviraghiID1, Maria Beatriz S. Mota2, Willy Jablonka1, Carlu´cio Rocha-Santos1, Rodrigo D. NunesID1¤, Thayane da Encarnac¸ão Sa´-Guimarães2, Daniele S. OliveiraID2, Ana C. A. MeloID2,4, Monica F. MoreiraID2,4, Patrı´cia FampaID5, Marcus F. OliveiraID1,4, Mario Alberto C. da Silva-Neto1,4†, Rafael D. MesquitaID2,4*, Georgia C. Atella1,4* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Instituto de Bioquı´mica Me´dica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil, 2 Departamento de Bioquı´mica, Instituto de Quı´mica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil, 3 Laborato´rio de Fisiologia e Controle de Artro´podes Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil, 4 Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil, 5 Departamento de Ciências Farmacêuticas, Instituto de Ciências Biolo´gicas e da Sau´de, Universidade Federal Rural do Rio de Janeiro, Seropedica, Rio de Janeiro, Brazil † Deceased. ¤ Current address: Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland—United States of America * rdmesquita@iq.ufrj.br (RDM); atella@bioqmed.ufrj.br (GCA) † Deceased. † Deceased. ¤ Current address: Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland—United States of America * rdmesquita@iq.ufrj.br (RDM); atella@bioqmed.ufrj.br (GCA) Author summary Aedes aegypti is a vector of several human diseases such as Dengue, Zika, Chikungunya, and Yellow Fever. Only the adult females can feed on blood, important for the production of their offspring, and therefore transmitting these pathogens for the human host. Inter- estingly, right after their emergence as adults, females show a preference of feeding on nectar, and only after three days, they are fully capacitated to perform a blood meal. Understanding the molecular mechanisms that orchestrate this physiological and bio- chemical switch is the main topic of the present study. The transcriptome analysis of males and females during the first hours post-emergence reveals that the gene expression in females is tightly regulated, showing three time-dependent profiles of expression. There is an increase in genes related to the oxidative phosphorylation pathway in the female head. Assessment of mitochondrial function revealed a gradual increase in respiration linked to ATP synthesis and mitochondrial content. Also, there is an increase in genes related to the muscular function, suggesting a putative role in muscle development and contraction, required, for example, for pumping of blood. The female body showed an increase in salivary gland related genes and serine proteases, probably related to the inges- tion and digestion of the blood. Also, the increase in DNA replication, ribosome biogene- sis, and juvenile hormone signaling pathways together with changes in cell cycle control suggest the gonotrophic capacitation for the massive synthesis of yolk proteins precursors during vitellogenesis. All these genes were enhanced even before the first blood meal, which reveals insightful information about the biology of anautogenous mosquitoes. Our data showed the molecular machinery that stands the females hematophagy and gonotro- phy, leading to potential new targets for vector control. Competing interests: The authors have declared that no competing interests exist. Author Mario Alberto C da Silva-Neto, was unable to confirm their authorship contributions. On their behalf, the corresponding author has reported their contributions to the best of their knowledge. PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Cientı´fico e Tecnolo´gico (hhtp://www.cnpq.br) PhD scholarship to SSdC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Abstract Funding: Funding from Fundac¸ão Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (http://www.faperj.br) PENSA-RIO-E26/ 010.003003/2014 to GCA, MACdSN, RDM, MFM and ACAM; Conselho Nacional de Desenvolvimento 1 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Abstract The adult females of Aedes aegypti mosquitoes are facultative hematophagous insects but they are unable to feed on blood right after pupae emergence. The maturation process that takes place during the first post-emergence days, hereafter named hematophagic and gono- trophic capacitation, comprises a set of molecular and physiological changes that prepare the females for the first gonotrophic cycle. Notwithstanding, the molecular bases underlying mos- quito hematophagic and gonotrophic capacitation remain obscure. Here, we investigated the molecular and biochemical changes in adult Ae. aegypti along the first four days post-emer- gence, prior to a blood meal. We performed a RNA-Seq analysis of the head and body, com- paring male and female gene expression time courses. A total of 811 and 203 genes were differentially expressed, respectively in the body and head, and both body parts showed early, mid, and late female-specific expression profiles. Female-specific up-regulation of genes involved in muscle development and the oxidative phosphorylation pathway were remarkable features observed in the head. Functional assessment of mitochondrial oxygen consumption in heads showed a gradual increase in respiratory capacity and ATP-linked respiration as a consequence of induced mitochondrial biogenesis and content over time. This pattern strongly suggests that boosting oxidative phosphorylation in heads is a required step towards blood sucking habit. Several salivary gland genes, proteases, and genes involved in DNA replication and repair, ribosome biogenesis, and juvenile hormone signaling were up-regulated specifi- cally in the female body, which may reflect the gonotrophic capacitation. This comprehensive description of molecular and biochemical mechanisms of the hematophagic and gonotrophic capacitation in mosquitoes unravels potentially new targets for vector control. Editor: Jose´ M. C. Ribeiro, National Institute of Allergy and Infectious Diseases, UNITED STATES Received: March 31, 2020 Accepted: October 22, 2020 Published: January 6, 2021 Copyright: © 2021 de Carvalho et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files. The bioproject accession is PRJNA659517and available at https://www.ncbi. nlm.nih.gov/bioproject/PRJNA659517. PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 Introduction Mosquitoes are vectors of several human diseases since these insects possess a remarkable human feeding preference [1]. The disease transmission occurs during the blood meal, required by anautogenous female mosquitoes for egg development [2]. Aedes aegypti females h i di t kill i t h i b t fl id f l t d bl d l Mosquitoes are vectors of several human diseases since these insects possess a remarkable human feeding preference [1]. The disease transmission occurs during the blood meal, human feeding preference [1]. The disease transmission occurs during the blood meal, required by anautogenous female mosquitoes for egg development [2]. Aedes aegypti females have a unique dietary skill interchanging between sugary fluids from plants and blood along the gonotrophic cycle. This cycle was named by Beklemishev in 1940 and comprises the host seeking, blood feeding, egg development, and oviposition [3]. Although the first gonotrophic cycle is unique, as the mosquito has never fed on blood before, in the first hours post-emergence (PE) they are unable to feed on blood, acquiring nutrients essentially from plant sap [4]. To get the first blood meal, females must undergo a maturation process in the first three days PE that comprises a series of physiological and molecular adaptations that take place in many tissues [5], named here hematophagic and gonotrophic capacitation (HGC). Juvenile hormone III (JH) is a master regulator PE develop- ment, participating in the maturation of newly emerged females towards blood feeding and vitellogenesis [6]. JH acts through its intracellular receptor Methoprene-tolerant (Met), a basic Helix-Loop-Helix/Per-Arnt-Sim (bHLH/PAS) transcription factor [7]. Met forms a heterodi- mer with Taiman, another bHLH-PAS protein, promoting the transcriptional regulation of several genes [8–10]. The fat body is extremely affected by JH signaling, increasing the expres- sion of ribosomal proteins and driving ribosome biogenesis, nucleolus enlargement, Golgi complex development, and invaginations of the plasma membrane, priming for vitellogenesis [11,12]. JH also induces the immature primary follicles [13,14] to grow twice in length to PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 2 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation mature follicles in 48-72h PE and the development of an endocytic complex by the oocytes given them the competence to acquire proteins [13,14]. The JH role on the female fat body was characterized by a post-emergence (PE) microarray in wild-type and Met-depleted females [15]. Introduction Three major profiles of expression were observed in the fat body of Ae. aegypti and in Culex quinquefasciatus adult females with an early, mid, and late profiles of transcript abundance [16,17]. The absence of Met revealed a similar profile of gene expression as JH deprived females for a subset of genes. Thus, JH regulates gene expres- sion for several genes through Met during PE development [15]. In a similar approach, the car- bohydrate and lipid metabolisms were assessed, through microarray analysis, in the female fat body in order to understand the energy supply for the physiological changes that occur during the PE phase. JH promotes an accumulation of glycogen in the fat body and the transcript abun- dance of pathways related to carbohydrate metabolism, such as glycolysis and citric acid cycle were high until 24h PE, declining from 36h until 72h PE. Met silencing promotes an increase in carbohydrate metabolism transcripts [18]. Met is also a key regulator of lipid metabolism during the PE hours leading to an accumulation of triacylglycerol (TAG) in the fat body and a reduc- tion in the ß-oxidation and lipid catabolism [12]. Thus, JH plays a role in regulating both carbo- hydrate and lipid metabolisms during PE development on Ae. aegypti female mosquitoes. Some other authors explored the female PE period. The Culex quinquefasciatus transcrip- tome evaluated immediately after the emergence in whole adult females, identified odorant binding proteins, salivary proteins, trypsins, lipases, uricases, among others [17]. The prote- ome of newly emerged females midgut revealed proteins involved in the metabolism of pro- teins and amino acids, serine proteases, and cell signaling, suggesting that there is a biochemical adaptation for the digestion of blood in the PE developmental phase [19]. The sal- ivary glands transcriptome compared female to male in a single time-point PE revealing sex- Some other authors explored the female PE period. The Culex quinquefasciatus transcrip- tome evaluated immediately after the emergence in whole adult females, identified odorant binding proteins, salivary proteins, trypsins, lipases, uricases, among others [17]. The prote- ome of newly emerged females midgut revealed proteins involved in the metabolism of pro- teins and amino acids, serine proteases, and cell signaling, suggesting that there is a biochemical adaptation for the digestion of blood in the PE developmental phase [19]. The sal- ivary glands transcriptome compared female to male, in a single time-point PE, revealing sex- specific proteins [20]. Introduction Tallon et al assessed the expression of main chemosensory gene families comparing female to male antennae, in a post-emergence time course using a transcriptome. Odorant binding proteins, odorant receptors, and ionotropic receptors gene expression were sex-specific and time-dependent [21] biochemical adaptation for the digestion of blood in the PE developmental phase [19]. The sal- ivary glands transcriptome compared female to male, in a single time-point PE, revealing sex- specific proteins [20]. Tallon et al assessed the expression of main chemosensory gene families comparing female to male antennae, in a post-emergence time course using a transcriptome. Odorant binding proteins, odorant receptors, and ionotropic receptors gene expression were sex-specific and time-dependent [21] Given the inability to feed on blood right after emergence, and the voracious hematophagous habit on mature stages, an important gap of knowledge exists on the molecular and biochemical mechanisms that mediate hematophagic capacitation in mosquitoes. The HGC occurs in the PE phase before the first blood feeding and are female-specific features, so only the comparison of female and male time-course transcriptomes will target the genes related to them. In the present work, we used RNA-Seq to investigate the effect of sex and time on the dynamics of gene expression in the first 96 hours PE, during HGC. The separated analysis of heads and bodies provided a global view of the complex and tightly regulated molecular remodeling that the females undergo along the first post-emergence hours. The transcriptome analysis revealed sex- and time-dependent changes in transcript abundance, with 203 genes differentially expressed in the head and 811 in the body. The up-regulation of the oxidative phosphorylation pathway in female heads lead us to perform a functional assessment of mitochondrial function in mosqui- toes heads, revealing an increase in respiration linked to ATP synthesis and mitochondrial con- tent. We discuss our findings in relation to the current knowledge of the physiological features concerning blood feeding behavior and the gonotrophic cycle in mosquitoes. Ethics statement All animal care and experimental protocols were conducted following the guidelines of the institutional care and use committee (Committee for Evaluation of Animal Use for Research 3 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation at the Federal University of Rio de Janeiro, CAUAP-UFRJ), Fundac¸ão Oswaldo Cruz Animal Use Ethics Committee (CEUA Fiocruz), and the NIH Guide for the Care and Use of Labora- tory Animals (ISBN 0-309-05377-3). The protocols were approved by CAUAP-UFRJ under the registry #IBQM067-05/16 and 24154319.5.0000.5257 and CEUA Fiocruz LW-20/14. Tech- nicians dedicated to the animal facility at both places conducted all the aspects related to ani- mal husbandry under strict guidelines to ensure their careful and consistent handling. Seeking assay The human host proximity assay was adapted from [23]. Aedes Rio female mosquitoes (F8-F10 generation) were kept with 10% sucrose ad libitum, but not blood fed. The post-emergence time points tested were 2, 12, 24, 48, and 96 hours. Fifteen minutes before each assay, 10 adult females were placed in an acrylic cage (16 x 16 x 16 cm) and human volunteers (N = 5, 2 females, aged 20–29) placed their right forearm approximately 2.5 cm away from the cage for 5 minutes. There was no direct contact between mosquitoes and the volunteers. A Sony Cyber- shot camera was positioned right across the cage, allowing a plain view of the mosquitoes and the forearm. This system was isolated with styrofoam at all sides, preventing interference from the environment and blocking not-exposed net areas. For each assay a 10-minute video was recorded, 5 minutes without and 5 minutes with the human forearm. The number of mosquito visits to the net was counted, with and without the forearm, considering only the exposed net area. P<0.005; Kruskal-Wallis corrected one-way ANOVA test comparing the hours post- emergence were performed using GraphPad Prism software v.6.0. Mosquito rearing All experiments were performed with a colony previously established by our group designated as Aedes Rio [22]. Ovitrap collected eggs from 5 different places around the Guanabara Bay: Paqueta´ Island, São Gonc¸alo, Prac¸a XV, Nitero´i, and Governador Island were hatched, raised into adults, identified as from Ae. aegypti, and then sorted into males and females. A pool of 20 males from each site was mated with 20 virgin females of every other location, for 5 days. After mating, all females were placed in a cage for blood feeding and egg laying (Aedes Rio F1 genera- tion). The Aedes Rio F1 generation mating was performed with 500 males and 500 females (1:1). From F2 generation onwards the natural female/male proportion (1:2) was not manipulated. The eggs were hatched in deoxygenated filtered water for 2 h and maintained at the Laboratory of Physiology and Control of Arthropods Vectors (LAFICAVE-Fiocruz), under BOD controlled conditions (27˚C ± 1˚C, 12:12h light:dark cycle, and 75% ± 10% relative humidity). First instar larvae were pooled in groups of ~300 per tray, in 1 liter of deoxygenated filtered water, and 1 g of cat food (Friskies, Purina) was provided every three days. Pupae were collected only once, on the day in which their number was the highest, and transferred to cardboard cages (17 cm diameter x 18.5 cm high). Aedes Rio F4 generation was used in the transcriptome, the details about mos- quito collecting and sample preparation are in the topic "Sample preparation and RNA-Seq". For the other experiments, Aedes Rio F8 to F10 generation eggs were hatched at the Federal Univer- sity of Rio de Janeiro and maintained as described above. Adult mosquitoes were collected in a two-hour window, i.e., from 1 hour before until 1 hour after each time point. The adult mosqui- toes were maintained with 10% sucrose ad libitum. Females and males, heads and bodies, were collected 2, 12, 24, 48, and 96 hours after the emergence from pupae. Bioinformatics analysis Sequenced reads were analyzed using FastQC version 0.11.5 [25] to evaluate their quality, before and after trimming with Cutadapt version 1.16 [26]. Adaptors and regions with quality scores smaller than 32 were removed, the remaining reads were dropped if the length was below 40 bp. These high-quality reads were aligned using Bowtie2 version 2.2.6 [27] to the Ae. aegypti tran- scripts (version 5.1—downloaded from VectorBase https://www.vectorbase.org/downloadinfo/ aedes-aegypti-lvpagwgtranscriptsaaegl51fagz). Salmon version 0.9.1 [28,29] was used with stan- dard parameters to quantify the transcripts due to the high amount of isoforms in this Ae. aegypti transcript version. The R package DESeq2 [30] allowed the identification of differentially expressed genes (DEG). The likelihood ratio test (LRT) (p-value <0.05) was used to time course DEG identification (male x female) while the Wald test (p-value <0,05; LogFoldChange > 1 or 2) followed by a false discovery rate (FDR—p-value <0.05) to compare each time point individ- ually between males and females. Only DEG identified by both methods were considered. Hier- archical clusterization and heatmaps used Expander version 7.1 [31]. Enrichment analysis of the three principal categories (Biological Process, Molecular Function, and Cellular Component) of gene ontology (GO) was performed with Panther Scoring Tool [32]. Statistical support was pro- vided by the FDR corrected Fisher test (p-value <0.1). The KEGG Mapper–Search&Color Path- way tool, from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, was used to highlight the differentially expressed genes in pathways [33–35]. Sequenced reads were analyzed using FastQC version 0.11.5 [25] to evaluate their quality, before and after trimming with Cutadapt version 1.16 [26]. Adaptors and regions with quality scores smaller than 32 were removed, the remaining reads were dropped if the length was below 40 bp. These high-quality reads were aligned using Bowtie2 version 2.2.6 [27] to the Ae. aegypti tran- scripts (version 5.1—downloaded from VectorBase https://www.vectorbase.org/downloadinfo/ aedes-aegypti-lvpagwgtranscriptsaaegl51fagz). Salmon version 0.9.1 [28,29] was used with stan- dard parameters to quantify the transcripts due to the high amount of isoforms in this Ae. First feeding assay This assay was adapted from [17]. Aedes Rio mosquitoes (F8-F10 generation) were tested at the following post-emergence time points: 2, 12, 24, 48, and 96 hours. All mosquitoes were 4 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation kept with 10% sucrose ad libitum and sugar-starved for 12h before each blood meal offer, except for the 2-hour post-emergence time point. For each time point, a cage containing approximately 60 mosquitoes of both sexes (~1:2 ratio) was fed in an artificial membrane feed- ing system with rabbit blood at 37˚C for 30 minutes. Mosquitoes were not manipulated from their emergence to the blood meal offer. The number of fed females was evaluated right after each assay. Midguts from fed and unfed mosquitoes were dissected and stored at -70˚C in pro- tease inhibitors cocktail until protein quantification by Lowry assay [24] (4 independent exper- iments were performed). P<0.05; Kruskal-Wallis corrected one-way ANOVA test comparing the hours post-emergence. P<0.0001; Tukey’s corrected one-way ANOVA test comparing the protein midgut contents in blood fed and non-blood fed female mosquitoes in the hours post- emergence. Both tests were performed using GraphPad Prism software v.6.0. Sample preparation and RNA-Seq Aedes Rio mosquitoes (F4 generation) were kept with 10% sucrose ad libitum, but not blood fed. The post-emergence time points tested were 2, 12, 24, 48, and 96 hours. All samples were col- lected at the same time each day (8:30 a.m.), except for the 12 hours time point that was collected twice—at day (8:30 a.m.) and at night (8:30 p.m.). Males and females were immobilized by chill- ing on ice onto a pre-cooled Petri dish and then dissected to obtain the heads and body (Pools of 10, N = 3). The samples were stored in RNAlater (Invitrogen) at -70˚C, and then total RNA was extracted with the miRNAeasy Mini Kit (Qiagen) following the manufacturer’s instructions. The 72 cDNA libraries were prepared with Truseq RNA Library Preparation (Illumina) and RNA-Seq sequencing was performed in Illumina HiSeq 4000, with 50 bp single-read, by the AgriLife Geno- mics and Bioinformatics Service (https://www.txgen.tamu.edu/) at Texas A&M University. Raw sequence reads were deposited at SRA under bioproject accession PRJNA659517. Quantitative PCR (qPCR) validation Aedes Rio mosquitoes (reared from F9-F10 eggs) were kept with 10% sucrose ad libitum, but not blood fed. The post-emergence time points tested were 2, 24, and 96 hours. Mosquitoes PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 5 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation were immobilized by chilling on ice and then dissected to obtain the heads and body (two pools of 5 mosquitoes from each of three independent cages). The samples were immediately fixed on TRIzol Reagent (Thermo Fisher Scientific) and the tissues were homogenized with pistils. The samples were stored at -70˚C for about 5 days until RNA extraction according to manufacturer instructions. RNA was analyzed through a nanodrop spectrophotometer (Thermo Fisher Scientific) for quality and quantity and 1μg of RNA of each sample was treated with DNAse I (Thermo Fisher Scientific). cDNA was prepared using High Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific) according to the manufacturer instruc- tions and the qPCR was performed in a StepOnePlus Real-Time PCR System (Thermo Fisher Scientific). The qPCR reactions were performed with HOT FIREpol EvaGreen qPCR Mix Plus (Solis Biodyne) with a final volume of 10μL, using 2μL of the reagent, 0.1μM of each primer, and 5μL of cDNA (1:50). The primers efficiency was established through calibration curves and determined from slope. The genes for qPCR validation were selected based Li et al (2019) [36]. One gene for each female enhanced cluster was chosen, except B4, H2, and H3 that did not fit the method criteria. The reference genes were selected based on the analysis of the tran- scriptome expression levels [36]. The Cq values were analyzed in Refinder software that also calculates ΔCq. The less variable genes were eukaryotic translation factor 1A (eiF1A) and eukaryotic translation factor 3, subunit J (eiF3j) that were used as reference genes following MIQE guidelines [37] The primers used for this analysis were provided in S3 Table. Expres- sion levels were calculated using 2-ΔCT. p-value <0.05; two-way ANOVA test was used to ana- lyze the factors time and sex. Tukey´s (time) and Sidak´s (sex) were used to correct the multiple comparisons. Tests were performed using GraphPad Prism software v.6.0. Respirometry analyses on mechanically permeabilized heads Respiratory activity of mechanically permeabilized heads from Aedes Rio mosquitoes was per- formed using a two-channel titration injection respirometer (Oxygraph-2k, Oroboros Instru- ments, Innsbruck, Austria) according to a method previously established by our group [38,39]. Aedes Rio mosquitoes (reared from F8-F10 eggs) were kept with 10% sucrose ad libitum, but not blood fed. The post-emergence time points tested were 2, 12, 24, 48, and 96 hours. Males and females were dissected and a pool from 15 heads was placed into the O2K chamber filled with 2 mL of respiration buffer (120 mM KCl, 5 mM KH2PO4, 3 mM HEPES, 1 mM EGTA, 1.5 mM MgCl2, and 0.2% fatty acid free bovine serum albumin, pH 7.2). The samples were subjected to a mechanical permeabilization inside the respirometer chamber by stirring at 750 rpm for about 10 minutes. The analysis was performed at 27.5˚C and 750 rpm. The substrate– uncoupler–inhibitor titration (SUIT) protocol was started by adding 10 mM pyruvate followed by 10 mM proline (Pyr+Pro). This combination of substrates was used because pyruvate and proline represent two of the main substrates used by Ae. aegypti as was shown previously by our group [40]. Then, 2 mM ADP was added and the oxygen consumption coupled to ATP synthesis (ATP linked respiration) was calculated by subtracting the oxygen consumption after substrate addition from ADP-stimulated oxygen consumption rates. The maximum uncoupled respiration was induced by stepwise titration of carbonyl cyanide p-(trifluoro- methoxy) phenylhydrazone (FCCP) to reach final concentrations of 0.8 μM. After that, the contribution of complex I on the electron flow was determined by the addition of 0.5 μM rote- none. Finally, respiratory rates were inhibited by the injection of 2.5 μg/mL antimycin A and the residual oxygen consumption (ROX) represents the oxygen consumed by the cells, not due to respiration. The maximum respiratory rates (ETS) were calculated by subtracting the anti- mycin resistant oxygen consumption from FCCP-stimulated oxygen consumption rates. The “leak” respiratory states, that represents the oxygen consumption in the presence of high PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 6 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation substrate concentration but in the absence of ADP, was calculated by subtracting the antimy- cin resistant oxygen consumption from the oxygen consumption after Pyr+Pro addition. Respirometry analyses on mechanically permeabilized heads An injection of the oxygen enriched gaseous mixture (70% O2 and 30% N2 mol/mol) was per- formed once the oxygen concentration fell down below 150 nmol/mL into the O2k-chamber. This is important to avoid the potential effects of oxygen diffusion and electron transfer due to oxygen shortage during measurements [41]. Cytochrome c oxidase activity was measured polarographically at the end of the routine of respiratory analysis using 2 mM ascorbate and 0.5 mM N,N,N’,N’-Tetramethyl-p-phenylene- diaminedihydrochloride (TMPD), as an electron-donor regenerating system. To discriminate the oxygen consumption due to complex IV from the self-oxidation of TMPD, 5 mM of KCN was added at the end of each experiment, and cytochrome c oxidase activity was considered as the oxygen consumption rate cyanide sensitive. Since cytochrome c oxidase activity is limited by low oxygen concentrations [42], the oxygen enriched gas mixture was also injected before measuring cytochrome c oxidase activity. All oxygen consumption rates were normalized for the protein content, using another pool of heads collected in the respective hours after emer- gence, and quantified using the Lowry assay [24]. P<0.05; two-way mixed-effect ANOVA model was used to analyze the factors of time and sex. Tukey´s were used to correct the multi- ple comparisons. Tests were performed using GraphPad Prism software v.6.0. Citrate synthase activity Aedes Rio mosquitoes (reared from F8-F10 eggs) were kept with 10% sucrose ad libitum, but not blood fed. The post-emergence time points tested were 2, 12, 24, 48, and 96 hours. Males and females were immobilized by chilling on ice onto a pre-cooled Petri dish and then dis- sected to obtain the heads (Pools of 15, N = 4). Citrate synthase activity was determined in whole cell lysates following methods described in the literature [40] with minor modifications. The heads were homogenized with a tissue grinder in a Teflon pestle in 0.05 mL of hypotonic buffer (25 mM potassium phosphate and 5 mM MgCl2, pH 7.2) and subsequently subjected to three freeze-thawing cycles. The enzyme activities were measured spectrophotometrically [43] at room temperature, in 75 mM Tris-HCl pH 8.0, 0.03 mM acetyl-CoA, and 0.25 mM DTNB, using a SpectraMax M3 Multi-Mode Microplate Reader spectrophotometer (Molecular Devices, California, USA). Enzyme activities were determined using samples corresponding to about 10 μg of protein. The rate of reduced coenzyme A (CoASH) production was determined using the thiol reagent 5,5’ -dithiobis (2-nitrobenzoic acid) (DTNB), which has an absorption maximum at 412 nm. P<0.05; two-way ANOVA test was used to analyze the factors time and sex. Tukey´s were used to correct the multiple comparisons. Tests were performed using GraphPad Prism software. Differential gene expression along the post-emergence phase is time and sex-dependent RNA-Seq transcriptome analysis was performed to understand the molecular maturation pro- cesses that occur during HGC. We evaluated the transcriptome of 72 libraries from heads and bodies of males and females, after 2, 12, 24, 48, and 96 hours PE. The time course was estab- lished based on the host seeking behavior and first blood feeding (S1 Fig) in agreement with the literature (reviewed by [44]). While at 2h PE females do not feed on blood, at 96h PE almost all insects are able to full blood engorgement. Using this timeframe, we were able to assess all molecular parameters during the transition period from sugar to blood meals. A total of 1,160,614,703 raw reads were generated from heads and 1,164,028,130 from the bodies of males and females combining all time points. After removing adaptors, poor quality, and/or small reads, a total of 1,141,101,980 clean reads were obtained for the heads and 1,139,254,496 for the bodies. Almost 90% of the Ae. aegypti coding sequences (version 5.1) had aligned reads for both head and body data (S1 Table). Differentially expressed genes (DEGs) were searched comparing the male and female time courses, considering genes modulated by time and sex (p-value <0.05). We also compared male x female data, for each of the five PE time points, using a minimum fold change of 2 and 4 (head and body, respectively) and the false discovery rate (p-value <0.05). The intersection of these statistical analyses resulted in a total of 203 and 811 DEGs identified in the head and body, respectively, in a time- and sex-dependent manner (S2 Table). The expression profile clustering analysis identified female-specific time-dependent clusters showing decrease, increase, and transient modifications (Fig 1). The clusters H1, H2, H3, and H4 for the head and clusters B1, B2, B3, and B4 for the body showed very little (or absent) male-specific time- dependent expression variation. Otherwise, the same clusters showed time-dependent expres- sion variation for the females, suggesting they contain the genes that are most likely related to the HGC, since its expression is sex-dependently modulated. We also observed clusters with very low male-specific variations (Hm and Bm), with the same profile for both males and females (Hb and Bb), and with opposite profiles (Ho) (Fig 1). The female gene expression during the PE period was very dynamic, in contrast to what was observed for males. Differential gene expression along the post-emergence phase is time and sex-dependent The clusters B2 (59 genes) peaked at 24h and clusters B3 (484 genes) and B4 (19 genes) showed gradual expression increase from 24h until 96h. The body clusters also presented a gradually decreased profile from 2h to 24h (B1–15 genes) (Fig 1A). Some head clusters had a similar profile as the H2 (43 genes) that peaked at 24h and the H4 (26 genes) that showed gradual expression increase until 96h. Other clusters comprised the clus- ters H1 (35 genes) and H3 (4 genes) that had the expression peak about 12h but with different time variations (Fig 1B). The expression profiles were validated by qPCR (S3 Fig) suggesting a fine regulation of gene expression in females, compared to males. Among the female-specific DEGs we observed an up-regulation of genes involved in the gonotrophic cycle, comprising hematophagic features such as blood ingestion and digestion, the juvenile hormone pathway, and the molecular machinery for the biosynthesis of yolk proteins. Hematophagic habit manifests along the first post-emergence days The Aedes Rio emerged mosquitoes exhibited a delayed response to blood feeding, becoming able to acquire blood only after 1-day post-emergence (S1A Fig). Only a small number of females (13%) fed on blood on the first 24h PE, and about 36% and 61% fed respectively 48h and 96h PE. The host seeking behavior showed that females start to seek the host with a minimum of 24h PE (S1B Fig). A significant increase is observed only 96h PE when seeking behavior to a human host reaches approximately 75 cumulative visits, within a 5-minute window. Most of the females were enabled to search, find, and acquire their first blood meal upon 96h PE. PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 7 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Despite this, some females can feed before 96h with the same efficiency, as the ones that fed 24, 48, or 96h PE ingest equal blood amounts (S2 Fig). Expression of protease genes in females is enhanced late upon emergence Vertebrate blood is a rich source of proteins that are digested into amino acids and subse- quently used to complete the gonadotrophic cycle in adult females. The main enzymes involved in the digestion of blood proteins are endoproteolytic serine proteases, carboxypepti- dases, and aminopeptidases [51,52]. Among the DEGs present in clusters B2, B3, and B4, three carboxypeptidases, two aminopeptidases, and nineteen serine proteases that were significantly up-regulated in females upon 48-96h PE (Fig 2B). We also found one aminopeptidase and eight serine proteases which expression increased in males (cluster Bm) (Fig 2B). From the twelve serine proteases known to be expressed in the midgut [53–58], eight were up-regulated in females at 48-96h PE in cluster B3 (Fig 2B), even prior to a blood meal. They were the early phase trypsin (AaET) (AAEL007818), Aa5G1 (AAEL013712), female-specific chymotrypsin (AAEL003060), JHA15 (AAEL001703), AaSPIII (AAEL013623), AaSPIV (AAEL0013628), AaSPV (AAEL008085) and AaSPVI (AAEL010196). Although AaSPI (AAEL007432) and AaSPVII (AAEL010202) were not differentially expressed, they showed a profile similar to the B3 cluster (S4 Fig). Interestingly, the late phase trypsin (AaLT—AAEL013284) did not follow the same pattern, being up-regulated in males but not in females (Fig 2B). Since the AaSPII gene (AAEL008093) was removed from the last version of the Ae. aegypti transcripts gene pre- diction tool (5.1), its expression was not assessed. To determine a clear pattern of serine proteases expression upon emergence, we assessed the expression profile of 90 serine proteases gene sequences previously described in the litera- ture [59]. We observed that the expression of ~ 18% of the serine proteases analyzed was differ- entially up-regulated in females, mostly belonging to cluster B3. Additionally, 36% of these sequences followed the same profile of expression, increasing in females only at 48-96h (S4 Fig). In combination, they represent ~ 54% of the 90 serine proteases sequences investigated, some of them with confirmed roles in blood digestion. The huge increase in protease expres- sion observed suggests that females activate a molecular program to enable massive blood digestion. However, some of the up-regulated genes involved in proteolysis may also partici- pate in other processes including hemostatic regulation in saliva and/or in signaling cascades. Expression of salivary gland anti-hemostatic genes is enhanced in females early upon emergence The salivary glands (SG) produce molecules with anti-hemostatic properties including vasodi- lators, anticoagulants, platelet aggregation inhibitors, among others [20,45–49]. 8 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Fig 1. Clustering of differentially expressed genes (DEGs). Expression profiles of DEGs during the 96-h post-emergence (PE) time course. The body data generated 6 clusters (A) while the head data was grouped in 7 clusters (B). The y-axis shows normalized log2 expression values and the x-axis shows female (F) and male (M) time courses from 2 to 96 hours PE. https://doi.org/10.1371/journal.pntd.0008915.g001 Fig 1. Clustering of differentially expressed genes (DEGs). Expression profiles of DEGs during the 96-h post-emergence (PE) time course. The body data generated 6 clusters (A) while the head data was grouped in 7 clusters (B). The y-axis shows normalized log2 expression values and the x-axis shows female (F) and male (M) time courses from 2 to 96 hours PE. https://doi.org/10.1371/journal.pntd.0008915.g001 Fig 1. Clustering of differentially expressed genes (DEGs). Expression profiles of DEGs during the 96-h post-emergence (PE) time course. The body data generated 6 clusters (A) while the head data was grouped in 7 clusters (B). The y-axis shows normalized log2 expression values and the x-axis shows female (F) and male (M) time courses from 2 to 96 hours PE. https://doi org/10 1371/journal pntd 0008915 g001 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 9 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Notwithstanding, the feeding act is also an immune challenge, thus the saliva also contains lysozyme, antimicrobial peptides, angiopoietins, and lectins [49,50]. Most DEGs up-regulated in the female body and related to the SG (Fig 2A) belong to B2 and B3 clusters and were increased at 24h PE. Those include the salivary apyrase (AAEL006333), serpins (AAEL003182 and AAEL007420), c-type lectin (AAEL000556), angiopoietin (AAEL00749), antigen 5 related proteins (AAEL00793, AAEL003053 and AAEL003057), and mosquito specific families such as D7 (AAEL006417 and AAEL006423), Sialokinins (AAEL00229), aegyptins (AAEL010228 and AAEL010235) and 15–17 kDa proteins (AAEL004809). Notwithstanding, the feeding act is also an immune challenge, thus the saliva also contains lysozyme, antimicrobial peptides, angiopoietins, and lectins [49,50]. Most DEGs up-regulated in the female body and related to the SG (Fig 2A) belong to B2 and B3 clusters and were increased at 24h PE. Expression of salivary gland anti-hemostatic genes is enhanced in females early upon emergence Those include the salivary apyrase (AAEL006333), serpins (AAEL003182 and AAEL007420), c-type lectin (AAEL000556), angiopoietin (AAEL00749), antigen 5 related proteins (AAEL00793, AAEL003053 and AAEL003057), and mosquito specific families such as D7 (AAEL006417 and AAEL006423), Sialokinins (AAEL00229), aegyptins (AAEL010228 and AAEL010235) and 15–17 kDa proteins (AAEL004809). Previtellogenesis: Juvenile hormone signaling and ribosome biogenesis pathways JH is an endocrine regulator that induces the heterodimerization of the JH intracellular recep- tor Methoprene-tolerant (Met) and its coactivator Taiman (Tai) to bind to juvenile hormone regulating elements (JHREs), modulating the expression of several genes [9] (S5A Fig). The JH receptor (AAEL025915) is differentially expressed in the PE phase (B2) and Tai (AAEL023902) showed an increased profile in females, at 48-96h, for most isoforms (S5B Fig). JH signaling transcriptional repression indirectly requires the involvement of other tran- scription factors [16]. Hairy recruits the corepressor Groucho 1 (Gro1) down-regulating target genes [60] (S5A Fig). The Gro1 expression was not included in S5B Fig due to the very low 10 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Fig 2. Female-specific up-regulation of salivary gland and proteases genes. Hierarchical clusterization of salivary gland (A) and serine proteases, aminopeptidases, and carboxypeptidases (B) DEGs for the body. The heatmap y-axi shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B2, B3, B4, and Bm ar cluster names described in Fig 1. https://doi.org/10.1371/journal.pntd.0008915.g002 Fig 2. Female-specific up-regulation of salivary gland and proteases genes. Hierarchical clusterization of salivary gland (A) and serine proteases, aminopeptidases, and carboxypeptidases (B) DEGs for the body. The heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B2, B3, B4, and Bm are cluster names described in Fig 1. https://doi org/10 1371/journal pntd 0008915 g002 Fig 2. Female-specific up-regulation of salivary gland and proteases genes. Hierarchical clusterization of salivary gland (A) and serine proteases, aminopeptidases, and carboxypeptidases (B) DEGs for the body. The heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B2, B3, B4, and Bm are l d ib d i Fi 1 Fig 2. Female-specific up-regulation of salivary gland and proteases genes. Hierarchical clusterization of salivary gland (A) and serine proteases, aminopeptidases, and carboxypeptidases (B) DEGs for the body. The heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B2, B3, B4, and Bm are cluster names described in Fig 1. Fig 2. Female-specific up-regulation of salivary gland and proteases genes. Previtellogenesis: Juvenile hormone signaling and ribosome biogenesis pathways Hierarchical clusterization of salivary gland (A) and serine proteases, aminopeptidases, and carboxypeptidases (B) DEGs for the body. The heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B2, B3, B4, and Bm are cluster names described in Fig 1. https://doi.org/10.1371/journal.pntd.0008915.g002 https://doi.org/10.1371/journal.pntd.0008915.g002 11 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation expression level observed. It is know that Kr-h1 and Hairy work synergistically [61], we observed that Hairy expression had a more pronounced increase in females at 96h, however, Kr-h1 showed different profiles for the two isoforms, one of them increased for both sexes at 96h and the other only to males (S5B Fig). JH plays an essential role during the HGC stimulating the FB competence for protein syn- thesis. The FB priming involves nucleoli enlargement, development of Golgi complex, and an increase in the number of ribosomes [11,62]. One of the genes directly modulated by the JH signaling pathway is the Regulator of Ribosome synthesis 1 (RRS1), that regulates the proteins levels of Ribosomal protein large subunit 32 (RpL32), mediating ribosomal biogenesis [12]. The expression profile of RRS1 (AAEL012185) and RpL32 (AAEL003396) was increased in females at 48-96h PE (S5B Fig). The expression of the major and minor ribosome subunits genes (S6 Fig) and those from the ribosomal biogenesis pathway (Figs 3 and S7) were increased at 48-96h PE (B3). Nine genes (13%) were significantly up-regulated in female bod- ies (B3 cluster) (Fig 3A) from a pathway containing 66 genes (Fig 3B), and another 54 (81%) had the same expression pattern (S7 Fig). JH coordinates a series of events in the ovaries during the PE phase, including the develop- ment of a robust receptor-mediated endocytic pathway, required by the ovaries for Vg uptake [63]. Three genes regulated by this pathway were analyzed: the vitellogenin receptor (VgR), the lipophorin receptor (LpR) and a Heavy-Chain Clathrin (CHC) [64] (S5A Fig). The VgR (AAEL007657) was differentially expressed (B3). The LpR (AAEL019755) has 18 isoforms in the current version (5.1) of Ae. aegypti genome gene prediction, where five isoforms were enhanced in females at 48-96h PE and eight in males (two were DEGs). We could not observe expression at a detectable level for the other isoforms. Previtellogenesis: Juvenile hormone signaling and ribosome biogenesis pathways The CHC (AAEL022819) had two iso- forms and both were expressed similarly in males and females (S5B Fig). Functional enrichment analysis of the DEGs Functional enrichment analysis was based on DEGs gene ontology (GO) classification (p- value <0.05, hypergeometric test; FDR 10% corrected Fisher’s exact test). The enriched GO terms in the body were associated with cell growth, involving cell cycle and division, DNA metabolism, and structure (S8A Fig). The GO terms enriched in the head covered two major functions: (1) movement and muscle contraction; and (2) mitochondrial function, including metabolic pathways, and transport systems related to this organelle (S8B Fig). The functional enrichment analysis did not find gene classes obviously related to hematophagy, however they might reflect new basic and necessary functions that support this habit. The DNA replication pathway/system and the oxidative phosphorylation pathway were analyzed in more detail fur- ther in this work. Increase in DNA metabolism in the female body at 48-96h post-emergence The functional enrichment analysis showed the overrepresentation of the genetic information processing genes in the body. The classes included "nucleus", "chromosome", "nuclear chromo- some", "nuclear envelope", "protein-DNA complex", "cell cycle", "DNA metabolic process", "DNA replication", "cell proliferation", "chromatin assembly" and "single-stranded DNA bind- ing". The DNA replication pathway belongs to the DNA metabolic process and their genes were almost all more expressed in the female body over time when compared to males. This group contains approximately 31% of DEGs from Clusters B2 and B3 and more 66% following the DEG expression profile (Figs 4A and S9A), summing almost all genes. We also observed an increase in gene expression of cell cycle regulators in the female body at 48-96h PE (cluster B3), such as cyclins and cyclin-dependent kinases (Cdk), and PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 12 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Fig 3. Female-specific up-regulation of the ribosome biogenesis pathway. Heatmap of differentially expressed g (DEGs) for the body (A). The y-axis shows gene codes and the x-axis the female (F) and male (M) time courses fro to 96 hours; B3 is a cluster name described in Fig 1. Ribosome biogenesis pathway (B). DEG gene names are in re boxes (significantly upregulated in female bodies, B3 cluster), genes not DEG but with similar expression profile i pink, dissimilar or invariable profile in green and absent genes in white (Source: KEGG Mapper tool). The compl heatmap was included in S7 Fig. https://doi.org/10.1371/journal.pntd.0008915.g003 Fig 3. Female-specific up-regulation of the ribosome biogenesis pathway. Heatmap of differentially expressed (DEGs) for the body (A). The y-axis shows gene codes and the x-axis the female (F) and male (M) time courses f to 96 hours; B3 is a cluster name described in Fig 1. Ribosome biogenesis pathway (B). DEG gene names are in r boxes (significantly upregulated in female bodies, B3 cluster), genes not DEG but with similar expression profile pink, dissimilar or invariable profile in green and absent genes in white (Source: KEGG Mapper tool). The comp heatmap was included in S7 Fig. https://doi org/10 1371/journal pntd 0008915 g003 Fig 3. Female-specific up-regulation of the ribosome biogenesis pathway. Heatmap of differentially expressed genes (DEGs) for the body (A). Muscle development in females head at 2-12h post-emergence The H1 cluster (Figs 1B and S11) had 18 genes (51%) associated with movement and struc- tural functions, including cytoskeleton, muscle contraction and development. The gene ontol- ogy analysis of the head DEGs (S8B Fig) revealed the enrichment of "cytoskeleton" and "actin cytoskeleton" as cellular components and "muscle contraction" as a biological process. Among the proteins identified within these groups were myosins, tropomyosins, paramyosins, muscle lim proteins and myofilins. The genes coding these proteins were significantly up-regulated on females from 2 to 24h PE (S11 Fig). Increase in DNA metabolism in the female body at 48-96h post-emergence The y-axis shows gene codes and the x-axis the female (F) and male (M) time courses from 2 to 96 hours; B3 is a cluster name described in Fig 1. Ribosome biogenesis pathway (B). DEG gene names are in red boxes (significantly upregulated in female bodies, B3 cluster), genes not DEG but with similar expression profile in pink, dissimilar or invariable profile in green and absent genes in white (Source: KEGG Mapper tool). The complete heatmap was included in S7 Fig. https://doi.org/10.1371/journal.pntd.0008915.g003 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 13 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation chromosome associated proteins such as histones (S9B Fig). The Cyclin-dependent kinase 2 (Cdk2)—Cyclin E complex is required for G1/S transition and endoreplication in Drosophila [65,66]. The transcription factor E2F1 stimulates the entry in the S phase by regulating the expression of cyclin E and genes related to DNA synthesis [67]. We observed the significant up-regulation of Cyclin E (AAEL009057), and the expression increase of Cdk2 (AAEL023423) and four isoforms of E2F (AAEL022462B-E) (S9 Fig). The DNA mismatch repair pathway is responsible for the repair of mismatched base pairs during DNA replication [68] and was already described in Ae. aegypti [69]. Among its 21 genes, 5 were significantly up-regulated in females (cluster B3) and 15 more were enhanced with a similar profile (S10 Fig). Altogether, our data suggests that the cells of the female’s body may be either proliferating or increasing their DNA content through the modulation of cell cycle regulators expression and the increase in DNA replication and repair pathways. Activation of mitochondrial biogenesis increases respiratory capacity and ATP-linked respiration early upon emergence in females Among the 43 genes in cluster H2, 21 (48%) belong to the oxidative phosphorylation (OXPHOS) pathway. These genes correspond to subunits of complexes I, II, III, IV and F1Fo ATP synthase (Figs 4B and S11). Remarkably, these genes were those that were significantly up-regulated in the females head over time when compared to males. We also observed that 63 genes (70%) had the same H2 group expression profile, but not differentially expressed. Only a small fraction of genes (6%) in the OXPHOS pathway presented an expression profile that did not fit the H2 cluster (Figs 4B and S12). Globally, we observed a female-specific expression increase of genes involved in OXPHOS pathway along maturation. Since the expression of genes involved in OXPHOS pathway was remarkably increased in female heads along PE, we next wondered whether this would be reflected in a gain of meta- bolic function. We then determined oxygen consumption rates (OCR) using pyruvate and proline (Pyr+Pro) as substrates along the same time course in mechanically permeabilized male and female heads (Fig 5). The reason to use these substrates lies in the fact that respira- tion coupled to ATP synthesis in Ae. aegypti flight muscle mostly uses proline and pyruvate to sustain respiration rates [38,40]. Indeed, we observed a trend towards an increase in expression of genes coding for pyruvate/proline transport and/or oxidation in the female upon PE (Figs 5A and S13A). Examples include proline dehydrogenase, subunits of pyruvate dehydrogenase complex, and mitochondrial pyruvate carrier (Fig 5A). The expression profile of these genes was very close to the H2 cluster, the same found for almost all genes of the OXPHOS pathway. Fig 5B shows a representative trace of oxygen consumption of mechanically permeabilized Ae. aegypti female heads using Pyr+Pro as substrates. The oxygen consumption coupled to ATP synthesis (ATP-linked) significantly increased in female heads over time (Fig 5C). This strongly indicates that increased expression of OXPHOS components in females head upon PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 14 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Fig 4. Female-specific up-regulation of DNA replication and oxidative phosphorylation genes. The DNA replication pathway was up-regulated in the female body (A) and the oxidative phosphorylation (OXPHOS) pathway in the head (B). Activation of mitochondrial biogenesis increases respiratory capacity and ATP-linked respiration early upon emergence in females Differentially expressed genes (DEG) names are in red boxes (upregulated in female body, clusters B2, B3, and H2), genes not DEG but with similar expression profile in pink, dissimilar or invariable in green and absent genes in white (Source: KEGG Mapper tool). The complete heatmaps were included in S9 and S12 Figs. https://doi.org/10.1371/journal.pntd.0008915.g004 Fig 4. Female-specific up-regulation of DNA replication and oxidative phosphorylation genes. The DNA replication pathway was up-regulated in the female body (A) and the oxidative phosphorylation (OXPHOS) pathway in the head (B). Differentially expressed genes (DEG) names are in red boxes (upregulated in female body, clusters B2, B3, and H2), genes not DEG but with similar expression profile in pink, dissimilar or invariable in green and absent genes in white (Source: KEGG Mapper tool). The complete heatmaps were included in S9 and S12 Figs. htt //d i /10 1371/j l td 0008915 004 Fig 4. Female-specific up-regulation of DNA replication and oxidative phosphorylation genes. The DNA replication pathway was up-regulated in the female body (A) and the oxidative phosphorylation (OXPHOS) pathway in the head (B). Differentially expressed genes (DEG) names are in red boxes (upregulated in female body, clusters B2, B3, and H2), genes not DEG but with similar expression profile in pink, dissimilar or invariable in green and absent genes in white (Source: KEGG Mapper tool) The complete heatmaps were included in S9 and S12 Figs Fig 4. Female-specific up-regulation of DNA replication and oxidative phosphorylation genes. The DNA replication pathway was up-regulated in the female body (A) and the oxidative phosphorylation (OXPHOS) pathway in the head (B). Differentially expressed genes (DEG) names are in red boxes (upregulated in female body, clusters B2, B3, and H2), genes not DEG but with similar expression profile in pink, dissimilar or invariable in green and absent genes in white (Source: KEGG Mapper tool). The complete heatmaps were included in S9 and S12 Figs. https://doi.org/10.1371/journal.pntd.0008915.g004 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 15 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Fig 5. Increased expression of genes involved in mitochondrial processes drive respiratory rates and OXPHOS. Activation of mitochondrial biogenesis increases respiratory capacity and ATP-linked respiration early upon emergence in females Heatmap of genes related to pyruvate and proline oxidation (A), the y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours, details in S13A Fig; typical traces of oxygen consumption rates (OCR) (B), the OCR (red line) and concentration (blue line) were obtained from mechanically permeabilized Aedes Rio female heads at 24 hours PE using Pyr+Pro as substrates; oxygen consumption linked to ATP synthesis (OXPHOS) (C); maximum respiratory rates (ETS) (D); Cytochrome c oxidase (COX) activity (E); Leak represents the oxygen consumption in the presence of high substrate concentration but in the absence of ADP (F); residual oxygen consumption (ROX) (G); citrate synthase activity (H). Bar graphs show mean (SEM) for male and female at different PE time points. Interaction p-value between sex and time factors (two-way ANOVA) are displayed above the bars. ns = not significant; p-value <0.05; p-value <0.01; p- value <0.001. htt //d i /10 1371/j l td 0008915 005 Fig 5 Increased expression of genes involved in mitochondrial processes drive respiratory rates and OXPHOS Heatmap of genes related to pyruvate and f genes involved in mitochondrial processes drive respiratory rates and OXPHOS. Heatmap of genes related to pyruvate an Fig 5. Increased expression of genes involved in mitochondrial processes drive respiratory rates and OXPHOS. Heatm Fig 5. Increased expression of genes involved in mitochondrial processes drive respiratory rates and OXPHOS. Heatmap of genes related to pyruvate and proline oxidation (A), the y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours, details in S13A Fig; typical traces of oxygen consumption rates (OCR) (B), the OCR (red line) and concentration (blue line) were obtained from mechanically permeabilized Aedes Rio female heads at 24 hours PE using Pyr+Pro as substrates; oxygen consumption linked to ATP synthesis (OXPHOS) (C); maximum respiratory rates (ETS) (D); Cytochrome c oxidase (COX) activity (E); Leak represents the oxygen consumption in the presence of high substrate concentration but in the absence of ADP (F); residual oxygen consumption (ROX) (G); citrate synthase activity (H). Bar graphs show mean (SEM) for male and female at different PE time points. Interaction p-value between sex and time factors (two-way ANOVA) are displayed above the bars. ns = not significant; p-value <0.05; p-value <0.01; p- value <0.001. Fig 5. Activation of mitochondrial biogenesis increases respiratory capacity and ATP-linked respiration early upon emergence in females Increased expression of genes involved in mitochondrial processes drive respiratory rates and OXPHOS. Heatmap of genes related to pyruvate and proline oxidation (A), the y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours, details in S13A Fig; typical traces of oxygen consumption rates (OCR) (B), the OCR (red line) and concentration (blue line) were obtained from mechanically permeabilized Aedes Rio female heads at 24 hours PE using Pyr+Pro as substrates; oxygen consumption linked to ATP synthesis (OXPHOS) (C); maximum respiratory rates (ETS) (D); Cytochrome c oxidase (COX) activity (E); Leak represents the oxygen consumption in the presence of high substrate concentration but in the absence of ADP (F); residual oxygen consumption (ROX) (G); citrate synthase activity (H). Bar graphs show mean (SEM) for male and female at different PE time points. Interaction p-value between sex and time factors (two-way ANOVA) are displayed above the bars. ns = not significant; p-value <0.05; p-value <0.01; p- value <0.001. PE reflects in improved energy supply by mitochondria. The maximum respiratory rates (ETS), induced by uncoupling of respiration from ATP synthesis, also increased significantly in females over PE time points (Fig 5D). Interestingly, the slight differences between ATP- linked and ETS respiratory rates indicate that ATP synthesis through OXPHOS requires almost the maximal capacity provided by mitochondria, similarly to flight muscle mitochon- dria [38,40]. Cytochrome c oxidase (COX) activity (Fig 5E), leak (Fig 5F), and residual respi- ratory rates (Fig 5G) followed the same trend, significantly increasing in females’ heads over time. Remarkably, respiratory rates in males´ heads were not significantly altered upon PE for any of the mitochondrial metabolic states investigated (Fig 5). Therefore, increased expression of OXPHOS pathway genes (Fig 4B) resulted in a female-specific gain of function in Ae. aegypti head in the first days after emergence, underscoring the key role of OXPHOS to HGC (Fig 5). The simultaneous increase in all mitochondrial metabolic states assessed is suggestive of induction of mitochondrial biogenesis. We then measured citrate synthase (CS) activity, as a proxy of mitochondrial content [70]. A two-step increase in CS activity was observed in female 16 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation heads: the first one at 12-24h PE and a second and higher one at 48-96h PE. Activation of mitochondrial biogenesis increases respiratory capacity and ATP-linked respiration early upon emergence in females Curiously, the pat- tern of increased CS activity is sex-independent, although at the end of the maturation process (96h) was significantly higher in females compared to males (Fig 5H). Despite this, the overall comparison between the female and male CS time curves was not significant. We then consid- ered whether mitochondrial biogenesis would be responsible for the differences observed in respiratory rates, by normalizing OCR by their respective CS activities in each sex group and time points. S13B–S13F Fig show that all significant time-sex-related differences observed in Fig 5 were completely abolished, regardless the mitochondrial metabolic state. Together, these results indicate that the maturation process upon emergence in females´ head involves the activation of mitochondrial biogenesis that ultimately increase mitochondrial content, respira- tory rates and energy provision by OXPHOS. The expression of genes involved in mitochondrial electron transport system, heme biosyn- thesis and mitochondrial DNA metabolism are regulated by transcriptional factors such as peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1ɑ), mitochon- drial transcription factor A (TFAM) and dimethyladenosine transferase 2 (TFB2M) [71–73]. Interestingly, the Ae. aegypti orthologues of PGC-1ɑ (AAEL003768), TFAM (AAEL013643) and TFB2M (AAEL012582) were up-regulated in female heads earlier than those involved in OXPHOS pathway (S14 and S12 Figs). We also observed the expression of the first enzyme of the heme biosynthetic pathway, 5-aminolevulinate synthase (ALAS2—AAEL007787), that had two of three isoforms with a similar expression profile as the OXPHOS pathway genes, a tran- sient increase peaking at 12-24h (S14 Fig). Therefore, we propose the hypothesis that activa- tion of specific transcription factors involved in mitochondrial biogenesis is an early event that results in later increases in expression of OXPHOS pathway components, and ultimately enhancing respiratory rates and energy supply through the oxidative phosphorylation. Discussion The understanding of the hematophagic and gonotrophic capacitation (HGC) as a maturation process that occurs in newly emerged females is fundamentally important to conceptually identify specific new targets for vector control. Previous transcriptomic, microarray and prote- omic studies have studied the post-emergence (PE) phase in females, revealing altered meta- bolic pathways in midgut, fat body and salivary glands [16–20,74], but just the mosquito antenae transcriptome compared gene expression based both on sex and time [21]. Notwith- standing, the available knowledge did not consider the sexual dimorphism in the time context of PE phase and were mostly focused on the fat body. To fill this gap we performed time- dependent molecular and biochemical analyses to comprehensively identify mechanisms involved in Ae. aegypti HGC comparing both sexes upon emergence. Our transcriptomic anal- yses showed that genes involved in blood feeding were significantly up-regulated exclusively in females even prior to the first blood meal, in a time-dependent manner. We observed that cell growth and DNA metabolism related genes were more expressed in the female body than in males. We also showed that the OXPHOS pathway and consequently the respiration rates enhanced in females head, compared to the male, due to a remarkable increase in mitochon- drial content. Collectively, the data presented here support the notion the activation of a sex- biased program in female´s head involving mitochondrial biogenesis and OXPHOS activity is a key mechanism underlying HGC process. Although the mechanisms involved in the activa- tion of mitochondrial biogenesis genes remain elusive, we envisage that targeting such mecha- nisms would represent new avenues for vector control strategies. The Aedes Rio colony started recently from field mosquitoes captured in Rio de Janeiro state, Brazil. The assessment of the females blood feeding and host seeking behaviours showed PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 17 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation that both started at 24h and increased until 96h (S1 Fig). These results are in agreement with reported data. Early studies determined the pattern of the first blood-feeding for Ae. aegypti, where most of the individuals (~50%) acquired the first blood meal upon 24–48 h PE (reviewed by [44]. The host seeking behavior has been described after 18-24h PE [75]. Here we observed cohorts of gene expression unique to females in the PE phase in the head and body (Fig 1). Discussion It is remarkable that each cluster was mainly associated with a specific func- tion/system, except cluster B3 that contained 484 genes, and therefore more functions. The H1 cluster (Fig 1B) was associated with movement function, with proteins related to the cytoskele- ton and to muscle contraction. The head actually has several muscles associated with sensory organs and mouthparts, including the salivary pump that connects the esophagus, neck and tho- rax [44]. From 2 to 24h PE there was an up-regulation of proteins associated with muscular func- tion (S11 Fig) previously to the blood-feeding behaviour start (S1 Fig), suggesting that the head muscles development after the adult emergence is necessary for the blood ingestion. The decision of using the whole head and decapitated body prevented the identification of the origin tissues of DEG in some cases, but also avoided a priori exclusions that allowed findings like this related to the muscular tissue. The H2 cluster (Fig 1B) had a very marked relationship with the OXPHOS pathway (Fig 4B), almost 50% of the H2 genes coded proteins to this pathway. The salivary pro- tein coding genes are in the cluster B2 (16 genes, representing 27% of the cluster) and cluster B3 (7 genes, representing 1.5% of the cluster) (Figs 1A and 2). The cluster B3 (Fig 1A) was not only the biggest cluster with 484 genes, but also the most functionally diverse. This particular cluster contained proteases, cell cycle, DNA replication and repair, ribosome and ribosome biogenesis, transcription factors and signaling genes, among others (Figs 3–5 and S4–S8). The remarkable changes in gene expression that females experienced upon emergence can be observed by the inflection present at the 24h time point in almost all cluster gene expression curves (Fig 1: B1, started baseline at 24h; B2 and H2, sine wave top; B3 and B4, started expres- sion increase). These gene expression changes at 24h were synchronized and very closely related to the female ability to start to feed on blood at this time (reviewed by [44]) (S1 Fig). Among the genes found up-regulated in females were those related to blood feeding, so we decided to evaluate the expression of genes previously associated with the gonotrophic cycle, such as sali- vary proteins, proteases, ribosome biogenesis and JH signaling pathways (Figs 2–4 and S4–S6). Salivary genes were up-regulated in females as preparation for blood meal intake Salivary sex-specific proteins of 2 to 5 days old adult Ae. aegypti were already described [20] and our data confirmed the up-regulation in the female body of 25 salivary genes from the 84 described (B2 and B3 clusters, Fig 2A). The difference probably was due to the samples, while we used the mosquito whole body (that contains the salivary glands), Ribeiro used only the sal- ivary glands. One example of up-regulated gene is aegyptin (AAEL10235-RA), the coded pro- tein binds to collagen, inhibiting platelet aggregation and adhesion. Its down-regulation promotes longer probing time and reduction on feeding success [48]. All of the salivary up- regulated genes have the same transient expression, peaking at 24h or 48 PE. Their maximum production matches the time that the females are enabled to acquire a blood meal, showing again that the saliva is obviously a piece of the HGC. Proteases involved in blood digestion are highly up-regulated in females body After the ingestion of a blood meal, proteases, especially trypsins, play an important role in protein digestion [52,76]. The literature has many descriptions of trypsins that have their 18 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation protein level/activity triggered by a blood meal, such as AaET, AaSPI, AaSPVI, AaSPVII, AaLT, and female-specific chymotrypsin [52–55,57,77]. Although we did not include blood- fed females, we could find 18% of all proteases (listed by [59]) significantly up-regulated in the body at 48-96h (B3 cluster) and other 36% with an expression increase (Figs 2B and S4). These results suggest that some proteases are up-regulated by the HGC, previously to the first blood feeding, complementary to the common-sense knowledge of protease regulation by the blood diet ingestion. Two serine proteases with trypsin-like activities account for the majority of the blood meal digestion [52,53]. AaET, that shows an intense proteolytic activity between 1 and 6h after a blood meal, and AaSPVI, that belong to the 5G1 family, has it’s main activity (75%) from 12- 36h after a blood meal [52,53]. Evidence indicates that AaET is transcriptionally regulated by JH and translationally regulated by a blood meal [78,79]. Our results suggest that this feature could not be exclusive from AaET since the proteases AeET (AAEL007818), female-specific chymotrypsin (AAEL003060), AaSPVI (AAEL010196) and AaSPVII (AAEL010202) had expression peaking at 48h PE (Fig 2B) and were already described to have their activity increased by the blood meal. Despite the classical role of serine proteases in midgut blood digestion, we cannot rule out their potential involvement in key biological functions in other tissues. For instance, it was already described the presence of serine proteases in the salivary glands of adult females and it was suggested they play a role in immunity [48]. The male expression increase of several trypsins analyzed (Fig 2, cluster Bm) was not an expected result. For example, the late phase trypsin (AaLT—AAEL013284) is known as a midgut-specific pro- tein that increases in content and activity after a blood meal in females [79,80]. Interestingly, it was significantly up-regulated in males after the emergence, raising questions about its biologi- cal role and tissue origin on the males, that are not under HGC. Juvenile Hormone signaling differs between female and male mosquitoes The JH drives the shift of unfed Culex nigripalpus females from nectar to blood-host odour [81]. This hormone acts regulating gene expression during the PE phase, where the genes/pro- teins involved in the signaling were already identified in the female fat body and ovaries [82,83]. Our results revealed these genes have expression differences between the female and male mosquitoes (S5B Fig). One isoform of the key gene Met (AAEL025915-RC) is signifi- cantly up-regulated in the female body. Some isoforms of Tai (AAEL023902) and Hairy (AAEL027674) were also increased at 48-96h PE in the female body, but others showed expres- sion on the male body. The gene Kr-h1 was previously classified as late PE phase gene [16]. We observed the same late expression pattern to both sexes for Kr-h1 isoform A (AAEL002390-RA) while the other isoform was increased only in males (AAEL002390-RB) (S5B Fig). These time-sex differences highlight the relevance of JH signaling pathway for the female HGC and also are closely related to the striking difference in the gene expression clus- tering between the sexes (Fig 1). An important molecular machinery regulated by JH signaling is the ribosome biogenesis pathway. This machinery is important for vitellogenesis, including the synthesis of Vitello- genin (Vg), a major yolk protein. The female time-dependent expression increase of ribosomal genes was shown on the fat body [12]. Here, we revealed that the expression of almost all genes of the ribosome biogenesis, including the ribosome subunits themselves have significant up- regulation or increased expression not only based on time, but also on sex (Figs 3 and S6 and S7). The vitellogenin receptor (VgR) has a known expression profile in the ovary by Northern blot [84]. Our observations confirmed the VgR (AAEL007657) female expression profile, sig- nificantly up-regulated in the body (S5B Fig), due to the vitellogenesis preparation. PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 19 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation The lipid metabolism is also related to the JH signaling [74]. In Ae. aegypti female fat body there is a known TAG accumulation until 72h PE and a decrease in β-oxidation and lipid catabolism [74]. Here, we observed sex-specific expression increase of the lipophorin receptor isoforms (LpR) (AAEL019755) (S5B Fig). Cell cycle control during previtellogenesis Cells in endoreplication suppress mitosis and cytokinesis repeating S and G phases succes- sively, increasing their size and ploidy [85]. In Locusta migratoria, the endoreplication in fat body is regulated by JH signaling that induces the transcription of chromosome maintenance (Mcm) genes Mcm4 and 7, cell-division-cycle 6 (cdc6), cyclin-dependent kinase 6 (Cdk6) and E2F [86,87]. The G2 to M phase progression can be avoided down-regulating the expression of the Mitotic cyclin-dependent kinase (M-CDK), also known as cdc2/CDK1, or their protein levels by anaphase promoting complex (APC) ubiquitin-mediated proteolysis of cyclins or cyclin kinase inhibitors [65]. We observed the significant up-regulation of Mcm4 (AAEL10086), Mcm7 (AAEL000999), and the expression increase of cdc6 (AAEL010855), Cdk4/6 (AAEL001407), and APC complex proteins (S9 Fig). Besides the regulation, the DNA replication pathway itself had 97% of its genes significantly up-regulated or with enhanced expression in the female body (Figs 4A and S9A). Other proteins associated with the cell cycle regulation and progression were also up- regulated, such as cyclins, cyclin-dependent kinases, and structural proteins that associate with the DNA such as histones (S9B Fig). These observations suggest the control of the G1 to S pro- gression, possibly avoiding M phase, which could be a sign of endoreplication engagement [88,89]. This regulation is crucial to the HGC, and some changes can severely impact those processes, such as the depletion of Cdk6 and E2F that are known to reduce the endoreplication in the fat body arresting oocyte maturation [90]. Juvenile Hormone signaling differs between female and male mosquitoes The five isoforms more expressed in females might be related to the fat body lipid stock increase and/or the oocytes preparation for the uptake of lipophorin during vitellogenesis [64]. In males, the other eight isoforms of LpR had increased expression compared to females, pointing that the lipid distribution may differ strongly between sexes in the first days PE (S5B Fig). Muscle changes in females’ heads Miofilin is a core protein that interacts with myosins sub filaments that is required for the cor- rect assembly of thick filaments in insects striated muscles [93]. Flightin is essential for the sta- bility of thick filaments in the indirect flight muscle of Drosophila by regulating the filament and sarcomere length [94,95]. It also contributes to stiffness and performance of oscillatory work [96]. The contraction in thin filaments striated muscles are associated with the activation of the tropomyosin-troponin complex through Ca2+ binding [97]. Here we observe a significant up-regulation of myofilin (AAEL001082), flightin (AAEL004249), myosin light chain 1 (AAEL012207), myosin heavy chain (AAEL026217), tro- ponins I, C and T (AAEL010850, AAEL06572 and AAEL026967) and tropomyosin (AAEL002761) in females at 2-24h PE (S11 Fig). Notwithstanding the mentioned proteins, the H1 cluster (Fig 1) sums 51% of its proteins associated with the actin cytoskeleton and muscle contraction, as identified by GO enrichment (S5B Fig). The sex differences in gene expression observed in the head suggest that females muscle thick filaments had improvement assembly, stability and/or strength. There are many muscles at the mosquito head, they allow movements in sensory organs and mouthparts. Likewise the diet intake and saliva injection are coordinated by the cibarial and pharyngeal pumps that con- tract in alternation, oscillating at a frequency of 4.3 Hz [98]. The physiological differences between sexes demands from females more sensory and feeding challenges, since they need to find the blood source and suck a fluid that is more viscous than sap, needing higher pump power [99]. It is important to notice that the higher female expression of the genes related to muscular function (S11 Fig) occurs during HGC, previously to the observation of the first engagement in a blood meal and may be needed for it but further investigation is necessary to define their relation. Increasing of the DNA mismatch repair pathway and decreasing of apoptosis Considering the pathways we found regulated (ribosome biogenesis, ribosome subunits, JH signaling, MMR, DNA 20 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation replication, cell cycle regulators, and apoptosis) (Figs 3 and S5–S9) and the literature insights in L. migratoria and Drosophila, we suspect the fat body and midgut as possible sights of endoreplication [88,90]. The polyploid phenotype provides an advantage to synthesize and secrete a huge amount of macromolecules [85]. We show that during HGC there is an expres- sion increase in the machinery for protein synthesis (ribosome biogenesis and ribosomes) trig- gered by JH signaling pathway, possibly supporting the known fat body huge and rapid biosynthesis after the first blood meal. Increasing of the DNA mismatch repair pathway and decreasing of apoptosis The endoreplication process is also related to changes on the DNA maintenance and apoptosis pathways in eukaryotic cells [91]. The key genes of the DNA mismatch repair pathway (MMR) activation MLH1 (AAEL005858) and PMS2 (AAEL026487) were significantly up-regulated in the female body together with the expression increase of 71% of the other genes from this path- way (S10 Fig). They followed the same expression pattern of the endoreplication genes already mentioned (S9 Fig), indicating a possible enhancement of the DNA replication and repair in the females in the first hours PE. The apoptosis is controlled to avoid the death of the polyploid cells [91]. At 48–96 PE, one isoform of the inhibitor of apoptosis 1 gene (Aeiap1) The endoreplication process is also related to changes on the DNA maintenance and apoptosis pathways in eukaryotic cells [91]. The key genes of the DNA mismatch repair pathway (MMR) activation MLH1 (AAEL005858) and PMS2 (AAEL026487) were significantly up-regulated in the female body together with the expression increase of 71% of the other genes from this path- way (S10 Fig). They followed the same expression pattern of the endoreplication genes already mentioned (S9 Fig), indicating a possible enhancement of the DNA replication and repair in the females in the first hours PE. The apoptosis is controlled to avoid the death of the polyploid cells [91]. At 48–96 PE, one isoform of the inhibitor of apoptosis 1 gene (Aeiap1) (AAEL009074-RE) was significantly up-regulated in females, while the other isoforms were relevant to males (AAEL09074-RB/AAEL009074-RC) (S9B Fig). The core caspases activated during apoptosis, AeCASP7 (AAEL012143) and AeCASP8 (AAEL014348) [92] are down-reg- ulated in females at 48-96h PE (S9B Fig). The enhancement of Aeiap1 and decrease of AeCASP7 and AeCASP8, suggests that apoptosis pathway was down-regulated, corroborating with the hypothesis of endoreplication activation. (AAEL009074-RE) was significantly up-regulated in females, while the other isoforms were relevant to males (AAEL09074-RB/AAEL009074-RC) (S9B Fig). The core caspases activated during apoptosis, AeCASP7 (AAEL012143) and AeCASP8 (AAEL014348) [92] are down-reg- ulated in females at 48-96h PE (S9B Fig). The enhancement of Aeiap1 and decrease of AeCASP7 and AeCASP8, suggests that apoptosis pathway was down-regulated, corroborating with the hypothesis of endoreplication activation. Altogether, our data suggests that endoreplication is activated. Mitochondrial biogenesis triggers an increase in mitochondrial content and respiratory rates A remarkable observation was the early increase in expression of mitochondrial biogenesis transcription factors peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1ɑ; AAEL003768), the mitochondrial transcription factor A (TFAM) (AAEL013643) and dimethyladenosine transferase 2 (TFB2M) (AAEL012582) (S14 Fig). PGC-1ɑ is known to induce mitochondrial biogenesis by increasing the expression of genes involved in electron transport system, heme biosynthesis, mitochondrial DNA (mtDNA) transcription and replica- tion [71–73]. Interestingly, the expression of PGC-1ɑ occurred early to the OXPHOS pathway components, suggesting a regulatory role in our model. Similarly, the expression of TFAM and TFB2M, which are key activators of transcription and replication of mtDNA [100], exhib- ited an expression profile similar to PGC-1ɑ (S14 Fig). On the other hand, the expression of nuclear respiratory factors 1 and 2 (NRF1/2) did not follow this trend, since their expression was reduced in female heads (S14 Fig). Indeed, we observed a significant up-regulation of elec- tron transport system genes (Fig 4B). We also observed expression increase of many other PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 21 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation genes involved in OXPHOS including mitochondrial pyruvate carrier 1 and 2, proline dehy- drogenase, TCA cycle enzymes, as well as many components of the electron transport system (Figs 4B, 5A and S12). Importantly, these events culminated with a striking increase in mito- chondrial content, respiratory rates and ATP-linked respiration (Figs 5 and S13). Although the mechanisms that trigger PGC/Tfam expression remain elusive, the activation of a con- certed program towards energy provision through OXPHOS in female heads is clear. Conceiv- ably, increased ATP demand is synced with the start of the blood feeding and host seeking behaviors (S1 Fig) during the HGC. The aforementioned muscle differences together with the female sensory neuronal activity (required for host seeking) may be the source of the extra energy demand that could be met by a more robust energy provision process (OXPHOS). The synapses require a huge energy requirement. The regulation of ion contents across the membrane, the synaptic vesicles trafic, the neurotransmitters secretion and reuptake are very high energy demands, that is provided by the mitochondrial metabolic activity [101]. Addi- tionally, the mitochondria responds to energy requirements and are transported through the neuron as needed [102–105]. Specialized cells, such as the photoreceptors cells, have a high mitochondrial density that can be redistributed according to energy demand [106]. Mitochondrial biogenesis triggers an increase in mitochondrial content and respiratory rates In newly emerged females, this energy power system might be adjusting to be able to support the per- ception of huge amounts of new environmental clues, and contributing to the maturation of the host seeking behavior, that occurs at 24h PE (S1 Fig) during HGC. More research needs to be done in order to determine the tissue specificity of the phenotype and the relationship with the blood feeding and host seeking behaviors. HGC and vector control In the female head, PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 22 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation at 2-24h PE (cluster H1) there was an up-regulation of genes related to muscle development and contraction, suggested to be associated with the feeding/sucking pumps strengthening for the blood ingestion, denser than sap. At 24h PE (cluster H2) there was the up-regulation of the oxidative phosphorylation pathway. Functional assessment of mitochondrial function revealed a gradual increase in respiration capacity, ATP-linked respiration and mitochondrial content until 96h, suggesting the activation of mitochondrial biogenesis in heads is a required step towards blood sucking habit. The increase in ATP offer could supply the intense muscle con- traction, brain activity and chemosensory responses required before or during the blood feed- ing. Considering the female body, at 24h PE (cluster B2) there was an increase in salivary gland genes that allow the blood ingestion by their antihemostatic properties. Several pathways were enhanced at 48-96h PE (cluster B3). The huge increase in trypsins is probably related to blood digestion, and the cell cycle, DNA metabolism, ribosome biogenesis, and juvenile hor- mone signaling pathways are possibly related to polyploidization (endoreplication) and intense biosynthesis preparation for the vitellogenic stage. Our data showed a strong relationship between the up-regulation of female-specific genes along the first days PE and the hematopha- gic capacitation and maturation process, unraveling not only new mosquito biological aspects but also new potential targets for vector control. HGC and vector control The hematophagic and gonotrophic capacitation (HGC) is a female-specific process that takes place in the first days after the emergence, resulting in a large number of differentially expressed genes (DEG) peaking at different times during this period. We envisage that identification of critical molecular mediators of HGC as potential targets to be explored in the future, represent- ing innovative and valuable tools aiming the reduction in Ae. aegypti fitness and vector control. In this sense, we suggest a small set of genes involved in HGC considering those DEG with the strongest sex-dependent expression (highest in females and lowest in males) as the most inter- esting ones to be targeted by available genetic interventions. These include the salivary antigen- 5 protein AG5-4 (AAEL000793-RA) and the salivary basic peptide 4 (AAEL008310-RA), both with expression levels very close to Aegyptin (AAEL010235-RA). Among the proteases, JHA15 (AAEL001703-RA) and female-specific chymotrypsin (AAEL003060-RA) are good candidates as both have expression levels quite close to AaETs (AAEL007818-RA-B). The tubulin beta chain gene (AAEL002848-RA—Muscle group), RFC3/5 (AAEL007581-RA and AEL009465-RA —DNA repair group), Cyclin B (AAEL010094-RA—Cell cycle group) had the highest and sig- nificant expression difference between sexes. Notwithstanding, genes with sex-specific expres- sion can also highlight CRISPR-Cas9 gene disruption candidates, like the Histone H3 (AAEL019635-RA) which is barely expressed in males, and lipophorin receptor (AAEL019755) that have 13 isoforms predicted. The transcripts RA and RP were DEG on the male (cluster Bm) while the transcript RO despite not DEG was the one with the highest female expression. Finally, despite clear sex-dependent increases in mitochondrial metabolism gene expression toward the females were observed (S12 Fig), the overall changes were not as high as those iden- tified in other mechanisms. For this reason, we could not suggest any particular mitochondrial mechanism to be further explored as a valuable target at this point. Finally, despite clear sex-dependent increases in mitochondrial metabolism gene expression toward the females were observed (S12 Fig), the overall changes were not as high as those iden- tified in other mechanisms. For this reason, we could not suggest any particular mitochondrial mechanism to be further explored as a valuable target at this point. The present study provides insightful information about sex and time effects on the gene expression dynamics during the first four days after mosquito emergence. S2 Fig. Blood intake by Aedes Rio females during post-emergence phase. Total protein amount was quantified per midgut of fed and unfed females after offering an artificial blood meal for 30 minutes. "X", at 2 and 12h PE none mosquito took the blood meal. (Tukey’s cor- rected one-way ANOVA;  P<0.0001. N = 4). S2 Fig. Blood intake by Aedes Rio females during post-emergence phase. Total protein amount was quantified per midgut of fed and unfed females after offering an artificial blood meal for 30 minutes. "X", at 2 and 12h PE none mosquito took the blood meal. (Tukey’s cor- rected one-way ANOVA;  P<0.0001. N = 4). amount was quantified per midgut of fed and unfed females after offering an artificial blood meal for 30 minutes. "X", at 2 and 12h PE none mosquito took the blood meal. (Tukey’s cor- rected one-way ANOVA;  P<0.0001. N = 4). (TIF) S3 Fig. Validation of female-specific expression profiles by qPCR analysis. One gene was selected to represent the profile of clusters: B1 (A), B2 (B), B3 (C), H1 (D), and H4 (E). Bar graphs show mean (SEM) for males and females. The post-emergence time points tested were 2, 24, and 96 hours. Interaction p-values between sex and time factors (two-way ANOVA) are dis- played above the bars. ns = not significant; p-value <0.05; p-value <0.01, p-value <0.001. (TIF) S4 Fig. Serine proteases expression profile. Hierarchical clusterization of the serine protease genes in the post-emergence time points of 2, 12, 24, 48, and 96 hours. Heatmap y-axis shows gene codes and x-axis the female (F) and male (M) time courses from 2 to 96 hours. B2, B3, and Bm are cluster names described in Fig 1. Up-regulated genes are highlighted by red arrows for females and blue arrows for males. (TIF) S5 Fig. Juvenile hormone (JH) signaling pathway and its target genes in the fat body and ovary. Summarized juvenile hormone (JH) signaling pathway (A) The JH biosynthesis occurs S3 Fig. Validation of female-specific expression profiles by qPCR analysis. One gene was selected to represent the profile of clusters: B1 (A), B2 (B), B3 (C), H1 (D), and H4 (E). Bar graphs show mean (SEM) for males and females. The post-emergence time points tested were 2, 24, and 96 hours. Interaction p-values between sex and time factors (two-way ANOVA) are dis- played above the bars. ns = not significant; p-value <0.05; p-value <0.01, p-value <0.001. (TIF) S4 Fig. Serine proteases expression profile. Hierarchical clusterization of the serine protease genes in the post-emergence time points of 2, 12, 24, 48, and 96 hours. Heatmap y-axis shows gene codes and x-axis the female (F) and male (M) time courses from 2 to 96 hours. Supporting information S1 Fig. Aedes Rio females take at least 24 hours to mature the host seeking behavior and take the first blood meal. (A) Percent females freely feeding on an offered artificial blood meal; and (B) Cumulative number of female visits to the net in the area exposed to a human arm. The post-emergence time points tested were 2, 12, 24, 48, and 96 hours. Bars upper and lower whiskers represent the highest and lowest observations. The line inside the bar repre- sents the median. (Kruskal-Wallis corrected one-way ANOVA comparing the hours post emergence; (a) P<0.005 (b) P<0.05). N = 5). S2 Fig. Blood intake by Aedes Rio females during post-emergence phase. Total protein amount was quantified per midgut of fed and unfed females after offering an artificial blood meal for 30 minutes. "X", at 2 and 12h PE none mosquito took the blood meal. (Tukey’s cor- rected one-way ANOVA;  P<0.0001. N = 4). (TIF) S2 Fig. Blood intake by Aedes Rio females during post-emergence phase. Total protein amount was quantified per midgut of fed and unfed females after offering an artificial blood meal for 30 minutes. "X", at 2 and 12h PE none mosquito took the blood meal. (Tukey’s cor- rected one-way ANOVA;  P<0.0001. N = 4). B2, B3, and Bm are cluster names described in Fig 1. Up-regulated genes are highlighted by red arrows for females and blue arrows for males. (TIF) S4 Fig. Serine proteases expression profile. Hierarchical clusterization of the serine protease genes in the post-emergence time points of 2, 12, 24, 48, and 96 hours. Heatmap y-axis shows gene codes and x-axis the female (F) and male (M) time courses from 2 to 96 hours. B2, B3, and Bm are cluster names described in Fig 1. Up-regulated genes are highlighted by red arrows for females and blue arrows for males. (TIF) S5 Fig. Juvenile hormone (JH) signaling pathway and its target genes in the fat body and ovary. Summarized juvenile hormone (JH) signaling pathway (A) The JH biosynthesis occurs S5 Fig. Juvenile hormone (JH) signaling pathway and its target genes in the fat body and ovary. Summarized juvenile hormone (JH) signaling pathway (A) The JH biosynthesis occurs PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 23 / 32 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation in the corpora allata (CA), a pair of endocrine glands with neural connections to the brain. There is a relevant JH increase in hemolymph 12h PE leading the fat body (FB) priming and maturation of oocytes for vitellogenesis. JH has an intracellular receptor Methoprene-tolerant (Met), which binds to Taiman (Tai), this heterodimer binds to Juvenile hormone response ele- ments (JHREs) modulating gene expression. Hairy and Kruppel homolog 1 (Kr-h1) are tran- scription factors that will regulate the expression of other genes. In the FB, this pathway will activate Ribosome Biogenesis Regulator 1 Homolog (RRS1) and Ribosomal protein L32 (RpL32), required for Ribosome biogenesis pathway and subsequently the production of vitel- logenin (Vg). In the ovary, the activation of this pathway will regulate the expression of genes such as vitellogenin receptor (VgR), Heavy-Chain Clathrin (CHC) and the lipophorin receptor (LpR), related to the uptake of vitellogenin (Vg); Heatmap of Juvenile hormone signaling path- way and the cited target genes for the body (B). Heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B2, B3, and Bm are cluster names described in Fig 1. Up-regulated genes are highlighted by red arrows for females. (TIF) S6 Fig. Ribosome large and small subunits expression profile. S2 Fig. Blood intake by Aedes Rio females during post-emergence phase. Total protein amount was quantified per midgut of fed and unfed females after offering an artificial blood meal for 30 minutes. "X", at 2 and 12h PE none mosquito took the blood meal. (Tukey’s cor- rected one-way ANOVA;  P<0.0001. N = 4). Differentially expressed genes (DEG) names are in red boxes (up-regulated in female body—group B3), genes not DEG but with similar expression profile in pink, dissimilar or invariable in green and absent genes in white (Source: KEGG Mapper tool) (A). The hierarchical clusterization heatmap for the large (B) and small (C) subunits. The y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B3 is a cluster name described in Fig 1. Up-regulated genes are highlighted by red arrows for females. (TIF) S7 Fig. Ribosome Biogenesis Pathway expression profile. Hierarchical clusterization of the ribosome biogenesis pathway in the post-emergence time points of 2, 12, 24, 48, and 96 hours. Heatmap y-axis shows gene codes and x-axis the female (F) and male (M) time courses from 2 to 96 hours. B3 is a cluster name described in Fig 1. Up-regulated genes are highlighted by red arrows for females. (TIF) S8 Fig. Enriched Gene Ontology (GO) categories for the differentially expressed genes (DEGs). Enrichment analysis was performed with Panther scoring tool. The y-axis shows the GOs enriched for each ontology, as the x-axis the number of genes for the body (A) and the head (B). (TIF) S9 Fig. DNA replication pathway, genes that regulate the cell cycle progression, apoptosis and histones. Hierarchical clusterization heatmap for the DNA replication pathway (A) and body differentially expressed genes (DEGs) for cell cycle progression, apoptosis and histones (B). The y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B2 and B3 are cluster names described in Fig 1. Up-regulated genes are highlighted by red arrows for females. (TIF) S10 Fig. DNA mismatch repair pathway expression profile. The hierarchical clusterization heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B3 is a cluster name described in Fig 1. Up-regulated genes are highlighted by red arrows for females (A). Differentially expressed genes (DEG) names are in red boxes (up-regu- lated in female body—group B3), genes not DEG but with similar expression profile in pink, S10 Fig. DNA mismatch repair pathway expression profile. The hierarchical clusterization heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. B3 is a cluster name described in Fig 1. S2 Fig. Blood intake by Aedes Rio females during post-emergence phase. Total protein amount was quantified per midgut of fed and unfed females after offering an artificial blood meal for 30 minutes. "X", at 2 and 12h PE none mosquito took the blood meal. (Tukey’s cor- rected one-way ANOVA;  P<0.0001. N = 4). Up-regulated genes are highlighted by red arrows for females (A). Differentially expressed genes (DEG) names are in red boxes (up-regu- lated in female body—group B3), genes not DEG but with similar expression profile in pink, 24 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation S11 Fig. Muscle development and movement. The hierarchical clusterization heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. H1 and H2 are cluster names described in Fig 1. Up-regulated genes are highlighted by red arrows for females. (TIF) S12 Fig. Oxidative phosphorylation pathway. The hierarchical clusterization heatmap y-axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. H2 is a cluster name described in Fig 1. Up-regulated genes are highlighted by red arrows for females. S13 Fig. Electron transport chain and normalized oxygen consumption rates (OCR). The mitochondrial pyruvate carrier (MPC 1 and MPC2) transports the pyruvate across the mito- chondrial inner membrane into the mitochondrial matrix. The pyruvate dehydrogenase com- plex is composed by pyruvate dehydrogenase A (PDHA) and B (PDHB), dihydrolipoyllysine- residue acetyltransferase oxydase (DLAT) and dihydrolipoyl dehydrogenase (DLD). This com- plex mediates de oxidative decarboxylation of pyruvate to acetyl-CoA, producing CO2 and NADH. Proline is a main energy source for ATP synthesis in insects through OXPHOS. Although the molecular nature of mitochondrial proline transporter remains unknown, the first step of proline metabolism is mediated by proline desidrogenase (ProDH), generating 1-pyrroline-5-carboxylate (Δ1PC) and ubiquinol. Δ1PC is then oxidised to a-ketoglutarate (a- KG), producing NADH and glutamate. The expression profile of the MPCs and the pyruvate dehydrogenase complex can be observed in Fig 5A. Blunted arrows indicate the inhibitors used for each complex in our experiments (A). The head OCRs were normalized by CS activ- ity. Oxygen consumption coupled with oxidative phosphorylation (OXPHOS) (B); maximum respiratory rates (ETS) (C); Cytochrome c oxidase activity (D); Leak represents the oxygen consumption in the presence of high substrate concentration but in the absence of ADP (E); residual oxygen consumption (ROX) (F). Bar graphs show mean (SEM) for males and females at 2, 12, 24, 48, and 96h post-emergence. Interaction p-value between sex and time factors (two-way ANOVA) were not significant (p>0.05) for all panels. (TIF) S14 Fig. Mitochondrial biogenesis related genes. Acknowledgments We thank Paula F C Borges, Luciana S Dias and Jose´ Bento P Lima for the mosquito capture and colony establishment efforts at FIOCRUZ. We also thank Geane C Braz for mosquito rear- ing at UFRJ. S2 Fig. Blood intake by Aedes Rio females during post-emergence phase. Total protein amount was quantified per midgut of fed and unfed females after offering an artificial blood meal for 30 minutes. "X", at 2 and 12h PE none mosquito took the blood meal. (Tukey’s cor- rected one-way ANOVA;  P<0.0001. N = 4). The hierarchical clusterization heatmap y- axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. (TIF) S14 Fig. Mitochondrial biogenesis related genes. The hierarchical clusterization heatmap y- axis shows gene codes and x-axis shows female (F) and male (M) time courses from 2 to 96 hours. (T ) S1 Table. Summary of the sequencing performance across 72 samples represented by the number of reads generated (Raw reads), the number of reads that have quality enough to be analysed (Cleaned reads), the number of reads actually mapped against Ae. aegypti (ver- sion 5.1) transcripts (Mapped reads), the percentage of reads that actually mapped against Ae. aegypti (version 5.1) transcripts (% Mapped reads); the number of transcripts (Ae. aegypti version 5.1) that actually had mapped reads. (XLSX) S1 Table. Summary of the sequencing performance across 72 samples represented by the number of reads generated (Raw reads), the number of reads that have quality enough to be analysed (Cleaned reads), the number of reads actually mapped against Ae. aegypti (ver- sion 5.1) transcripts (Mapped reads), the percentage of reads that actually mapped against Ae. aegypti (version 5.1) transcripts (% Mapped reads); the number of transcripts (Ae. aegypti version 5.1) that actually had mapped reads. (XLSX) 25 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation References 1. Takken W, Verhulst NO. Host preferences of blood-feeding mosquitoes. Annu Rev Entomol. 2013; 58: 433–453. https://doi.org/10.1146/annurev-ento-120811-153618 PMID: 23020619 2. Hansen IA, Attardo GM, Park J-H, Peng Q, Raikhel AS. Target of rapamycin-mediated amino acid sig- naling in mosquito anautogeny. Proc Natl Acad Sci U S A. 2004; 101: 10626–10631. https://doi.org/10. 1073/pnas.0403460101 PMID: 15229322 3. Beklemishev WN. Gonotrophic rhythm as a basic principle of the biology of Anopheles. Vopr.Fiziol. Ekol. Malar. Komara. 1940; 1: 3–22.http://paperpile.com/b/x4BkJW/53Fli 4. Foster WA. Mosquito sugar feeding and reproductive energetics. Annu Rev Entomol. 1995; 40: 443– 474. https://doi.org/10.1146/annurev.en.40.010195.002303 PMID: 7810991 5. Klowden MJ. 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J Biol Chem. 2017; 292: 10306–10315. https://doi.org/10.1074/jbc.M116.761387 PMID: 28446607 13. Raikhel AS, Lea AO. Hormone-mediated formation of the endocytic complex in mosquito oocytes. Gen Comp Endocrinol. 1985; 57: 422–433. https://doi.org/10.1016/0016-6480(85)90224-2 PMID: 3988025 14. Gwadz RW, Spielman A. Corpus allatum control of ovarian development in Aedes aegypti. Author Contributions Moreira, Patrı´cia Fampa, Marcus F. Oliveira, Mario Alberto C. da Silva-Neto, Rafael D. Mesquita, Georgia C. Atella. Mesquita, Georgia C. Atella. Mesquita, Georgia C. Atella. Author Contributions Conceptualization: Cynara M. Rodovalho, Mario Alberto C. da Silva-Neto, Georgia C. Atella. Data curation: Stephanie S. de Carvalho, Cynara M. Rodovalho, Maria Beatriz S. Mota, Willy Jablonka, Carlu´cio Rocha-Santos, Rodrigo D. Nunes, Thayane da Encarnac¸ão Sa´-Gui- marães, Daniele S. Oliveira, Ana C. A. Melo, Monica F. Moreira, Patrı´cia Fampa, Rafael D. Mesquita. Formal analysis: Stephanie S. de Carvalho, Cynara M. Rodovalho, Alessandro Gaviraghi, Maria Beatriz S. Mota, Willy Jablonka, Carlu´cio Rocha-Santos, Rodrigo D. Nunes, Marcus F. Oliveira, Rafael D. Mesquita. Funding acquisition: Mario Alberto C. da Silva-Neto, Georgia C. Atella. Investigation: Stephanie S. de Carvalho, Cynara M. Rodovalho, Alessandro Gaviraghi, Maria Beatriz S. Mota, Willy Jablonka, Carlu´cio Rocha-Santos, Rodrigo D. Nunes, Thayane da Encarnac¸ão Sa´-Guimarães, Daniele S. Oliveira, Ana C. A. Melo, Monica F. Moreira, Patrı´- cia Fampa, Marcus F. Oliveira, Mario Alberto C. da Silva-Neto, Rafael D. Mesquita, Georgia C. Atella. Methodology: Stephanie S. de Carvalho, Cynara M. Rodovalho, Willy Jablonka, Carlu´cio Rocha-Santos, Marcus F. Oliveira, Mario Alberto C. da Silva-Neto, Rafael D. Mesquita. Project administration: Mario Alberto C. da Silva-Neto, Rafael D. Mesquita, Georgia C. Atella. Resources: Marcus F. Oliveira, Mario Alberto C. da Silva-Neto, Rafael D. Mesquita, Georgia C. Atella. Software: Stephanie S. de Carvalho, Maria Beatriz S. Mota, Rafael D. Mesquita. Supervision: Mario Alberto C. da Silva-Neto, Rafael D. Mesquita, Georgia C. Atella. Validation: Stephanie S. de Carvalho, Alessandro Gaviraghi, Maria Beatriz S. Mota, Willy Jablonka, Carlu´cio Rocha-Santos, Rodrigo D. Nunes, Thayane da Encarnac¸ão Sa´-Gui- marães, Daniele S. Oliveira, Ana C. A. Melo, Monica F. Moreira, Patrı´cia Fampa, Marcus F. Oliveira, Rafael D. Mesquita, Georgia C. Atella. Visualization: Stephanie S. de Carvalho, Maria Beatriz S. Mota, Marcus F. Oliveira, Rafael D. Mesquita. Writing – original draft: Stephanie S. de Carvalho. 26 / 32 PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0008915 January 6, 2021 PLOS NEGLECTED TROPICAL DISEASES Aedes aegypti post-emergence hematophagic and gonotrophic capacitation Writing – review & editing: Stephanie S. de Carvalho, Cynara M. Rodovalho, Alessandro Gaviraghi, Maria Beatriz S. 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Melamine in the environment: a critical review of available information
Environmental sciences Europe
2,023
cc-by
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© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. Abstract Large numbers of chemicals and products thereof are used in our daily routine to ensure a good quality of life. Sub- stances may even serve as raw materials to produce daily life articles including electronic hardware, green houses, cars etc. Melamine is used for a great variety of products, such as wood panels, paints, coatings, foam seating’s and mattresses (as flame retardant), automotive brake tubes and hose. Based on the latest discussions, melamine has been concluded in the European Union to be classified as “carcinogenic to humans” (Carc. 2, H351) and “may cause damage to organs (urinary tract) through prolonged or repeated exposure” (STOT RE 2, H737). In addition, there is a self-classi- fication of the European industry as suspect Repr. CAT2. Furthermore, the substance is considered a potential ground- water contaminant, due to a low log octanol carbon coefficient ­(Koc). However, the underlying data require further evaluation. Therefore, a review of available information related to the presence of melamine (M) and cyromazine (CM, of which M is a transformation product) in surface, ground and drinking water was conducted and the data were criti- cally analysed for plausibility. Available monitoring data are scarce and investigated for the Netherlands and Germany mainly. Measurements in the catchment area of the river Rhine and Maas revealed, that both substances (M, CM) were not ubiquitously found in surface, ground and drinking water in these countries. All in all, it can be concluded that the available monitoring data are considered as conclusive, and thus requiring further investigation before a clear relationship between emission and occurrence of melamine in the environment can be drawn. Keywords  Melamine, Cyromazine, Monitoring data, PMT Keywords  Melamine, Cyromazine, Monitoring data, PMT as a plasticiser in concrete and in automobile brake tubes and hose. It is also included in thermally fused mela- mine paper and shelves, whiteboards and flakeboards, paints, sealants for mechanical, electrical and plumb- ing applications, and in inkjet ink. It is primarily used in the synthesis of melamine–formaldehyde resins for the manufacture of laminates, coatings, plastics, commer- cial filters, glues or adhesives, and moulding compounds (dishware and kitchenware) [1]. Furthermore, melamine– formaldehyde resins are used as coatings for seeds, plant protection products and fertilizers [2, 3]. The use of mela- mine–formaldehyde in shells for fragrance encapsulation such as fabric softeners or laundry detergents represents another application [4]. Lütjens et al. Environmental Sciences Europe (2023) 35:2 https://doi.org/10.1186/s12302-022-00707-y Lütjens et al. Environmental Sciences Europe (2023) 35:2 https://doi.org/10.1186/s12302-022-00707-y (2023) 35:2 Environmental Sciences Europe Lütjens et al. Environmental Sciences Europe https://doi.org/10.1186/s12302-022-00707-y Open Access Introduction In our modern world, large numbers of chemical sub- stances are daily used to ensure a good quality of life. Those substances include pharmaceuticals, personal hygiene products, sunscreens, plant protection prod- ucts, feed and food supplement as well as detergent and cleaning agents. Furthermore, chemicals are used as raw materials to produce daily life articles including elec- tronic hardware, green houses, cars, etc. Melamine has a variety of industrial and domestic uses: it is used in paints and coatings in consumer and commercial prod- ucts, in foam seating and bedding and it has applications *Correspondence: Laura H. Lütjens laura.luetjens@basf.com BASF SE, 67056 Ludwigshafen, Germany Melamine can be contained in fertilisers and algaecides but can also trimerize from calcium cyanamide fertiliz- ers [5]; European Food Safety Authority [6]. In addition, Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 2 of 12 Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 2 of 12 Lütjens et al. Environmental Sciences Europe melamine is the main metabolite/degradation product of cyromazine, which is used as insecticide and biocide [5– 7]. Based on conclusions drawn from a misuse of mela- mine in adulterate milk, dairy products and in powdered infant formula in China and Africa, and the directly linked adverse effects in kidneys and urinary tracts of the exposed children, a re-assessment of the available data was performed in the European Union (EU) by the Mem- ber State Competent Authority of Germany (BAuA). Within the re-evaluation, especially the incidences and findings in humans were considered together with all available animal data for other endpoints, such as car- cinogenicity. Consequently, a Harmonized Classifica- tion and Labeling Dossier (CLH dossier) was announced and submitted. Finally, the ECHA (European Chemicals Agency) Committee for Risk Assessment (RAC) [8] has proposed a harmonized classification and labelling at EU as “carcinogenic to Humans (Carc. 2, H351)” and “may cause damage to organs (urinary tract) through prolonged or repeated exposure (STOT RE 2, H373)”. In addition, melamine may be considered as a potential groundwater contaminant following the criteria defined by the German Environmental Protection Agency [8, 9]. Although the substance has been detected in drink- ing water, the extent and relevance of such detections remains unclear and thus requires further elaboration [9, 10]. Notably, since the conclusions drawn on both persis- tency and mobility were based on screening information only, not considering eventually available higher tier data and assessments [11]. Therefore, in light of these exist- ing uncertainties, the aim of this work was to review and evaluate available information related to the environmen- tal occurrence and fate of melamine and, furthermore, identify and address potentially relevant data gaps. Based on the results, the question should be answered whether melamine is ubiquitous and widely detectable in the envi- ronment, or its occurrence is primarily related to point source emissions. It was decided to start with a focus on data related to Germany and the Netherlands, given the availability of data and the presence of melamine produc- tion sites. information, such as the location of the monitoring sites in Germany and the Netherlands. Furthermore, informa- tion on melamine concentration in soil, crops and veg- etables and the release from use products into food and beverages are taken into account. The data collection was conducted from 22 February 2021 to 24 June 2021. The databases were checked for the keywords melamine and cyromazine in relation to monitoring data. A second search was conducted on 19 and 20 October for the key- word’s melamine and cyanuric acid. Publicly available data bases Surface water and wastewater Publicly available databases (see Additional file  1: Table  S1) were searched for relevant information using the keywords “melamine” and “cyromazine” to gain information on the presence and the concentration of these substances in surface and wastewater.h The available measured concentrations from the Inter- national Commission for the Protection of the Rhine (ICPR), were subsequently used to calculate an average melamine concentration up- and downstream of indus- trial production sites at the Rhine. In particular, the mon- itoring data allow an analysis of the impact of melamine production and formulation sites as point sources on the melamine concentrations in the rivers Rhine and Maas. Groundwater Data on melamine concentrations in groundwater were available only to a limited extent. Monitoring data in Germany for melamine were only available from German federal state North Rhine-Westphalia [12] and some data are represented by one publication [13]. According to feedback of German water suppliers, anthropogenic influences on groundwater used for drink- ing water purposes is unlikely due to the geological struc- tures at two locations. Another water supplier from the Netherlands pointed out that melamine is not monitored at stations, where groundwater is used for drinking water production. Soil, crops and vegetables To obtain monitoring data from soil, crops and vegetables associated with the use of biocides or plant protection products (PPP) containing cyromazine and/or fertilizers containing melamine and calcium cyanamide, relevant publicly accessible literature and databases were evalu- ated. In addition, websites of the Environmental Minis- tries of the German Federal States, the German Federal Institutions and relevant Dutch institutions (Additional file 2: Table S2) were screened for relevant data. Releases of melamine from use of articlesh The websites of the German Environmental Ministries were screened for publications and additional informa- tion on the migration of melamine from packaging mate- rial and tableware into food and beverages. In a next step, different scenarios were used to calculate the releases attributable to the production of melamine, the use as intermediate and the manufacturing of articles including melamine. For this purpose, data on emissions as indicated in the Safety Data Sheet (SDS) of melamine from the OCI Company were used. The release rates indicated are representative for one plant carrying out the respective activity. Since no data are available for the production of melamine in the SDS, the same release rate as for formulating and re-packing activities were used.f Surface water monitoring sites Most of the available surface water monitoring data refer to the rivers Rhine and Maas. However, for many other European rivers or even lakes, no such data were publicly available. Due to several monitoring stations installed along the river Rhine, numerous data were available from Switzerland, Germany and the Netherlands. Monitoring data for the Maas are available from several monitoring stations located along the course of the river.h 1. Information on melamine releases during the pro- duction of melamine. 2. Additional information related to the manufacturing sites for melamine applications (also the production of intermediates). 3. Information on melamine releases during the use phase (downstream applications). 4. Information on melamine releases during the waste phase. The average measured melamine surface water concen- trations for the river Rhine (2017) ranged from 0.30 to 3.23 µg/L at the locations Weil at the Rhein and Worms, respectively [16] (see Table  1). The average concentra- tions at the Maas (2020) ranged from 1.49 µg/L (Harin- qvliet) to 20 µg/L (Roosteren) [17]. Furthermore, even in tributaries of the river Rhine higher melamine concen- trations were measured at lowland rivers (i.e., 1.4  µg/L at river Main at Frankfurt, Main, Germany) compared to those rather upstream (i.e., 1.14  µg/L at river Aare, 5. General monitoring data. Drinking water Th d k The drinking water supply in Germany is managed by 5845 companies [14]. In the Netherlands only 10 compa- nies are responsible for the water supply [15]. The avail- able data from water suppliers were analyzed according to the scope of the review. In Germany and the Nether- lands, 20 and 9 companies, respectively, were selected for this study (Additional file 2: Table S2). On request, some drinking water suppliers kindly provided available moni- toring data on surface, ground and/or drinking water as For the purpose of this review, various data sources related to Germany and the Netherlands were evalu- ated for the presence of measured levels of melamine and cyromazine in the aquatic environment. This report focuses mainly on the catchment area of the rivers Rhine (Germany) and Maas (France, Belgium, the Netherlands). The aim of the data collection was to collect monitor- ing data of melamine and cyromazine in surface, ground and drinking water and possible associated background Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 3 of 12 Lütjens et al. Environmental Sciences Europe well as the related background information (time and type of the sample, location of the sampling site, etc.). and exports of crop protection products and their active ingredients published by German Federal institutions were evaluated. For the Netherlands, available informa- tion published by the Netherlands Food and Consumer Product Safety Authority under the Ministry of Agricul- ture, Nature and Food Quality on sales data for plant pro- tection products and as far as available on biocides were screened. Comparing data on emission and monitoring data on melamine in the environmenth The annual freight of melamine present in the waterbod- ies of the rivers Maas and Rhine was estimated based on the discharge rate of water into the river and the concen- tration of melamine in the water body and the flow-rate of rivers.f Emissions from production, formulation and waste Production, use and waste data of melamine Data related to production, use and waste of melamine and melamine containing products were kindly pro- vided by the European Melamine Producers Association (EMPA). The melamine manufacturers provided relevant information on the emission of melamine to water and air, which can arise during the manufacturing processes as confidential information (i.e., data not shown). Con- cerning the production of intermediates and the manu- facturing of articles, a worst-case emission scenario was calculated using the data and assuming that all steps including all sources of release take place within one plant. In particular, EMPA was asked for information related to: For each scenario, a different quantity of melamine producers and downstream users (e.g., manufacturers of melamine-containing articles) was assumed. Based on these scenarios, the total release of melamine to water associated with the industrial point sources indi- cated above was calculated. Production and use data of cyromazine To obtain data of the production and use of products containing the active ingredient (AI) cyromazine, the ECHA website was screened for relevant information and literature. In addition, the reports on domestic sales Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 4 of 12 Table 1  Summary table of the concentrations of melamine and cyromazine in the different water compartments (surface water, wastewater, groundwater and drinking water) Substance Water compartment Location Concentration [µg/L] Years Source Melamine Surface water Weil am Rhein, Germany (Rhine) 0.30 2017 [16] Worms, Germany (Rhine) 3.23 2017 [16] Harinqvliet, Netherlands (Maas) 1.49 2020 [17] Roosteren, Netherlands (Maas) 20.0 2020 [17] Frankfurt, Germany (Main) 1.4 2016 [16] Felseneau, Swiss (Aare) 0.14 2016 [16] Dinslaken, Germany (Emscher) 21.0 2019 [16] Wastewater Augsburg, Germany  < 0.001 2017 [18] Groundwater NWR, Germany 1.2 n.a. [12] Near the river Thur, Swiss 0.06 2018 [26] Drinking water Netherlands  > 1.0 n.a. [10] Cyromazine Surface water Netherlands 0.05 2019 [19] Germany 0.8 2019 [20] Wastewater n.a. Groundwater Netherlands 0.05 2017 [27] Nord-Brabant and Limburg, Netherlands  < 0.03 n.a. [27] Drinking water n.a. Table 1  Summary table of the concentrations of melamine and cyromazine in the different water compartments (surface water, wastewater, groundwater and drinking water) Surface water monitoring data from the Netherlands on cyromazine indicated that the concentrations were below the maximum permissible risk (MTR) of 1.9 μg/L. In gen- eral, a decreasing trend for cyromazine concentrations in surface waters from 0.25 to 0.05 mg/L was observed in this country between the years 2006 and 2019 [19]. The surface water concentrations of melamine in Germany was constant during the observation period from 2015 to 2020, but increased from 0.5 µg/L to more than 0.8 µg/L during the period of 2017 to 2020 [20]. In the Nether- lands, an overall decreasing trend can be observed. The average concentration of all available measurements in Dutch surface water decreased from above 1.8  µg/L in 2017 to less than 1.1 µg/L in 2020 [20]. Felsenau, Switzerland). In the river Emscher (Germany) maximum melamine concentrations of 21  µg/L were detected. However, it has to be mentioned that this river is characterised by a high proportion of municipal waste- water [17]. Publicly available databases Surface and wastewaterh The search for “melamine” in the publicly available Nor- man Empodat Database from 2017 to 2020 for measure- ments in surface and wastewater resulted in 1,004 hits (673 in Germany and 331 in the Netherlands), whereas only 1 hit was in fact related to wastewater in Germany (Augsburg, 2017), respectively. For wastewater, meas- ured concentrations were below the limit of detection (LOD) of 0.001 μg/L [18]. 61 of the 673 measurements of surface water in Germany were below the LOQ of 0.025  µg/L. From 331 measurements in Dutch surface waters, 8 measurements were below the LOQ (ranging from ≤ 0.0005  µg/L). The detectable median concentra- tions were 0.31 and 1.14 µg/L for Germany and the Neth- erlands, respectively [18]. Groundwater Th i The review revealed that the number of freely available ground water monitoring data on melamine is very lim- ited. However, these data demonstrated that compared to 1,4-dioxane and perfluorinated substances [21–25] melamine is not ubiquitous in groundwater rather than being detected more locally. In fact, it was detected in some of the samples, whereas in others, it was not. The data from German federal state North Rhine-Westphalia [12] showed average melamine concentrations in some ground water bodies of 1.2  µg/L. On the other hand, more recent investigations did not detect any melamine above the LOD/LOQ (no specific value indicated) in the groundwater [10]. In Switzerland, melamine was detected in groundwater at individual monitoring sites in 2017 and In an upstream/downstream comparison by the Inter- national Commission for the Protection of the Rhine (ICPR) [16] average melamine concentrations ranged from 0.30 to 0.55  µg/L (upstream) and from 0.86 to 3.23 µg/L (downstream), respectively. Melamine was fre- quently detected in German and Dutch surface waters, although it was not a ubiquitous substance. Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 5 of 12 Lütjens et al. Environmental Sciences Europe (2023) 35:2 Lütjens et al. Environmental Sciences Europe (2023) 35:2 Based on the website of the German Federal Institu- tion, more than 3100 German plant-based food products were analyzed for residues of cyromazine and melamine from 2013 to 2017. In none of the samples was cyroma- zine detected. Melamine residues were detected in 21% of the samples, with levels above 0.01 mg/kg [5]. Products from organic farming in particular showed high concen- trations of 17.0 mg/kg in potatoes (2015). In addition, a study from China, cereals were tested for melamine. Mel- amine concentrations above 0.1 mg/kg were measured in less than 20% of the samples. Only 3 out of 557 crop sam- ples contaminated more than 1  mg/kg melamine, with the highest level of 2.05 mg/kg in a wheat sample [30]. 2018 as part of a pilot study on the screening of micropo- llutants ICPR [26]. Melamine was detected in groundwa- ter near the river Thur in concentrations of 0.06 µg/L and downstream of Lake Thun in concentrations of 0.03 µg/L. At these sites, the proportion of river water infiltrate to groundwater is more than 60%. Groundwater Th i As the concentrations of melamine upstream of the estuary of the Rhine into Lake Constance and at the confluence of the Emme and Reuss rivers were below 0.015 µg/L, the ICPR [26] concludes, that melamine is likely to have entered the groundwater through the infiltration of river water at the locations mentioned above. Measured groundwater concentrations for cyroma- zine were only available for the Netherlands (prov- inces of Nord-Brabant and Limburg) and the overall amount of data was very limited. These monitoring data revealed concentrations below 0.03 µg/L [27]. In another study, groundwater concentrations up to 0.05 µg/L were detected [27]. Melamine migration through the use of melamine‑based productsh The review of articles published by the Landeslabor Schleswig–Holstein [31] and the VerbraucherFenster Hessen [32] revealed that no significant migration of mel- amine from melamine formaldehyde resin (MFR) table- ware occurs, when the equipment is used at temperatures below 70  °C. In another study, however, the amount of leached melamine ranged from < 0.03 to 49.0 ng/cm2 and from 0.37 to 70.2 ng/cm2 at water temperatures of 25 and 90–100 °C, respectively [33]. The authors also found out that acidic or methanolic water at 25 °C did not enhance extraction of melamine from the product. The study by Hanhi et al. tested a new method to measure the level of melamine migration in melamine-tableware products by HPLC method and the effect of the food-type on migra- tion [34]. The study showed that although melamine migration occurred in all samples and acidic conditions had a significant influence, the levels were not higher than the European standard (125 µg/L). Drinking water Th The amount of available monitoring data for melamine in drinking water is limited and only available for the Netherlands. In Germany melamine is not among the substances monitored regularly during drinking water production. According to monitoring data from Flanders (Belgium) and the Netherlands melamine was detected in 2 out of 12 drinking water samples indicating that this substance might be present in drinking water samples in concentrations > 1 µg/L (in 1 out of the 12 drinking water samples) [10]. For cyromazine, no data related to measured drinking water concentrations were identified for Germany and the Netherlands. Investigations from the German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung, BfR) in 2020 showed an increase in melamine concen- trations in food and drinks after repeated contact, which suggests that materials degrade by contact with hot liquids [35]. Furthermore, the median release for con- ventional MFR was 0.69  mg/L ranging from < LOQ to 8.37 mg/L and for bambooware the median release was 1.55  mg/L ranging from < LOQ to 20.7  mg/L [35]. The tolerable daily intake (TDI) for melamine was 0.2 mg/kg body weight per day [28]. Taking this TDI into account, it was concluded that the average melamine concentrations released from the products did not pose a human health risk to adults. Especially, since the specific migration limit of melamine from those products has been lowered from 30 to 2.5 mg/kg food [36]. Emissions from production, formulation and waste As this information was provided by the various stake- holders as confidential information, no details were pro- vided within this manuscript. Soil, crops and vegetables monitoring datah The EFSA (European Food Safety Authority) [28] col- lected and summarized data on food and feed samples from different EU Member States including Germany. Melamine was detected in 96% of the 136 food samples but only in 5% of the 52 feed samples. The agency con- cluded that consumers might be exposed to melamine via food due to the use of cyromazine as pesticide and as vet- erinary drug [29]. Furthermore, due to use of calcium cyanamide ferti- lizer in conventional agriculture may result in the forma- tion of the degradation products melamine and cyanuric acid [5]. Consequently, the analysis of melamine in fer- tilizers showed concentrations up to 7.3 mg/kg and high concentrations of cyanuric acid [5]. The same author concluded that the high concentrations of both transfor- mation products were due to the high persistency in soil. Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 6 of 12 Lütjens et al. Environmental Sciences Europe (2023) 35:2 Lütjens et al. Environmental Sciences Europe Comparing data on emission and monitoring data on melamine in the environmenth The calculated annual freight of melamine in waterbodies of the Rivers Maas and the Rhine ranges between 3.0 and 22.6 and 82,6 tons/year, respectively, depending on the calculation parameters (water discharge and melamine concentration) (see Additional file 3: Table S3). Based on its Freundlich distribution coefficient (kfoc), which ranges from 40.2 to 1.784  mL/g, the adsorption potential of cyromazine varies depending on the soil type [29]. i For checking the plausibility of this result, an addi- tional calculation was performed. The annual freight of melamine was calculated based on the average freight of melamine of 1.93 g/s [17] (at the location of Lobith). This resulted in an annual melamine freight of approximately 60.9 tons/year in the waterbody of the Rhine. Thus, the annual freight of melamine calculated on the basis of the average flow rate and melamine concentration was about 26% lower compared to the value calculated based on the average melamine freight. In soil, melamine may be considered as non-persis- tent or very persistent with half-life ranging from 46 to 211 days at 20 °C depending on the soil type [1, 29]. The European Commission (calculated a geometric mean half-life of melamine in aerobic soil ranging from 37.89 to 307.6 days, respectively, based on the literature used for the assessment [37, 39, 40]. Based on its kfoc which was reported to be between 54 and 423  mL/g it was assumed that melamine is mostly bound to the soil matrix [29]. Out of 100% cyromazine application < 12% melamine was found to be distributed to the receiving water. Degradation/Formation processes of cyromazine and melamine However, in a worst-case scenario considering the application in the case of rainfall, a cyromazine loss of 23.7% due to run-off was concluded [7]. In water, cyrom- azine was considered as being persistent, while it was slowly partitioning from water to sediment compartment [29]. Accordingly, a half-life for rivers and ponds of 401 and 464 days, respectively, were reported [39]. However, ECHA [41] reported no unacceptable risk to the aquatic compartment (including surface water and sediment) due to cyromazine use in PPPs. In both Germany and the Netherlands, cyromazine is authorized as an AI in biocidal products (BPs). The use in plant protection products (PPPs) is not approved in Germany. The substance likely enters the environment through these pesticide applications via soil, food and feed and surface run-offs [7, 37]. Several studies have indicated that melamine is the primary metabolite and degradation product of cyromazine [5, 7, 29] (Fig. 1). Cyromazine is stable to hydrolysis and photolysis in aqueous solutions [29]. In soil, it has a low to moderate persistence under aerobic conditions. A geometric mean half-life in the soil through aerobic solid degradation of 37.89 days at 20 °C was calculated by the European Com- mission [39]. After 190 days a maximum melamine con- centration of 36% was found in anaerobic soils, whereas under aerobic conditions, between 60% and 74.5% mela- mine were formed [39]. This indicates that the presence of oxygen favored the formation of melamine during the degradation of cyromazine. Discussionh The analysis of surface water monitoring data of both the river Rhine and Maas revealed that melamine indeed is present in both rivers. Considering additional monitoring Fig. 1  Degradation pathway of cyromazine via melamine and cyanuric acid (according to [38]) Fig. 1  Degradation pathway of cyromazine via melamine and cyanuric acid (according to [38]) Fig. 1  Degradation pathway of cyromazine via melamine and cyanuric acid (according to [38]) Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 7 of 12 Lütjens et al. Environmental Sciences Europe drawn regarding the correlation between monitored sur- face and groundwater concentrations of melamine. data from the Norman Empodat database, it can be con- cluded that the entry path via wastewater seems to be rather low (i.e., below the LOD). However, it has to be acknowledged that the number of measurements is also rather low. In surface waters, melamine was not detected in all samples, but in approximately 90% of the samples above the LOQ, indicating its presence in the aquatic freshwater environment, although the concentrations were in the Rhine between 0.30 and 3.23 µg/L and in the Maas 1.49–20 µg/L. Considering the presence of melamine in drinking water, it has to be emphasized that there are currently no freely available monitoring data available as this substance is not part of measurements campaigns car- ried out on regular base. Despite this fact, some authors already stated that based on its substance properties mel- amine belongs to PM (persistent and mobile) substances, which cannot be removed by conventional or advanced treatment processes, such as activated carbon [46]. Due to this assumption, it was concluded that melamine may reach drinking water and associated resources. However, as mentioned previously this assumption lacks a causality check and/or a proof of concept as the few monitoring data available are not conclusive at this stage. Further- more, it has to be emphasized that melamine may be con- sidered as persistent in water using a standardized OECD 309 lab test but was shown to be non-persistent under realistic field conditions with half-life of 39 days [47]. In a study from the USA, melamine and cyanuric acid were measured in a river and a lake in New York State. Melamine was the most abundant compound in river water with concentrations between 0.017 and 3.650 µg/L [42]. Discussionh It can be seen that the concentrations are in a simi- lar range compared to the Rhine and the Maas. Unfortu- nately, it is not clear from the paper by Zhu et al. what the flow rate of the river was and at what time the measure- ments were carried out. However, the data suggest that the rivers in large American cities have similar melamine concentrations as in Europe. The presence of cyanuric acid in American surface waters (river 0.147 µg/L, lakes 1.068 µg/L und seawater 0.157 µg/L) can be explained by the direct discharge of wastewater. In the USA, cyanu- ric acid is used in dishwashing detergents, sanitizer and drinking water treatment products [42]. i In a study from the USA, melamine and cyanuric acid were detected in tap water and bottled water. Melamine was found with a mean concentration of 0.033  µg/L in tap water and 0.075 µg/L in bottled water. Cyanuric acid was detected at a mean concentration of 0.515  µg/L in tap water and 0.075 µg/L in bottled water [42]. According to the authors, the occurrence of melamine in tap water could be due to the presence of indoor dust [48]. Since it is not clear from the article what material the drinking bottles are made of, it cannot be ruled out that melamine or cyanuric acid has dissolved from the bottles. Drinking water in the USA is usually purified with chlorine [49]. Cyanuric acid is commonly used as a drinking water treatment product to stabilize the chlorine [42]. It has been also reported that drinking water can contain up to 1.6–3.2 mg/L cyanuric acid form the use of disinfectants (sodium dichloroisocyanurate) [50]. This use can explain the high concentrations in drinking water from the tap and the bottle. In summary, it can be concluded that there is a good database concerning monitoring data in surface water along the rivers Rhine and Maas. Based on these meas- urements, it was concluded that there is a correlation between industrial production sites and melamine con- centration in surface water [43–45]. Nevertheless, no clear trend in the annual melamine surface water con- centrations during the entire observation period (from 2015 to 2020) was identified. Overall, it should be noted that the analysis of trends based on annual averages does not provide a complete picture of the melamine concen- trations in surface water. Discussionh Melamine concentrations are subject to strong fluctuations throughout the year. There might be a correlation between the melamine concentra- tions and the flow-rate of the river indicating low mela- mine concentrations a high flow-rates.h Cyromazine, was not measured in drinking water at all. In summary, there is a lack of data regarding melamine and cyromazine measured concentrations in drinking water.h l The number of available melamine groundwater detec- tions are scarce, and the results are not consistent across various water bodies, as it was present in some areas, whereas it was not in others (i.e., below LOQ/LOD). This indicates that the occurrence of melamine in some groundwater areas is likely to be more dependent on local conditions and possible point sources than on a general soil leachability issue. Due to the lack of sufficient groundwater monitoring data and relevant additional information, however, no reliable conclusions can be The presence of melamine in agricultural soil is due to use of the plant protection product active ingredient (AI) cyromazine and the use of fertilizers. Whereas, melamine is a relevant transformation product of the AI, it is also freely available within the fertilizer. Based on the results from a soil leachability study, a horizontal transfer of both cyromazine and melamine through the soil column was considered negligible [7]. If degradation to melamine already took place within the soil, melamine is primarily bound to the soil and hence, does not present a dominant Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 8 of 12 Lütjens et al. Environmental Sciences Europe entry path for melamine into waterways. Thus, it can be assumed that the presence of melamine in crops and veg- etables is linked to the agricultural use of cyromazine and the use of fertilizers rather than by an uptake of mela- mine leached from surface water to the agricultural area [30]. A study from Korea shows that melamine and cya- nuric acid were measured in high concentrations in the sediment of a lake near Seoul. The mean concentration was 0.182 µg/g dw for melamine and 0.0262 µg/g dw for cyanuric acid [51]. In a study from Japan, melamine con- centrations between 10 and 400 ng/g dw were measured in river sediment (OECD, 1998, Primary source no longer available) [51]. Discussionh The high concentrations can be explained by the fact that melamine and cyanuric acid were added to fish feed to increase the protein content [52, 53]. temperature but seems to be not affected by acidity. This suggests that melamine resin products can contribute to releases into the environment, but only at a low emis- sion rate. However, the available data did not allow for an assessment of specific quantities or shares. i Waste from melamine production is mainly inciner- ated, which leads to the thermic destruction of melamine. However, no detailed information on releases regarding waste from the manufacturing of intermediates, mix- tures and articles was available but it is suggested to be also incinerated. Concerning professional and consumer use, the contribution to waste is considered negligible as products should typically be incinerated and not dis- posed of in landfills. However, releases from existing landfills may be relevant as they may even be connected to ground water resources [57–59]. i Releases to the soil from production have not been reported and is considered as negligible. If releases occur, melamine would primarily be bound to the soil reducing the risk of introduction into waterways. However, a run- off from the agricultural field straight into nearby surface waters after heavy rain falls could not be excluded. This was also demonstrated in another study, where 23.7% cyromazine was observed in the run-off water [7]. It can be assumed that the soil does not present a domi- nant entry path for melamine into waterways including groundwater taking into account that melamine release from the degradation of cyromazine is negligible. In conclusion, quantified figures regarding releases of melamine into the environment can only be established for releases from the production of melamine, its use in the manufacturing of articles. Although a correlation between releases from indus- trial point sources and the concentrations of melamine in surface water has been identified, the presence of mela- mine in surface water cannot exclusively be ascribed to a specific segment of the production and manufactur- ing chain. Further research should, therefore, also focus on other possible emission pathways of melamine to the environment. A comparison with the potential impact of agriculture is limited due to the lack of available monitoring data. Discussionh Environmental Sciences Europe (2023) 35:2 Lütjens et al. Environmental Sciences Europe (2023) 35:2 there is no known industrial discharger of melamine into the Emscher [17, 21]. This is further substantiated by the available monitor- ing data, which shows elevated melamine concentrations downstream of industrial point sources. In a study from China, wastewater from 37 production plants was ana- lysed for its melamine content. Melamine was measured in only 9 samples with a content of 22–100  µg/L [30]. Therefore, a correlation between discharges of industrial point sources and the concentrations of melamine in sur- face water may be plausible. However, significant con- centrations are already detected upstream of such point sources, indicating the presence of other sources. The available data also show that melamine is not detected in all surface water samples in the rivers Rhine and Maas above the corresponding LODs. It can, there- fore, be concluded that melamine is not a ubiquitous sub- stance in surface waters in Germany and the Netherlands. Monitoring data for melamine in groundwater are scarce. The available data demonstrate that the presence of melamine in groundwater depends on local condi- tions (such as infiltration rates or the presence of point sources). Therefore, it is concluded that melamine is not ubiquitously found in ground water. Due to existing data gaps, no reliable conclusion can be drawn regarding the correlation between monitored surface and groundwater concentrations of melamine. Hence, while a connection between releases from industrial point sources and the concentrations of mela- mine in surface water has been identified, the presence of melamine in surface water and the environment as a whole may not exclusively be allocated to the produc- tion of melamine, the production of intermediates and the manufacturing of articles using melamine. Further research on sources and pathways of melamine to the environment should, therefore, also focus on other pos- sible sources, such as: The rather large number of melamine detections in sur- face water did not comply with the low detection rate in groundwater (GW) and drinking water (DW), although it has to be acknowledged that the data from latter two are rather rare (i.e., 1 out of 12 for DW). In areas with high river water infiltration rates, detection of melamine in such filtrates (RWF) occur, but more on a local rather than on a general basis. Discussionh The local occurrence in RWFs depends also on the melamine concentrations present in the surface water and as the concentrations may increase during the course of the river, it may result in exceedance of any threshold at the lower end of larger rivers (i.e., river Rhine: the Netherlands), rather than at the upper or middle region (i.e., Switzerland, Germany). However, river water infiltrations often lead to rather constant water flow from the river to the well. The associated soil, therefore, may be considered as fully saturated, which means that both physical and chemical absorption of sub- stances may be limited. Furthermore, in case of high flow rates in combination with short distances (i.e., 1–10 m), the biodegradation does not play a relevant role. This result in the detection of substances such as caffeine typi- cally not being considered as persistent or a substance of low absorption [8, 9, 11, 60, 61]. On the other hand, substances such as long-chain perfluoroalkyl carboxylic acids (PFOAs) considered as highly absorptive (log Koc of > 4) [21–23], may end up in groundwater, river filtrates and associated drinking water resources if they (a) are particle bound and/or (b) are highly persistent (i.e., half- life of several decades) so that they may travel through the horizontal and/or the vertical soil layer, respectively [21–23, 62]. i) The degradation/metabolization of melamine from cyromazine resulting from its use as PPP and bioc- ide and the emission to surface water via the feed and food chain and organic slurry. ii) Potential releases of melamine from the use of cyana- mide-containing fertilizers. iii) Emissions from consumer uses such as tableware made from melamine–formaldehyde–resin. iv) Emissions from the degradation of incapsulated fra- grances or. v) Emissions from waste. v) Emissions from waste. Regarding the question whether melamine in the envi- ronment is ubiquitous and widely dispersive detectable or primarily occurs in direct relation to point sources, the following can be concluded. g As regards surface water, data are mainly available for monitoring stations related to the rivers Rhine and Maas. The data indicate that melamine concentrations at these locations frequently exceed the ERM target value of 1 μg/L and that higher melamine concentrations can be observed downstream of industrial point sources. Thus, the available data suggest a relationship between releases from industrial point sources and the measured concentrations of melamine in surface water. Discussionh In this context, another author refers to the decreasing and low concentrations of cyromazine in surface waters, indicating that agricultural use of cyromazine most likely does not significantly contribute to the observed melamine concentrations in Dutch surface waters [1]. Another major gap is the lack of data for surface water in remote areas.h However, when interpreting these shares, it must be kept in mind that no full picture including all emis- sions of melamine into the environment rather than a proportionate allocation of melamine emissions based on known (and assumed) emissions, i.e., a relative com- parison of known sources and their (assumed) emis- sions is possible. Furthermore, it should be noted that the releases from the production of intermediates and manufacturing of articles using melamine might be over- estimated as these are solely based on worst-case releases presented within the SDS for melamine and data submit- ted by EMPA members within the questionnaires. The available data on the occurrence of melamine due to the use of cyromazine as PPP suggest that the presence of melamine in plant food can rather be attributed to environmental contamination or residues from fertilizers and disinfectants than to the use of cyromazine as PPP [5, 54]. Cyromazine is commonly added to animal feed in concentrations up to 0.5 mg/kg to control the hatching from flies in the manure [55, 56]. However, data indicate that agricultural activities (manure/slurry treatment and veterinary purposes) might contribute to the occurrence of melamine in food and feed and hence, to melamine background exposure. Studies on consumer exposure to melamine indicate that consumers are exposed to low levels of melamine (migration from food contact mate- rials and from feed ingredients). Data evaluated suggest that melamine can leach from melamine resin prod- ucts, such as tableware. The rate increases with water Other contributions to melamine in the environ- ment cannot be calculated or estimated due to the data gaps identified above (contributions resulting from the use of cyromazine) or as they were not the focus of this assessment (contribution from cyanamide containing fertilizers). Based on the data presented in this report, the main contributions to surface water resulted from the pro- duction of melamine, intermediates and from the man- ufacture of melamine-containing products, while the significance of contributions from other sources (e.g., waste, landfill) to the release of melamine to water remains unclear. Page 9 of 12 Lütjens et al. References 1. CE Smit (2018) Water quality standards for melamine. A proposal in accordance with the methodology of the Water Framework Directive. RIVM Letter report 2018-0077. https://​doi.​org/​10.​21945/​RIVM-​2018-​0077 1. CE Smit (2018) Water quality standards for melamine. A proposal in accordance with the methodology of the Water Framework Directive. RIVM Letter report 2018-0077. https://​doi.​org/​10.​21945/​RIVM-​2018-​0077 2. Giroto AS, Garcia RHS, Colnago LA, Klamczynski A, Glenn GM, Ribeiro C (2020) Role of urea and melamine as synergic co-plasticizers for starch composites for fertilizer application. Int J Biol Macromol 144:143–150. https://​doi.​org/​10.​1016/j.​ijbio​mac.​2019.​12.​094 3. Yuan H, Li G, Yang L, Yan X, Yang D (2015) Development of melamine-for- maldehyde resin microcapsules with low formaldehyde emission suited for seed treatment. Colloids Surf B 128:149–154. https://​doi.​org/​10.​1016/j.​ colsu​rfb.​2015.​02.​029 3. Yuan H, Li G, Yang L, Yan X, Yang D (2015) Development of melamine-for- maldehyde resin microcapsules with low formaldehyde emission suited for seed treatment. Colloids Surf B 128:149–154. https://​doi.​org/​10.​1016/j.​ colsu​rfb.​2015.​02.​029 4. ECHA (2019) ANNEX to the ANNEX XV RESTRICTION REPORT—intention- ally added microplastics. 1.2 edn. Helsinki, Finland. https://​echa.​europa.​ eu/​docum​ents/​10162/​db081​bde-​ea3e-​ab53-​3135-​8aaff​e66d0​cb 5. Adam S (2017) Dünger, Biozid oder Insektizid? Woher kommen Melamin- und Cyanursäure-Rückstände? GIT Labor Fachz 11:16–21 6. EFSA (2007) EFSAs provisional statement on a request from the European commission related to melamine and structurally related compounds such as cyanuric acid in protein-rich ingredients used for feed and food. EFSA J 5(6):1–11 The online version contains supplementary material available at https://​doi.​ org/​10.​1186/​s12302-​022-​00707-y. org/​10.​1186/​s12302-​022-​00707-y. Additional file 1: Table S1. List of used databases and additional sources. Additional file 2: Table S2. Identified and contacted water suppliers in Germany and the Netherlands. Additional file 3: Table S3. Calculated annual freight of melamine pre- sent in the Maas and in the Rhine based on the discharge and melamine concentration in the rivers. Additional file 1: Table S1. List of used databases and additional sources. Additional file 2: Table S2. Identified and contacted water suppliers in Germany and the Netherlands. Additional file 3: Table S3. Calculated annual freight of melamine pre- sent in the Maas and in the Rhine based on the discharge and melamine concentration in the rivers. 7. Pote DH, Daniel TC, Edwards DR, Mattice JD, Wickliff DB (1994) Effect of drying and rainfall intensity on cyromazine loss from surface-applied caged-layer manure. J Environ Qual 23(1):101–104. https://​doi.​org/​10.​ 2134/​jeq19​94.​00472​42500​23000​10015x 7. Pote DH, Daniel TC, Edwards DR, Mattice JD, Wickliff DB (1994) Effect of drying and rainfall intensity on cyromazine loss from surface-applied caged-layer manure. Acknowledgements The authors would like to thank the members of the EMPA consortium and Nico Watzek and Olga Lemke (both BASF SE) for providing useful comments on the manuscript. Furthermore, the authors would like to thank Carina Broneder, Felix Strauss, Dominik Höhne and Alexander Potrykus (all Ramboll Deutschland GmbH for preparing the report entitled “Melamine in the environment” from 02.02.2022 on behalf of EMPA, which was taken as a data source for preparing this manuscript. 10. Kolkman A, Vughs D, Sjerps R, Kooij PJF, vd Kooi, B M., K., J Louisse, P de Voogt, (2021) Assessment of highly polar chemicals in Dutch and Flemish drinking water and its sources: presence and potential risks. ACS EST Water 1(4):928–937. https://​doi.​org/​10.​1021/​acses​twater.​0c002​37 11. Arp HP, Hale SE (2019) REACH improvement of guidance and methods for the ideification and assessment of PMT/vPvM substances. vol Texte 126/2019. Umweltbundesamt, Dessau-Roßlau, Germany Availability of data and materials Availability of data and materials All data used are either publicly available through published articles or avail- able through the Ramboll report entitled “Melamine in the environment”, issued on 02.02.2022 on behalf of EMPA. Availability of data and materials All data used are either publicly available through published articles or avail- able through the Ramboll report entitled “Melamine in the environment”, issued on 02.02.2022 on behalf of EMPA. References J Environ Qual 23(1):101–104. https://​doi.​org/​10.​ 2134/​jeq19​94.​00472​42500​23000​10015x 8. Berger U, Ost N, Sättler D, Schliebner I, Kühne R, Schüürmann G, Neu- mann M, Reemtsma T (2018) Assessment of persistence, mobility and toxicity (PMT) of 167 REACH registered substances, vol 1. Texte, vol 9, 1st edn. German Environment Agency, Dessau-Roßlau, Germany 9. Neumann M, Schliebner I (2019) Protecting the sources of our drinking water—The criteria for identifying Persistent, Mobile, and Toxic (PMT) substances and very Persistent, and very Mobile (vPvM) substances under EU REACH Regulation (EC) No 1907/2006. Umweltbundesamt, Dessau-Roßlau Author contributions LHL and SP were involved in the conceptual framework and the writing of the manuscript. All other authors reviewed and provided comments on the manuscript. IR was the project lead. All authors read and approved the final manuscript. 12. LANUV (2020) ECHO News Melamin. Recklinghausen, Germany 13. Seitz W, Winzenbacher R (2017) A survey on trace organic chemicals in a German water protection area and the proposal of relevant indicators for anthropogenic influences. Environ Monit and Assess. https://​doi.​org/​10.​ 1007/​s10661-​017-​5953-z Funding Not applicable. Discussionh However, high melamine concentrations can also be observed in surface water, where no discharge of melamine is known. In the river Emscher (Germany) are high concentrations of melamine (max. value of 21 µg/L) detected. The river is characterised by a high proportion of wastewater, but Taking the available information into account, it remains questionable whether melamine is an abundant potential groundwater contaminant or whether the indi- vidual detections are due to high local emission rates in combination with high local river-water infiltrations, thus Lütjens et al. Environmental Sciences Europe (2023) 35:2 Page 10 of 12 Lütjens et al. Environmental Sciences Europe requiring further elaboration and research. If the addi- tional data indicate that local sources are the main driver for melamine detections in groundwater further site-spe- cific emission reduction are considered necessary. requiring further elaboration and research. If the addi- tional data indicate that local sources are the main driver for melamine detections in groundwater further site-spe- cific emission reduction are considered necessary. Competing interests All authors are employed by BASF SE, a producer of melamine. All authors are employed by BASF SE, a producer of melamine. Received: 3 August 2022 Accepted: 26 November 2022 Received: 3 August 2022 Accepted: 26 November 2022 Declarations Abbreviations AI Active ingredient BAuA Member State Competent Authority of Germany (Bundesansta für Arbeitsschutz und Arbeitsmedizin) BfR German Federal Institute for Risk Assessment (Bundesinstitut fü Risikobewertung) BPs Biocidal products CLH Classification and labeling CM Cyromazine DW Drinking water ECHA European chemicals agency EFSA European Food Safety Authority EMPA European Melamine Producers Association EU European Union GW Groundwater ICPR International Commission for the Protection of the Rhine Kfoc Freundlich distribution coefficient Koc Octanol carbon coefficient LOD Limit of detection LOQ Limit of quantification M Melamine MFR Melamine formaldehyde resin OECD Organization for Economic Co-operation and Development PFOA Perfluoroalkyl carboxylic acids PM Persistent and mobile PPP Plant protection products RAC​ Risk assessment committee RWF River water filtration SDS Safety data sheet TDI Tolerable daily intake Not applicable. 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UDK: 37.03 ; 159.922.7 ID: 191662348 Pregledni rad UDK: 37.03 ; 159.922.7 ID: 191662348 Pregledni rad Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. Zorica MATEJIĆ ĐURIČIĆ1 Univerzitet u Beogradu Fakultet za specijalnu edukaciju i rehabilitaciju Zorica MATEJIĆ ĐURIČIĆ1 Univerzitet u Beogradu Fakultet za specijalnu edukaciju i rehabilitaciju NOVE KONCEPTUALIZACIJE RAZVOJA I VASPITANJA2 U ovom radu izvršena je teorijsko-konceptualna analiza dva kom- plementarna procesa humane ontogeneze: razvoja i vaspitanja. Na osnovu kritičkog pregleda vodećih nativističkihi i empirističkih teori- ja u razvojnoj psihologiji i pedagogiji, ukazuje se na osnovne pristupe o ulozi socijalne sredine na psihički razvoj deteta. Nova antropologija deteta i detinjstva izvedena je iz klasičnih postavki kulturno-istorijske teorije L. S. Vigotskog, uz pokušaj dobijanja odgovora na pitanje zašto je vaspitanje biološki nužno. U zaključnom delu, dokazuje se teza po kojoj nove konceptualiizacije razvoja i vaspitanja poništavaju discipli- narne podele između psihologije i pedagogije, jer se ovi procesi sagleda- vaju kao dve linije jedinstvenog procesa humane ontogeneze. Ključne reči: razvoj, vaspitanje, dete kao animal educandum Ključne reči: razvoj, vaspitanje, dete kao animal educandum Ključne reči: razvoj, vaspitanje, dete kao animal educandum 2 Rad je proistekao iz projekta „Unapređenje kvaliteta i dostupnosti obra- zovanja u procesima modernizacije Srbije“ broj 47008 (2011-2014) čiju realizaciju finansira Ministarstvo prosvete i nauke Republike Srbije 1 E-mail: graphos@sbb.rs UVOD Klasičan pristup problemima vaspitanja grubo je disciplinarno podelio pojmove vaspitanja i razvoja na dve nauke: pedagogiju i dečju psihologiju. Iako je reč o jedinstvenom procesu humane ontogeneze, taj proces je istraživan sa različitim fokusima, uz razvijanje vrlo razli- čitih, pa i oprečnih shvatanja o detetu i detinjstvu. „Dete samo zna da živi svoje detinjstvo. Proučavanje, pak, detinj- stva pripada odraslom. Ali šta će prevagnuti u tom proučavanju: stano- višta odraslog ili deteta? zabeležio je francuski psiholog Anri Valon. 267 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. (Wallon,1964, p.7). U ovom kratkom tvrđenju kriju se sve opasnosti adultocentrističkog razumevanja procesa koji se događa detetu, pre svega, procenjivanje opterećeno brojnim projekcijama koje dolaze sa pozicija odraslog. Koncept deteta, detinjstva i psihičkog razvoja u celini, određen je društvenim i istorijskim kontekstom koji formira određene kolektiv- ne predstave (preovlađujuće društvene poglede na dete), a koje dalje definišu izbor referentnog okvira proučavanja, zasnivanje teorija o ra- zvoju i vaspitanju, pa i sam plan konkretno-empirijskih istraživanja. Klasična pedagogija, koja se primarno bavi proučavanjem proce- sa vaspitanja deteta, zasnovana je, pre svega, kao normativna nauka. Otuda, umesto osnovnog fokusa na dete, fokus je pomeren na odra- slog: šta to roditelji i vaspitači treba da čine kako bi ostvarili propisane (normirane) ciljeve vaspitanja usmerene ka izgradnji jedne svestrane i celovite ličnosti. Paradoksalno je otkriće da se značajan deo „stare“ pedagogije više bavi vaspitačima nego samimm detetom, te da je nau- ka o vaspitanju prevalentno više usmerena na odraslog nego na dete. U takvoj nauci o vaspitanju - dete ostaje naučno nevidljivo. U definisanju vaspitnog procesa, u ciljevima i postupcima vaspitanja, u vaspitnim sredstvima i merama, u izvorima vaspitanja - „vidljivija“ je uloga odraslog (roditelja, porodice, različitih društvenih subjekata i agenasa) od pozicije samog deteta koje se vaspitava. U ovakvoj pro- jektovanoj slici vaspitanja, dete je samo pasivni primalac spoljašnjih uticaja, a sam proces njegovog vaspitavanja izjednačen je sa „modelo- vanjem“ ličnosti pod pritiskom grupe socijalnih činilaca. Kolektivna predstava o detetu i detinjstvu ne otkriva dete kao subjekt vaspitnog procesa, već samo kao objekt vaspitanja, „predmet“ na kome različiti vaspitni agensi (vaspitači) ostavljaju svoj trag, uprkos proklamovanih stavova o tome da je vaspitanik i objekt i subjekt vaspitanja. (opširnije; Šmit, 1991). UVOD Pored toga, vaspitanje je često posmatrano u suženim okvirima, kao proces usvajanja pozitivnih društvenih vrednosti (u svakodnev- nom životu, ostaci klasičnih pedagoških shvatanja sačuvani su u ko- lokvijalnom govoru u kome se značenje „vaspitane osobe“ vezuje za ličnost koja je usvojila pozitivne društvene vrednosti, standarde i nor- me ponašanja) što je za posledicu imalo potpunu disocijaciju procesa razvoja i vaspitanja deteta. 268 Matejić Đuričić, Z.: Nove konceptualizacije razvoja i vaspitanja Sedamdesete godine prošlog veka donele su snažan obrt u (re)de- finisanju temeljnih pedagoških polazišta. U tom reformatorskom pro- cesu, ideje Paola Freira i njegovo kapitalno delo Pedagogy of Oppresed (Freire, 1970) imali su presudnu ulogu i značaj. Freire razvija novi konstruktivistički pristup vaspitanju i obrazo- vanju, i polazeći od suštine ontološkog bića čoveka u prvi plan ističe aktivnost subjekta, saradnju (kolaboraciju) i kritiku, umesto konfor- mizma kao pasivnog prijema i apsorpcije sadržaja koji dolaze iz spo- ljašnje sredine. Pristalice Pijažeovog učenja lako će prepoznati visok nivo slaganja dva autora, a upravo iznete stavove izvorno pripisati Pi- jažeu. j Novi vokabular pratio je pojavu nove kritičke pedagodije; interak- tivna pedagogija, pedagogija konstruktivizma, aktivno učenje, obra- zovanje usmereno na učenika itd., samo su deo spoljašnjih indikatora reforme pedagoških načela. (Hausfather, S.,2001; Smith, H. J., Hig- gins, S., Wall, K., & Miller, J., 2005; Ivić i sarad., 1997). U sklopu no- vih terminološko-.konceptualnih razgraničenja, neki autori predlažu termin „edukacija“ kao dovoljno opšti i obuhvatan, umesto klasičnog termina „vaspitanje“. (uporedi: Šmit, 1991). Edukacija (engl. education) obuhvata i procese podizanja, odgoja, formalnog i neformalnog obra- zovanja, vaspitanja, učenja i školovanja, ukratko: razvoj deteta u soci- jalnom kontekstu. Razvoj i vaspitanje: klasični psihološki teorijski izvori Tradicionalna dečja psihologija „zarobila“ je istraživanja psihičkog razvoja deteta na okvire „organizma“ ili pojedinca, postavljajući za cilj sistematsko istraživanje promena koje se dešavaju na unutrašnjem planu, bilo da se te promene objašnjavaju kao rezultat organskog sa- zrevanja i/ili učenja. Principi vaspitanja postavljani su post hoc, i zbog toga se ne može govoriti o postojanju čvrste i prirodne vezi između procesa razvoja i vaspitanja deteta. Naprotiv, pre bi se moglo reći da su ovi procesi sagledavani kao izdvojene i različite celine jedinstvenog procesa humane ontogeneze. U okviru klasične dečje psihologije, pitanja odnosa razvoja i vas- pitanja pokrenuta su u okviru opšte teorijske kontroverze o osnovnim 269 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. determinantama psihičkog razvoja, na liniji trajućeg teorijskog spora nativizam vs. empirizam. Za maturacioniste, poput Gezela, vaspitanje je „prevedeno“ u proces podizanja, negovanja ili odgoja dece (engl. - raising children, care-taking, care-rearing). Drugim rečima, budući da je razvoj deteta sveden na predeterminirano i zakonito ispoljavanje naslednih karak- teristika koje se odvijaju na unutrašnjem planu organizma, od rodi- telja i vaspitača se očekuje samo pomoć u smislu pozitivne podrške i podsticanja razvoja. Tako na primer, Gezel u svojoj „teoriji vaspitanja“ preporučuje roditeljima da je „najbolji metod podizanja dece jedno razumno vođstvo“. Previše popustljivosti ili preterena rigidnost samo mogu štetiti pri- rodnom razvoju deteta. Ovaj stav Gezel objašnjava na sledeći način: „Ličnost deteta se razvija u procesu postepenog rasta. Sazreva- nje nervnog sistema se odvija postupno i obuhvata prirodne sekvence razvoja. Dete sedi pre nego što počne da hoda i govori; ono izmišlja i fantazira pre nego što počne da govori istinu; ono prvo crta krug, pa tek onda kvadrat; dete je sebično pre nego što postane altruista; ono je zavisno od drugih, pre nego što je postalo samostalno. Sve njegove spo- sobnosti, uključujući i moral, podređene su zakonima rasta. Zadatak odgoja dece ne sastoji se u tome da forsiramo javljanje predetermini- ranih obrazaca, već da ih podržavamo i vodimo“. (Gesell et.all., 1946, rev.,1977, p. 17). Ideje o prirodnom, unapred determiniranom procesu psihičkog razvoja deteta ne ostavljaju mnogo prostora za proučavanje vaspitno- obrazovnog procesa, tj. edukacije shvaćene u najširem smislu kao pro- ces socijalnog formiranja ličnosti. Ipak, značajni postulati nativističke orijentacije ne samo da su prihvaćeni, već i direktno ugrađeni u kon- cept nove interaktivne pedagogije. Gezelove postavke o gotovosti (ili spremnosti) deteta za učenje pretočene su u operacionalizovane principe novog vaspitanja. Razvoj i vaspitanje: klasični psihološki teorijski izvori Fokusi- ranost na dete (ili: student centered learning), dobro poznavanje stvar- nih mogućnosti deteta, prihvatanje deteta onako kakvo jeste, bez projektovanih slika roditelja i vaspitača kao deo nerealnih očekivanja, „osluškivanje“ dečjih potreba, visok stepen osetljivosti za potrebe de- 270 Matejić Đuričić, Z.: Nove konceptualizacije razvoja i vaspitanja teta, sve su to zahtevi koji predstavljaju direktne derivate nativistič- kih ideja o prirodnom razvoju deteta. S druge strane, kako to jezgrovito i tačno ocenjuje V. H. O. Šmit, rusoovske ideje o prirodnom razvoju imale su i svoj ozbiljan negativ- ni eho, jer „romantična vera u mudrost Prirode i nepoverenje u Društvo, dovode do preteranih pojednostavljenja odnosa između društva, kulture i razvoja deteta“. (Šmit, 1991, str.6). Drugačiji, gotovo suprotan, model proučavanja psihičkog razvo- ja, u okviru tradicionalne dečje psihologije, ponudili su empiristi, sa Votsonom na čelu. Bihejvioristički koncept psihičkog razvoja deteta izjednačio je ovaj proces sa procesom individualno sticanog isku- stva, odnosno učenja. U tom kontekstu, umesto istraživanja samog procesa vaspitanja, rasprava je pomerena na istraživanje vaspitne sredine. Pored velikog broja popularnih članaka namenjenih roditeljima, Votson je za sobom ostavio monumentalno delo „Psihološka nega odojčeta i deteta“ (Psychological Care of Infant and Child, Watson, 1928). Nakon ozbiljne kritike vaspitnih stavova iznetih u knjizi, naročito preporuke da decu ne treba mnogo maziti i da je emocionalna distan- ca poželjniji oblik brige, da se treba oglušiti o dečja pitanja ostavljajući dete da se samo zabavlja rešavanjem problema, da ne treba praviti od dece „invalide“ pripremajući ih za svet idealizovanih očekivanja itd., Votson je odustao od svojih ideja, pravdajući da u to vreme „nije do- voljno znao da bi dobro obavio posao“. Uključujući se u raspravu „nasleđe-sredina“, eksplicitno je zastu- pao stanovište po kome „ništa nije instinktivno, sve je stečeno u okviru in- terakcija koje dete gradi sa svojom sredinom“. Otuda je potpuna odgovor- nost za rezultate razvoja i vaspitanja deteta u rukama roditelja, pošto od njih zavisi kakvu će sredinu za razvoj pružiti svojoj deci. (Votsonu se pripisuje poznati slogan: Not more babies but better brought up babies! Ne veći broj dece, već više bolje odgojene dece!) Roditelji i vaspitači su ti koji preuzimaju kontrolu nad oblikovanjem ponašanja deteta jer oni utiču na to koje će vrste S-R veza i koliki će broj asocijacija „draž-reak- cija“ dete izgrađivati. U odnosu na stavove jednog nativiste, Votsonove predstave o vas- pitanju bez sumnje stavljaju veći akcenat na faktore sredine u proce- sima razvoja i vaspitanja dece. Razvoj i vaspitanje: klasični psihološki teorijski izvori Međutim, i dalje, sredina je shvaćena 271 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. samo kao bolji ili lošiji okvir razvoja, ali ne i kao sam izvor psihičkog razvoja deteta. Sredina modeluje procese učenja (razvoja), pa dete ostaje pasivni primalac uticaja „spolja“, a ne aktivni kreator vlastitog razvoja i vaspitanja. Šta je ostalo od klasičnih empirističkih ideja o razvoju i vaspita- nju? Zahtevi nove interaktivne pedagogije, fokusirane na mrežu od- nosa koje dete gradi u socijalnoj sredini, u prvi plan ističu veću odgo- vornost odraslih (vaspitača) za kvalitet relacija i opšti vaspitni odnos. Roditelji i svi značajni Drugi odgovorni su za obezbeđivanje uslova i pružanje najrazličitijih mogućnosti za sticanje iskustava, od kojih će dete iskoristiti tek neke, saobražene vlastitim mogućnostima i razvoj- nim dostignućima. Ističe se, takođe, i spoljašnji lokus kontrole kao re- gulator vaspitnih relacija, naročito u ranim godinama razvoja deteta. Konačno, definiše se plan optimalne ili obogaćene sredine kao kon- tekst realizacije razvojnih i vaspitnih procesa deteta. Sve su to tekovi- ne ili implikativni nastavci empirizma u psihologiji. Grandiozna teorija Žana Pijažea dovela je do značajnog pomaka u ovoj oblasti. Razvoj deteta Pijaže definiše kao epigenetički, autoregulativni tok, spontani i prirodni proces koji, sledeći svoju unutrašnju logiku, ne uključuje mehanizme socijalnog uticaja i regulacije. U kritičkoj oceni, Valon će pronaći zgodnu metaforu koja opisuje ovakav razvoj kao „ro- binzijadu“, kako bi predstavio dominantnu predstavu Pijažea o detetu kao malom Robinzonu koji vodi usamljenu borbu sa fizičkim univer- zumom, zahvaljujući vlastitim saznajnim kompetencijama. Sredina, fizička i socijalna, imaju isto značenje i važnost, a njihova uloga je da potpomažu i „alimentiraju“ (hrane) unutrašnji razvoj. Roditelj, nastavnik ili vaspitač treba samo da podstiče dete da sa- mostalno razvija strategiju otkrića... ... „jer samo slobodno istraživanje i samostalni napori deteta mogu proizvesti pozitivne rezultate, kako na planu školskog uspeha, tako i na planu opštih tokova socijalizacije“. (Piaget,1973, p.92). ... „jer samo slobodno istraživanje i samostalni napori deteta mogu proizvesti pozitivne rezultate, kako na planu školskog uspeha, tako i na planu opštih tokova socijalizacije“. (Piaget,1973, p.92). Pijažeova teorija izvršila je snažan uticaj na teoriju i praksu vas- pitanja (za opsežan kritički pregled, vidi: Satterly, 1987). Ideje kogni- tivnog konstruktivizma lako su svodive na prvi i osnovni postulat Pi- jažeove pedagogije: edukacija je proces stvaranja kreatora, inventora Pijažeova teorija izvršila je snažan uticaj na teoriju i praksu vas- pitanja (za opsežan kritički pregled, vidi: Satterly, 1987). Razvoj i vaspitanje: klasični psihološki teorijski izvori Ideje kogni- tivnog konstruktivizma lako su svodive na prvi i osnovni postulat Pi- jažeove pedagogije: edukacija je proces stvaranja kreatora, inventora 272 Matejić Đuričić, Z.: Nove konceptualizacije razvoja i vaspitanja i inovatora. Ovakva teorijska projekcija otkriva dete kao aktivni su- bjekt ne samo procesa unutrašnjeg (psihološkog) razvoja, već i opštih procesa vaspitanja (psihosocijalnog razvoja). Dete kao animal educandum: revitalizacija Vigotskovih ideja U okviru novih konceptualizaija razvoja i vaspitanja, granica iz- među procesa razvoja i vaspitanja se gotovo poništava: razvoj deteta se posmatra nužno u socijalnom i kulturnom kontekstu, dok se vaspi- tanje sagledava kroz mrežu socijalnih interakcija koje dete ostvaruje sa svojim socijalnim okruženjem, dakle, u čvrstoj sprezi sa psihičkim napredovanjem deteta. Da bi se razvijalo, dete mora da uči i da se vaspitava, čime vaspi- tanje postaje nužni konstituent psihičke ontogeneze. S druge strane, da bi se ostvario proces vaspitanja, potrebno je razvojno napredova- nje deteta, čime razvoj postaje nužni konstituent procesa vaspitanja, budući da dete nije pasivan primalac uticaja koji dolaze „spolja“, već je aktivno uključeno u zajedničku aktivnost sa odraslima i socijalno opštenje. Vaspitavajući se, dete se razvija; razvijajući se, dete se vaspitava. Tako shvaćena socijalna sredina, u kojoj se ostvaruje proces pre- obražaja deteta od biološkog u socijalno biće, nije samo bolji ili lošiji okvir, sa ulogom podsticanja ili usporavanja tokova prirodnog razvoja deteta; socijalna sredina je nužni formativni činilac razvoja. Rad Lava Semjonoviča Vigotskog, tvorca moderne ruske psihologije (i savremene defektologije) radikalno je uticao na tok savremenih rasprava o procesima razvoja i vaspitanja. U istraživanjima u ovoj oblasti, Vigotskove ideje su sveprisutne, čak i kada autori pripadaju drugačijim teorijskim orijentacijama i ne iskazuju eksplicitno svoju „naklonost“ prema Vigotskom (Farquhar, 2007; Santrock, 2004; Van der Veer, & Valsiner, 1991). Prema Vigotskom, socijalna sredina ima formativnu ulogu u procesima razvoja deteta, čime se odbacuje teza o njenoj podsticajnoj ulozi u prirodnom razvoju deteta (koju zastupaju maturacionisti) i teza o socijalnoj sredini koja modeluje ponašanje deteta, obezbeđiva- njem uslova za procese individualnog učenja (koju zastupaju empiri- sti, odnosno teoretičari učenja). 273 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. Individualni razvoj ne može se razumeti bez uvođenja društvenog i kulturnog konteksta u koji je psihička ontogeneza prirodno ugrađe- na. Za dete, to najbespomoćnije biće u čitavom živom svetu, prirodna sredina (habitat) jeste društveno oblikovana sredina koja obezbeđuje, u prvom redu, biološki opstanak, a potom i psihološki i socijalni op- stanak deteta. Sva druga mladunčad opremljena su gotovim obrascima pona- šanja koja im obezbeđuju relativno brzu adaptaciju fizičkim uslovima sredine, od nekoliko sati do nekoliko dana i nedelja. Visok stepen bespomoćnosti deteta pri rođenju, koje zahteva ne- ophodnu pomoć i podršku odraslih u procesu zadovoljenja osnovnih potreba, prestavlja specifičnu poziciju „ljudskog mladunčeta“ u odnosu na mladunčad svih ostalih životinjskih vrsta. Dete kao animal educandum: revitalizacija Vigotskovih ideja Tu i takvu poziciju Vi- gotski je odredio kao socijalnu situaciju razvoja, a potrebu deteta da odmah po rođenju stupi u socijalni odnos sa drugim ljudima koji o njemu preuzimaju brigu i odgovornost za njegov opstanak – kao pri- marnu socijalnost. U tom kontekstu, zabeležio je: „Odojče nije u stanju da samo zadovolji nijednu životnu potrebu „Odojče nije u stanju da samo zadovolji nijednu životnu potrebu. Najelementarnije i najosnovnije životne potrebe ne mogu biti zadovo- ljene drugačije nego uz pomoć odraslih koji o njemu brinu...Put preko drugih, put preko drugog čoveka jeste osnovni put u ovom periodu“. (Vigotski, 1984, IV, str. 62) Specifičnost dečijih potreba, u odnosu na potrebe odraslih, Vi- gotski ne vidi u sadržaju i vrsti, već u načinu na koji se vrši proces njihovog zadovoljenja. Dete ima potrebu za hranom, ali i potrebu da bude nahranjeno - sažeto, paradigmatski, objašnjava Vigotski osnovni postulat duševnog razvoja kao socijalno posredovanog procesa. Socijalna situacija novorođenčeta predstavlja prvi paradoks ra- zvoja: dete ima snažnu potrebu da komunicira sa socijalnom sredi- nom, a da, pritom, još uvek ne poseduje razvijena sredstva komunika- cije, tj. „postoji protivrečnost između potpune socijalnosti deteta i minimal- nih mogućnosti za komunikacijom.“ Novorođenče ne poseduje urođene mehanizme, specijalizovane i gotove oblike ponašanja, niti instinktivni prirodni komunikativni si- stem, kao mladunčad drugih vrsta. Ipak, broj urođenih šema ponaša- nja, na koji reaguju odrasli, iako sasvim ograničen, sasvim je dovoljan 274 Matejić Đuričić, Z.: Nove konceptualizacije razvoja i vaspitanja da otpočne proces socijalne razmene. U okviru zajedničke (praktič- ne) aktivnosti, u okviru socijalnog odnosa i socijalne interakcije, dete može da razvije sredstva razmene sa sredinom (jezik i druga simbolič- ka sredstva). Osnovni dokazi na kojima se zasniva postojanje primarne socijal- nosti deteta su: −− autonomna motivacija za uspostavljanje komunikacije i ini- ciranje socijalnog kontakta (pozitivni signali na prisustvo odraslih i negativni signali deteta prilikom odlaska odraslog); −− rana pojava specifičnih socijalnih reakcija (socijalni osmeh, motorička živost, pojačana vokalizacija, gukanje i sl. Dete kao animal educandum: revitalizacija Vigotskovih ideja u prisu- stvu odraslih ili, na drugoj strani, kod napuštanja, pojava pla- ča i drugih signala kojima dete doziva odraslog da se ponovo vrati); −− rana osetljivost na socijalne draži (diferenciranje fizičkih i so- cijalnih draži, uz preferenciju stimlusa koji dolaze od drugog čoveka, kao što su ljudski lik i karakteristike glasa i govora, u odnosu na senzorne i akustičke draži iz fizičke okoline); −− postojanje kapaciteta za emocionalno vezivanje, i −− relativno rano ispoljavanje sposobnosti deteta za uspostavlja- nje lančane reakcije, tj. dvosmerne komunikacije sa odraslima. Primarna socijalnost deteta proističe iz činjenice da dete, iako ne poseduje urođene obrasce ponašanja, jeste spremno za razvijanje zajedničke aktivnosti sa odraslima. Upravo u tom procesu socijalnog opštenja ono pristupa otkriću spoljašnje realnosti. Tako Vigotski obra- zlaže tezu da je individualni razvoj deteta nužno socijalno posredo- van proces. „Komunikacija sa odraslima predstavlja osnovni put ispoljavanja sopstvene aktivnosti deteta...Ne postoji individualani razvoj deteta - postoji samo socijalno posredovan proces psihičke ontogeneze deteta“. (op. cit.) „Komunikacija sa odraslima predstavlja osnovni put ispoljavanja sopstvene aktivnosti deteta...Ne postoji individualani razvoj deteta - postoji samo socijalno posredovan proces psihičke ontogeneze deteta“. (op. cit.) Psihičke funkcije koje dete razvija najpre se pojavljuju kao interp- sihičke kategorije, i one postoje u funkciji razmene i socijalnog opšte- nja sa sredinom, a tek potom, mehanizmom prenošenja na unutrašnji plan, one postaju intrapsihičke kategorije, sa ulogom regulacije indivi- dualnog ponašanja. 275 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. Kratka geneza govora : socijalizovani govor  egocentrični govor  unutrašnji govor - verovatno je najilustrativniji primer kojim Vi- gotski objašnjava vezu između interpsihičkog (socijalnog odnosa) i in- trapsihičkog (individualnog ponašanja i razvoja). U tumačenju odnosa učenja i razvoja, ova zakonitost prestavlja stub Vigotskovog sistema. Za razliku od Pijažea, koji je zastupao stanovište da procesi ra- zvoja prethode svakom učenju, jer da bi bilo spremno da uči dete treba da konstruiše za to potrebne saznajne strukture, Vigotski je čvrsto verovao da učenje vodi ili vuče razvoj deteta. Drugim rečima, učenje u socijalnoj sredini prethodi razvoju, tj. stoji ispred razvoja. „Učenje je nužan i univerzalan aspekt procesa razvoja kulturalno organizovanih, specifično humanih psiholoških funkcija“. (Vigotski, 1978, p.277). Ulogu učenja u procesu psihičke ontogeneze Vigotski je definisao uz pomoć novokonstruisanog pojma - pojma zone narednog razvoja. Zona narednog razvoja (ZNR) govori o tome šta dete može uz po- moć odraslih, a još uvek ne može samostalno da izvede. Dete kao animal educandum: revitalizacija Vigotskovih ideja Iako se ovaj pojam primarno odnosi na sferu saznajnog razvoja, čini se da on ima gotovo univerzalnu primenu u razvoju detinjih kompetencija. Uzmi- mo, na primer, motoričku aktivnost uspravljanja i prohodavanja. Dete koje se nalazi u fazi neposrednog prohodavanja, uz pomoć roditelja slobodno korača iako ga oni tek malo pridržavaju za krajičak odeće dok „razvoj u sadašnjem danu“ signalizira roditeljima da dete iako još uvek ne hoda - „samo što nije prohodalo“. j p Pred vaspitačima se nalazi odgovoran zadatak da tačno prepo- znaju zonu narednog razvoja, u svakom trenutku, i u svim domenima razvoja. Podsticanje i ohrabrivanje deteta da se samostalno oproba u nekoj radnji, veštini, rešavanju problema i sl. ima važnu vaspitnu ulo- gu u razvoju. Osetljivost za prepoznavanje dečjih potreba, na čemu se danas toliko insistira u okviru savremene porodične pedagogije, znači upravo to: ponuditi prave sadržaje koji se nalaze u okviru zone nared- nog razvoja deteta, umesto onih koji pripadaju zoni davno pređenog puta (jer dete ih je „preraslo“) i onih koji se, eventualno nalaze u zoni dalekog budućeg razvoja (jer dete im nije „doraslo“). 276 Matejić Đuričić, Z.: Nove konceptualizacije razvoja i vaspitanja Nova antropologija deteta i detinjstva Iako govore „drugim jezikom“, ove Vigotskove ideje čvrsto su ugrađene u nove konceptualizacije razvoja i vaspitanja, i pre svega, u novu antropologiju deteta i detinjstva. Redefinisanje procesa humanog razvoja u vaspitnom (socijalnom, kulturnom) kontekstu i nove konceptualizacije vaspitanja najbolje su iskazane u novim predstavama o detetu kao biću koje mora da uči i da se vaspitava da bi razvilo osnovne mogućnosti ljudskog roda. Dete je animal educandum, prvi ističe ovu tezu u okviru svoje „an- tropologije vaspitanja“ holandski psiholog M.J. Langafeld (prema: Šmit, 1991). Ovim se tvrdi nešto znatno više od toga da je dete vaspit- ljivo ili da je vaspitanje važno. Nova antropologija deteta kaže da dete mora da uči i da se vaspitava, te da je vaspitanje biološki nužno za razvoj. O tome Ešli Montegju eksplicitno izveštava: „Nijedan organizam iz vrste koja je tako preuranjeno nazvana homo sapiens nije rođen sa ljudskom prirodom. Biti čovek nije status sa kojim, već status prema kome se neko rađa. Mora se naučiti da se bude čovek“ (Montague, 1955). Razvijajući opsežnu raspravu o ovom problemu, Šmit zaključuje da je redefinisanje procesa razvoja kao kulturno i socijalno posredova- nog procesa dovelo i do novog pristupa procesima vaspitanja. Za razli- ku od klasičnih stanovišta prema kojima dete trpi raznorodne uticaje odraslih koji preuzimaju ulogu vaspitača, vaspitanje se danas razume- va kao proces zajedničkog interaktivnog izgrađivanja jedne specifič- ne humane relacije u kojoj dete aktivno preuzima odgovornost za svoje razvojno napredovanje. Lako se zapaža da se ovim stavom gotovo poništavaju granice iz- među razvoja i vaspitanja. O tome Langefeld eksplicitno izveštava: „Dečja psihologija, ili opštije, razvojna psihologija, predstavlja važnu dimenziju pedagogije ili vaspitanja. Međutim, i razvojna psi- hologija je suštinski prepoznala da su činjenice o njenom predmetu proučavanja (psihološki razvoj deteta) uvek činjenice o detetu koje se vaspitava. Langefeld, 1988, p. 2). Ovakvim pristupom, prirodni razvoj čoveka se sagledava kao sa- svim „artificijelna“ kategorija, jer humani razvoj znači mnogo više od prostog fizičkog održanja organizma čoveka. Razvijanje individualne, samosvojne, neponovljive ličnosti, s jedne strane, i izgradnja za datu 277 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. kulturu karakterističnih oblika ponašanja, dve su osnovne linije u ko- jima se ostvaruje razvoj, čvrsto vezane za vaspitno u kulturno okruže- nje u kome pojedinac živi. Drugim rečima, vaspitanje je proces koji se ostvaruje na dva pla- na, i uključuje dve linije: a) hominizaciju b) individualizaciju. Nova antropologija deteta i detinjstva Proces hominizacije podrazumeva izgradnju osnovnih osobina ili svojstava karakterističnih za čoveka kao živu vrstu, uz sve kultur- no specifične dorade i stilizacije obrazaca ponašanja koje izviru iz date kulture i ukupnog društveno-istorijskog konteksta. Proces indivudalizacije odnosi se na izgradnju posebne, jedin- stvene individue, ličnosti sa neponovljivim idiosinkratskim karakte- ristikama. Za ova dostignuća u „postajanju čovekom“ (Montegju) odgovorni su procesi vaspitanja. Etolozi su ukazali na osnovne činjenice koje vaspitni proces čini nužnim za opstanak i razvoj pojedinca. Sažimajući nalaze velikog bro- ja etoloških studija, možemo zaključiti da su se u procesima evolucio- nog razvoja čoveka kao vrste (antropogenzi) događale obostrano važ- ne promene koje su „biološki opremili“ i roditelje i decu da odmah po detinjem rođenju ostvare, za dete nužan, socijalni odnos. Prvo, u odnosu na trajanje perioda detinjstva kod ostalih živo- tinjskih vrsta, detinjstvo deteta produženo traje, najmanje sedam go- dina. (mački je potrebno samo godinu dana da postigne punu seksu- alnu i fizičku zrelost, za mladunče šimpanze to je period od samo dve godine). Ovu činjenicu ne treba posmatrati i tumačiti kao „evolucionu grešku“ ili „luksuz evolucije“, već, naprotiv, u kontekstu dubokog smi- sla evolucionih procesa koji su vodili ka produženju perioda za učenje i isprobavanje različitih mogućnosti organizma, kao deo pripreme za život u zajednici odraslih. Odgovornost odraslih ogleda se u tome da optimalno pomognu detetu u toj pripremi za život, tako što će od sa- mog početka adekvatno izlaziti u susret i zadovoljavati potrebe deteta. Drugo, dete se ne rađa sa gotovim (instinktivnim) specijalizova- nim obrascima i šemama ponašanja, koji bi mu omogućili brzo pri- lagođavanje složenim sredinskim uslovima, ali zato, mladunče čo- veka poseduje najviši stepen plasticiteta mozga, što omogućava 278 Matejić Đuričić, Z.: Nove konceptualizacije razvoja i vaspitanja najveći opseg varijacija u ponašanju i najšire mogućnosti za učenje. U ovaj proces, takođe, nužno su uključeni odrasli (roditelji i svi drugi za dete važni Odrasli) koji preuzimaju odgovornost za proces šta, koliko i kada dete uči. Treće, dete se rađa sa najvišim stepenom bespomoćnosti (pojava neotenije, novog rođenja) zbog čega je nužno upućeno na druge ljude u procesima učenja u periodu detinjstva. Nova antropologija deteta i detinjstva Rana osetljivost za socijalne draži (preferiranje karakteristi- ka draži koje dolaze od drugog čoveka, kao što su lice, glas, dodir, u odnosu na stimuluse koji dolaze iz fizičke sredine) i biološki predeter- miniran kapacitet za emocionalno vezivanje, omogućavaju novo- rođenčetu da prve socijalne interakcije ostvaruje odmah po rođenju, i pre nego što je razvilo osnovna sredstva za komunikaciju. S druge strane, biološka oprema odraslih uključuje spremnost da se reaguje i odgovori na signale koje emituje beba, stavom koji uključu- je naklonost, brigu i zaštitu. O ovome etolozi izveštavaju serijom ogle- da o pojavi babyshness-a. Iako teško prevodiv na naš jezik, ovaj feno- men se može opisati kao sistem pozitivnog emocionalnog reagovanja na „bebasti izgled“, pozitivnog reagovanja na mladunče, na bebu, ali i na sve drugo što je malo, majušno i nezaštićeno. Promena osnovnih fizioloških parametara (puls, arterijski pritisak, vlažnost kože, pro- mena temerature tela, itd.) kao fizioloških supstrata emocija, beleže se ne samo prilikom reagovanja na „bebasti izgled“ ljudske bebe, već i na mladunčad iz celog životinjskog sveta: pile, ptiče, tele, prase, čak i pupoljak u odnosu na uvenule latice cveta. (Istraživanja su ukazala na izvesne razlike između muškaraca i žena, što bi potkrepljivalo klasične teorije o materinskom instinku: takođe, osetljivije, sa jačim promenama fizioloških parametara reagu- ju trudnice, u odnosu na žene koje nisu rađale; kod očeva se registruje istaknutija slika pozitivnog reagovanja na „bebasti izgled“ u odnosu na muškarce koji nemaju svoju decu, itd. (pregled: Hess, 1970). Ovi podaci skupno potkrepljuju postavke o tome da je ljudska vr- sta biološki opremljena kapacitetom za prihvatanje mladunaca, neza- visno od činjenica koje određuju složenu prirodu humane motivacije za roditeljstvom. Šta vaspitanje čini posebnim socijalnim odnosom među ljudima? 279 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. Za razliku od drugih odnosa među ljudima, vaspitanje je specifič- na humana relacija za koju je karakteristično to da se odvija između jedne ili više odraslih zrelih (i pretpostavlja se, odgovornih) osoba kao vaspitača i deteta kao još neizgrađene, nezrele osobe koju će vaspita- nje učiniti sposobnim, kompetentnim i zrelim članom društva. Najdirektnije empirijske dokaze u prilog ovim postavkama pru- žaju studije o deci odrasloj u „divljini“, u uslovima ekstremno teške socijalne deprivacije. Čitav smisao i nužnost vaspitanja posmatra se izoštreno, kao druga strana ogledala. Rezultati ovih studija pokreću jedno opšte metodološko pitanje. Nova antropologija deteta i detinjstva Naime, ako je tačno da ljudska beba barem prve dve godine ne može da preživi bez pomoći drugih ljudi, onda je krajnje sumnjiva pretpostav- ka o valjanosti studija o „divljoj deci“ i o objektivnosti i pouzdanosti podataka dobijenih praćenjem dece koja su rasla u uslovima socijalne izolacije. Rana socijalna izolacija nikada ne može da bude potpuna. Zato je ispravnije govoriti o ekstremno teškim uslovima socijalnog lišavanja i posledicama koje takva sredina ostavlja na ukupan razvoj dece. Nezavisno od moguće kritike ovih studija, ne postoje jači i ubed- ljiviji dokazi za tezu da Priroda Čoveka vaspitanje čini nužnim za dete. Sva druga mladunčad živih vrsta brzo se prilagođavaju spoljašnjim uslovima, opstaju i razvijaju se zahvaljujući automatizovanom delova- nju mehanizama kolektivnog i individualnog iskustva, samo dete ne može da se razvija bez delovanja faktora socijalnog iskustva.i Socijalno iskustvo fiksirano je u produktima materijalne i duhov- ne kulture jednog naroda, pa se kao jedan od osnovnih zadataka koji stoji pred svakim ljudskim bićem postavlja zahtev za „prisvajanjem dostignuća kulturno-istorijskog razvoja čovečanstva“, kako to ističe Vigotski u svojoj teorijskoj skici. U tome se ogleda osnovna specifič- nost plana humanog razvoja. Roditelji (drugi ljudi) koji posreduju u procesu zadovoljavanja deč- jih potreba, u okviru stalnih interakcija sa detetom pojavljuju se kao prenosioci produkata date materijalne i duhovne kulture, uključujući jezik kao vrhunsku istorijsku tvorevinu. U tome se ogleda plan huma- nog vaspitanja. Završni cilj vaspitanja je preuzimanje vaspitne odgovornosti za izgrađivanje novih relacija u kojoj vaspitanik postaje vaspitač. 280 Matejić Đuričić, Z.: Nove konceptualizacije razvoja i vaspitanja UMESTO ZAKLJUČKA: UMESTO ZAKLJUČKA: nove konceptualizacije - stari teorijski izvori Kratak istorijski presek osnovnih ideja ugrađenih u raspravu o procesima psihičkog razvoja i vaspitanja jasno otkriva tendenciju pre- vazilaženja početne disociranosti i disciplinarne podeljenosti u prou- čavanju dva konstitutivna segmenta humane ontogeneze. Savremene konceptualizacije vaspitanja integrišu naučno nasle- đe različitih psiholoških teorija razvoja, uključujući i klasične teorijske izvore. Pri tome, presudan uticaj u oblikovanju novih teorija vaspita- nja i obrazovanja (edukacije) imala je Vigotskova teorija kulturno-isto- rijskog razvoja, koja, takođe, pripada klasičnim teorijskim izvorima od kojih nas deli gotovo čitavo stoleće. Središnje ideje nove antropologije vaspitanja jezgrovito objašnja- va Langefeldov koncept deteta kao animal educandum-a. Dete je biće koja mora da uči i da se vaspitava da bi razvilo osnovne karakteristike ljudskog roda (proces hominizacije ili nastajanja čovekom) i sve speci- fične, idiosinkratske karakteristike ličnosti (proces individuacije). Nova antropologija deteta i detinjstva i Umesto izlolovanog fokusa na dete (vaspitanika) ili odraslog (vaspitača) – novi pristupi akcentiraju sam proces, odnosno uzajamni odnos dete-odrasli. Na taj način, može se prepoznati i posebno ana- lizirati uloga deteta ka aktivnog kreatora vlastitih procesa razvoja i vaspitanja. Šmit (op. cit.) navodi odeljak iz Boldvinovog romana „Ko- liko voz dugo putuje“, koji bolje od svake stručne analize, objašnjava smisao, svrhu i cilj vaspitanja: „Pa, da, ja sam konačno uvideo šta se od mene traži. Ja moram da napravim gnezdo, ja moram da znam i da budem spreman da ga branim životom, i da nahranim to majušno stvorenje, i da ga držim či- stim, i da njegovo gnezdo držim čistim: i da prepoznam trenutak kada je ono spremno da poleti i da dam snagu tim zaplašenim krilima da se dokopaju zraka.“ 281 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. NEW CONCEPTS ON DEVELOPMENT AND EDUCATION Zorica Matejić Đuričić University of Belgrade – Faculty of Special Education and Rehabilitation LITERATURA 1. Farquhar, S. E. (2007). Assessing the Evidence on Childcare/Early Childhood Effects. Published by ChildForum, New Zealand. 2. Freire, P. (2007). Pedagogy of the Oppressed. New York: Continuum. (first pub.,1968) 3. Gesell, A. (1924, rev. 1977). 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Psychological Care of Infant and Child. New York: W. W. Norton Company, Inc. 283 Specijalna edukacija i rehabilitacija (Beograd), Vol. 11, br. 2. 267-284, 2012. Summary In this article, the theoretical analysis of two complementary processes of human ontogenesis, development and education, was made. Starting by the leading biological and social theory in developmental psychology and pedagogy, the main approaches to the role of social environment factors in child development had been investigated. New anthropology of a child and childhood was derived from cultural-historical theory of L.S. Vygotsky, as the way of looking for the answer on the question: Why is the education of biological necessity? The conclusion deals with the new concepts of the new developments and education, which abolish the boundaries between psychology and pedagogy, for it treats these processes as the unique human ontogenesis. Key words: development, education, child as animal educandum Primljeno, 29. 12. 2011. Prihvaćeno, 23. 4. 2012. Prihvaćeno, 23. 4. 2012. 284
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Improving Reading TOEFL Score through Note Taking Strategy
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*) Corresponding Author Keywords: TOEFL reading; note-taking strategy; reading skills; ELT; standardized tests. How to Cite: Ismail, N., & Fata, I. (2021). Improving Reading TOEFL Score through Note Taking Strategy. Al- Ta lim Journal, 28(1). doi:https://doi.org/10.15548/jt.v28i1.668 How to Cite: Ismail, N., & Fata, I. (2021). Improving Reading TOEFL Score through Note Taking Strategy. Al- Ta lim Journal, 28(1). doi:https://doi.org/10.15548/jt.v28i1.668 © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Nyak Mutia Ismail, Ika Apriani Fata; Improving Reading TOEFL… Nyak Mutia Ismail, Ika Apriani Fata; Improving Reading TOEFL… AL-TA’LIM JOURNAL, 28 (1), 2021, (46-54) (Print ISSN 1410-7546 Online ISSN 2355-7893) Available online at http://journal.tarbiyahiainib.ac.id/index.php/attalim Received: 06th November 2020; Revised: 05th February 2021; Accepted: 28 th February 2021 Received: 06th November 2020; Revised: 05th February 2021; Accepted: 28 th February 2021 P li k/DOI h //d d i /10 15548/j 28i1 668 Received: 06th November 2020; Revised: 05th February 2021; Accepted: 28 th February 2021 Permalink/DOI: http://dx.doi.org/10.15548/jt.v28i1.668 Permalink/DOI: http://dx.doi.org/10.15548/jt.v28i1.668 Nyak Mutia Ismail Abstract: There are still a number of less skilled readers in higher degree education where academic texts are staple needs (Hellekjaer, 2009). This study investigated a technique to help students increase their reading ability in TOEFL reading section. A technique named Notetaking technique was implemented during two cycles of classroom action research. There were 3 meetings for each cycle. The participants were 17 Economics students who are taking TOEFL Preparation course at Universitas Syiah Kuala, Aceh, Indonesia. The result from cycle one showed no increase since the average only incline to 38.58. Then in cycle 2, there was a significant increase reaching 45.11 (which is the minimum TOEFL standard for the university). It can be deduced that this technique might not be appropriate for large classes as it demands individual assistance. Besides, a good skill of organizing information is fundamental in this strategy to maximize the students’ effort in answering the TOEFL questions during the test. y Universitas Syiah Kuala, Banda Aceh, Indonesia. E-mail: nyakmutiaismail2020@gmail.com Ika Apriani Fata*) Universitas Syiah Kuala, Banda Aceh, Indonesia. Ika Apriani Fata*) Universitas Syiah Kuala, Banda Aceh, Indonesia. Ika Apriani Fata*) Universitas Syiah Kuala, Banda Aceh, Indonesia. E-mail: ika.unsyiah@gmail.com *) Corresponding Author E-mail: ika.unsyiah@gmail.com E-mail: ika.unsyiah@gmail.com INTRODUCTION was poor. From the pre-test, it was obtained that the reading average score of the students was 36.17. Indonesian students are known to have below average ability in mastering literacy. This fact is shown in the result of PISA in 2012 and 2015. In PISA’s result 2012, Indonesia got 396 for reading while the average score for reading was 497; while in 2015, Indonesia reached 397 while the average score was 493. The result of the huge observation shows that from year to year, Indonesia is still struggling with the issues of literacy. To be more specific, similar conditions also happen to a university class where the authors teach. The class was a TOEFL preparation class in Economics faculty, Universitas Syiah Kuala, Indonesia. The students’ reading score in reading section As a matter of fact, reading is seen as an important part of language skills. Students can develop other language skills such as speaking and writing through reading (Hatch, 2001). There are five aspects comprising reading, they are main idea, detail information, reference, vocabulary and inference (Mickulecky & Jeffries, 2007). Likewise, TOEFL also tests these subskills of reading. The main problem in reading comprehension for these mentioned students is comprehension, where their concentration can easily collapse during the reading time. Besides, there are also vast thoughts come to 46 © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Nyak Mutia Ismail, Ika Apriani Fata; Improving Reading TOEFL… 47 their mind at the moment they read. Simply, they cannot resist the temptation to stay grounded on their concentration. Besides, Putra et al., (2017) found that for Acehnese university students, reading—especially vocabulary—is a part of TOEFL that students need to focus more. and the test performance. It was found that there is a significant relationship between notetaking strategies and the students’ test performance, especially concerning to the number of words in the note. Reading is a complex activity involving perception and thoughts. Besides, it also involves two stages which are word decoding and text comprehending (Pang, et.al, 2011). Reading is message transactions between writers and readers through visualization where readers need to convert all kinds of messages such as emotion, culture, information, and experience during their reading (Kader, 2008). INTRODUCTION It is important since it does not only give readers understanding and clarification, but it also exposes readers to gaining new experience— even though the ones that the readers have never undergone before. This mostly happen in literary reading (Lems, 2010). Meanwhile in academic reading, readers are exposed to the concepts and understandings of theories intertwined to a certain field of discipline. Similarly, in Reading Section of the TOEFL test, reading comprehension also refers to academic reading types with various topics. A worth-to-try strategy called note- taking technique was examined whether it met the students’ need in handling comprehension problems (Fata, et.al, 2020). Note taking is an elaborate process demanding comprehension in selecting the most important information (Piolat, et al., 2005). Piolat, et.al (2005) further clarify that note taking activity involves working memory procedures and timing in order to get a task done. Multitasking activities such as reading, comprehending, regulating knowledge to select vital information, and jot it down are involved in this strategy. Previous studies on the note-taking technique are described in the following. First, it is a study by Teng (2011) which sought the note-taking strategies used in listening. There were 80 university students involved as the participants in Taiwan. He used questionnaires in collecting the data. The result suggested that the strategy mostly used during note-taking by the students was trying to absorb what is being taught in class as much as possible. Next, it is a study by Rahmani & Sadeghi (2011). This study examined the effects of note taking strategy training on students’ comprehension and retention. There were 108 respondents who were Iranian EFL learners which were divided into experimental and control group. The experimental group was assigned with note taking strategy while the control group was not. The result unveiled that the experimental group performed better at both comprehension and retention test. Finally, the last one mentioned in this study is a study by Carrel (2007). A group of TOEFL examinees who were taking computer-based listening comprehension were involved as the participants. The instrument used during the data collection was a set of questionnaires. Besides, this study also investigated the relationship between the note taking strategies The interest in reading is one important factor that can lead an EFL student to become a successful reader. INTRODUCTION However, most students are not fond of reading, especially academic reading, which most likely brings about the problems around TOEFL reading. When the term ‘comprehension’ is a demand, it means that the students are obliged to identify five reading subskills, namely: main ideas, inferences, references, details, and vocabulary (Brown, 2001). Main idea is the writer’s idea and the readers are supposed to catch it in order to convey the messages in the passages (Mikulecky and Jeffries, 2007). Then inference means that readers should be able to predict the preceding and following issue(s) before or after the passage; it is crucial because inferring is employing the sense of comprehension (Duffy, 2009). Reference word is one of the cohesive devices of reading that helps tie sentences together to create a cohesive text. There are anaphoric and cataphoric reference, anaphoric is the backward pointing while cataphoric forward © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Volume 28, Number 1, February, 2021, Page 45-54 48 pointing (Erwin, 2004). Mikulecky and Jeffries (2007) further state that details are important part in a reading passage since readers can obtain specific and clear information that clarify the main idea. Finally, vocabulary is an essential part in reading. Readers should grab the meaning of vocabulary first in order to figure out the next level in reading comprehension (Lehr, 2009). students also have to follow the speed of their eyes during reading; and at the same time, they have to select and write down the points that they deliberate to be essential. The cognitive effort involved during several reading activities can be seen in the following chart. Figure 1. Mean of Cognitive Effort To juxtapose the propositions above, instructors should be able to provide additional materials in reinforcing students’ needs in class, especially in reading comprehension. This is worth to be in consideration since Ness (2009) has found that, on the contrary, most instructors do not understand the responsibility to do so. Further, Pang et.al (2011) place twelve key issues in enhancing reading comprehension, they are oral language (as it influences early reading ability), phonological and phonemic awareness, fluency in reading, vocabulary, prior knowledge, comprehension, motivation and purpose, the integration of reading and writing, text choice, assessments and feedback, cultural factors, and practice. INTRODUCTION In addition, integrating writing into reading is a good suggestion as Khaki (2014) revealed that asking students to do summary in readings and generate questions could improve their ability in reading comprehension. Figure 1. Mean of Cognitive Effort In the figure above, it can be seen that the highest cognitive effort happens during taking notes in lecturers using usual method, followed by the similar notetaking activity by pre-planned method. Meanwhile, taking notes during reading leads to almost 300 efforts per mili-second. This is considered as a high cognitive activity. There are several essential keywords in notetaking as suggested by Jones & Mort (1994). A note-taker should: 1). be selective and systematic, 2). comprehend the passage purpose, 3). understand the information organization, and 4). include his/her own insights for justification. They further propose several models that can be used during notetaking such as using symbols, abbreviate and drawing maps and charts. Interpolating notetaking strategy, research has shown its usefulness in learning. Taking note is a process that involved information comprehension, selection, and organization (Piolat, et al., 2005). This strategy is beneficial for students whether in in-class learning process or in figuring out the information from aural and visual sources. Mostly, note taking does not have to be exactly linear with the original text, but what comes to be the most important is the quality of the information selection. The memory would easily be recalled; hence, more organized review can be gained when the information is about to be performed. METHOD This study was conducted using classroom action research (CAR) design. CAR is strategy used by a teacher or an instructor to solve the actual problems faced in class; CAR is also seen as a tool to develop teaching techniques (Ferrance, 2000). According to Kemmis and McTaggart (2014), Piolat, et.al (2005) further clarify that noticing involves a highly cognitive consuming ability. While taking notes, the © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Nyak Mutia Ismail, Ika Apriani Fata; Improving Reading TOEFL… 49 were still some shortcomings in the teaching process—as well as informed by the collaborator, the second cycle was repeated for three more meetings before the students had their final post-test. The success indicator was at least 60% (10 out of 17) of the students get 6 points increase. Concerning to the research instrument, the diagnostic test and post-test developed by Philips (2001) were used. there are four steps in a CAR design, they are planning, acting, observing, and reflecting, and this cycle may repeat as necessary. The class used was a TOEFL preparation class consisted of 17 first year Economics students majoring in Management at the Universitas of Syiah Kuala. In addition, the first author was the teacher and the second author was the collaborator in this study. The collaborator is also an experienced-English instructor who has taught TOEFL preparation class. The research procedure conducted was as follows. Initially, a pretest was administered to the class. Later, the note-taking technique was implemented for three meetings. Then, the students had the initial post-test to see how far the technique had helped them. Since there RESULT AND DISCUSSION Below is provided the result of TOEFL reading section of the pretest, cycle one test, and cycle two test. © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Table 1. Reading Score in Pretest, Cycle 1 Test, and Cycle 2 Test Student Pretest Mid-test (Cycle 1) Increasae in Cycle 1 Post-test (Cycle 2) Increase in Cycle 2 1 39 39 0 47 8 2 39 38 -1 48 9 3 44 43 -1 49 5 4 37 43 6 50 13 5 40 40 0 47 7 6 33 37 4 43 10 7 39 35 -4 47 8 8 35 44 9 49 14 9 31 34 3 40 9 10 35 40 5 50 15 11 38 43 5 48 7 12 31 34 3 46 15 13 34 38 4 38 4 14 35 39 4 45 7 15 30 32 2 34 4 16 40 38 -2 44 4 17 35 40 5 42 7 Average 36.17 38.58 2.47 45.11 8.58 © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Volume 28, Number 1, February, 2021, Page 45-54 Volume 28, Number 1, February, 2021, Page 45-54 50 The table above shows that the average score of the TOEFL reading section in pretest was 36.17, from which there were supposed to be only 16 correct answers out of 50 question Gear & Gear (2006). The average score that Syiah Kuala university demands for non-English major is 450 which Reading section should reach at least score 45 for non- English major. Hence, 36.17 is still below the university average score. In addition, the researcher did not observe the class herself. After she explained and exemplified the strategy of notetaking, she asked the students to do notetaking on their own. She only provided a little help and she did not assist every single student. The collaborator advised to give individual assistance to every student since their limited ability in reading. The next idea being reflected is the researcher’s ability. It it reflected in students’ score in cycle 1. Table 1 above shows that the average score is 38.58 which is still below average score that the university demands. It can be seen there are score increase from 11 students but only two students reached 6 point-increase; meanwhile, it was set up in the success indicator that there, at least, 10 students who can reach 6 point-increase. RESULT AND DISCUSSION It was concluded that this cycle did not yet succeed and needed to continue. Besides, the table shows there are 2 students who barely got any increase, and 4 students even degrade score. So, it was essential that the researcher refine her teaching ability using the notetaking technique in teaching TOEFL reading. Below is an example of a student’s note from Cycle 1. Cycle 2 In the phase of planning for cycle 2, the researcher prepared six TOEFL reading passages for the next three meetings. The topic was randomly assigned since it is important to familiarize students with topic shifts as it happens regularly in TOEFL reading section. In the acting process, the three meetings were carried out on April 4, April 11, and April 18, 2017. Like the previous cycle, in the first meeting, the researcher explained again the strategy used in notetaking. Of course, this time she explained more slowly and made sure that all students were engaged with her explanation. When the students looked confused, she immediately questioned them for clarification. More individual assistances were enhanced in this cycle. From the observing phase done by the collaborator, it was concluded that the process was mostly feasible. One point that can be noted is that, students who were already good at notetaking—only one or two students—felt bored as they could finish fast so that they might chat about something else during the process. However, this was not any meaningful trouble. The other key point being considered in the reflecting phase is the researcher’s ability in implementing the technique, which is portrayed in the students’ score of cycle 2. From the table above, it can be seen that the mean score after cycle 2 is 45.11 and there is definitely an increase. This score is the minimum standard for the non-English department students at the university. The table shows that there are 4 students who did not reach the six-point increase; while there are 13 students who reached above six points increase. This indicates that the cycle is successful since the success indicator has stipulated that there has to be, at least, 60% (10 out of 17) of the students get 6 points increase. Besides, there is no downgrading score after cycle 2. Regarding the students who did not reach the six-point increase, they informed the researcher that it was hard for them to grab, organize, and rewrite information they got from the passage(s) at once. It was a burdening activity for them. Hence, they could not carry on those activities together without getting confused. Below is the note from the same student whose note is also presented earlier in cycle 1. What differentiates is that the following note is made after cycle 2. Cycle 1 When planning the action for cycle 1, the researcher prepared a topic about sports for the students. She prepared four TEOFL reading texts for the process. The acting phase was carried out on March 10, March 17, and March 24, 2017. In the first meeting, she explained to the students how to do notetaking while doing reading and later, the students were given chances to practice notetaking using the passages from their learning module. In the second and the third meeting, the students had to do notetaking by themselves and at the end of the class, the researcher—together with the class—checked the students’ work. The researcher also gave some revisions and suggestions when checking the students’ work. In the phase of observing, the collaborator observed both the students’ participation and teacher’s ability in applying the technique during the teaching and learning process. And the results from the collaborator were later being discussed with the researcher after the cycle ended. Figure 2. Student’s note after Cycle 1 Finally, in reflecting phase, there are two ideas being reflected. The first one—also answering the first research question—is the students’ participation and the second one is the researcher’s ability in using notetaking technique in teaching TOEFL reading, which is implied in students’ score stated in the second research question. From the initial idea, it was suggested by the observer that the researcher taught so fast that most students could not keep up the pace, so there were several students who were left behind and did not understand the idea of notetaking; however, there were some students who could stay focus and followed the researcher’s explanation and found no obstacles on it. Figure 2. Student’s note after Cycle 1 From the figure above, it can be seen that the student wrote down every first line in each paragraph. It is more like text-copying instead of notetaking. Indeed, there was an outline that is understandable after reading this note; however, it is needlessly to use complete sentences when notetaking. As in notetaking strategy, there are only © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Nyak Mutia Ismail, Ika Apriani Fata; Improving Reading TOEFL… 51 paraphrasing, outlining, using abbreviations, and understanding the gists (Hughes & Suritsky, 1993)—there is no word-copying. recognizing parts of the outlining—which ideas belonged to which. Cycle 1 The researcher did not enhance this issue since the focus of this study was only implementing the notetaking strategy to help them handle potential problems in TOEFL reading. Hopefully future research might want to probe this condition. Cycle 2 In the last phase of the cycle, which is reflecting cycle, there were still two key points being reflected: students’ participation and the researcher’s ability in applying notetaking strategy in teaching TOEFL reading. The initial one is intended to fetch answer for the first research question and the latest is to answer the second research question. Firstly, the students’ participation was considered excellent during this second cycle. All students were fully engaged and the researcher paid attention and provided help to every student. So that, as soon as they got a problem, the researcher was around them to be asked about it. The researcher found that frequent problems that were asked by the students were vocabulary and making decision on which cues are more important. It seemed that they still have problems in Figure 3. Student’s note after Cycle 2 Figure 3. Student’s note after Cycle 2 Figure 3. Student’s note after Cycle 2 © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Volume 28, Number 1, February, 2021, Page 45-54 Volume 28, Number 1, February, 2021, Page 45-54 52 Woolley (2011), picture provisions might help students who considered as less-skilled readers as numerous research has proven that visual pictures can help readers to understand text-based cues. The figure above shows that the student did not copy anymore. Now she tried to understand the cues instead of copying. It is depicted in her note that the passage narrates about the differences between Engineering and Science. And in the pointers, she listed some differences between the work of engineers and that of scientist. From other notetaking formats the researcher urged the outline format to be taught to the students as it is more precise and helpful during reviewing. Bahrami & Nohratzadeh (2017) found that students who took notes tend to remember the reason of why they learned and they also remembered the information during the learning process. Besides, it also increased their attention, comprehension, and memorization which would certainly enhance their study to be better. Accordingly, the researcher adopted the outline format of notetaking to be implemented. Cycle 2 In addition, the implementation of metacognitive strategies is also important in taking notes during reading as indicated by Fata & Ismail (2017) and Karbalei (2010) that strategic readers generally employ knowledge regulation more often compared to their knowledge alone and they have higher awareness of the strategies they encounter while reading. This means that while notetaking, the students need to regulate the information they obtain as well as arrange them into the form of notes while reading. Based on the findings elaborated above, there are some points of discussion that can be raised. Fundamentally, from both cycles, it is understood that the students needed extra attention during the learning process as supported by Hughes & Suritsky (1993). They suggest that students with low ability in learning should be facilitated even for providing notebooks. Besides, they have to be clearly taught the step-by-step process, including in this technique. In notetaking technique, they proposed four types, which are paraphrasing, outlining, using abbreviations, and understanding the cues. In the first cycle, the researcher only introduced the technique using outlining strategy since the students only read printed reading, not listening to lectures. The students had to make outline of the reading passage(s) provided by the researcher. Apparently, most of them copied the passages and lost the main ideas of the passage(s). As Goodman (2010) points out that reading is not an exact process. Readers can still miss cues and details; it depends on the readers’ condition at the time of reading. In addition, he asserts that reading is not a single-factor-interfered activity. The graphic, phonic and morphemic knowledge, as well as syntactic, semantic, and pragmatic knowledge also play important roles while reading. REFERENCES REFERENCES Hatch, B. (2001). From Practice to Perform – A Mannual of Teacher Training Workshop Volume Two. Washington DC: The Office of English Language Program. Bahrami, F., & Nohratzadeh, H. (2017). The effectiveness of note-taking on reading comprehension of iranian EFL learners. International Journal of Applied Linguistics & English Literature, 6(7), 308-317 Hellekjaer, G. O. (2009). Academic English reading proficiency at the university level: A Norwegian case study. Reading in a Foreign Language, 21(2), 198-222. Brown, H. D. (2001). Teaching by principles: An interactive approach to language pedagogy. London: Longman. Carrel, P. L. (2007). Notetaking strategies and their relationship to performance on listening comprehension and communicative assessment tasks. TOEFL Monograph Series. Princeton: Educational Testing Service. Hughes, C. A., & Suritsky, S. K. (1993). Notetaking Skills and Strategies for Students with Learning Disabilities. Preventing School Failure, 38(1), 7- 11. Duffy, L. (2009). A Brief Description of Language. New York: The Guilford Press. Ismail, N. M. (2016). Using the Process Approach for teaching English descriptive writing. English Education Journal, 7(4), 535-548. Erwin, J. C. (2004). The Classroom of Choice: Giving Students What They Need and Getting What You Want. Alexandria: ASCD press. Jones, G., & Mort, P. (1994). Study skills for academic writing. Phoenix: The Learning Center. Fata, I. A., & Ismail, N. M. (2017). “Watching English movie helps me!” Language exposure and metacognitive awareness on TOEFL. Lingua Cultura, 11(1), 7-12. Kader, C. C. C. (2008). Teaching reading in the foreign language classroom. VIDYA, 28(1), 105-112. Karbalei, A. (2010). A Comparison of the Metacognitive Reading Strategies Used by EFL and ESL Readers. The Reading Matrix, 10(2), 165-180. Fata, I.A, Gani, S. & Husna, N. (2020). Cultural elements: A textbook evaluation in Indonesia, International Journal of Language Studies, 14 (4), 93-104, ISSN: 2157-4898; EISSN: 2157-4901. Kemmis, S., and McTaggart, R. (2014). The Action Research Planner. Victoria: Deakin University Press. Ferrance, E. (2000). Themes in Education: Action Research. Rhode Island: Brown University Press. Khaki, N. (2014). Improving reading comprehension in a foreign language: strategic reader. The Reading Matrix, 14(2), 186-200. Gear, R., & Gear, J. (2006). Cambridge preparation for the TOEFL test. Cambridge: Cambridge University Press. Lehr, M. (2009). Developing Reading Skill for the Learners. New York: Cambridge University Press. Goodman, K. S. (2010). Reading: A psycholinguistic guessing game. Journal of the Reading Specialist, 6(4), 126-135. Lems, K. (2002). Teaching Reading to English Language Learners. New Lems, K. (2002). CONCLUSION AND RECOMMENDATION There are three premises that can be taken as the conclusions of this study after implementing notetaking strategy in teaching TOEFL reading through a classroom action research for less-skilled readers. Firstly, this strategy indeed worked if the students are given individual assistance—merely for less strategic readers. Second, if individual assistance is consistently needed, then large classes are not recommended to use this technique unless the students are autonomous reader-writer themselves. Lastly, even for skilled-readers, organizing skill is a crucial component in notetaking. Basically, during the process of writing, there is a process that emphasizes more on recalling information and making decision on what to write (Ismail, 2016). Similar activity also occurs in notetaking, the students have to recall information from the passage they just read a few seconds ago and organize the information. Although it does sound simpler than writing, it takes students to manage and familiarize with recognizing and organizing information. As suggested by © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Nyak Mutia Ismail, Ika Apriani Fata; Improving Reading TOEFL… 53 © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) REFERENCES Teaching Reading to English Language Learners. New © 2021 by Al-Ta’lim. This work is licensed under (CC-BY-SA) Volume 28, Number 1, February, 2021, Page 45-54 54 York: A Division of Guilford Publications, Inc. York: A Division of Guilford Publications, Inc. Applied cognitive psychology, 19(3), 291-312. Putra, T. M., Kasim, U., & Mustafa, F. (2017). Reading comprehension in the PBT TOEFL: Which sub-skills deserve more intensive training? In the proceedings of the International Conference on the Teaching and Learning of Languages, pp. 771-783, 3-4 April, Sarawak, Malaysia. Mikulecky, B. S. & Jeffries, L. (2007). Advanced reading power: Extensive reading,vocabulary building, comprehension skills, reading faster. New York: Longman. Putra, Ness, M. K. (2009). Reading comprehension strategies in secondary content area classrooms: Teacher use of and attitudes towards reading comprehension instruction. Reading Horizons, 49(2), 57-85. Rahmani, M., & Sadeghi, K. (2011). Effects of note taking training on reading comprehension and recall. The Reading Matrix, 11(2), 116-128. Pang, E. S., Muaka, A., Bernhardt, E. B., & Kamil, M. L. (2011). Teaching reading. Geneva: International Bureau of Education. Teng, H. (2011). Exploring notetaking strategies of EFL listenerst. Procedia Social and Behavioral Sciences, 15, 480-484. Philips, D. (2001). Longman complete course for the TOEFL test: preparation for the computer and paper tests. New York: Addison-Wesley Longman, Inc. Woolley, G. (2011). Reading Comprehension: Assisting Children with Learning Difficulties. Springer Science & Business Media. Piolat, A. Olive, T. Kellogg, R. T. (2005). Cognitive effort during note taking.
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Blood plasma lipidome profile of dairy cows during the transition period
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© 2015 Imhasly et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Abstract Background: The transition period of dairy cows, around parturition and the onset of lactation, involves endocrine and metabolic changes to compensate for an increased energy requirement aggravated by reduced feed intake. Transition cows adjust to the resulting negative energy balance with the mobilization of lipids from the adipose tissues yielding increased blood levels of non-esterified fatty acids and ketone bodies like β-hydroxybutyrate. Results: To study the biochemical adaptations underlying this physiologic adjustment and possible pathologic derangements, we analyzed the blood plasma lipidome of transition cows by ultra-pressure liquid chromatography coupled to high-resolution quadrupole time-of-flight mass spectrometry. The resulting data were processed by principal component analysis, revealing over 60 lipid masses that change in abundance over the test period ranging from two weeks before calving to four weeks postpartum. Further characterization of analytes by tandem mass spectrometry demonstrated that the concentration of triacylglycerides in plasma drops at the day of parturition whereas the plasma level of many phosphatidylcholines and two sphingomyelins increases steadily during early lactation. Conclusion: This newly identified shift in phospholipid composition delivers a potential biomarker to detect aberrant metabolic pathways in transition cows and also provides insights into how to prevent and treat associated disorders like fatty liver disease. Blood plasma lipidome profile of dairy cows during the transition period S. Imhasly1, C. Bieli2, H. Naegeli1*, L. Nyström3, M. Ruetten4 and C. Gerspach2* S. Imhasly1, C. Bieli2, H. Naegeli1*, L. Nyström3, M. Ruetten4 and C. Gerspach2* RESEARCH ARTICLE Open Access Blood plasma lipidome profile of dairy cows during the transition period S. Imhasly1, C. Bieli2, H. Naegeli1*, L. Nyström3, M. Ruetten4 and C. Gerspach2* Imhasly et al. BMC Veterinary Research (2015) 11:252 DOI 10.1186/s12917-015-0565-8 RESEARCH ARTICLE Open Access Blood plasma lipidome profile of dairy cows during the transition period S. Imhasly1, C. Bieli2, H. Naegeli1*, L. Nyström3, M. Ruetten4 and C. Gerspach2* Imhasly et al. BMC Veterinary Research (2015) 11:252 DOI 10.1186/s12917-015-0565-8 Imhasly et al. BMC Veterinary Research (2015) 11:252 DOI 10.1186/s12917-015-0565-8 * Correspondence: naegelih@vetpharm.uzh.ch; cgerspach@vetclinics.uzh.ch 1Institute of Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland 2Department of Farm Animals, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland Full list of author information is available at the end of the article * Correspondence: naegelih@vetpharm.uzh.ch; cgerspach@vetclinics.uzh.ch 1Institute of Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland 2Department of Farm Animals, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland Full list of author information is available at the end of the article Background esterified fatty acid (NEFA) concentrations, which are linked to greater incidences of ketosis, displaced aboma- sum and retained placenta (Dyk 1995). Many transition period disorders, including fatty liver, also occur in a subclinical form affecting the overall health status, milk production and reproductive performance of dairy cows. During the last few weeks before parturition and the first weeks post partum, dairy cows have to undergo the physiologic transition from pregnancy to lactation, which involves many endocrine and metabolic adapta- tions related to parturition and the onset of milk pro- duction (Grummer et al. 1995; Huzzey et al. 2005). A key problem during this transition period is the dramatic increase in energy requirements for milk production, paralleled by a decreased feed intake, occurring around parturition and the first week after calving (Moyes et al. 2013). This condition results in a negative energy bal- ance, to which dairy cows adjust by lipid mobilization from the adipose tissue representing a major fuel source during the transition period (Sordillo and Raphael 2013). However, lipid mobilization leads to an increase in non- Fatty liver is a multifactorial metabolic disorder resulting from an increased flux of NEFAs to the liver, followed by their reconversion to triacylglycerides and storage as intra- cellular lipid droplets (Bobe et al. 2004). The development of fatty liver disease in cows with a negative energy bal- ance depends on the level of overall lipid mobilization, the rate of fatty acid oxidation in the liver and the efficiency of fatty acid elimination from the liver, either as ketone bodies reflecting the fatty acid breakdown or as full tria- cylglycerides exported in the form of very low density lipoproteins (VLDLs) (Ingvartsen 2006). Fatty liver is re- lated to other diseases including retained placenta, uterine infection, milk fever, abomasal displacement and mastitis. These pathological changes affect up to Imhasly et al. BMC Veterinary Research (2015) 11:252 Page 2 of 14 Fig. 2 NEFA levels. History of NEFA concentrations in the plasma of the 12 cows over the experimental period (median values with range). The time points are indicated relative to the date of calving. ***P < 0.001 compared to NEFA concentrations at the beginning of the study (day −14). ANOVA: F (6,77) = 14.74, P value < 0.0001 50 % of dairy cows during early lactation (Sejersen et al. 2012; Jorritsma et al. 2001). Background A liver biopsy remains the only diagnostic tool to deter- mine the lipid content of the liver and, as a consequence, the extent of the disease is in practice frequently uncertain. A non-invasive and accurate test for the diagnosis of fatty liver disease would, therefore, be helpful for the manage- ment of this disorder in individual animals as well as on a herd level. Such a simplified test would also allow to inves- tigate the incidence and risk factors of the disorder (Ingvartsen 2006). Because the lipid metabolism is a key as- pect of the physiology of transition cows (Drackley 1999; Gross et al. 2013), we conducted a comprehensive analysis of the plasma lipidome of cattle during the time before and after parturition. This study reveals that the physiologic adaptation to an increased energy requirement of transition cows involves a post partum elevation of phosphatidylcho- lines and sphingomyelins in their blood plasma. Fig. 2 NEFA levels. History of NEFA concentrations in the plasma of the 12 cows over the experimental period (median values with range). The time points are indicated relative to the date of calving. ***P < 0.001 compared to NEFA concentrations at the beginning of the study (day −14). ANOVA: F (6,77) = 14.74, P value < 0.0001 Methods study. Also, they had to be confirmed pregnant with a known breeding date. Their health status was assessed by the herd veterinarian and clinicians of the Department of Farm Animals. All cows of the study were fed exactly the same diet and kept in the same barn. During the preceding dry period, the cows were fed grass silage, straw, hay and a mineral supplement. Two weeks before parturition, the cows were regrouped Animals and management Twelve dairy cows of the Holstein Frisian breed were included in this study. In order to reduce variability, all cows were selected from the same farm. The ani- mals were housed in an open spaced barn comprising a total of 75 dairy cows. To be included in the study, the cows had to be multiparous, clinically healthy and not receiving any treatments at the beginning of the Fig. 1 Clinical examination. History of the body condition score of the 12 cows over the experimental period (median values with range). The time point of clinical examination is indicated relative to the date of calving Fig. 1 Clinical examination. History of the body condition score of the 12 cows over the experimental period (median values with rang The time point of clinical examination is indicated relative to the date of calving Imhasly et al. BMC Veterinary Research (2015) 11:252 Page 3 of 14 Fig. 3 Ketone bodies. History of β-hydroxybutyrate (BHB) concentrations in the plasma of the 12 cows over the experimental period (median values with range). The time points are indicated relative to the date of calving. **P < 0.01 and ***P < 0.001 compared to β-hydroxybutyrate concentrations at the beginning of the study (day −14). ANOVA F (6,77) = 3.333, P value = 0.0057 to the lactating animals receiving increasing amounts of a concentrate (0–1.5 kg). Post partum, the cows were fed grass and corn silage, beet pulp, soybean, grass, mineral supplement, and up to 4 kg concentrate. The body condi- tion score was recorded concurrently with each blood sample collection. The study was approved by the Veterinary Office of the Kanton Zurich and conducted in accordance with guidelines established by the Animal Welfare Act of Switzerland (permission No. 27/2013). Consent was ob- tained from the owner of the dairy farm to collect sam- ples from his cows for the current study. Collection of blood samples and liver tissue l b d f h l Fig. 3 Ketone bodies. History of β-hydroxybutyrate (BHB) concentrations in the plasma of the 12 cows over the experimental period (median values with range). The time points are indicated relative to the date of calving. **P < 0.01 and ***P < 0.001 compared to β-hydroxybutyrate concentrations at the beginning of the study (day −14). ANOVA F (6,77) = 3.333, P value = 0.0057 Fig. 3 Ketone bodies. History of β-hydroxybutyrate (BHB) concentrations in the plasma of the 12 cows over the experimental period (median values with range). The time points are indicated relative to the date of calving. **P < 0.01 and ***P < 0.001 compared to β-hydroxybutyrate concentrations at the beginning of the study (day −14). ANOVA F (6,77) = 3.333, P value = 0.0057 Samples were obtained from the jugular vein at days −14, −7, 0, +7, +14, +21 and +28 relative to parturition. 14, 7, 0, +7, +14, +21 and +28 relative to parturition. The samples were drawn always at the same time in the afternoon. Tubes supplemented with lithium heparin (Sarstedt AG and Co., Nümbrecht, Germany) were used to collect 10 ml of blood. The heparinized blood was centrifuged at 4000 g for 5 min. Separated plasma was stored in 2-ml tubes at −80 °C until analysis. Plasma samples were used for lipidome evaluation and measure- ment of -hydroxybutyrate and NEFA. vacuoles), moderate fatty liver (fatty degeneration of the periportal to midzonal or midzonal to centrolobular areas), severe fatty liver (all three zones affected including the Kupffer cells). Liver biopsies were taken as described (Mølgaard et al. 2012) under ultrasonographic control and stained with hematoxylin-eosin (H & E). The histological lesions were staged into four categories: no abnormalities, mild fatty liver (only cells from one liver zone affected by lipid Lipid nomenclature For the designation of lipids, the common standard lipid language described by the Lipidomics Gateway (http:// www.lipidmaps.org, National Institute of General Medical Sciences, National Institutes of Health) and by Schmelzer et al. (2007) was applied. Table 1 Identified masses by tandem mass spectrometry Class Formula m/z Annotation Lonization mode lysoPC C24H50NO7P 496.341 LPC 16:0 [M + H]+ C26H50NO7P 520.340 LPC 18:2 [M + H]+ C26H52NO7P 522.355 LPC 18:1 [M + H]+ C28H48NO7P 542.324 LPC 20:5 [M + H]+ C26H48NO7P 518.324 LPC 18:3 [M + H]+ PC C42H80NO7P 742.574 PC P-34:2 [M + H]+ C42H84NO8P 762.599 PC 34:0 [M + H]+ C44H78NO7P 764.551 PC P-36:5 [M + H]+ C44H80NO7P 766.568 PC P-36:4 [M + H]+ C44H76NO8P 778.537 PC 36:6 [M + H]+ C46H90NO8P 816.645 PC 38:1 [M + H]+ C48H90NO8P 840.642 PC 40:3 [M + H]+ C50H88NO8P 862.620 PC 42:6 [M + H]+ SM C48H91N2O6P 773.649 SM 39:1 [M + H]+ C48H91N2O6P 823.665 SM 43:3 [M + H]+ Fatty amides C18H33NO 280.264 Linoleamide [M + H]+ C20H33NO2 320.256 Anandamide [M + H]+ TG C51H92O6 818.717 TG 48:3 [M + NH4]+ C51H96O6 822.753 TG 48:1 [M + NH4]+ C52H96O6 834.759 TG 49:2 [M + NH4]+ C52H98O6 836.771 TG 49:1 [M + NH4]+ C53H94O6 844.726 TG 50:4 [M + NH4]+ C53H96O6 846.751 TG 50:3 [M + NH4]+ C53H98O6 848.769 TG 50:2 [M + NH4]+ C54H98O6 860.772 TG 51:3 [M + NH4]+ C54H100O6 862.788 TG 51:2 [M + NH4]+ C54H102O6 864.801 TG 51:1 [M + NH4]+ C55H98O6 872.761 TG 52:4 [M + NH4]+ C55H100O6 874.785 TG 52:3 [M + NH4]+ C56H102O6 888.806 TG 53:3 [M + NH4]+ C57H98O6 896.779 TG 54:6 [M + NH4]+ C59H102O6 924.809 TG 56:6 [M + NH4]+ Chemicals and internal standards All solvents were liquid chromatography-grade. Leucine- enkephalin was used as the lock mass at a concentration of 1 ng/μl in a solution of acetonitrile/water (50:50, v/v) supplemented with 0.1 % formic acid. For the internal standards, an exogenous mixture of lipids was added to the organic solvent during the initial extraction step. These standards consisted of 1- heptadecanoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC 17:0/0:0), 1-nonadecanoyl-2-hydroxy-sn-glycero- 3-phosphocholine (LPC 19:0/0:0), 1,2-dipentadecanoyl-sn- glycero-3-phosphoethanolamine (PE 15:0/15:0), 1,2-dihep- tade-canoyl-sn-glycero-3-phosphoethanolamine (PE 17:0/ 17:0), 1,2-dipentadecanoyl-sn-glycero-3-phospho-(1’-rac- glycerol) sodium salt (PG 15:0/15:0), 1,2-diheptadecanoyl- sn-glycero-3-phospho-rac-(1-glycerol) sodium salt (PG 17:0/17:0), 1,2-ditridecanoyl-sn-glycero-3-phospho- choline (PC 13:0/13:0), 1,2-ditricosanoyl-sn-glycero- 3-phosphocholine (PC 23:0/23:0), 1,2-dinona-decan- oyl-sn-glycero-3-phosphocholine (PC 19:0/19:0) and 1,2-di-(3,7,11,15-tetramethylhexadecanoyl)-sn-glycero- 3-phosphocholine [PC 16:0 (3me,7me,11me,15me)/ 16:0 (3me,7me,11me,15me)] purchased from Avanti Polar Lipids (Alabaster, AL, USA); 1,2,3-tripentadeca- noylglycerol (TG 15:0/15:0/15:0) and 1,2,3-trihepta- decanoylglycerol (TG 17:0/17:0/17:0) were from Sigma-Aldrich (Buchs, Switzerland). The concentra- tion of internal standards (350 nM) was calculated relative to the final amount of organic solvent in the extraction tube. Measurement of NEFA and β-hydroxybutyrate Plasma concentrations of NEFA and β-hydroxybutyrate were determined by enzymatic analyses using the Wako Fig. 4 Principal component analysis. Principal components were determined with all 579 detected masses of the 82 measured samples and arranged in 7 groups according to the time of sampling relative to the date of calving (−14 days to +28 days) Fig. 4 Principal component analysis. Principal components were determined with all 579 detected masses of the 82 measured samples and arranged in 7 groups according to the time of sampling relative to the date of calving (−14 days to +28 days) Page 4 of 14 Imhasly et al. BMC Veterinary Research (2015) 11:252 NEFA-HR (2) (Wako Chemicals GmbH, Neuss, Germany) and the β-Hydroxybutyrate LiquiColor® kit (Stanbio Laboratory, Boerne, TX, USA), respectively. Spectrophoto- metric measurements were performed for both NEFA and β-hydroxybutyrate, using a Cobas Mira S Chemistry Analyzer (Roche, Basel, Switzerland). The mixtures were supplemented with 500 μl of methyl- tert-butyl ether and incubated for 60 min at room temperature in a thermo shaker (Vaudaux-Eppendorf AG, Schönenbuch, Basel) at 800 rpm. Then, a phase separation was induced by adding 125 μl of water and further vortexing. The samples were centrifuged for 10 min at 1000 g and 4 °C; 300 μl of the upper (or- ganic) phase containing the lipids and non-polar com- ponents were collected and transferred into a new tube. The organic phases were dried in a vacuum centrifuge (Savant Speed Vac Plus SC 110A, Savant Instruments Inc., Holbrook, NY, USA), dissolved in 300 μl methanol and stored at −80 °C until measurements. Liquid chromatography was carried out following the protocol of Castro-Perez and Kamphorst (2010), whereby electrospray ionization (ESI) was employed in the positive and negative mode. A capillary voltage of 3 kV and cone voltage of 30 V were used for both polarities. The desolvation source conditions involved desolvation gas at 700 L/h and a temperature of 400 °C. The mass range during acquisition was 50– 1200 Da and the signals were acquired in the centroid mode. Leucine-enkephalin was used as internal reference in each measurement. Liquid chromatography An Acquity UPLC (Waters, Milford, MA, USA) sys- tem was used for ultra-pressure chromatographic sample separations. The plasma extracts were injected as triplicates and in a random order onto a HSS T3 column (Waters, Milford, MA, 1.8-μm particle, 100 × 2.1 mm id) heated to 55 °C. The average column pressure was 7000 psi. A binary gradient of two solv- ent mixtures was used for elution. Eluent A consisted of acetonitrile and water (50:40, v/v) with 10 mM am- monium acetate; eluent B consisted of acetonitrile and isopropanol (10:90, v/v) with 10 mM ammonium acetate. Eluent A was used for weak needle washes, whereas isopropanol was used for strong needle washes. The flow rate was 0.4 ml/min and the injec- tion volume 10 μl. A linear gradient was performed for the sample analysis. The initial portion of the gra- dient was held at 60 % A and 40 % B. In the next 10 min, the composition was changed in a linearly ramped gradient (curve 6)–100 % B and held for 2 min. The system was switched back to the initial proportion (60 % A, 40 % B) and the column was equilibrated for 3 min. The total run time was 15 min. During data acquisition, the first quadrupole was op- erated in a wide band RF mode, such that all ions were able to enter the T-wave collision cell. In this cell, two acquisition functions were applied. The first function with 5 eV resulted in non-fragmented ion molecules while the second function used a collision energy ramp of 20–30 eV to generate fragmented ions (MSE method). Argon gas was used for collision-induced dissociation. Using this interleaved acquisition, fragmen- ted and non-fragmented ions could be used for quantifica- tion and initial ion identification. Liquid chromatography For final ion identi fication, a tandem mass spectrometry (MS/MS) method was applied by setting the energy ramp for collision- induced dissociation at 15–40 eV. The fragmentation pattern resulting from each parental mass was identified using the mass spectrometry database provided online the Lipidomics Gateway (http://www.lipidmaps.org, National Institute of General Medical Sciences, National Institutes of Health). Sample extraction Lipids were extracted from bovine plasma following a published protocol (Matyash et al. 2008). The extraction was validated by the addition of internal standards. For that purpose, 127 μl methanol was placed into 1.5-ml Eppendorf tubes and 23 μl of the 10 μM internal stand- ard mixture was added (final concentration of 350 nM in the organic phase). A sample aliquot of 20 μl was added to each tube and the mixtures vortexed for 10 s. Imhasly et al. BMC Veterinary Research (2015) 11:252 Page 5 of 14 Mass spectrometry The UPLC inlet was coupled to a quadrupole time-of- flight mass spectrometer (SYNAPT G2 HDMS, Waters, MS Technologies Manchester, U.K.). Mass spectrometry Fig. 5 Principal component analysis. Principal components were re-calculated focusing on the 32 identified masses and arranged in 7 groups according to the time of sampling relative to the date of calving (−14 days to +28 days) Fig. 5 Principal component analysis. Principal components were re-calculated focusing on the 32 identified masses and arranged in 7 groups according to the time of sampling relative to the date of calving (−14 days to +28 days) Imhasly et al. BMC Veterinary Research (2015) 11:252 Page 6 of 14 Fig. 6 Plot of the variable factors. Values were extracted from the principal component analysis obtained with 32 identified masses. The time of sampling is indicated relative to the date of calving (−14 days to +28 days) Fig. 6 Plot of the variable factors. Values were extracted from the principal component analysis obtained with 32 identified masses. The time of sampling is indicated relative to the date of calving (−14 days to +28 days) Fig. 7 Ultra-pressure liquid chromatogram. This chromatographic profile of a representative sample demonstrates the distinct elution windows of different lipid classes identified by mass spectrometry. LPC, lyso-phosphatidylcholines; PC, phosphatidylcholines; SM, sphyngomyelins; PE, phosphoethanolamines; TG, triacylglycerides Fig. 7 Ultra-pressure liquid chromatogram. This chromatographic profile of a representative sample demonstrates the distinct elution windows of different lipid classes identified by mass spectrometry. LPC, lyso-phosphatidylcholines; PC, phosphatidylcholines; SM, sphyngomyelins; PE, phosphoethanolamines; TG triacylglycerides Fig. 7 Ultra-pressure liquid chromatogram. This chromatographic profile of a representative sample demonstrates the distinct elution windows of different lipid classes identified by mass spectrometry. LPC, lyso-phosphatidylcholines; PC, phosphatidylcholines; SM, sphyngomyelins; PE, phosphoethanolamines; TG, triacylglycerides Page 7 of 14 Imhasly et al. BMC Veterinary Research (2015) 11:252 Data analysis the blood plasma lipidome occurring during the peripartal transition phase. The selected cows were aged between 3 and 12 years (mean age: 5 ± 2.6 years) and undergoing their 2nd to 10th lactation (mean number of lactations 3 ± 2.3). The mean dry period lasted 64 ± 14.27 days. The animals were clinically healthy at the beginning of the study, but the histologic findings by means of liver biopsies taken four weeks after calving showed that only one animal remained completely devoid of fatty degeneration of hepatocytes; 7 cows displayed a mild and 4 cows a moderate degree of lipid deposition in hepatocytes. Importantly, however, none of these animals developed clinical symptoms of fatty liver disease although several cows experienced other health problems after parturition including hypocalcemia (n = 7), retained placenta with subsequent metritis (n = 2), mastitis (n = 1), and lameness (n = 4). Accordingly, the overall body Descriptive statistics of the concentrations of NEFA and -hydroxybutyrate was performed using graphpad GraphPad Prism 6 (Graph Pad Software, La Jolla, CA, USA). The open source program MZmine (http:// mzmine.sourceforge.net; Project GNU free software foun- dation, Boston, USA) was used for automatic alignment, denoising, deconvolution and extraction of peaks (Pluskal et al. 2010). All data were standardized using exogenous standards. The follow-up statistics were performed with the open source program R (R_Core_Team R Foundation for Statistical Computing 2014) and GraphPad Prism 6. Results A total of 12 multiparous cows of the Holstein Frisian breed, kept in the same farm, were tested for changes in Fig. 8 Plasma concentration of triacylglycerides (TG 48:3, TG 48:1, TG 49:2, TG 49:1, TG 50:4 and TG 50:3) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; **P < 0.01 and ***P < 0.001 compared to triacylglyceride concentrations at the beginning of the study (day −14) Fig. 8 Plasma concentration of triacylglycerides (TG 48:3, TG 48:1, TG 49:2, TG 49:1, TG 50:4 and TG 50:3) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; **P < 0.01 and ***P < 0.001 compared to triacylglyceride concentrations at the beginning of the study (day −14) Page 8 of 14 Imhasly et al. BMC Veterinary Research (2015) 11:252 condition score of the 12 cows deteriorated slightly with progression of the transition period (Fig. 1). as the transition period progressed could be detected with significantly higher concentrations in the plasma post partum (for example 1814 ± 1407 μmol/l on day +28) compared to the samples taken ante partum (for example 632 ± 299 μmol/l on day −14) (Fig. 3). Clinical chemistry analysis Blood samples were obtained ante partum (on days −14 and −7) on the day of calving and post partum (on days +7, +14, +21 and +28). The blood plasma con- centration of NEFAs increased from low values before calving (for example 360 ± 190 μmol/l on day −7) to significantly higher values post partum, reaching a max- imum at day +7 (770 ± 160 μmol/l). These NEFA concen- trations remained at high levels until at least day +28 (Fig. 2). The plasma concentrations of -hydroxybutyrate displayed some variability among the individual cows. However, a trend of increasing -hydroxybutyrate levels Plasma lipidome analysis The lipid composition of plasma samples obtained at the different time points were compared by liquid chromatog- raphy coupled to quadrupole time-of-flight mass spec- trometry. This analysis yielded over 500 masses detected in the positive ion mode, and over 200 masses in the nega- tive ion mode, representing lipids and other non-polar metabolites. To illustrate the differences in the lipidome profile at different stages of the transition period, from Fig. 9 Plasma concentration of triacylglycerides (TG 50:2, TG 51:3, TG 51:1, TG 53:4, TG 52:4 and TG 52:3) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Fig. 9 Plasma concentration of triacylglycerides (TG 50:2, TG 51:3, TG 51:1, TG 53:4, TG 52:4 and TG 52:3) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Page 9 of 14 Imhasly et al. BMC Veterinary Research (2015) 11:252 separation between the different time points around par- turition (Fig. 6). 14 days ante partum to 28 days post partum, the multi- variate data were subjected to principal component ana- lysis (PCA), which is an unsupervised clustering method that provides an overview of the results by reducing the dimensionality of complex findings. The principal compo- nents of the data acquired in the positive ion mode were graphically plotted as a score plot (Fig. 4), thus revealing that the samples from each time point cluster together forming distinguishable groups. Instead, the masses ac- quired in the negative ion mode did not shown any such clustering (data not shown). As the next step, the lipids responsible for this separ- ation were characterized and quantified. In Fig. 7, the chromatographic retention time windows of lipid classes are indicated to illustrate how their classification is sim- plified by the respective position in the elution profile (Ogiso et al. 2008). Plasma lipidome analysis One class of lipids that discriminates between the different time points around parturition consisted of triacylglycerides (TGs), including TG 48:3, TG 48:1, TG 49:2, TG 49:1, TG 50:4, TG 50:3, TG 50:2, TG 51:3, TG 51:2, TG 51:1, TG 52:4, TG 52:3, TG 53:3, TG 54:6 and TG 56:6. All these TGs displayed high plasma levels in cows before calving but, on the day of parturition, their levels dropped instantaneously and remained low for up to 28 days post partum (Figs. 8, 9 and 10). Lyso-posphatidylcholine (LPC) and phosphat- idylcholine (PC) levels, in contrast, increased progres- sively post partum. This increment was significant for LPC 16:0, LPC 18:3, LPC 18:2, LPC 18:1, LPC 20:5, PC P-34:2, PC P-36:5, PC P-36:4 and PC 36:6 (Figs 11 and 12). In addition, the sphingomyelines SM 39:1 and 43:3 were increased post partum in the same manner as described for phosphatidylcholines (Fig. 13). There is an intriguing although not statistically significant drop of PC levels at the day of parturition. It should be noted The data of 40 masses that best correlate with the principal component 1 (PC1), and collections of 20 masses that each correlate best with the principal com- ponents 2 and 3 (PC2 and PC3) were extracted. These 80 masses accounted for all the observed separation be- tween the seven time points in the PCA score plot. Due to duplicate representations of the same masses in the different PCs, finally 62 masses were selected for further investigation. From these, 32 masses could be identified by tandem mass spectrometry (Table 1). The score plot was then replicated using the data of these 32 identified masses, yielding a closer clustering of the samples ob- tained from individual time points (Fig. 5). An additional vector plot of the variables evidenced the particular con- tribution of each of the 32 identified masses to the overall Fig. 10 Plasma concentration of triacylglycerides (TG 53:3, TG 54:6 and TG 56:6) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Fig. 10 Plasma concentration of triacylglycerides (TG 53:3, TG 54:6 and TG 56:6) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Plasma lipidome analysis Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Page 10 of 14 Imhasly et al. BMC Veterinary Research (2015) 11:252 that not all identified phosphatidylcholines showed this same pattern of increased concentrations post partum compared to ante partum. In the case PC 38:1, PC 40:3 and PC 42:6, there was first a drop in plasma levels from day −14 to calving, followed by a slow recovery post par- tum (Fig. 14). For PC 34:0, we observed an exceptionally sharp increase at the day of calving followed by a pro- gressive reduction to reach the starting level measured at the beginning of the study (Fig. 14). Finally, we also identified the two fatty acid amides linoleamide and anandamide, whose plasma levels are transiently de- pressed only at the time of calving (Fig. 15). energy requirements for maintenance, fetal growth in late pregnancy, mammary tissue remodeling and early lactation (Herdt 2000; Esposito et al. 2014). Despite the enhanced nutritional demands, this period coincides with a reduction in dry matter intake (Ingvartsen and Andersen 2000). The resulting negative energy balance is considered a normal occurrence in dairy cows after calving (McArt et al. 2013), but only animals poorly adapting to these changing physiologic conditions are at risk of developing various production disorders. Several potential biomarkers have already been evalu- ated for their ability to predict which cows are at risk of diseases related to the transition period. Most tested pa- rameters reflect the negative energy balance and the rate of hepatic fatty acid oxidation, which can be demon- strated by measuring NEFAs and β-hydroxybutyrate, Discussion During the transition from pregnancy to lactation, dairy cows experience a challenging period with increasing Fig. 11 Plasma concentration of lyso-phosphatidylcholines (LPC 16:0, LPC 18:3, LPC 18:2, LPC 18:1 and LPC 20:5) and phosphatidylcholines (PC P-34:2) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Fig. 11 Plasma concentration of lyso-phosphatidylcholines (LPC 16:0, LPC 18:3, LPC 18:2, LPC 18:1 and LPC 20:5) and phosphat (PC P-34:2) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05 d ***P 000 d h l h b i i f h d (d ) Fi 11 Pl t ti f l h h tid l h li (LPC 16 0 LPC 18 3 LPC 18 2 LPC 18 1 d LPC 20 5) d h h tid l h li Fig. 11 Plasma concentration of lyso-phosphatidylcholines (LPC 16:0, LPC 18:3, LPC 18:2, LPC 18:1 and LPC 20:5) and phosphatidylcholines (PC P-34:2) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Imhasly et al. BMC Veterinary Research (2015) 11:252 Page 11 of 14 Fig. 12 Plasma concentration of phosphatidylcholines (PC P-36:5, PC P-36.4 and PC 36:6) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Fig. 12 Plasma concentration of phosphatidylcholines (PC P-36:5, PC P-36.4 and PC 36:6) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) change by the end of gestation (Holtenius et al. 2003; Bos- saert et al. 2008), this investigation focused on a period of 6 weeks around parturition. Discussion Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Fig. 14 Plasma concentration of phosphatidylcholines (PC 38:1, PC 40:3, PC 42:6 and PC 34:0) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) (Van den Top et al. 2005; Kessler et al. 2014). In contrast, the plasma concentration of the vast majority of the iden- tified phospholipids (five lyso-phosphatidylcholines, four phosphathidylcholines and two sphingomyelins) increased steadily with progression of early lactation post partum (see for example Fig. 12). A common feature of these phospholipids is their requirement for the secretion of hepatic triacylglycerides as VLDL particles, indicating that a reduced level of phosphatidylcholines and other phos- pholipids may directly cause an excessive accumulation of triacylglycerides in the liver (Artegoitia et al. 2014; Côté et al. 2014). The transient drop of phosphatidylcholine (Van den Top et al. 2005; Kessler et al. 2014). In contrast, the plasma concentration of the vast majority of the iden- tified phospholipids (five lyso-phosphatidylcholines, four phosphathidylcholines and two sphingomyelins) increased steadily with progression of early lactation post partum (see for example Fig. 12). A common feature of these phospholipids is their requirement for the secretion of hepatic triacylglycerides as VLDL particles, indicating that a reduced level of phosphatidylcholines and other phos- pholipids may directly cause an excessive accumulation of triacylglycerides in the liver (Artegoitia et al. 2014; Côté et al. 2014). The transient drop of phosphatidylcholine parallel, the overall lipidome profile changed abruptly on the day of calving with further intriguing adaptations post partum (Fig. 5). Our large-scale approach demon- strates that two main lipid classes undergo significant shifts in their plasma concentration during the transition period of dairy cows, i.e., triacylglycerides and phospho- lipids. The 15 unequivocally identified triacylglycerides were all characterized by a sharply reduced plasma con- centration on the day of calving and post partum com- pared to ante partum values (see for example Fig. 8). This observation reflects the suddenly enhanced energy requirement and is in agreement with previous studies Fig. 15 Plasma concentration of fatty acid amides in the 12 transition period cows. Discussion There was no overt effect of age on lipid metabolism across the 12 cows of this study. respectively. Increased concentrations of these metabo- lites ante partum have been associated with higher odds of displaced abomasum, poor lactation and reduced fer- tility (Chapinal et al. 2012; Ospina et al. 2010). However, there is an urgent need for a non-invasive and accurate test to diagnose early alterations in the lipid metabolism leading to fatty liver disease. For that specific purpose, we used a large-scale and untargeted metabolomic approach, based on high-resolution quadrupole time-of-flight mass spectrometry, to analyze the physiologic lipidome of healthy dairy cows. Since metabolic profiles begin to As expected (Ospina, P a et al. 2010; McArt, Jessica a a et al. 2013), the tested animals responded to their negative energy balance by mobilizing large amounts of body fat, leading to increased NEFA concentrations in plasma starting from the day of calving (Fig. 2). Simi- larly, −hydroxybutyrate levels in plasma increased post partum (Fig. 3) as a marker of lipid catabolism. In Fig. 13 Plasma concentration of sphingomyelines (SM 39:1 and SM 43:3) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Fig. 13 Plasma concentration of sphingomyelines (SM 39:1 and SM 43:3) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Imhasly et al. BMC Veterinary Research (2015) 11:252 Page 12 of 14 Fig. 14 Plasma concentration of phosphatidylcholines (PC 38:1, PC 40:3, PC 42:6 and PC 34:0) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; *P < 0.05, **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Fig. 14 Plasma concentration of phosphatidylcholines (PC 38:1, PC 40:3, PC 42:6 and PC 34:0) in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Competing interests Grummer RR, Hoffman PC, Luck ML, Bertics SJ. 1995. “Effect of Prepartum and Postpartum Dietary Energy on Growth and Lactation of Primiparous Cows.” J Dairy Sci 78(1). Elsevier: 172–80. doi:10.3168/ jds.S0022-0302(95)76627-9. Grummer RR, Hoffman PC, Luck ML, Bertics SJ. 1995. “Effect of Prepartum and Postpartum Dietary Energy on Growth and Lactation The authors declare that they have no potential competing interests to disclose. Abbreviations Abbreviations NEFA: Non-esterified fatty acid; VLDL: Very low density lipoprotein; MTBE: Methyl-tert butyl ether; UPLC: Ultra-performance liquid chromatography; ESI: Electrospray ionization; MS/MS: Tandem mass spectrometry; PCA: Principal component analysis; TG: Triacylglycerid; LPC: Lyso-phosphatidylcholine; PC: phosphatidylcholine. Gross JJ, Schwarz FJ, Eder K, van Dorland HA, Bruckmaier RM. 2013. “Liver Fat Content and Lipid Metabolism in Dairy Cows during Early Lactation and during a Mid-Lactation Feed Restriction.” J Dairy Sci 96(8). Elsevier: 5008–17. doi:10.3168/jds.2012-6245. Gross JJ, Schwarz FJ, Eder K, van Dorland HA, Bruckmaier RM. 2013. “Liver Fat Content and Lipid Metabolism in Dairy Cows during Early Lactation and during a Mid-Lactation Feed Restriction.” J Dairy Sci 96(8). Elsevier: 5008–17. doi:10.3168/jds.2012-6245. References Artegoitia VM, Virginia M, Middleton JL, Harte FM, Campagna SR, de Veth MJ. Choline and Choline Metabolite Patterns and Associations in Blood and Milk during Lactation in Dairy Cows. PLoS One. 2014;9(8):e103412. doi:10.1371/ journal.pone.0103412. Bobe G, Young JW, Beitz DC. Invited review: pathology, etiology, prevention, and treatment of fatty liver in dairy cows. J Dairy Sci. 2004;87(10):3105–24. doi:10.3168/jds.S0022-0302(04)73446-3. Bossaert P, Leroy JL, De Vliegher S, Opsomer G. 2008. “Interrelations between Glucose-Induced Insulin Response, Metabolic Indicators, and Time of First Ovulation in High-Yielding Dairy Cows.” J Dairy Sci 91(9). Elsevier: 3363–71. doi:10.3168/jds.2008-0994. Discussion The time of sampling is indicated relative to the date of calving. Mean values ± SEM; **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Fig. 15 Plasma concentration of fatty acid amides in the 12 transition period cows. The time of sampling is indicated relative to the date of calving. Mean values ± SEM; **P < 0.01 and ***P < 0.001 compared to the values at the beginning of the study (day −14) Imhasly et al. BMC Veterinary Research (2015) 11:252 Page 13 of 14 levels at the day of parturition may be due to a sudden in- crease of phospholipase activity in order to gain energy from PCs (Jacobs et al. 2013). In addition to insufficient hepatic VLDL secretion, the drop in triacylglycerides and concomitant rise of phosphatidylcholines around parturi- tation can be due to an increase in mammary lipoprotein lipase activity as reported by Van den Top et al. (2005). interpretation, MR was responsible for assessment of liver biopsies, SI and CG drafted the manuscript, which was read and approved by all authors. interpretation, MR was responsible for assessment of liver biopsies, SI and CG drafted the manuscript, which was read and approved by all authors. Acknowledgements The lipidomic platform is supported by a grant from the Bundesamt für Landwirtschaft (BLW) and the Bundesamt für Lebensmittelsicherheit und Veterinärwesen (BLV). The project was also supported by the “Forschungskredit” of the University of Zurich (grant 8873). Further studies are now required to confirm a causal relationship between reduced phospholipid concentra- tions and fatty liver disease in dairy cows. On that line, we recently reported that dairy cows affected by fatty liver disease during the transition period display lower levels of phosphatidylcholines and sphingomyelins in their blood plasma than control animals (Imhasly et al. 2014). Thus, the abnormal decline of certain specific phosphatidylcholines and sphingomyelins could be regarded as a promising biomarker indicative of fatty liver disease. Conversely, dietary supplementation of biochemical precursors of phosphatidylcholines and sphingomyelins may help to prevent the occurrence of fatty liver disease in dairy cows. Additionally, it should be tested if direct intravenous infusion of missing phos- phatidylcholines and sphingomyelins may serve as a new therapeutic strategy for the management of animals af- fected by severe-grade fatty liver disease. Author details 1Institute of Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland. 2Department of Farm Animals, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland. 3Institute of Food, Nutrition and Health, Swiss Federal Institute of Technology, Schmelzbergstrasse 9, 8092 Zurich, Switzerland. 4Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, Zurich, Switzerland. Received: 12 February 2015 Accepted: 28 September 2015 Received: 12 February 2015 Accepted: 28 September 2015 Conclusion h “Interactions between Negative Energy Balance, Metabolic Diseases, Uterine Health and Immune Response in Transition Dairy Cows.” Anim Reprod Sci 144(3–4). Elsevier B.V.: 60–71. doi:10.1016/j.anireprosci.2013.11.007. Conclusion h In the present study, a new lipidomic approach was used to demonstrate adaptations in the lipid metabolism to high energy demands, during the transition period. With this approach, using multivariate statistics and tandem mass spectrometry, we identified 32 masses, discriminat- ing between time points, during the transition period. Most intriguing was the alteration in phosphatidylcho- lines, which can be linked to altered VLDL formation, which is a key factor in the pathogenesis of fatty liver disease. This newly identified shift in phospholipid com- position delivers a potential biomarker to detect aberrant metabolic pathways in transition cows and provides in- sights into how to prevent and treat associated disorders. Future studies with larger animal groups will be needed, to validate the potential new biomarkers. 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Authors’ contributions doi:10.1016/S0076- 6879(07)32007-7 Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Schmelzer K, Fahy A, Subramaniam S, Dennis EA. 2007. “The Lipid Maps Initiative in Lipidomics.” Methods Enzymol 432(07): 171–83. doi:10.1016/S0076- 6879(07)32007-7 Submit your next manuscript to BioMed Central and take full advantage of: Submit your next manuscript to BioMed Central and take full advantage of: Sejersen H, Sørensen MT, Larsen T, Bendixen E, Ingvartsen KL. 2012. “Liver Protein Expression in Dairy Cows with High Liver Triglycerides in Early Lactation.” J Dairy Sci 95(5). 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CG and CB were responsible for sample collection, SI, CB, and LN participated in lipidomics analysis, SI, HN, and CG participated in identification, statistical evaluation and biological Page 14 of 14 Imhasly et al. BMC Veterinary Research (2015) 11:252 Imhasly et al. BMC Veterinary Research (2015) 11:252 Holtenius K, Agenäs S, Delavaud C, Chilliard Y. Effects of Feeding Intensity during the Dry Period. 2. Metabolic and Hormonal Responses. J Dairy Sci. 2003;86(3):883–91. doi:10.3168/jds.S0022-0302(03)73671-6. Huzzey JM, von Keyserlingk MA, Weary DM. 2005. “Changes in Feeding, Drinking, and Standing Behavior of Dairy Cows during the Transition Period.” J Dairy Sci 88(7). Elsevier: 2454–61. doi:10.3168/jds.S0022- 0302(05)72923-4. Imhasly S, Naegeli H, Baumann S, von Bergen M, Luch A, Jungnickel H, et al. Metabolomic Biomarkers Correlating with Hepatic Lipidosis in Dairy Cows. BMC Vet Res. 2014;10(1):122. doi:10.1186/1746-6148-10-122. 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Authors’ contributions “Fatty Liver in Dairy Cows Post Partum Is Associated with Decreased Concentration of Plasma Triacylglycerols and Decreased Activity of Lipoprotein Lipase in Adipocytes.” J Dairy Res 72(2): 129–37. doi:10.1017/S0022029905000774.
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Prognostic impact of urokinase-type plasminogen activator system components in clear cell renal cell carcinoma patients without distant metastasis
BMC cancer
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cc-by
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RESEARCH ARTICLE Open Access * Correspondence: susanne.fuessel@uniklinikum-dresden.de †Equal contributors 1Department of Urology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany Full list of author information is available at the end of the article Prognostic impact of urokinase-type plasminogen activator system components in clear cell renal cell carcinoma patients without distant metastasis Susanne Fuessel1*†, Kati Erdmann1†, Helge Taubert2, Andrea Lohse-Fischer1, Stefan Zastrow1, Matthias Meinhardt3, Karen Bluemke4, Lorenz Hofbauer5, Paolo Fornara6, Bernd Wullich2, Gustavo Baretton3, Viktor Magdolen7, Manfred P Wirth1 and Matthias Kotzsch3 Abstract Background: Members of the urokinase-type plasminogen activator (uPA) system including uPA, its receptor uPAR and the plasminogen activator inhibitor 1 (PAI-1) play an important role in tumour invasion and progression in a variety of tumour types. Since the majority of clear cell renal cell carcinoma (ccRCC) shows distant metastasis at time of diagnosis or later, the interplay of uPA, uPAR and PAI-1 might be of importance in this process determining the patients’ outcome. Methods: Corresponding pairs of malignant and non-malignant renal tissue specimens were obtained from 112 ccRCC patients without distant metastasis who underwent tumour nephrectomy. Tissue extracts prepared from fresh-frozen tissue samples by detergent extraction were used for the determination of antigen levels of uPA, uPAR and PAI-1 by ELISA. Antigen levels were normalised to protein concentrations and expressed as ng per mg of total protein. Results: Antigen levels of uPA, uPAR, and PAI-1 correlated with each other in the malignant tissue specimens (rs=0.51-0.65; all P<0.001). Antigen levels of uPA system components were significantly higher in tissue extracts of non-organ confined tumours (pT3+4) compared to organ-confined tumours (pT1+2; all P<0.05). Significantly elevated levels of uPAR and PAI-1 were also observed in high grade ccRCC. When using median antigen levels as cut-off points, all three uPA system factors were significant predictors for disease-specific survival (DSS) in univariate Cox’s regression analyses. High levels of uPA and uPAR remained independent predictors for DSS with HR=2.86 (95% CI 1.07-7.67, P=0.037) and HR=4.70 (95% CI 1.51-14.6, P=0.008), respectively, in multivariate Cox’s regression analyses. A combination of high antigen levels of uPA and/or uPAR further improved the prediction of DSS in multivariate analysis (HR=14.5, 95% CI 1.88-111.1, P=0.010). Moreover, high uPA and/or uPAR levels defined a patient subgroup of high risk for tumour-related death in ccRCC patients with organ-confined disease (pT1+2) (HR=9.83, 95% CI 1.21-79.6, P=0.032). Conclusions: High levels of uPA and uPAR in tumour tissue extracts are associated with a significantly shorter DSS of ccRCC patients without distant metastases. Keywords: PAI-1, Prognostic biomarker, Renal cell carcinoma, uPA, uPAR, uPA system Keywords: PAI-1, Prognostic biomarker, Renal cell carcinoma, uPA, uPAR, uPA system * Correspondence: susanne.fuessel@uniklinikum-dresden.de †Equal contributors 1Department of Urology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany Full list of author information is available at the end of the article © 2014 Fuessel et al.; licensee BioMed Central. Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Background were observed between high immunoexpression of PAI-1 in tumour tissue of ccRCC patients and older age, advanced tumour stage, high nuclear grade, and disease progression [20,21]. In survival analyses, strong PAI-1 immunostaining was associated with a shorter disease-free survival of ccRCC patients [20]. Furthermore, high PAI-1 immunoexpression was identified as an independent predictor of cancer- specific survival in a cohort of 172 ccRCC patients [21]. Renal cell carcinoma (RCC), comprising 3-4% of all ma- lignant neoplasms, is the third most common urological tumour entity and the 13th most common malignancy worldwide [1,2]. Clear cell RCC (ccRCC) is the most common and the most aggressive subtype of this disease [3]. About one third of the patients already present dis- tant metastases at the time of diagnosis, whereas nearly another third develops metastases during the course of the disease [1,4]. Although the application of target- directed therapeutics improved the outcome of pa- tients with metastatic ccRCC their prognosis remains unfavourable [5]. Increased uPA, uPAR and/or PAI-1 antigen levels in tumour tissue extracts, as determined by ELISA, were found to be related to high tumour grade of RCC [22,23]. Hofmann et al. [24,25], who also measured antigen levels of uPA, uPAR and PAI-1 in renal tissue extracts from RCC patients by ELISA, revealed all three factors as strong and independent predictors for early relapse. Since the disease progression of RCC is still not suffi- ciently predictable by clinical and histopathological pa- rameters, there is an urgent need for additional powerful biological prognostic factors that may help to refine indi- vidual risk stratification of RCC patients. A reliable pre- diction of outcome after nephrectomy by such markers would be valuable to tailor individualised follow-up schedules and to provide adjuvant therapies to patients at high risk of relapse [6]. Several clinicopathological pa- rameters and molecular biomarkers or their combination have been described to be prognostically useful for RCC [7-9]. Nevertheless, further research and validation of these molecular markers for diagnostic and prognostic purposes in RCC patients are still necessary. Thus, the above-mentioned studies point to a rather strong clinical relevance of the members of the uPA- system in RCC, however, with some important limita- tions. Most of these data were obtained using tissue samples originating from different RCC subtypes, incon- sistent cohort sizes, optimised cut-off points, the use of non-detergent tissue extracts or the three factors were not analysed in parallel. Abstract This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Page 2 of 12 Background Therefore, in the present study, uPA, uPAR and PAI-1 antigen levels were determined in detergent tissue extracts derived from corresponding malignant and non-malignant renal tissues of 112 RCC patients of the clear-cell subtype without clinically de- tectable distant metastases at the time of diagnosis by ELISA. The antigen concentrations of uPA system com- ponents in tissue extracts were analysed for correlations between these factors themselves and for potential associations with clinicopathological parameters. In addition, we assessed the prognostic power of these markers for the prediction of disease-specific survival (DSS) and overall survival (OS) to validate their use- fulness for outcome prediction of ccRCC patients without distant metastasis. The urokinase-type plasminogen activator (uPA) sys- tem consisting mainly of uPA, the uPA receptor (uPAR) and the plasminogen activator inhibitor-1 (PAI-1) has been shown to play a key role in physiological and pathological pathways including carcinogenesis [10-12]. In addition to extracellular proteolysis, uPA in concert with uPAR and/or PAI-1 induces cell signaling pathways that affect multiple steps of cancer progression such as angiogenesis, cell growth, cell adhesion and migration, chemotaxis and cell survival [10,11,13,14]. High expression levels of uPA and/or PAI-1 in tumour tissue extracts have been found to be strong predictors of poor prognosis in patients afflicted with different types of solid malignant tumours [15,16]. High uPAR levels are also associated with poor prognosis in a var- iety of cancer types, however, the prognostic impact of uPAR expression is not as pronounced as that of uPA and PAI-1 [17,18]. Study population In total, 112 patients with ccRCC were included in this retrospective study that was approved by the institu- tional review boards of the Technische Universität Dresden and the Martin Luther University Halle- Wittenberg. Written informed consent was obtained from all patients. Patients were treated by partial or radical tumour nephrectomy between 1994 and 2001 at either the Department of Urology of the Technische Universität Dresden or the Department of Urology of the Martin Luther University Halle-Wittenberg. Tumours were restaged according to the UICC-classification 2010 [26]; tumour grading was performed according to Fuhrman et al. [27]. The patient cohort consisted of 65 men (58%) To date, only few studies exist that characterise the role of uPA system members in RCC and analyse their association with clinicopathological parameters and their impact on the outcome of RCC patients. High uPA, uPAR and/or PAI-1 protein expression in tumour tissue of RCC patients, detected by immunohistochemistry, was significantly associated with higher tumour stage, me- tastasis and poor disease-specific survival in a cohort of 106 RCC patients [19]. Furthermore, significant associations Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Page 3 of 12 Table 1 Clinical and histopathological characteristics of the ccRCC patients Clinicopathological parameters No. patients (%) Total 112 Gender male 65 (58.0) female 47 (42.0) Age (years) ≤64 57 (50.9) >64 55 (49.1) Tumour stage pT1 73 (65.2) pT2 14 (12.5) pT3 22 (19.6) pT4 3 (2.7) Tumour grade G1 5 (4.5) G2 63 (56.3) G3 35 (31.2) G4 9 (8.0) Lymph node status positive 6 (5.4) negative 106 (94.6) Disease-specific death (DSS) alive 91 (81.2) died of ccRCC 21 (18.8) Death of any cause (OS) alive 74 (66.1) died of any cause 38 (33.9) Table 1 Clinical and histopathological characteristics of the ccRCC patients and 47 women (42%). Median age was 64.4 years (range 38–88 years). Organ-confined tumours (pT1+pT2) were found in 87 patients (78%), and non-organ confined tu- mours (pT3+pT4) in 25 patients (22%). 68 patients (61%) had low grade tumours (G1+G2), whereas 44 patients (39%) displayed high grade tumours (G3+G4). None of the patients included in the study showed clinically detectable distant metastasis at the time of diagnosis, but 6 patients (5%) had tumour-positive lymph nodes (pN1). Furthermore, patients with distant metastases detected within six months after primary surgery were excluded from the study. Follow-up data were collected with regard to death of patients and cause of death. Determination of tissue antigen levels by ELISA Matched pairs of malignant and non-malignant renal tis- sue specimens obtained directly after surgery were snap- frozen and stored in liquid nitrogen until further use. Detergent tissue extracts were prepared from frozen renal tissue specimens as previously described [28,29]. The use of detergent-containing extraction buffer was recommended by the manufacturer, since it allows the reliable extraction of uPA, PAI-1 and the membrane- bound uPA receptor and the parallel determination of all three factors in one tissue extract [28,30]. Briefly, after solubilisation of membrane-bound proteins using Tris-buffer containing the non-ionic detergent Triton X- 100 (1%), cell debris was separated by centrifugation and the supernatant was stored at -80°C until use. The uPA, uPAR and PAI-1 antigen content in tissue extracts of ccRCC patients was determined applying commercially available ELISA kits (IMUBIND uPA ELISA # 894, IMU- BIND uPAR ELISA # 893 and IMUBIND Tissue PAI-1 ELISA # 821; American Diagnostica/Sekisui Diagnostics, Stamford, CT, USA) according to the manufacturer’s in- structions. IMUBIND ELISA tests for uPA and PAI-1 have previously been extensively validated in quality assessment trials by an EORTC study group [31]. The protein content of tumour tissue extracts was determined using the BCA protein assay (Sigma, Deisenhofen, Germany). Antigen con- centrations in tissue extracts were expressed as ng analyte per mg of total protein. is presented by boxplots. The Wilcoxon test was used to test for significant differences in antigen levels between both sample groups. Correlations between continuous variables of the three uPA system components were assessed by Spearman's rank correlation coefficients (rs). The relationship of anti- gen levels with clinicopathological parameters was evalu- ated using the non-parametric Mann–Whitney test. DSS and OS of ccRCC patients were used as follow-up end points for survival analyses. The median levels were set as cut points to separate ccRCC patients in groups with low or high marker expression. For statistical analyses of the association between expression of uPA system compo- nents and patients’ prognosis univariate and multivariate Cox’s proportional hazard regression models were used to calculate the hazard ratio (HR) and its 95% confidence interval (CI) in the analysis of OS and DSS. The multivari- ate Cox’s regression models were adjusted to known clin- ical prognostic factors in ccRCC patients such as gender, Study population Median follow up for all pa- tients comprised 101 months (range 9–188 months) with 38 deaths of any cause (33.9%; median survival 61.5 months) in the analysis of OS and with 21 patients (18.8%; median survival 32.0 months) who died of ccRCC in the analysis of DSS. All clinical and histo- pathological characteristics of the ccRCC patients are given in Table 1. Comparison of uPA system component levels in corresponding malignant and non-malignant tissue specimens of ccRCC patients The median normalised antigen levels (ng/mg protein) of uPA, uPAR, and PAI-1 were 0.41 (range 0.03 - 7.44), 0.51 (range 0.16 - 8.31), and 10.3 (range 1.28 – 3738.3), respectively, in the ccRCC tissues. In tissue extracts of the adjacent non-malignant tissue median antigen levels of 0.61 (range 0.09 - 4.99), 0.52 (range 0.10 - 6.17), and 3.13 (range 1.17 – 34.5) were determined for uPA, uPAR, and PAI-1, respectively (Figure 1). Significantly reduced antigen levels of uPA were ob- served in the tumour tissue specimens compared to the corresponding non-malignant tissues (P = 0.002), whereas PAI-1 antigen levels were significantly increased in tumour tissue specimens (P < 0.001). In contrast, no significant differences in protein levels between malig- nant and non-malignant tissue samples were observed for uPAR (P = 0.306). The distribution of the uPA, uPAR, and PAI-1 antigen levels in tissue extracts of the corresponding tissue pairs is shown in Figure 1. Antigen levels of the uPA system components in tumour tissue specimens showed a moderate, significant correlation amongst each other. Spearman’s correlation coefficients of rs = 0.51 (P < 0.001) were calculated for the association between uPA and uPAR, of rs = 0.54 (P < 0.001) for uPA with PAI-1 and of rs = 0.65 (P < 0.001) for uPAR with PAI-1. Conversely, only a low correlation (rs < 0.28) was observed between uPA system component levels in non-malignant tissue specimens. Figure 1 Protein levels in matched pairs of malignant and non-malignant renal tissue specimens. Distribution of protein Figure 1 Protein levels in matched pairs of malignant and non-malignant renal tissue specimens. Distribution of protein levels of A) uPA, B) uPAR and C) PAI-1 in malignant (Tu) and non-malignant (Tf) renal tissues from 112 ccRCC patients assessed by ELISA is presented by boxplots. The boxes represent the 25th – 75th percentiles, the whiskers indicate the 10th and 90th percentiles. The median values are depicted as solid lines within the boxes. The Wilcoxon test was used to test for significant differences in antigen levels between Tu and Tf. Statistical analyses h d b The distribution of protein levels of uPA, uPAR and PAI-1 in malignant and non-malignant tissue specimens Page 4 of 12 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Figure 1 Protein levels in matched pairs of malignant and non-malignant renal tissue specimens. Distribution of protein levels of A) uPA, B) uPAR and C) PAI-1 in malignant (Tu) and non-malignant (Tf) renal tissues from 112 ccRCC patients assessed by ELISA is presented by boxplots. The boxes represent the 25th – 75th percentiles, the whiskers indicate the 10th and 90th percentiles. The median values are depicted as solid lines within the boxes. The Wilcoxon test was used to test for significant differences in antigen levels between Tu and Tf. age, tumour stage and tumour grade. Survival curves were generated using Kaplan-Meier analysis applying the log- rank test to look for differences in survival. All calcula- tions were performed using the StatView 5.0 statistical package (SAS Institute, Cary, NC, USA). P-values < 0.05 were considered as statistically significant. Association of uPA system component levels in tumour tissue with clinicopathological parameters of ccRCC patients non-malignant renal tissue specimens. Distribution of protein levels of A) uPA, B) uPAR and C) PAI-1 in malignant (Tu) and non-malignant (Tf) renal tissues from 112 ccRCC patients assessed by ELISA is presented by boxplots. The boxes represent the 25th – 75th percentiles, the whiskers indicate the 10th and 90th percentiles. The median values are depicted as solid lines within the boxes. The Wilcoxon test was used to test for significant differences in antigen levels between Tu and Tf. Associations of uPA, uPAR and PAI-1 antigen levels in tumour tissue extracts with relevant clinicopathological factors are summarised in Table 2. Levels of uPA in tumour tissue samples differed significantly between male and female patients (P = 0.002), whereas the associ- ation of uPAR and PAI-1 with gender was not significant. Significantly higher levels of uPAR, but not of uPA and PAI-1, were observed in patients at higher age (older than the median of 64 years) compared to younger patients (P = 0.029). Furthermore, antigen levels of all three uPA system factors were significantly elevated in tumour tissue from non-organ confined tumours (pT3+4) compared to organ- confined tumours (pT1+2; all P < 0.05). High grade tu- mours (G3+4) displayed significantly increased levels of uPAR (P = 0.008) and PAI-1 (P = 0.011) in compari- son to low grade tumours (G1+2). However, uPA levels in tumour tissue extracts were not related to tumour grade (Table 2). Page 5 of 12 Page 5 of 12 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Table 2 Protein levels of uPA system components in tumour tissue specimens in relation to clinicopathological parameters of the ccRCC patients Clinicopathological parameters No. Association of uPA system component levels in tumour tissue with clinicopathological parameters of ccRCC patients patients uPAa uPARa PAI-1a Total 112 0.41 (0.4) 0.51 (0.7) 10.31 (20.7) Genderb P = 0.002 P = 0.065 P = 0.056 male 65 0.47 (0.6) 0.60 (0.7) 12.58 (29.1) female 47 0.30 (0.3) 0.42 (0.5) 7.18 (13.9) Age (years)b P = 0.117 P = 0.029 P = 0.242 ≤64 57 0.36 (0.3) 0.43 (0.4) 8.98 (13.4) >64 55 0.46 (0.7) 0.63 (0.7) 11.74 (54.7) Tumour stageb P = 0.003 P = 0.021 P = 0.010 pT1+2 87 0.36 (0.3) 0.47 (0.5) 8.33 (14.0) pT3+4 25 0.63 (0.9) 0.81 (1.4) 18.05 (62.3) Tumour gradeb P = 0.122 P = 0.008 P = 0.011 G1+2 68 0.40 (0.3) 0.43 (0.5) 7.83 (12.8) G3+4 44 0.43 (0.9) 0.68 (1.1) 14.57 (62.9) Disease-specific survivalb P = 0.220 P = 0.002 P = 0.007 alive 91 0.37 (0.4) 0.46 (0.5) 7.91 (14.4) died of ccRCC 21 0.50 (0.7) 0.94 (0.8) 16.08 (65.0) Overall survivalb P = 0.568 P = 0.013 P = 0.037 alive 74 0.38 (0.4) 0.45 (0.4) 7.59 (17.7) died of any cause 38 0.46 (0.5) 0.69 (0.7) 12.57 (57.1) aMedian values (interquartile range), ng analyte/mg protein; bMann-Whitney test. levels of uPA system components in tumour tissue specimens in relation to clinicopathological h RCC ti t es (interquartile range), ng analyte/mg protein; bMann-Whitney test Median values (interquartile range), ng analyte/mg protein; bMann-W Association of uPA system component levels with survival of ccRCC patients Association of uPA system component levels with survival of ccRCC patients factors separately to a base model consisting of clinico- pathological parameters including gender, age, tumour stage and tumour grade. Strikingly, uPA and uPAR anti- gen levels in tumour tissue extracts were significantly associated with shorter DSS, whereas none of the clini- copathological parameters showed a significant predict- ive value towards DSS (Table 3). For ccRCC patients with either high uPA (HR = 2.86; 95% CI 1.07-7.67; P = 0.037) or uPAR antigen levels (HR = 4.70; 95% CI 1.51- 14.6; P = 0.008) we observed a significantly increased risk of cancer-related death compared with those pa- tients who displayed low uPA or uPAR antigen levels in ccRCC tissue (Table 3). PAI-1 antigen levels were associ- ated with DSS only by trend in multivariate analysis (HR = 2.59; 95% CI 0.95-7.08; P = 0.064). When adding all three factors simultaneously to the basic model, only uPAR remained an independent prognostic factor for DSS with HR = 3.54 (95% CI 1.02-12.2, P = 0.046). In contrast, uPA system members did not emerge as inde- pendent prognosticators for OS (Table 3). Among the clinicopathological parameters only age displayed an in- dependent prognostic value for OS (Table 3). of ccRCC patients For statistical analyses of the impact of uPA system components on patients’ survival, the median protein ex- pression levels of uPA, uPAR, and PAI-1 were used as cut-off points to classify the ccRCC patients into groups with low or high antigen levels in tumour tissue extracts. In univariate Cox’s regression analyses, high antigen levels of all three uPA system components in tumour tis- sue were significantly associated with both shorter DSS and OS of ccRCC patients, except for uPA, for which an association of high antigen levels was observed with OS only (Additional file 1: Table S1). These findings were con- firmed by the log-rank test which also revealed signifi- cantly shorter DSS of patients with high levels of uPA system components (P = 0.013, P = 0.001, and P = 0.022 for uPA, uPAR, and PAI-1, respectively) as exemplarily visualised by the respective survival curves (Figure 2). In univariate Cox’s regression analyses, high antigen levels of all three uPA system components in tumour tis- sue were significantly associated with both shorter DSS and OS of ccRCC patients, except for uPA, for which an association of high antigen levels was observed with OS only (Additional file 1: Table S1). Analysis of combined uPA system component levels in tumour tissues for survival of ccRCC patients tumour tissues for survival of ccRCC patients In the next step, we assessed whether the pair-wise com- bination of uPA, uPAR and PAI-1 antigen levels could improve the prognostic power of either single marker. For this, the ccRCC patient cohort was divided into two groups: a group with low levels of each of both markers analysed, and another with high levels of one or both markers. In the whole patient cohort, the marker combi- nations of high antigen levels of either uPA and/or uPAR, uPA and/or PAI-1 or uPAR and/or PAI-1 were found to be significantly associated with shorter DSS in univariate Cox’s regression analyses (Additional file 1: Table S1). Particularly, the co-detection of high antigen levels of uPA and/or uPAR added significant prognostic information for DSS in ccRCC patients with a HR of 12.6 (95% CI 1.69-94.1; P = 0.013). Moreover, in multi- variate analyses using the base model mentioned above (comprising gender, age, tumour stage and tumour grade), we found that combined high antigen levels of uPA and/or uPAR resulted in an even better prediction of DSS represented by a HR of 14.5 (95% CI 1.88-111.1, P = 0.010), which was independent of other factors (Table 4). The combined antigen levels of high uPA and/or PAI-1 (HR = 4.24, 95% CI 1.21- 14.9, P = 0.024) did also provide additional prognostic information (Table 4). In addition, in the subgroup of patients with organ- confined disease, those with low antigen levels of both uPA and uPAR were characterised by a longer DSS than patients with tumours with high levels of one or both markers (Table 5). Patients with pT1+2 tumours with high levels of uPA and/or uPAR showed a significantly increased risk of cancer-related death (HR = 9.83; 95% CI 1.21-79.6, P = 0.032) compared to pT1+2 patients who had low uPA and uPAR levels (Table 5). Thus, a pronounced additive effect on prognosis of pT1+2 ccRCC patients, i.e. patients with an assumed lower risk of cancer-related death, was identified when combining uPA and uPAR antigen levels in tumour tissue. The other combinations of high uPA and/or PAI-1 or uPAR and/or PAI-1 did not provide any additional prognostic information for ccRCC patients with organ-confined disease (Table 5). Figure 2 Disease-specific survival of the ccRCC patients in relation to the uPA system components. Association of uPA system component levels with survival of ccRCC patients These findings were con- firmed by the log-rank test which also revealed signifi- cantly shorter DSS of patients with high levels of uPA system components (P = 0.013, P = 0.001, and P = 0.022 for uPA, uPAR, and PAI-1, respectively) as exemplarily visualised by the respective survival curves (Figure 2). Furthermore, the relevant clinicopathological parame- ters age, tumour stage and tumour grade were univariate predictors for DSS. However, in univariate analysis of OS only age and tumour grade reached statistical significance, whereas gender did not affect outcome of ccRCC patients in neither DSS nor OS (Additional file 1: Table S1). In addition, we performed statistical analyses in the subgroup of ccRCC patients with organ-confined tu- mours (pT1+2; n = 87). Here, the clinicopathological variables were not significantly related to the patients’ survival, except for age, which was a significant predictor The independent relationship of uPA system compo- nents with DSS and OS of ccRCC patients was evaluated by multivariate Cox’s regression analyses by adding these Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Page 6 of 12 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Figure 2 Disease-specific survival of the ccRCC patients in relation to the uPA system components. Kaplan-Meier curves show the dependence of disease-specific survival (DSS) on the protein levels of A) uPA, B) uPAR and C) PAI-1. Differences in DSS between patients with low and high levels of the uPA system components were assessed using the log-rank test. p with a trend towards significance for patients with organ- confined tumours in either univariate or multivariate Cox regression analysis with HRs of 3.15 (95% CI 0.97-10.2, P = 0.057) and 3.09 (95% CI 0.88-10.8, P = 0.077), respectively (Additional file 1: Tables S2 and S3). Analysis of combined uPA system component levels in tumour tissues for survival of ccRCC patients Kaplan-Meier curves show the dependence of disease-specific survival (DSS) on the protein levels of A) uPA, B) uPAR and C) PAI-1. Differences in DSS between patients with low and high levels of the uPA system components were assessed using the log-rank test. for OS in uni- and multivariate analyses (Additional file 1: Tables S2 and S3). Likewise, no significant associa- tions were observed between uPA system component levels in tumour tissue extracts and OS (Additional file 1: Tables S2 and S3). On the contrary, in the analysis of DSS we found an association between high uPAR anti- gen levels and an increased risk of cancer-related death For overall survival, none of the marker combinations represented a significant predictor in univariate or multivariate Cox’s regression analyses neither in the whole cohort nor in the subgroup of ccRCC patients Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Page 7 of 12 Table 3 Associations of uPA system components in tumour tissue specimens with disease-specific survival (DSS) and overall survival (OS) of patients with ccRCC (n = 112) assessed by multivariate Cox’s regression analysis Factor No. cases Disease-specific survival HR (95% CI)a P Overall survival HR (95% CI)a P Gender male 65 1 1 female 47 0.93 (0.38-2.28) 0.880 1.65 (0.79-3.45) 0.179 Age (years) ≤64 57 1 1 >64 55 2.31 (0.89-5.99) 0.085 2.52 (1.26-5.07) 0.009 Tumour stage pT1+2 87 1 1 pT3+4 25 1.85 (0.73-4.69) 0.192 1.17 (0.56-2.44) 0.670 Tumour grade G1+2 68 1 1 G3+4 44 2.08 (0.83-5.19) 0.118 1.61 (0.82-3.14) 0.165 uPAb low 53 1 1 high 59 2.86 (1.07-7.67) 0.037 1.28 (0.66-2.51) 0.467 uPARb low 55 1 1 high 57 4.70 (1.51-14.6) 0.008 1.60 (0.80-3.23) 0.185 PAI-1b low 56 1 1 high 56 2.59 (0.95-7.08) 0.064 1.71 (0.85-3.46) 0.135 aHR: hazard ratio; 95% CI: 95% confidence interval of multivariate Cox’s regression analysis; uPA system factors were separately added to the base model consisting of gender, age, tumour stage and tumour grade. bDichotomised into groups with high and low levels of uPA system factors by the median values. with organ-confined disease (Additional file 1: Tables S1 and S2, Tables 4 and 5). from matched malignant and corresponding non- malignant tissue kidney specimens in a cohort of 112 ccRCC patients without distant metastasis and at assessing their potential associations with clinicopath- ological parameters and the prognostic relevance in ccRCC patients. Discussion Conversely, in cytosolic tumour tissue extracts, consider- ably lower uPA concentrations were measured, whereas the PAI-1 antigen levels were comparable [22]. compared to benign renal tissue in previous reports [23,24]. These discrepancies might originate from differ- ences in the numbers of analysed tissue samples. While 112 pairs of corresponding malignant and non-malignant renal tissues were used in our study, Hofmann et al. [24] assessed uPAR levels only in 49 matched tissue pairs and Swiercz et al. [23] compared 52 RCC tissues with 28 nor- mal tissues of different origin (Table 6). Furthermore, levels of uPA system components might differ between the RCC subtypes. We analysed only patients with ccRCC, but no in- formation on the subtype is given in the mentioned reports [23,24]. Interestingly, Chautard et al. [22] observed clear differences in uPA and PAI-1 levels between tissue speci- mens from ccRCC (n = 85), papillary RCC (n = 11) and sar- comatoid RCC (n = 4) indicating that the RCC subtype is of importance and the use of mixed patient cohorts ham- pers the drawing of definite conclusions (Table 6). The concentration of uPA system components has been reported to differ between malignant and non- malignant renal tissues (see Table 6). All mentioned studies including our present analyses demonstrated sig- nificantly higher protein levels of PAI-1 in RCC tissues compared to normal renal tissues (see Table 6). With re- gard to uPA and uPAR, the observations in the different studies vary. While Swiercz et al. [23] observed signifi- cantly elevated uPA levels in the tumour specimens, others found no significant differences between malig- nant and non-malignant renal tissues [22,24,25,32]. In contrast, in our study uPA protein levels were signifi- cantly decreased in ccRCC tissues compared to the cor- responding non-malignant specimens. The reasons for these discrepancies between the different reports remain unclear so far. Hofmann et al. [24,25], who used the same strategy and analysed a similar number of patients as we did, measured comparable uPA levels in the corre- sponding renal tissue specimens, whereas Span et al. [32] obtained a similar trend of uPA levels in malignant and non-malignant renal tissues as in our study, which did not reach statistical significance (P = 0.081). In the tumour tissues, we found significant, moder- ately high correlations between the antigen levels of all three components of the uPA system (rs values between 0.51 and 0.65). Discussion cases Disease-specific survival HR (95% CI) a P Overall survival HR (95% CI) a P uPA/uPARb uPA and uPAR low 35 1 1 uPA and/or uPAR high 52 9.83 (1.21-79.6) 0.032 1.03 (0.45-2.37) 0.942 uPA/PAI-1b uPA and PAI-1 low 37 1 1 uPA and/or PAI-1 high 50 3.23 (0.79-13.1) 0.101 1.30 (0.56-3.02) 0.541 uPAR/PAI-1b uPAR and PAI-1 low 35 1 1 uPAR and/or PAI-1 high 52 2.68 (0.67-10.8) 0.164 1.39 (0.58-3.29) 0.460 aHR: hazard ratio; 95% CI: 95% confidence interval of multivariate Cox’s regression analysis; combinations of uPA system factors were separately added to the base model consisting of gender, age and tumour grade. bDichotomised into groups with high and low levels of uPA system factors by the medians. Table 5 Association of the combination of uPA system component levels in tumour tissue specimens with disease-specific survival (DSS) and overall survival (OS) in the subgroup of ccRCC patients with organ-confined tumours (tumour stage pT1+2, n = 87) assessed by multivariate Cox’s regression analysis Factor No. cases Disease-specific survival HR (95% CI) a P Overall survival HR (95% CI) a P uPA/uPARb uPA and uPAR low 35 1 1 uPA and/or uPAR high 52 9.83 (1.21-79.6) 0.032 1.03 (0.45-2.37) 0.942 uPA/PAI-1b uPA and PAI-1 low 37 1 1 uPA and/or PAI-1 high 50 3.23 (0.79-13.1) 0.101 1.30 (0.56-3.02) 0.541 uPAR/PAI-1b uPAR and PAI-1 low 35 1 1 uPAR and/or PAI-1 high 52 2.68 (0.67-10.8) 0.164 1.39 (0.58-3.29) 0.460 aHR: hazard ratio; 95% CI: 95% confidence interval of multivariate Cox’s regression analysis; combinations of uPA system factors were separately added to the base model consisting of gender, age and tumour grade. bDichotomised into groups with high and low levels of uPA system factors by the medians. aHR: hazard ratio; 95% CI: 95% confidence interval of multivariate Cox’s regression analysis; combinations of uPA system factors were separately added to the base model consisting of gender, age and tumour grade. bDichotomised into groups with high and low levels of uPA system factors by the medians. The antigen levels of uPA, uPAR and PAI-1 (ng ana- lyte/mg of total protein) determined in detergent ex- tracts of corresponding malignant and non-malignant kidney tissues in our study were comparable to those re- ported in previous studies applying the same commercially available ELISA kits (IMUBIND from Sekisui/American Diagnostica) or using in-house ELISA formats (see Table 6). Discussion In the present study, we aimed at analysing the protein levels of uPA system components in tissue extracts Table 4 Associations of combinations of uPA system components in tumour tissue specimens with disease-specific survival (DSS) and overall survival (OS) of patients with ccRCC (n = 112) assessed by multivariate Cox’s regression analysis Factor No. cases Disease-specific survival HR (95% CI)a P Overall survival HR (95% CI)a P uPA/uPARb uPA and uPAR low 41 1 1 uPA and/or uPAR high 71 14.5 (1.88-111.1) 0.010 1.34 (0.64-2.82) 0.438 uPA/PAI-1b uPA and PAI-1 low 43 1 1 uPA and/or PAI-1 high 69 4.24 (1.21-14.9) 0.024 1.63 (0.78-3.40) 0.196 uPAR/PAI-1b uPAR and PAI-1 low 40 1 1 uPAR and/or PAI-1 high 72 3.47 (0.98-12.2) 0.053 1.56 (0.73-3.36) 0.255 aHR: hazard ratio; 95% CI: 95% confidence interval of multivariate Cox’s regression analysis; combinations of uPA system factors were separately added to the base model consisting of gender, age, tumour stage and tumour grade. bDichotomised into groups with high and low levels of uPA system factors by the median values. Table 4 Associations of combinations of uPA system components in tumour tissue specimens wit (DSS) and overall survival (OS) of patients with ccRCC (n = 112) assessed by multivariate Cox’s re f combinations of uPA system components in tumour tissue specimens with disease-specific survival val (OS) of patients with ccRCC (n = 112) assessed by multivariate Cox’s regression analysis g g g g g bDichotomised into groups with high and low levels of uPA system factors by the median values. Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Page 8 of 12 Table 5 Association of the combination of uPA system component levels in tumour tissue specimens with disease-specific survival (DSS) and overall survival (OS) in the subgroup of ccRCC patients with organ-confined tumours (tumour stage pT1+2, n = 87) assessed by multivariate Cox’s regression analysis Factor No. Discussion Similar positive correlations have in fact been previously reported between uPA, uPAR, and PAI- 1 in tumour tissue extracts of RCC patients [24,25]. Strikingly, significant correlations between antigen levels of these factors in tumour tissues have been also ob- served in various other types of cancer [33-35]. The reg- ulated expression of uPA system components in a concerted manner in tumour growth and metastasis may be attributed to the various interactions within the uPA system [11,16]. In contrast, we found only low correlations between uPA system components in non-malignant renal tissues, which is in line with observations on tumour-free samples of other tumour entities [32,36]. This may be caused by various mechanisms of expression regulation and functional interplay between these factors under physiological conditions [11]. For uPAR, we found no differences between corre- sponding malignant and non-malignant tissue of ccRCC patients. In contrast, significantly higher uPAR antigen concentrations have been observed in RCC tissues Page 9 of 12 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Table 6 Overview of median protein levels of uPA, uPAR and PAI-1 determined by different ELISA formats in malignant and non-malignant renal tissue specimens Parameter Hofmann et al. [24,25] Swiercz et al. [23]a Chautard et al. [22]b,c Span et al. [32] Present study Number and type of Tu tissue samples 152 RCC (not specified): 105 for uPA, 49 for uPAR, 96 for PAI-1 52 RCC (not specified) 100 RCC: 85 ccRCC, 11 papillary RCC, 4 sarcomatoid 55 RCC (not specified) 112 ccRCC Number and type of Tf tissue samples matched normal tissues from RCC kidneys n = 28: 3 RCC-free kidneys, 18 normal tissues from RCC-kidneys, 7 tissues adjacent to RCC matched normal tissues from RCC kidneys matched normal tissues from RCC kidneys matched normal tissues from RCC kidneys ELISA for uPA American Diagnostica American Diagnostica BYK Sangtec Medical (Nichols Laboratory) self-designed ELISA American Diagnostica ELISA for uPAR American Diagnostica American Diagnostica n.d. n.d. American Diagnostica ELISA for PAI-1 self-designed ELISA American Diagnostica American Diagnostica, self-designed ELISA American Diagnostica Tissue processing detergent tissue extracts detergent tissue extracts cytosolic tissue extracts detergent tissue extracts detergent tissue extracts uPA in Tu 0.29 n.p. 0.091 (0.043 in ccRCC) 0.50 0.41 in Tf 0.286 n.p. 0.078 0.71 0.61 Difference between Tu vs Tf n.s. (Tu = Tf) P = 0.01 (Tu > Tf) n.s. (Tu > Tf) n.s. Discussion (Tu < Tf) P = 0.001 (Tu < Tf) uPAR in Tu 0.78 n.p. n.d. n.d. 0.51 in Tf 0.30 n.p. n.d. n.d. 0.52 Difference between Tu vs Tf P = 0.018 (Tu > Tf) P = 0.007 (Tu > Tf) n.d. n.d. n.s. (Tu = Tf) PAI-1 in Tu 11.08 n.p. 40.8 (38.7 in ccRCC) 7.26 10.3 in Tf 4.221 n.p. 5.8 0.92 3.13 Difference between Tu vs Tf P = 0.02 (Tu > Tf) P = 0.001 (Tu > Tf) P < 0.001 (Tu > Tf) P < 0.001 (Tu > Tf) P = 0.001 (Tu > Tf) n.d.: not determined; n.p.: not provided; n.s.: not significant; Tf: non-malignant tissues; Tu: malignant tissues. aOnly P-values were given for differences between malignant and non-malignant tissue samples, which are presented in box plots. bResults are converted from pg/mg to ng/mg. cMean levels are shown since medians were not provided. L l f PA PAR d PAI 1 li d l i i d d l f l i Table 6 Overview of median protein levels of uPA, uPAR and PAI-1 determined by different ELISA formats in malignant and non-malignant renal tissue specimens b Table 6 Overview of median protein levels of uPA, uPAR and PAI-1 determined by different ELISA formats in malignant and non malignant renal tissue specimens s of uPA, uPAR and PAI-1 determined by different ELISA formats in malignant n.d.: not determined; n.p.: not provided; n.s.: not significant; Tf: non-malignant tissues; Tu: malignant tissues. aOnly P-values were given for differences between malignant and non-malignant tissue samples, which are presented in box plots. bResults are converted from pg/mg to ng/mg. cMean levels are shown since medians were not provided. Levels of uPA, uPAR and PAI-1 were normalised to total protein concentration and expressed as ng analyte per mg of total protein. between the immunoreactive scores of uPA, uPAR or PAI-1 and tumour grade, tumour stage or metastasis was described by Ohba et al. [19] who performed immu- nohistochemical analyses on 106 RCC patients. Two other immunohistochemical studies on ccRCC patients also described significant positive associations of PAI-1 staining with tumour grade as well as with tumour stage [20,21]. On the contrary, the studies by Hofmann et al. [24,25] did not reveal any association between protein levels of uPA, uPAR or PAI-1 in tissue extracts and tumour grade or stage. Discussion Only few studies have analysed the protein levels of uPA system components in RCC specimens with regard to their dependence on clinicopathological parameters and to their impact on prognosis of RCC patients. In the present study, we observed significantly elevated antigen levels of all three uPA system components in tissue specimens from non-organ confined tumours compared to organ-confined tumours. Furthermore, significantly increased levels of uPAR and PAI-1 could be detected in high grade tumours in comparison to low grade tu- mours. In accordance to our results, Swiercz et al. [23] reported elevated protein levels of uPA, uPAR and PAI-1 in tissue extracts from high grade RCC. Chautard et al. [22] also detected a gradual increase of uPA and PAI-1 protein levels in RCC extracts with higher tumour grade and stage, whereas only the relation between PAI-1 and grade reached statistical significance. A positive relation between the immunoreactive scores of uPA, uPAR or PAI-1 and tumour grade, tumour stage or metastasis was described by Ohba et al. [19] who performed immu- nohistochemical analyses on 106 RCC patients. Two other immunohistochemical studies on ccRCC patients also described significant positive associations of PAI-1 staining with tumour grade as well as with tumour stage [20,21]. On the contrary, the studies by Hofmann et al. [24,25] did not reveal any association between protein levels of uPA, uPAR or PAI-1 in tissue extracts and tumour grade or stage. Moreover, data on the influence of the protein expres- sion of uPA system members on survival of RCC pa- tients are partially contradictory depending on the detection method used [19,22,24]. In the present study, all three uPA system components were significant pre- dictors for DSS in univariate Cox’s regression analyses Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Page 10 of 12 Moreover, Zubac et al. [21] could show that PAI-1 immunoexpression turned out to be a highly significant predictor for metastatic relapse in patients with organ- confined RCC. These results suggests that the deter- mination of protein levels of uPA system components in patients with pT1 and pT2 tumours may provide add- itional prognostic information that may allow for individ- ual, risk-adapted therapy decisions. Discussion Patients at higher risk of relapse could be treated by targeted agents in an adju- vant setting as currently evaluated in a number of ongoing prospective clinical trials [6]. For primary breast cancer, the determination of uPA and PAI-1 antigen levels in tumour tissue extracts has already entered clinical practice for risk stratification and individual therapy decisions in patients with lymph node-negative disease [16,38]. This approach might be also imaginable for ccRCC patients without distant metastasis, particularly for those with organ-confined tumours, but needs further elucidation in prospective clinical trials. and high levels of uPA and uPAR remained independent prognostic factors for DSS in multivariate analyses. The combination of both factors further improved the pre- diction of DSS in multivariate analysis considerably (Table 4; HR=14.5, 95% CI 1.88-111.1, P=0.010). These results are in line with the data of the immunohisto- chemical analyses reported by Ohba et al. [19] who re- vealed that increased protein levels of all three factors were associated with poor DSS. Nevertheless, only PAI-1 emerged as independent predictive factor in their multi- variate Cox’s regression analyses [19]. and high levels of uPA and uPAR remained independent prognostic factors for DSS in multivariate analyses. The combination of both factors further improved the pre- diction of DSS in multivariate analysis considerably (Table 4; HR=14.5, 95% CI 1.88-111.1, P=0.010). These results are in line with the data of the immunohisto- chemical analyses reported by Ohba et al. [19] who re- vealed that increased protein levels of all three factors were associated with poor DSS. Nevertheless, only PAI-1 emerged as independent predictive factor in their multi- variate Cox’s regression analyses [19]. In the report of Hofmann et al. [24] who considered – in contrast to our study – the time from surgery to tumour progression, all three factors appeared also as strong predictors for a higher risk of relapse. In contrast, uPA and PAI-1 protein levels in cytosolic tissue extracts were not independently predictive for metastasis as re- ported by Chautard et al. [22] but elevated uPA levels were significantly associated with a shorter disease-free survival (DFS) in univariate Cox’s regression analyses. Similarly, Choi et al. [20] described a significant relation between high PAI-1 immunoexpression and a shorter DFS, albeit this could not be confirmed in multivariate Cox’s regression analyses. In comparison to this, the im- munohistochemical study by Zubac et al. Conclusions Th The present study, to our knowledge, is the first report on the parallel assessment of protein levels of uPA, uPAR and PAI-1 in detergent tissue extracts of renal tissue speci- mens in a consistent cohort of 112 patients with ccRCC and without clinically detectable distant metastasis at the time of diagnosis. Comparable previous studies were per- formed using tissue samples originating from different RCC subtypes and follow-up endpoints, inconsistent co- hort sizes, optimised cut-off points or non-detergent tissue extracts or analysed not all three factors in parallel (see Table 6). Our study tried to overcome these shortcomings, and revealed a considerable, independent prognostic po- tential of uPA and uPAR protein levels in tumour tissue extracts for DSS. Best prediction of DSS might be achieved by the combination of elevated protein levels of uPA and/ or uPAR compared to low levels of both factors. Particu- larly, this holds true for the subgroup of ccRCC patients with organ-confined tumours, whose outcome in general is assumed to be favourable but can be further stratified on the basis of the protein levels of uPA and uPAR. Despite the strengths of our retrospective study on 112 ccRCC patients, future prospective validation studies have to elucidate independently the prognostic value of the uPA system components for ccRCC patients. Finally, we evaluated the predictive value of the three uPA system components for patients with an organ- confined tumour who are usually expected to have a favourable outcome but still can progress after tumour nephrectomy given the highly aggressive nature of ccRCC. Surprisingly, the DSS of those patients could be further stratified on the basis of combined tissue protein levels of uPA and uPAR (Additional file 1: Table S2, Table 5). The HR of 9.83 (P = 0.032) obtained for pa- tients with high levels of uPA and/or uPAR in multivari- ate analysis in the pT1+2 subgroup further emphasises the potential prognostic utility of uPA and uPAR protein expression for patients with ccRCC. Based on these find- ings, it might be also of interest to specifically determine the concentration of the uPA/uPAR complex with hybrid sandwich-type ELISAs and its relation to prognosis of the patients [37]. Discussion [21] revealed PAI-1 as a significant prognostic factor for disease-specific survival both in univariate and multivariate Cox’s regres- sion analyses. Taken together, previous studies demon- strated a prognostic potential of uPA and uPAR, and most obviously, for PAI-1 protein levels in RCC tissues. In con- trast, high levels of uPA and uPAR in ccRCC extracts were shown to be associated with a significantly shorter DSS of ccRCC patients in our study. The differing study results may originate from variances in the applied methods and used cut-off points as well as in the patient cohorts with regard to the inclusion of patients with diverse RCC sub- types, metastatic status and follow-up endpoints. Additional file 1: Table S1. Univariate Cox’s regression analysis for disease-specific survival (DSS) and overall survival (OS) in patients with ccRCC (n = 112). 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J Clin Pathol 2011, 64(10):893–897. 1Department of Urology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany. 2Department of Urology, Universität Erlangen, Hartmannstrasse 14, 91054 Erlangen, Germany. 3Institute of Pathology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany. 4Institute of Legal Medicine, Martin Luther Universität Halle-Wittenberg, Franzosenweg 1, 06112 Halle, Germany. 5Department of Medicine III, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany. 6Department of Urology, Martin Luther Universität Halle-Wittenberg, Ernst-Grube-Strasse 40, 06120 Halle, Germany. 7Clinical Research Unit, Department of Obstetrics and Gynecology, Technische U i i ä Mü h I i S 22 81675 Mü h G 1Department of Urology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany. 2Department of Urology, Universität Erlangen, Hartmannstrasse 14, 91054 Erlangen, Germany. 3Institute of Pathology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany. 4Institute of Legal Medicine, Martin Luther Universität Halle-Wittenberg, Franzosenweg 1, 06112 Halle, Germany. 5Department of Medicine III, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany. 6Department of Urology, Martin Luther Universität Halle-Wittenberg, Ernst-Grube-Strasse 40, 06120 Halle, Germany. 7Clinical Research Unit, Department of Obstetrics and Gynecology, Technische Universität München Ismaninger Strasse 22 81675 München Germany 21. 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Cancer 1996, 78(3):487–492. Published: 18 December 2014 Authors’ contributions Authors contributions SF, KE, HT, VM and MK designed the study, collected data, performed statistical analyses and drafted the manuscript. SF, ALF and MK substantially contributed to data acquisition and analysis as well as patient data interpretation. KE, SZ, MM, KB, LH, PF, GB and MPW treated the patients, collected the material and data, and reviewed the manuscript. BW contributed substantially to the discussion and writing of the manuscript. All authors have read and approved the final manuscript version. 16. Schmitt M, Mengele K, Napieralski R, Magdolen V, Reuning U, Gkazepis A, Sweep F, Brunner N, Foekens J, Harbeck N: Clinical utility of level-of-evidence-1 disease forecast cancer biomarkers uPA and its inhibitor PAI-1. Expert Rev Mol Diagn 2010, 10(8):1051–1067. SF, KE, HT, VM and MK designed the study, collected data, performed statistical analyses and drafted the manuscript. SF, ALF and MK substantially contributed to data acquisition and analysis as well as patient data interpretation. KE, SZ, MM, KB, LH, PF, GB and MPW treated the patients, collected the material and data, and reviewed the manuscript. BW 17. de Bock CE, Wang Y: Clinical significance of urokinase-type plasminogen activator receptor (uPAR) expression in cancer. Med Res Rev 2004, 24(1):13–39. contributed substantially to the discussion and writing of the manuscript. All authors have read and approved the final manuscript version. contributed substantially to the discussion and writing of the manuscript. All authors have read and approved the final manuscript version. 18. Hoyer-Hansen G, Lund IK: Urokinase receptor variants in tissue and body fluids. Adv Clin Chem 2007, 44:65–102. 18. Hoyer-Hansen G, Lund IK: Urokinase receptor variants in tissue and body fluids. Adv Clin Chem 2007, 44:65–102. The authors declare that they have no competing interests. 15. 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Trends Immunol 2004, 25(8):450–455. 13. Duffy MJ, McGowan PM, Gallagher WM: Cancer invasion and metastasis: changing views. J Pathol 2008, 214(3):283–293. 14. Smith HW, Marshall CJ: Regulation of cell signalling by uPAR. Nat Rev Mol Cell Biol 2010, 11(1):23–36. Competing interests The authors declare that they have no competing interests. The authors declare that they have no competing interests. 31. Sweep CG, Geurts-Moespot J, Grebenschikov N, de Witte JH, Heuvel JJ, Schmitt M, Duffy MJ, Janicke F, Kramer MD, Foekens JA, Brunner N, Brugal G, Pedersen AN, Benraad TJ: External quality assessment of trans-European Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 multicentre antigen determinations (enzyme-linked immunosorbent assay) of urokinase-type plasminogen activator (uPA) and its type 1 inhibitor (PAI-1) in human breast cancer tissue extracts. Br J Cancer 1998, 78(11):1434–1441. multicentre antigen determinations (enzyme-linked immunosorbent assay) of urokinase-type plasminogen activator (uPA) and its type 1 inhibitor (PAI-1) in human breast cancer tissue extracts. Br J Cancer 1998, 78(11):1434–1441. multicentre antigen determinations (enzyme-linked immunosorbent assay) of urokinase-type plasminogen activator (uPA) and its type 1 inhibitor (PAI-1) in human breast cancer tissue extracts. Br J Cancer 1998, 78(11):1434–1441. 32. Span PN, Witjes JA, Grebenchtchikov N, Geurts-Moespot A, Moonen PM, Aalders TW, Vriesema JL, Kiemeney LA, Schalken JA, Sweep FC: Components of the plasminogen activator system and their complexes in renal cell and bladder cancer: comparison between normal and matched cancerous tissues. BJU Int 2008, 102(2):177–182. 33. Biermann JC, Holzscheiter L, Kotzsch M, Luther T, Kiechle-Bahat M, Sweep FC, Span PN, Schmitt M, Magdolen V: Quantitative RT-PCR assays for the determination of urokinase-type plasminogen activator and plasminogen activator inhibitor type 1 mRNA in primary tumor tissue of breast cancer patients: comparison to antigen quantification by ELISA. Int J Mol Med 2008, 21(2):251–259. 34. Foekens JA, Peters HA, Look MP, Portengen H, Schmitt M, Kramer MD, Brunner N, Janicke F, Meijer-van Gelder ME, Henzen-Logmans SC, van Putten WL, Klijn JG: The urokinase system of plasminogen activation and prognosis in 2780 breast cancer patients. Cancer Res 2000, 60(3):636–643. 35. Taubert H, Wurl P, Greither T, Kappler M, Bache M, Lautenschlager C, Fussel S, Meye A, Eckert AW, Holzhausen HJ, Magdolen V, Kotzsch M: Co-detection of members of the urokinase plasminogen activator system in tumour tissue and serum correlates with a poor prognosis for soft-tissue sarcoma patients. Br J Cancer 2010, 102(4):731–737. 35. Taubert H, Wurl P, Greither T, Kappler M, Bache M, Lautenschlager C, Fussel S, Meye A, Eckert AW, Holzhausen HJ, Magdolen V, Kotzsch M: Co-detection of members of the urokinase plasminogen activator system in tumour tissue and serum correlates with a poor prognosis for soft-tissue sarcoma patients. Br J Cancer 2010, 102(4):731–737. 36. Werle B, Kotzsch M, Lah TT, Kos J, Gabrijelcic-Geiger D, Spiess E, Schirren J, Ebert W, Fiehn W, Luther T, Magdolen V, Schmitt M, Harbeck N: Cathepsin B, plasminogenactivator-inhibitor (PAI-1) and plasminogenactivator-receptor (uPAR) are prognostic factors for patients with non-small cell lung cancer. References Luther T, Flossel C, Albrecht S, Kotzsch M, Muller M: Tissue factor expression in normal and abnormal mammary gland. Nat Med 1996, 2(5):491–492. 5. Di Lorenzo G, Autorino R, Sternberg CN: Metastatic renal cell carcinoma: recent advances in the targeted therapy era. Eur Urol 2009, 56(6):959–971 5. Di Lorenzo G, Autorino R, Sternberg CN: Metastatic renal cell carcinoma: recent advances in the targeted therapy era. Eur Urol 2009, 56(6):959–971 6. Pinto A: Adjuvant therapy for renal cell carcinoma. Clin Genitourin Cancer 2014, 12:408–412. 5. Di Lorenzo G, Autorino R, Sternberg CN: Metastatic renal cell carcinoma: recent advances in the targeted therapy era. Eur Urol 2009, 56(6):959–971 6. Pinto A: Adjuvant therapy for renal cell carcinoma. Clin Genitourin Cancer 2014, 12:408–412. 6. Pinto A: Adjuvant therapy for renal cell carcinoma. Clin Genitourin Cancer 2014, 12:408–412. 30. Bouchet-Bernet C, Spyratos F, Andrieu C, Deytieux S, Becette V, Oglobine J: Influence of the extraction procedure on plasminogen activator inhibitor-2 (PAI-2) and urokinase receptor (uPAR) assays in breast cancer tissues. Breast Cancer Res Treat 1996, 41(2):141–146. 7. Eichelberg C, Junker K, Ljungberg B, Moch H: Diagnostic and prognostic molecular markers for renal cell carcinoma: a critical appraisal of the current state of research and clinical applicability. Eur Urol 2009, 55(4):851–863. 7. Eichelberg C, Junker K, Ljungberg B, Moch H: Diagnostic and prognostic molecular markers for renal cell carcinoma: a critical appraisal of the current state of research and clinical applicability. Eur Urol 2009, 55(4):851–863. 31. Sweep CG, Geurts-Moespot J, Grebenschikov N, de Witte JH, Heuvel JJ, Schmitt M, Duffy MJ, Janicke F, Kramer MD, Foekens JA, Brunner N, Brugal G, Pedersen AN, Benraad TJ: External quality assessment of trans-European 31. Sweep CG, Geurts-Moespot J, Grebenschikov N, de Witte JH, Heuvel JJ, Schmitt M, Duffy MJ, Janicke F, Kramer MD, Foekens JA, Brunner N, Brugal G, Pedersen AN, Benraad TJ: External quality assessment of trans-European 8. Finley DS, Pantuck AJ, Belldegrun AS: Tumor biology and prognostic factors in renal cell carcinoma. Oncologist 2011, 16(Suppl 2):4–13. 8. Finley DS, Pantuck AJ, Belldegrun AS: Tumor biology and prognostic factors in renal cell carcinoma. Oncologist 2011, 16(Suppl 2):4–13. Page 12 of 12 Page 12 of 12 Fuessel et al. BMC Cancer 2014, 14:974 http://www.biomedcentral.com/1471-2407/14/974 Anticancer Res 2004, 24(6):4147–4161. 37. de Witte H, Pappot H, Brunner N, Grondahl-Hansen J, Hoyer-Hansen G, Behrendt N, Guldhammer-Skov B, Sweep F, Benraad T, Dano K: ELISA for complexes between urokinase-type plasminogen activator and its receptor in lung cancer tissue extracts. Int J Cancer 1997, 72(3):416–423. 37. de Witte H, Pappot H, Brunner N, Grondahl-Hansen J, Hoyer-Hansen G, Behrendt N, Guldhammer-Skov B, Sweep F, Benraad T, Dano K: ELISA for complexes between urokinase-type plasminogen activator and its receptor in lung cancer tissue extracts. Int J Cancer 1997, 72(3):416–423. 38. Harbeck N, Thomssen C: A new look at node-negative breast cancer. Oncologist 2011, 16(Suppl 1):51–60. doi:10.1186/1471-2407-14-974 Cite this article as: Fuessel et al.: Prognostic impact of urokinase-type plasminogen activator system components in clear cell renal cell carcinoma patients without distant metastasis. BMC Cancer 2014 14:974. doi:10.1186/1471-2407-14-974 Cite this article as: Fuessel et al.: Prognostic impact of urokinase-type plasminogen activator system components in clear cell renal cell carcinoma patients without distant metastasis. BMC Cancer 2014 14:974. 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The Implementation of Safeguard In Efforts to Protect Domestic Industrial Products
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THE IMPLEMENTATION OF SAFEGUARD IN EFFORTS TO PROTECT DOMESTIC INDUSTRIAL PRODUCTS Ufran University of Mataram email : ufranfh@unram.ac.id Abstract Trade security measures (safeguards) are government policies of importing countries to recover serious losses or prevent the threat of serious losses to domestic industries as a result of a surge in imports of similar goods are directly competitive. The purpose of this study is to analyze safeguard regulation in international trade, and to analyze the implementation of safeguards to protect domestic industries. This research is a normative legal research with a statute approach, a conceptual approach and a comparative approach. The technique of collecting legal materials is conducted by literature study. The analysis of legal materials was carried out in a qualitative descriptive manner. The results show that the safeguard arrangement is intended as a legal basis for the government to take security measures to recover serious losses and / or prevent the threat of serious losses from the domestic industry as a result of a surge in imports of similar goods which are directly competitors to domestic industrial products. The implementation of safeguards by importing countries is carried out by the Trade Safeguard Committee through stages, namely starting from investigation and evidence, determining the existence of a loss or threat of loss, and implementing security measures. Keywords: safeguard; international trade; domestic industry protection; tar- iff of import, serous injury. Jurnal IUS Kajian Hukum dan Keadilan Volume 9, Issue 1, April 2021, E-ISSN 2477-815X, P-ISSN 2303-3827 Nationally Accredited Journal, Decree No. 30/E/KPT/2018 open access at : http://jurnalius.ac.id/ojs/index.php/jurnalIUS INTRODUCTION International trade is one part of business activities which has recently progressed very rapidly. This can be seen from the growing circulation of goods, services, capital and labor between countries. This activity can occur through export-import relations, investment, trade in services, licenses and franchises, intellectual property rights and technology transfer, which in turn have an impact on other economic activities, such as banking, insurance, taxation and so on. The entry of Indonesia as a member of world trade through the ratification of Law Number 7 of 1994 concerning Ratification of the Agreement on Establishing DOI: http://dx.doi.org/10.29303/ius.v9i1.833 P-ISSN: 2303-3827, E-ISSN: 2477-815X The World Trade Organization (WTO) has consequences for Indonesia, namely that it must comply with all results of agreement in the WTO forum, as well as harmonize national laws and regulations. in accordance with the results of the WTO agreement. International trade greatly affects the economic growth and development of a country, because each country competes with each other in the international market. One of the advantages of international trade is that it allows a country to specialize in producing cheap goods and services. In addition, the real benefits of international trade can be in the form of an increase in state income, foreign exchange reserves, capital transactions and the breadth of employment opportunities. Economic growth is an achievement that is a top priority for a country in an effort to improve welfare for the community.1 Indonesian participation in free trade is intended to encourage domestic industrial products to be able to compete with imported products, both domestically and in the export market. However, Indonesian participation in the free market is still a problem, because the capacity of domestic products, both in terms of quality and quantity, is still weak. Another problem faced by Indonesia in facing free trade is the difficulty of stemming the surge in imported products, resulting in less competitive domestic industrial production-like goods which in turn will kill the domestic market for similar goods. Furthermore, there will be side effects such as termination of employment, unemployment and the bankruptcy of the domestic similar goods industry. Moreover, Indonesia is facing the ASEAN free market after AFTA since 2003 which was then followed by the ASEAN-China free market through the ACFTA agreement since the 1st January 2010.2 To anticipate these problems, it is necessary regulation and implementation of safeguards in an effort to protect domestic industries. 1 Mikhral Rinaldi, Abd. Jamal, dan Chenny Seftarita, Analysis of the Influence of International Trade and Macroeconomic Variables on Indonesian Economic Growth, Journal of Indonesian Economics and Pub- lic Policy, Volume 4 Number 1, E-ISSN. 2549-8355, May 2017 c o cy, Vo u e Nu be , E SSN. 25 9 8355, ay 20 7 2 Muhammad Sood, International Trade Law, Second Edition, Cet.3, (Depok: Rajawali Press). 2018 3 Hari Murti dan Mutiah Pramesi, Use of International Trade Safeguard Instruments and Global Compe- tition Strategy, JIEP: Journal of Economics and Development, Sebelas Maret University Solo, Vol 6, No 1, 2006, https://www.google.com/search. March 11, 2006 INTRODUCTION Security measures or known as safeguards are a trade policy instrument that is almost similar to anti-dumping and anti- subsidy policies. The three of them are both regulated in WTO approval, and both may be subject to additional import duties if they incur injury to the importing country. Base on the description above, the following problems can be formulated: a. How to regulate trade security measures (safeguards) in International Trade Law and Indonesia Legal System. b. How to implement trade safeguards in an effort to protect domestic industrial products. b. How to implement trade safeguards in an effort to protect domestic industrial products. This research is a normative legal research with the statutory approach, conceptual approach, and comparative approach. The technique of collecting legal materials is carried out through literature study, namely by analyzing various references in the form of statutory regulations and literature books in order to obtain legal materials that have Jurnal IUS Kajian Hukum dan Keadilan 35 Jurnal IUS Kajian Hukum dan Keadilan | Vol. 9 | Issue 1 | April 2021 | hlm, 36~5 relevance to the issues raised. Furthermore, the analysis of legal materials is carried out in a qualitative descriptive manner, namely examining in depth and thoroughly various references, and evaluating these legal materials as an elaboration of the regulations in the field of safeguards in an effort to protect the domestic industry. relevance to the issues raised. Furthermore, the analysis of legal materials is carried out in a qualitative descriptive manner, namely examining in depth and thoroughly various references, and evaluating these legal materials as an elaboration of the regulations in the field of safeguards in an effort to protect the domestic industry. Safeguard Regulations in International Trade Law Safeguards are actions taken by the government to recover serious losses and / or prevent the threat of serious losses to the domestic industry as a result of a surge in imports of similar goods or goods that are directly competitive, with the aim of enabling the industry in question to make structural adjustments. Domestic industry which produces goods of the same type as investigated goods and / or similar competitive goods; researched association of producers of similar goods and / or similar competitive goods; and labor organizations that represent the interests of domestic industry, can submit requests for investigations due to losses or threatening losses to the domestic industry.3 Based on the Agreement on Safeguard Article XIX of GATT 1994 that Safeguards are actions taken by governments of importing countries to recover serious losses and or prevent the threat of serious losses to domestic industries as a result of a surge in imports of similar goods. or goods that are directly competing. Furthermore, according to the Regulation of the Minister of Trade Number: 37 / M-Dag / Per / 9/2008, that Safeguards are actions taken by the government to recover serious losses and / or prevent the threat of serious losses from the domestic industry as a result of a surge. import of similar goods or goods that directly compete with domestic industrial products with the aim that domestic industries that suffer serious losses and / or threat of serious losses can make structural adjustments. Safeguard regulation aside from referring to Article XIX GATT (Emergency Action on Imports of Particular Products) Year 1947 as enhanced by Agremenn on Safeguard 1994, also refers to national regulations, namely Law Number 7 of 1994 concerning Ratification of the Agreement on Establishing the World Trade Organization ( WTO), Law Number 17 of 2006 concerning Amendments to Law Number 10 of 1995 concerning Customs, and Regulation of the Minister of Trade of the Republic of Indonesia Number 37 / M-Dag / Per / 9/2008 concerning Certificate of Origin against Imported goods subject to Safeguards. Based on Article XIX GATT 1947, one of the requerement for implementing safeguards by WTO member countries is to protect domestic industries and be non- discriminatory. 4 HS. Kartadjoemena (1), GATT, WTO and Uruguay Round Results. Cet. First. Jakarta: University of Indonesia (UI-Press), 1997, p. 155 5 Syariful Anam, Impact of Safeguard Measures Import Duty Policy on Protection and Competitiveness of Alu- minum Zinc Coated Steel Products, Fiscal Policy Agency, Ministry of Finance. Journal of Indonesian Treasury Review Vo. l.5, No.3, (2020), https://itrev.kemenkeu.go.id/index.php/ITRev/article/ view / 2020 p. 237. 6 HS. Kartadjoemena (2). GATT and WTO International Systems, Forums and Institutions in the Field of International Trade. Cet. First. Jakarta: University of Indonesia (UI-Press), 1996, pg. 165 Safeguard Regulations in International Trade Law This means that safeguard measures through import restrictions are 36 Jurnal IUS Kajian Hukum dan Keadilan P-ISSN: 2303-3827, E-ISSN: 2477-815X applied because there has been an increase in imported products, causing serious injury in the country (importing country). Thus, exporting countries must have limited access in the importing country market. In addition, another condition is that countries facing importing countries must be compensated. Furthermore, it was also determined that the remedies imposed in the safeguard efforts were tariffs, although quantitative restrictions were also allowed. According to H.S. Kartadjoemena, given the very strict requirements, since the 1947 GATT agreement the use of safeguard mechanisms is considered unsatisfactory. Rules for implementing safeguards are often ineffective, so this mechanism is used less and less. With unsatisfactory safeguard systems, more and more countries are using measures outside of GATT to stem imports. To achieve the same goal, namely limiting the increase in imports, what happens is the practice of agreements that are applied informally even though in essence they violate GATT but politically and technically it is difficult to prevent, this is known as gray area measures. 4 Safeguard measures are taken if a domestic industry faces difficulties due to a flood of imported products. However, developing countries are given special mitigating treatment. This is a principle that applies in the agreement as a special and differential treatment problem that must be resolved, among others, the safeguards time issue which also still requires political resolution, as well as the increasing number of countries joining the free trade area and custom union. Therefore, if the government does not implement a measurable trade protection policy, the domestic market will be dominated by imported products of relatively better quality at relatively lower prices due to advances in production technology which were previously controlled by advanced industrial countries. As a result, several domestic industries which are in the development stage will experience the threat of loss.5 With the implementation of the final round of the Uruguay negotiations in Marrakech (Morocco) on April 15, 1994, the results of the agreement in the field of safeguards were finally agreed. The summary of negotiation results in the safeguard sector is as follows.6 With the implementation of the final round of the Uruguay negotiations in Marrakech (Morocco) on April 15, 1994, the results of the agreement in the field of safeguards were finally agreed. Jurnal IUS Kajian Hukum dan Keadilan | Vol. 9 | Issue 1 | April 2021 | hlm, 38~5 c. Provisions such as voluntary export restraints (VER) should not be applied. c. Provisions such as voluntary export restraints (VER) should not be applied. d. Safeguards may not be applied for more than 4 (four) years unless it is still necessary to prevent injury and the affected industry is being restructured. d. Safeguards may not be applied for more than 4 (four) years unless it is still necessary to prevent injury and the affected industry is being restructured. e. Safeguards that exceed one year must be phased out and if they exceed 3 (three) years must be reviewed in one half year. f. Safeguards are not imposed for developing countries if the share of that country is 3% (three percent) or less of the total imports of the safeguards implementing country and if the collective share of developing countries is 9% (nine percent) or less of the country’s total imports. Thus, the Agreement on Safeguards which ended in Marrakech (Morocco) 15 April 1994 aimed to improve and strengthen the international trade system based on the provisions of the 1994 GATT with the following considerations: Thus, the Agreement on Safeguards which ended in Marrakech (Morocco) 15 April 1994 aimed to improve and strengthen the international trade system based on the provisions of the 1994 GATT with the following considerations: a. Clarify and strengthen the rules of the GATT 1994, and in particular Article XIX GATT (Emergency Measures for the Import of Certain Products), to re-enforce multilateral controls on security measures, and eliminate those that escape such control. b. The importance of structural adjustment and the need to increase rather than limit competition in international markets. b. The importance of structural adjustment and the need to increase rather than limit competition in international markets. c. Consider further that for this purpose, a comprehensive agreement that can be enforced by all members based on the principles of the GATT 1994. c. Consider further that for this purpose, a comprehensive agreement that can be enforced by all members based on the principles of the GATT 1994. With the ratification of regulations regarding safeguard agreements into national laws, each member country of the WTO members can implement safeguard measures for their domestic products if the domestic industry is unable to compete so that they suffer serious losses as a result of the increase in imported products. Safeguard Regulations in International Trade Law The summary of negotiation results in the safeguard sector is as follows.6 a. Developing countries fear more and more effective measures. (Morocco) on April 15, 1994, the results of the agreement in the field of safeguards were finally agreed. The summary of negotiation results in the safeguard sector is as follows.6 a. Developing countries fear more and more effective measures. a. Developing countries fear more and more effective measures. b. Safeguard provisions can be applied provisional during an investigation if: 1) There is clear evidence that the increase in imports has caused or will cause a serious injury. 2) If the delay in implementing the safeguard will result in losses that are diffi- cult to repair. 37 Jurnal IUS Kajian Hukum dan Keadilan 37 a. Investigation and Evidence Each member country can apply security measures after an investigation by the authorized party is carried out in accordance with the procedure and announced in accordance with Article X GATT 1994. This is stated in the Article 3 Agreement on Safeguard: “A member may apply a safeguard measure only following an investigation by the competent authorities of that Member pursuant to procedures previously established and made public in consonance with Article X of GATT 1994 ”. These investigations should include notification to all interested parties so that importers, exporters and other interested parties can present their evidence and views on whether the security measures protect the public interest. The competent authorities will then submit reports of their investigations and provide conclusions regarding all facts and applicable laws. The implementation of investigations into the existence of serious losses or the threat of serious losses to the domestic industry due to the surge in imports is carried out by a committee, which in Indonesia is called the Indonesian Trade Safeguard Committee (ITSC). For this reason, interested parties who are directly affected can submit a request for an investigation of security to the Committee. The interested parties who are directly affected by the increase in imported products can submit an investigation to the ITSC as follows: 7 The interested parties who are directly affected by the increase in imported products can submit an investigation to the ITSC as follows: 7 1) Indonesian domestic producers that produce goods of the same type as inves- tigated goods and / or goods that are directly competitive; 2) Investigated associations of producers of similar goods and / or goods that are directly competitive; ) Labor organizations representing the interests of domestic industrial workers If deemed necessary in the framework of protecting the domestic industry, the Government can even propose an investigation to the Committee. Furthermore, the Indonesian Trade Safeguard Committee (ITSC) on its own initiative can investigate the surge in imports which has resulted in serious losses and / or threats of serious losses to the domestic industry. If deemed necessary in the framework of protecting the domestic industry, the Government can even propose an investigation to the Committee. Furthermore, the Indonesian Trade Safeguard Committee (ITSC) on its own initiative can investigate the surge in imports which has resulted in serious losses and / or threats of serious losses to the domestic industry. Implementation of Safeguards to Protect Domestic Industrial Products. In the General provisions of the Agreement on Safeguards, it is stated that the safeguard agreement applies regulations for the implementation of security measures which must be interpreted as actions that will be regulated in Article XIX GATT 1994. Implementation of safeguards is intended to protect domestic industrial products from inflating. imported products that harm or threaten the loss of the domestic industry. The requirements for implementing safeguards as described in Article 2 of the Agreement on Safeguard are as follows: 1) The requirements for implementing safeguards as described in Article 2 of the Agreement on Safeguard are as follows: 1) The requirements for implementing safeguards as described in Article 2 of the Agreement on Safeguard are as follows: 2) Members can request security measures for a product if the product imported into the territory in such a number threatens domestic similar products, thus causing serious losses to domestic industries that produce similar products or direct products. 2) Members can request security measures for a product if the product imported into the territory in such a number threatens domestic similar products, thus causing serious losses to domestic industries that produce similar products or direct products. ) Safeguard measures will be applied to imported products regardless of the source 38 Jurnal IUS Kajian Hukum dan Keadilan P-ISSN: 2303-3827, E-ISSN: 2477-815X The policy of implementing safeguards by the importing country is carried out through several stages, including conducting investigations and proving, determining the existence of a loss or threat of loss, and implementing the following safeguards, this can be explained as follows: 7 Decree of the Minister of Industry and Trade of the Republic of Indonesia Number 85 / MPP / Kep / 2/2003 concerning Procedures and Requirements for Application for Industrial Safeguarding from the Impact of Surging Imports, Article 2 paragraph (2) a. Investigation and Evidence Based on Presidential Decree No. 84/2002 concerning Safeguard Measures for Domestic Industries from the Impact of Surging Imports, Article 3 paragraph (2) states, in order to facilitate the investigation process, the applicant must complete data at least containing the following: Jurnal IUS Kajian Hukum dan Keadilan Jurnal IUS Kajian Hukum dan Keadilan 39 1) identification of the applicant; 2) complete description of the investigated item; 3) complete description of similar goods or goods that are directly competitiv ) p p g g y p ; 4) name of exporter and exporting country and or country of origin of the goods; 5) domestic industries that are disadvantaged; ) name of exporter and exporting country and or country of origin of the goods 4) name of exporter and exporting country and or country of origin of the goods; 5) domestic industries that are disadvantaged; 5) domestic industries that are disadvantaged; 6) information regarding serious loss and or threat of serious loss; 7) information on investigated goods import data. For the purposes of collecting evidence and for the purposes of proof in exercising its authority, the Committee has the right to request data and information directly from interested parties or other sources deemed appropriate, either government or private agencies / institutions. In addition, the Committee may determine its own evidence based on available data and information (best information available) if the interested party investigates: 1) failing to provide the necessary responses, data or information within the time provided by the Committee; or In addition, the Committee may determine its own evidence based on available data and information (best information available) if the interested party investigates: data and information (best information available) if the interested party investigates: 1) failing to provide the necessary responses, data or information within the time provided by the Committee; or 1) failing to provide the necessary responses, data or information within the time provided by the Committee; or 2) obstructing the investigation process. The Committee treats any confidential data and information according to its nature. Confidential data and information cannot be disclosed publicly without the permission of the owner of the data and information. Interested parties submitting confidential data and information to the Committee must attach a brief note derived from confidential data and information. These brief notes are non-confidential summaries. a. Investigation and Evidence In carrying out the evidentiary process, the Committee must provide equal or equal opportunity to interested parties to submit written evidence and to provide information or other additional written information to the Committee. Then the Committee can verify data and information originating from or obtained from interested parties in the exporting country or in the country of origin of the investigated goods and the domestic industry. Furthermore, within a maximum period of 30 days after the submission of the application for security measures is received completely by the Committee, based on the results of the research and complete initial evidence as submitted by the applicant, the Committee shall issue a decision as stated in Article 3 paragraph (3) that: 1) rejecting the application in the event that the application does not meet the specified requirements; or 2) accept the application and initiate an investigation if the application meets the requirements. 2) accept the application and initiate an investigation if the application meets the requirements. If the committee determines whether or not to conduct an investigation into the request of an interested party, this is stated in Article (4), that the Committee must notify the interested parties in writing along with the reasons thereof and announce the decision in the printed media. Upon such notification, the interested party is given 40 P-ISSN: 2303-3827, E-ISSN: 2477-815X the opportunity to respond if it is deemed that there is a discrepancy for these reasons no later than 15 (fifteen) days after the Committee’s appointment Likewise, the postponement or termination of an investigation must be announced in print media with reasons and supported by facts and conveyed immediately to the interested parties. Furthermore, the party submitting the application can withdraw the request for investigation submitted to the Committee (Article 6). In terms of the results of the investigation it turns out that there is no solid evidence that shows that the domestic industry has suffered serious losses and or the threat of serious losses as a result of the surge in imports, the Committee shall stop investigating the safeguard measures. Based on the determination of the termination of the investigation of safety measures by the Committee, all import duties on the import of investigated goods subject to temporary security measures that have been paid by the importers of investigated goods must be returned to the importers of the investigated goods. a. Investigation and Evidence Then within a period of no later than 15 (fifteen) days from the determination of the termination of the investigation of security measures by the Committee, the Minister of Finance shall revoke the import duty for the investigated goods subject to temporary security measures. The return of the import duty must be carried out as soon as possible, not later than 15 (fifteen) days after the issuance of the Decree of the Minister of Finance regarding the lifting of the imposition of import duty (Article 7). Investigations conducted by the Committee must be completed within no later than 200 (two hundred) days after the determination of the commencement of the investigation. In the event that additional information is required for evidentiary purposes, the Committee may send a written list of questions to interested parties. The list of questions must be answered by the interested party within 15 (fifteen) days of sending the written questionnaire or within 20 (twenty) days in the event of a request from the interested party due to certain reasons. Jurnal IUS Kajian Hukum dan Keadilan | Vol. 9 | Issue 1 | April 2021 | hlm, 42~5 In determining the said loss or threat, ”domestic industry” is the overall producer that produces similar or directly competitive products operating within the territory of a member, or the production of similar products which directly competes constitutes the largest share of total production. Then, to identify serious losses or threat of serious loss the steps taken are First, identify domestically produced goods that are ”similar” or ”directly competitive” with the imported goods under investigation. Second, identify the domestic industries that produce these goods, and third, thoroughly assess the significant decline in the performance of the domestic industry.8 To realize the provisions of Article 4 Agreement on Safeguard, the Government has issued Presidential Decree Number 84 of 2002, Article 12 states: (1) Determination of serious losses and / or threats of serious losses to the domestic industry as a result of the surge in imports of investigated goods must be based on the results of an objective and measurable analysis of all relevant factors of the industry concerned, which includes: a. the rate and magnitude of the surge in investigated goods imports, either in ab- solute terms or relative to similar goods or goods that are directly competitive; b. domestic market share taken as a result of the surge in investigated goods im- ports; and c. changes in the level of sales, production, productivity, capacity utilization, profit and loss as well as employment opportunities. (2) In order to determine a surge in imports resulting in a threat of serious loss, the Committee may analyze other factors in addition to the factors referred to in paragraph (1), such as: a. Real and potential export capacity of the country or producing countries of or- igin of the goods; b. Inventory of goods in Indonesia and in the exporting country. (3) In the event of serious losses and / or threats of serious losses to domestic industries which arise at the same time as a surge in imports but are caused by factors other than the factors referred to in paragraph (1) and paragraph (2) serious and / or threat of serious loss cannot be stated as a result of a surge in imports. Furthermore, Article 13 states that the determination of the occurrence of a threat of serious loss as a result of a surge in imports must be based on facts and cannot be based on assumptions, forecasts or possibilities. 8 Theresia L. Pesulima, Safeguard Measures in the Asean Free Market as a Protection Effort for the Domestic Industry, S A S I, Scientific Journal of the Faculty of Law, Pattimura University, Ambon, Volume 23. Number 1. January - June 2017, ISSN 1693-006, pg. 23 b. Determination of the Existence of Loss or Threat of Loss Before security measures are put in place, it is necessary to prove that there has been a serious loss or threat of serious loss due to a surge in imported goods. Determination of the existence of a loss or threat of loss is regulated in Article 4 of the Agreement on Safeguard as follows: (1) The occurrence of ”serious loss” which is interpreted as being able to hinder the development or existence of domestic industry; (1) The occurrence of ”serious loss” which is interpreted as being able to hinder the development or existence of domestic industry; (2) The existence of ”threat of serious loss” which must be understood as a clear serious loss as meant in paragraph 2. Determination of the threat of serious loss must be based on facts and not on accusations, allegations or other undercover possibilities. 41 Jurnal IUS Kajian Hukum dan Keadilan Jurnal IUS Kajian Hukum dan Keadilan 41 41 c. Imposition of Security Measures Imposition of Safeguards is regulated in the Agreement on Safeguard, namely Article 5 (permanent security measures) and Article 6 (temporary security measures). Both articles allow each member country to implement safeguard measures to the extent necessary to prevent or remedy serious losses in order to facilitate adjustment or compensation. These security measures can take the form of tariffs, quotas and a combination of tariffs and quotas. According to Law Number 17 of 2006 concerning Amendment to Law Number 10 of 1995 concerning Customs, Article 23A states that “Safeguard duties may be imposed on imported goods in the event of a surge in imported goods, either in absolute terms or relative to domestically produced goods. similar products or goods that are directly competitive, and the surge in imported goods: 1) causing serious losses to domestic industries that produce goods similar to these goods and / or goods that are directly competitive; or 1) causing serious losses to domestic industries that produce goods similar to these goods and / or goods that are directly competitive; or 2) threatening serious losses to domestic industries that produce similar goods and / or goods that are directly competitive. Furthermore, Article 23B states that “The import duty for such security measures is the maximum amount required to overcome serious losses or prevent the threat of serious losses to domestic industries. The import duty is in addition to the import duty collected under Article 12 paragraph (1) of the Customs Law Number 10 of 1995. Based on the description above, security measures are taken for domestic industrial products because: 1) There has been a surge in imports of similar goods or goods that directly compete with domestic industrial products. 2) There is a serious loss or threat of serious loss to the domestic industry due to an influx of imported products. 3) There is a causal relationship between the increase in imports with serious losses or the threat of serious losses. Causality analysis based on economic indicators includes: production, domestic sales, market share, profit, capacity and labor utility. Based on the results of the investigation, if evidence is found that there has been a serious loss or threat of serious harm to the domestic industry due to a surge in imported products, the importing country must notify the Safeguard Committee before taking security measures. Jurnal IUS Kajian Hukum dan Keadilan | Vol. 9 | Issue 1 | April 2021 | hlm, 42~5 This means that in determining the existence of a serious loss or threat of loss, the Trade Safeguard Committee must carry out in-depth investigation and analysis in order to find accurate facts that the loss or threat of loss is really the result of a surge in imports, not based on allegations or mere 42 Jurnal IUS Kajian Hukum dan Keadilan P-ISSN: 2303-3827, E-ISSN: 2477-815X perception. Inaccurate investigations are not only detrimental to both the importing country but also the exporting country. c. Imposition of Security Measures Then the importing country first invites the exporting country as a member of the WTO to conduct consultations to give the country an opportunity to negotiate a solution to the problem. Jurnal IUS Kajian Hukum dan Keadilan 43 urnal IUS Kajian Hukum dan Keadilan | Vol. 9 | Issue 1 | April 2021 | hlm, 44~51 According to Bhagirath Lai Das in Cristhophorus Barutu, the form of security measures can be in the form of imposing import or non-tariff tariffs as follows: 1) The imposition of tariffs such as: increasing import obligations beyond the limit level, imposition of additional fees or additional taxes, reimbursement of production taxes, imposition of quota rates, namely quotas for imports at a lower rate and imposition of higher tariffs for imports that are in the over the quota. 1) The imposition of tariffs such as: increasing import obligations beyond the limit level, imposition of additional fees or additional taxes, reimbursement of production taxes, imposition of quota rates, namely quotas for imports at a lower rate and imposition of higher tariffs for imports that are in the over the quota. 2) The imposition of non-tariffs such as: determination of global quotas for imports, introduction of convenience in licensing, import authorization, and other similar measures to control imports. According to the Agreement on Safeguard, the implementation of safeguard measures for international trade includes two forms, namely: According to the Agreement on Safeguard, the implementation of safeguard measures for international trade includes two forms, namely: for international trade includes two forms, namely: 1) Temporary Security Measures 1) Temporary Security Measures Temporary security measures are in the form of tariffs (cash bonds) which are valid for a maximum of 200 days. However, if no evidence is found that the import of goods is causing serious losses or the threat of serious loss to the domestic industry, the tariff to be paid must be returned to the importer. The implementation of temporary security measures is carried out before the implementation of permanent security measures. Temporary security measures are implemented from the initiation or commencement of the investigation process which is preceded by notification. This action is carried out in case of an emergency which, if postponed or not implemented, will cause damage that is difficult to repair. The implementation of security measures is stated in Article 5 of the Agreement on Safeguard, that temporary security measures can be taken by importing countries of WTO members in case of an emergency and if it is postponed it will cause damage that is difficult to repair. Temporary security measures should not exceed 200 days, these measures are carried out in accordance with a provisional determination that clearly proves that increased imports have caused or threatened serious losses to the domestic industry. Furthermore, according to Article 9 of Presidential Decree Number 84 of 2002, that in the event there is strong evidence that the surge in imports of investigated goods has resulted in serious losses or the threat of serious losses; or the surge in imports of investigated goods caused serious losses to the domestic industry which would be difficult to recover if temporary safety measures were taken too late, the Committee may recommend temporary security measures in the form of import duties. In determining temporary countermeasures, the Minister of Industry and Trade can propose recommendations to the Minister of Finance. On the basis of this proposal, the Minister of Finance determined the amount of import duty as 44 Jurnal IUS Kajian Hukum dan Keadilan 44 44 P-ISSN: 2303-3827, E-ISSN: 2477-815X a temporary security measure. Temporary security measures can only be applied for a maximum period of 200 days (Article 10). Temporary security measures must be announced in the State Gazette and printed media and officially notified to the interested parties. 1) Temporary Security Measures The announcement must contain at least the following information as provided for in Article 11: (1) complete description of the investigated item including its technical characteristics and uses, and the tariff post number; (2) complete description of similar goods or goods that are directly competitive; (3) names of well-known domestic industries that produce similar goods or goods that are directly competitive; (4) names of exporters and exporting countries or countries of origin of the goods under investigation; (5) a summary of the loss determination process and its determinants, findings and conclusions. 2) Permanent Security Measures 2) Permanent Security Measures Security measures can still be defined in three forms including increasing import duties, establishing import quotas and a combination of the two forms. If the safeguard measures are still stipulated in the form of a quota, the quota must not be smaller than the average import in the last three years. Security measures can still be defined in three forms including increasing import duties, establishing import quotas and a combination of the two forms. If the safeguard measures are still stipulated in the form of a quota, the quota must not be smaller than the average import in the last three years. For the case of the imposition of a quota that is different from the average import in the last three years, it is necessary to have evidence or special justification as confirmed in Aticle 5 (1) Agreeme on Safeguard which states “A Member shall apply safeguard measures only to the extent necessary to prevent or remedy serious injury and to facilitate adjustment. If a quantitative restriction is used, such a measure shall not reduce the quantity of imports below the level of a recent period which shall be the average of imports in the last three representa- tive years for which statistics are available, unless clear justification is given that a different level is necessary to prevent or remedy serious injury. Members should choose measures most suitable for the achievement of these objectives. According to Article 5, “Each member can implement security measures as far as necessary to prevent or remedy serious losses and to facilitate adjustment or provision of compensation. If a quantitative restriction is used, then the measure shall not reduce the number of imports below the level of a recently enacted period which was the average of imports in the last three years based on available statistics, unless it is clear that a different level is required to prevent or make up for serious losses. The members must choose the most appropriate action to achieve the goal. Furthermore, countries that take safeguard measures in the form of quotas can make an agreement with the largest exporting country regarding the allocation of the quota. If there is no agreement, the quota of each country is determined on the export market share of each country in a certain period. 2) Permanent Security Measures This Agreement 45 Jurnal IUS Kajian Hukum dan Keadilan Jurnal IUS Kajian Hukum dan Keadilan 45 Jurnal IUS Kajian Hukum dan Keadilan | Vol. 9 | Issue 1 | April 2021 | hlm, 46~5 justifies action in special situations where member countries deviate from the non-discrimination rule in imposing quota restrictions on one or more countries whose imports originating from these countries increase the percentage of imports disproportionately in relation to the total increase in imports of goods in the period. which represents. To ensure that the intended action is taken in special situations, the agreement stipulates that the parties must carry it out after going through a consultation process and being approved by the Safeguard Committee. The committee is formed by approval. Based on Presidential Decree Number 84 of 2002, Article 20 paragraph (1- 3) that, the Committee can stipulate recommendations for permanent security measures after all investigative procedures for security measures have been carried out, and there are strong facts and evidence which state that the surge in imports of investigated goods is real and proven to have caused serious losses and or threat of serious harm to the domestic industry. The recommendation must be submitted to the interested parties no later than 10 days after the decision has been taken and published in the State Gazette and / or printed media. 2) Permanent Security Measures The announcement in the State Gazette and / or the printed media above must at least contain the information as referred to in Article 20 paragraph (4) as follows: The announcement in the State Gazette and / or the printed media above must at least contain the information as referred to in Article 20 paragraph (4) as follows: a) Complete description of the investigated item including its technical a) Complete description of the investigated item including its technical characteristics and uses and its tariff postal number; b) Complete description of similar goods or goods that are directly competitive; c) Names of well-known domestic industries that produce similar goods or goods b) Complete description of similar goods or goods that are directly competitive; b) Complete description of similar goods or goods that are directly competitive; c) Names of well-known domestic industries that produce similar goods or goods that are directly competitive; c) Names of well-known domestic industries that produce similar goods or goods that are directly competitive; d) Names of exporters and exporting countries or countries of origin of the goods under investigation; e) A summary of the process for determining serious harm and / or threat of serious loss, its determinants, findings and conclusions; f) Form, level and duration of security measures; g) The proposed date of implementation of permanent security measures; h) The amount of quota allocation for each supplying country if the form of security measure stipulated is not a tariff; and i) List of developing countries that are exempt from the said safeguard. Recommendations for permanent security measures as stated in Article 21, apart from being conveyed to interested parties after the decision has been taken and announced in the State Gazette and / or printed media, is also conveyed by the Committee to the Minister of Industry and Trade. Fixed security measures can be stipulated in the form of import duties by the Minister of Finance and / or quotas by the Minister of Industry and Trade. 46 Jurnal IUS Kajian Hukum dan Keadilan 46 P-ISSN: 2303-3827, E-ISSN: 2477-815X As for the permanent security measure in the form of a quota as emphasized in Article 22, it is stipulated that it cannot be less than the volume of imports calculated on average in the last 3 (three) years, unless there are clear reasons that the quota in the amount or volume of imports is smaller. 2) Permanent Security Measures necessary to recover serious losses and or prevent the threat of serious loss. If more than one country exports investigated goods to Indonesia, the import quota that is set must be allocated among the supplier countries. The quota must be allocated on a pro-rata basis in accordance with the average percentage of imports from each supplying country in the last 3 years. Safeguard measures remain only in effect as long as it is deemed necessary to recover serious losses and / or prevent the threat of serious loss and to allow time for structural adjustment for domestic industries that suffer serious losses or the threat of serious losses. The period of validity of security measures remains for a maximum of 4 years and can be extended. In the event that the security measures have been in effect for more than 3 (three) years, the Committee shall conduct an assessment of the security measures and notify the results of the assessment at least 6 (six) months before the validity period of said security measures ends to the interested parties (Article 23). Extension of the enforcement of security measures can be carried out based on an official request submitted by the domestic industry or on the basis of the Committee’s initiative in the event that there is a strong reason that the loss and or threat of loss suffered by the domestic industry due to the surge in imports will still continue and the domestic industry is still continuing. make structural adjustments. Security measures during the extension period shall not be more restrictive than previous security measures. The period of validity of security measures as a whole shall not exceed 10 years including the validity period of temporary security measures, the validity period of permanent security measures and the extension of permanent security measures. The security measures as referred to in Article 21 paragraph (2) will be gradually reduced or liberalized during the validity period of the permanent security measures. Permanent security measures as emphasized in Article 25, will not be re-applied to imported goods that have been subject to security measures. Jurnal IUS Kajian Hukum dan Keadilan | Vol. 9 | Issue 1 | April 2021 | hlm, 48~51 2) the permanent security measure has never been applied to the same imported goods more than 2 (two) times in a period of five years immediately after the date of the permanent security measure. 2) the permanent security measure has never been applied to the same imported goods more than 2 (two) times in a period of five years immediately after the date of the permanent security measure. In connection with the description above, that in an effort to protect the domestic industry from a surge in imported products, the Government through the Director General of Small, Medium and Miscellaneous Industry (IKMA) of the Ministry of Industry (Kemenperin) is committed to protecting the national small and medium- sized garment industry (IKM) as many as 569,745 business unit. One of the steps taken is the implementation of safeguards to safeguard the domestic garment market. According to BPS data for the 2017-2019 period, the import figure for garment products reached USD 2.38 billion. However, with the high number of imports in this sector, the Ministry of Trade must take it seriously because it can close the potential of the domestic market, especially since the imported products are relatively cheap. Therefore, the implementation of safeguards not only protects the garment industry from the entry of imported products, but can also encourage the growth of this potential sector, considering that the sector’s contribution to GDP is quite large, reaching 5.4 percent in 2019.9 Likewise with imported products in the form of aluminum foil from China, the Trade Safeguard Committee (ITSC) has conducted an investigation based on a request from the Association of Aluminum Extrusion Manufacturers and Aluminum Sheet & Foil (Apralex Sh & F). From the results of these investigations, ITSC found evidence of a surge in imports of aluminum foil with HS code 7607.11.00, during the 2015-2017 period with details in 2015 amounting to 19,438 tons (88.5%) and in 2017 it reached 30,647 tons (92, 4 %). However, until now, the government is still reviewing the imposition of security measures against aluminum foil, as well as kramik from China, with the consideration of maintaining the stability of domestic products, because domestic producers have not been able to meet consumer needs, while other imported products have not been touched at all by security measures. 10 Apart from garment products, various imported products that are subject to safeguard measures include Aluminum Foil Products (2018). 9 Ministry of Industry of the Republic of Indonesia, Ministry of Industry Supports Safeguards Imple- mentation for the Domestic Garment Industry, 12 June 2020. 9 Ministry of Industry of the Republic of Indonesia, Ministry of Industry Supports Safeguards Imple- mentation for the Domestic Garment Industry, 12 June 2020. 10 Andika Prasetyo, Media Indonesia, ITSC Investigates Imports of Aluminum Foil. https:// mediaindone- sia. com / read/ detail /190220, 13 August 2020 11 Grace Olivi, Imports of Aluminum Foil are subject to Safeguard Duties, https://national. kontan. co.id/news, 24 October 2019 sia. com / read/ detail /190220, 13 August 2020 11 Grace Olivi, Imports of Aluminum Foil are subject to Safeguard Duties, https://national. kontan. co.id/news, 24 October 2019 y, J 10 Andika Prasetyo, Media Indonesia, ITSC Investigates Imports of Aluminum Foil. https:// mediaindone- sia. com / read/ detail /190220, 13 August 2020 11 Grace Olivi, Imports of Aluminum Foil are subject to Safeguard Duties, https://national. kontan. co.id/news, 24 October 2019 2) Permanent Security Measures Except for fixed security measures with a maximum validity period of 180 days, imported goods may be imposed if: 1) at least 1 (one) year has been effective since the date of enactment of a security measure on the imported goods concerned; and 1) at least 1 (one) year has been effective since the date of enactment of a security 1) at least 1 (one) year has been effective since the date of enactment of a security measure on the imported goods concerned; and measure on the imported goods concerned; and Jurnal IUS Kajian Hukum dan Keadilan 47 9 Ministry of Industry of the Republic of Indonesia, Ministry of Industry Supports Safeguards Imple- mentation for the Domestic Garment Industry, 12 June 2020. 10 Andika Prasetyo, Media Indonesia, ITSC Investigates Imports of Aluminum Foil. https:// mediaindone- sia com / read/ detail /190220 13 August 2020 Jurnal IUS Kajian Hukum dan Keadilan | Vol. 9 | Issue 1 | April 2021 | hlm, 48~51 These products originated from China with a share of 92.4% in 2017, followed by the Republic of Korea with a share of 7.1%, and other countries with a share of 0.5%.11 Meanwhile in 2019 for textile products, such as curtain products (curtains), bed nets and other furniture items, yarn Jurnal IUS Kajian Hukum dan Keadilan 48 Jurnal IUS Kajian Hukum dan Keadilan 48 P-ISSN: 2303-3827, E-ISSN: 2477-815X products (other than sewing thread) from synthetic and artificial staple fibers, are still under investigation.12 Based on the above facts, it is imperative for Indonesia to be more proactive in utilizing instruments in the form of trade remedies in order to protect domestic industries. Trade remedies are government actions or policies to minimize the negative impact of imported products on domestic industrial products, whether those imports are carried out dishonestly, such as dumping and subsidies, or honestly, such as a surge in imported products. This can be detrimental to the domestic industry of the importing country. 13 Based on the description above, the implementation of safeguards carried out by the government of the importing country is to recover serious losses or prevent the threat of serious loss to the domestic industry as a result of a surge in imports of similar goods or goods that are directly competitive. This measure is used by WTO member countries to protect domestic industries and is non-discriminatory. Thus, the regulation and implementation of safeguards is aimed at protecting domestic industrial products from a surge in imported products that is detrimental or threatening to the loss of domestic industries that produce similar goods. 12 KPPI, Ministry of Trade of the Republic of Indonesia, Investigation of Curtain Products, Inner Sun- shade, Bed Nets and Other Furniture Items, http://kppi.kemendag.go.id/daftar_kasus/detail_produk, 12 October 2018. 13 Nandang Sutrisno, Strengthening the Legal System for Trade Remedies, Protecting Domestic Industries, Journal of Law, Faculty of Law, UII Yogyakarta, No. 2 Vol. April 14, 2007, https://media.neliti.com/media/publications/ 85149. Books Barutu, Christhophorus (1). (2007). Provisions for Antidumping, Subsidies and Safeguards in GATT and WTO. Cet. I. Bandung: PT. Citra Aditya Bakti HS Kartadjoemena (1), (1997). GATT, WTO and Uruguay Round Results. Cet.1. Jakarta: University of Indonesia (UI-Press). HS Kartadjoemena (1), (1997). GATT, WTO and Uruguay Round Results. Cet.1. Jakarta: University of Indonesia (UI-Press). ............. (2) (1996). GATT and WTO International Systems, Forums and Institutions in the Field of International Trade. Cet. 1. Jakarta: University of Indonesia (UI- Press) HS Kartadjoemena (1), (1997). GATT, WTO and Uruguay Round Results. Cet.1. Jakarta: University of Indonesia (UI-Press). ............. (2) (1996). GATT and WTO International Systems, Forums and Institutions in ............. (2) (1996). GATT and WTO International Systems, Forums and Institutions in the Field of International Trade. Cet. 1. Jakarta: University of Indonesia (UI- Press). Sood, Muhammad, (2018), International Trade Law, Second Edition, Cet. 3, Depok: Rajawali Press. CONCLUSION The regulation and application of safeguards is intended so that the government government can take action to recover serious losses and / or prevent the threat of serious losses from the domestic industry as a result of a surge in imports of similar goods or goods that are directly competing with domestic industrial products with the aim that the domestic industry those who experience serious losses and / or threat of serious losses can make structural adjustments. The policy of implementing safeguard measures by the importing country is carried out through stages, namely carrying out investigations and proving, determining the existence of a loss or threat of loss, and implementing security measures. The institution that has the authority to handle safeguard issues is the Indonesian Trade Safeguard Committee (KPPI). Efforts to socialize regulations are needed as one of the safeguards for domestic industry, especially for small and medium industry groups, because these two groups are part of the national manufacturing industry sector which will receive direct impact from the implementation of global market policies. 49 Jurnal IUS Kajian Hukum dan Keadilan 49 Journals and others Anam, Syariful, (2020), Impact of Safeguard Measures Import Duty Policy on Protection and Competitiveness of Aluminum Zinc Coated Steel Products, Fiscal Policy Agency, Ministry of Finance. Journal of Indonesian Treasury Review Vo.l.5, No.3, (2020), https://itrev. kemenkeu.go.id/index.php/ITRev/article/ view / 2020 p. 237. Mikhral, Abd. Jamal, dan Chenny Seftarita, (2017), Analysis of the Influence of International Trade and Rinaldi Macroeconomic Variables on Indonesian Economic Growth, Journal of Indonesian Economics and Public Policy, Volume 4 Number 1, E-ISSN. 2549-8355, May 2017 Murti, Hari dan Mutiah Pramesi, (2006), Use of International Trade Safeguard Instruments and Global Competition Strategy, JIEP: Journal of Economics and Development, Sebelas Maret University Solo, Vol 6, No 1, 2006, https://www.google. com/search. March 11, 2006 Pesulima, Theresia L. (2017), Safeguard Measures in the Asean Free Market as a Protection Effort for the Domestic Industry, S A S I, Scientific Journal of the Faculty of Law, Pattimura University, Ambon, Volume 23. Number 1. January - June 2017, ISSN 1693-006. Sutrisno, Nandang, (2007), Strengthening the Legal System for Trade Remedies, Protecting Domestic Industries, Journal of Law, Faculty of Law, UII Yogyakarta, No. 2 Vol. April 14, 2007, https://media.neliti.com/media/publications/ 85149. Prasetyo, Andika. Media Indonesia, ITSC Investigates Imports of Aluminum Foil. https:// mediaindonesia. com / read/ detail /190220, 13 August 2020 Indonesian Ministry of Industry, Ministry of Industry Supports Safeguard Implementation for Domestic Garments Industry, 12 June 2020. Olivi, Grace. Import-Aluminum Foil is subject to Safeguard Duties, https: // national. kontan.co.id/news, 24 October 2019 KPPI, Ministry of Trade of the Republic of Indonesia, Investigation of Curtain Products, Inner Sunshade, Bed Nets and Other Furniture Items, http: //kppi.kemendag. go.id, 12 October 2018. 50 Jurnal IUS Kajian Hukum dan Keadilan 50 P-ISSN: 2303-3827, E-ISSN: 2477-815X Law Number 7 of 1994 concerning the Agreement on Establishing the World Trade Organization/WTO (Ratification of the Approval for the Establishment of the World Trade Organization). Law Number 10 of 1995 concerning Customs Law Number 17 of 2007 concerning Amendments to Law Number 10 of 1995 on Customs Regulation of the Minister of Trade Number 37/M-Dag/ Per / 9/2008 concerning Certificate of Origin for Imported Goods subject to Safeguarding. Decree of the Minister of Industry and Trade Number 84 / MPP / Kep / 2003 concerning the Indonesian Legislative Protection Committee. Law Number 7 of 1994 concerning the Agreement on Establishing the World Trade Organization/WTO (Ratification of the Approval for the Establishment of the World Trade Organization). Journals and others Law Number 7 of 1994 concerning the Agreement on Establishing the World Trade Organization/WTO (Ratification of the Approval for the Establishment of the World Trade Organization). Law Number 7 of 1994 concerning the Agreement on Establishing the World Trade Organization/WTO (Ratification of the Approval for the Establishment of the World Trade Organization). Law Number 10 of 1995 concerning Customs Law Number 10 of 1995 concerning Customs Law Number 17 of 2007 concerning Amendments to Law Number 10 of 1995 on Customs Law Number 17 of 2007 concerning Amendments to Law Number 10 of 1995 on Customs Regulation of the Minister of Trade Number 37/M-Dag/ Per / 9/2008 concerning Certificate of Origin for Imported Goods subject to Safeguarding. Regulation of the Minister of Trade Number 37/M-Dag/ Per / 9/2008 concerning Certificate of Origin for Imported Goods subject to Safeguarding. Decree of the Minister of Industry and Trade Number 84 / MPP / Kep / 2003 concerning the Indonesian Legislative Protection Committee. 51 Jurnal IUS Kajian Hukum dan Keadilan 51 Jurnal IUS Kajian Hukum dan Keadilan
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Transplanting the Elderly: Mandatory Age- and Minimal Histocompatibility Matching
Frontiers in immunology
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REVIEW published: 12 March 2020 doi: 10.3389/fimmu.2020.00359 Transplanting the Elderly: Mandatory Age- and Minimal Histocompatibility Matching Geertje J. Dreyer and Johan W. de Fijter* Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, Netherlands Edited by: Caner Süsal, Heidelberg University Hospital, Germany Reviewed by: Stanislaw Stepkowski, The University of Toledo, United States Myra Coppage, University of Rochester, United States *Correspondence: Johan W. de Fijter j.w.de_fijter@lumc.nl; jwdefijter@lumc.nl Specialty section: This article was submitted to Alloimmunity and Transplantation, a section of the journal Frontiers in Immunology Received: 16 December 2019 Accepted: 14 February 2020 Published: 12 March 2020 Citation: Dreyer GJ and de Fijter JW (2020) Transplanting the Elderly: Mandatory Age- and Minimal Histocompatibility Matching. Front. Immunol. 11:359. doi: 10.3389/fimmu.2020.00359 Worldwide over 40% of patients receiving renal replacement therapy (RRT) are aged 65 years or older, a number that is still increasing. Renal transplantation is the preferred RRT, providing substantial survival benefit over those remaining on dialysis, including the elderly. Only 3% of patients aged 65 years or older accepted on the waiting list actually received a kidney transplant offer within the Eurotransplant allocation region. To increase the chance for elderly to receive a timely kidney transplant, the Eurotransplant Senior Program was introduced. The ESP supports local allocation of older kidneys to older donors in order to decrease cold ischemia time, while disregarding former exchange principles based on matching for HLA antigens. As a consequence, more elderly received a kidney transplant and a relative higher incidence of acute rejection resulted in additional courses of high steroids and/or depleting antibody therapy. Since death with a functioning graft due to infections is the dominant reason of graft loss in elderly, more intense clinical immunosuppression to prevent or treat acute rejection is not a very attractive option. Therefore in elderly kidney transplant candidates, we advocate reintroduction of minimal histocompatibility criteria (i.e., HLA-DR matching) followed by age-matching with mandatory local/regional allocation to also facilitate short cold ischemia. Keywords: kidney transplantation, elderly, allocation, histocompatibility, HLA, old-for-old program INTRODUCTION End stage renal disease (ESRD) is a rapidly becoming a critical problem worldwide. In The Netherlands, for instance, the prevalence of patients receiving renal replacement therapy (RRT) was 17531 or 1020 per million population (pmp) in the year 2017, an increase of almost 35% in the last decade (1). In countries contributing to the ERA-EDTA registry the prevalence of RRT was 592779 (854 pmp) in 2012, a number that also increased almost 30% in recent annual reports (2). In the US even greater numbers have been documented with a prevalence of 726331 patients (2206 pmp) on RRT in 2016, a number that almost doubled since 2000 [(3) USRDS annual data report: Epidemiology of kidney disease in the United States National Institutes of Health]. With increasing numbers of senior citizens and associated health care challenges, even more elderly with chronic kidney disease and need for RRT can be anticipated. Nowadays, according to the Dutch National Renal Replacement Database (Renine) and the ERA-EDTA registry, already 45% of patients on RRT are 65 years of age or older (2). Likewise, in the US 41% of the patients with ESRD is over the age of 65 years. Frontiers in Immunology | www.frontiersin.org 1 March 2020 | Volume 11 | Article 359 Dreyer and de Fijter Transplanting the Elderly acceptance on the active kidney waiting list. Secondly with increasing age, only very low proportions of these patients actually reach the end of the cue, while significant numbers of patients are removed from the list due to comorbidities and the majority die while waiting for a kidney transplant offer. Taken together, there is an important selection based on cardiovascular and/or oncological exclusion criteria. Where these issues are important long-term topics for younger transplant recipients, in elderly transplant candidates or recipients these are not the main reason for graft loss and therefore may require other strategies. It is known that patients aged 65 years or older, and especially those over 75 year, constitute a separate group with different views and needs regarding health care issues. This is also reflected in choice of RRT. Although kidney transplantation is generally the preferred treatment option when it comes to survival benefit across all ages (4–7), only 3% of the patients between 65 and 74 years were actually transplanted in 2017 and virtually none of the patients receiving a kidney transplant were over the age of 75 years (2). The majority of older transplant candidates are likely to die while on the waiting list before they get a transplant offer according to the Dutch Renine data. Mortality early after transplantation is also higher in elderly with a large French registry study reporting a 3-fold higher mortality risk in the first 3 postoperative months as compared to waitlisted counterparts (8). Another important cause of death after kidney transplantation is failure of the kidney allograft, which is an important independent risk factor of mortality. After graft loss, the risk of mortality in those relisted for a repeat transplant is also higher as compared to patients with a functioning graft or those listed for their first transplant (9–11). Since all-cause mortality increases with age, the longevity of the first kidney graft, even allowing less optimal renal function, is of critical importance. In this paper we reconsider the relative importance and causes of graft failure in the elderly as well as the challenges, hurdles and potential different approaches to prolong survival. We focus on the elderly and need for carefully balanced strategies in this vulnerable group of patients with ESRD. The Elderly and Mortality In elderly the most important reason for late allograft loss is death with a functioning graft (DWFG) (15, 16). In a large registry using UNOS and USRDS data, Ojo et al. (17) found that 42,5% of graft loss was due to DWFG. Age at transplantation was an obvious, strong and independent risk factor. When compared to those aged 18–29 years, recipients aged over 65 years had a 7-fold increased risk to die with a functioning graft. Besides age, ESRD caused by systemic vascular diseases such as hypertension or diabetes mellitus was an independent risk factor for premature death (17). This was confirmed in a study of ElZoghby et al. (18) where 43.4% of the grafts were lost due to death. Interestingly, the most important cause of death more than 5 years after transplantation was due to infectious causes. Transplant recipients who died due to infections were older (64.6 vs. 59.4 years) as compared to those due to cardiovascular diseases. This observation supports the fact that elderly kidney transplant recipients are an already highly selected group with excess infectious comorbidity and mortality, the downside of current potent clinical immunosuppressive drugs, and therefore a key consideration comparable to the increased cardiovascular risk in younger recipients (18). Death due to infectious causes is the consequence of clinical overimmunosuppression, especially in elderly with an already immunosenescent immune system in the context of aging (19). In the light of solid organ transplantation, the consequence of the aging immune system has been documented in a shift from naïve T-cells toward relatively more memory T-cells resulting in decreased immune reactivity (20–22). Indeed the incidence and severity of infections parallels the increase in age in patients (23). Regarding renal transplant recipients, several studies have reported that older patients have more infectious problems and that older recipients die more often due to infectious causes (24, 25). Recently, Lemoine et al. (16) studied renal recipients over 70 years of age and confirmed the mortality risk in elderly due to infections. In a total of 171 recipients death-censored 1-year graft survival was 82.6 and 9.9% of included patients died after the 1st year with infectious causes in 58.5% of cases (16). THE ELDERLY WITH A FAILING KIDNEY TRANSPLANT Overall, kidney graft survival improved significantly in the past decades and mainly due to the prevention of early acute rejection by the use of more potent immunosuppressive drugs like tacrolimus, mycophenolate and more frequent use of poly- or monoclonal antibodies as induction therapy. The improvement in short-term and long-term graft survival has not improved concomitantly and long-term graft survival more or less stabilized between 1988 and 2005 (12). This trend continued beyond 2005 with an approximate 5% annual loss of kidney allografts after the 1st year (13). An analysis of the Collaborative Transplant Study (CTS) registry confirmed that also in Europe graft survival has improved mainly due to short term outcome parameters. Since the year 2000, however, there has been a lack of improvement in short- and long-term graft survival, even after taking into account the changing donor and recipient demographics and donor or organ quality characteristics. This observation probably reflects a lack of further innovation in the management and treatment options around the kidney transplant procedure (14). Older kidney transplant recipients probably require different allocation and/or treatment strategies as compared to their younger counterparts. A critical first consideration is the notion that the elderly that actually do get a transplant offer are a highly selected subgroup of elderly patients with ESRD. First, these patients are generally rigorously medically selected before Frontiers in Immunology | www.frontiersin.org Kidney Transplant Failure The Elderly and Rejection It has become widely accepted that older transplant recipients may encounter less acute rejection episodes after transplantation as compared to younger recipients due to immunosenescence (26, 27). However, if they do experience acute rejection, this episode is more likely to compromise graft- and/or patient 2 March 2020 | Volume 11 | Article 359 Dreyer and de Fijter Transplanting the Elderly than pediatric patients. However, they found more dnDSA in patients treated with cyclosporine as compared to tacrolimus so regarding immunosuppressive protocols for elderly, their role is still important in long term graft survival. Multiple studies have been performed to address the prevalence, risk factors and consequences of dnDSA. Most studies report a prevalence of dnDSA of 10–19% after kidney transplantation and most are formed in the 1st year after transplantation with an annual incidence of 5% thereafter (39– 43). There are several risk factors for the formation of DSA and not surprisingly, non-adherence or lowering immunosuppressive drugs for clinical reasons play a crucial role (44–48). However, one can only form antibodies if there is a foreign HLA molecule and therefore the main risk factor is the degree of HLA mismatch between the recipient and the donor (49). Several studies show that HLA class II mismatch, in particular HLA-DQ, is most important (40, 41, 50). Other described risk factors for the formation of dnDSA are kidneys of deceased donors and younger age of the recipient. Despite the current knowledge there is still no clearly defined clinical advice regarding DSAs and the prevention of formation. Guidelines from the Transplantation Society, the sensitization in transplantation: assessment of risk (STAR) working group and the Heidelberg algorithm, based on the CTS and data from the Heidelberg Transplant Center, all advise to test posttransplantation in pre-specified patient groups. All agree that patients most at risk are patients with a pre-activated immune system, measured by pre-existing antibodies or soluble CD30, in combination with periods of under-immunosuppression and should be monitored closely (51–53). HLA compatibility between donor and recipient is currently assessed by the number of HLA mismatches on serologic level although HLA antibodies recognize accessible polymorphic sequences of amino acids rather than whole HLA antigens. These polymorphic sequences, so called epitopes, can be shared between HLA antigens so the true mismatch is much more complicated than serologic level shows. Therefore, the question can be raised whether current matching principles are reliable enough to reduce or minimize the risk of dnDSA formation. Using the original HLA Matchmaker algorithm (54), Wiebe et al. (55) evaluated the development of de novo class-II DSAs in 286 kidney transplant recipients. Epitope mismatches were significantly more frequent in the patients who developed dnDSAs. In this study the optimal threshold for development of antibodies against HLA-DR was 10 mismatched epitopes and for HLA-DQ 17 mismatched epitopes (55). In a second study they investigated the interaction between medication adherence and degree of epitope mismatch. In this study in 596 renal recipients the optimal threshold for development of class II dnDSAs was 11 epitope mismatches for both HLA-DR and HLA-DQ. The combination of a high alloimmune risk (> 11 epitope mismatches) and tacrolimus trough levels below 5 ng/ml led to development of dnDSAs whereas patients with less than 11 epitope mismatches tolerated low tacrolimus trough levels (56). Recently they published the result of a study in 664 renal recipients. This study confirmed that the risk of dnDSAs was more strongly correlated to epitope mismatches as compared survival, the latter in particular due to additional excessive immunosuppression (28). In a large registry, 5-year deathcensored graft survival after rejection was 59.9% in recipients aged 65 years or older as compared to 82.1% in recipients aged 18 to 35 years (29). Overall the frequency of rejection declines within subsequent age categories, but a higher donor age is significantly associated with higher rejection rates (30–32). A study in 2016 among 244 elderly also showed that although older recipient age was protective for the occurrence of acute rejection, this was clearly outweighed by the dominant negative effect of donor age and increased immunogenicity of the organ reflected by more rejection and more donor specific antibody (DSA) formation with increased HLA-DR mismatch (33). This study shows that 1 or 2 HLA-DR mismatches give a higher chance on TCMR and the development of DSAs which both results in decreased allograft survival (66% for TCMR and 63% for dnDSA compared to 82 and 80% resp). They also show a graded effect, patients with 2 HLA-DR mismatches had worse graft survival rates after 3 and 7 years after transplantation compared to 0 or 1 HLA-DR mismatch (80%, 76% and 73% for 0, 1 and 2 HLA-DR mismatches 7 years after transplantation). This complex interaction of risks for increased rejection incidences was confirmed by a Dutch group in 2017 where elderly recipients with an older DCD (donation after circulatory death) kidney had a 2.78 times higher risk of delayed graft function and rejection compared to elderly receiving a young DBD kidney (34). This increased immunogenicity in recipients of a more vulnerable kidney allograft could be due to more endothelial activation in the context of ischemia-reperfusion injury, bacterial and viral infections resulting in a more pro-inflammatory cytokine environment, increased expression of HLA molecules and/or recruitment of antigen-presenting cells (35). These data are especially relevant regarding renal transplantation in elderly, since expansion of the donor pool with older, high-risk kidney donors, is a key strategic policy for this subgroup of renal recipients. Especially in view of rejection treatment and higher risk on infections cumulating in the most important cause of death in elderly. Therefore, the optimal strategy to decrease rejection risks while still allowing a timely transplant in the elderly is of critical importance. Donor Specific Antibodies When addressing transplant failure, de novo donor specific antibodies against HLA antigens (dnDSAs) after transplantation gained more and more interest. Overall Lachmann et al. (36) reported significant a lower 10-year graft survival being 49% versus 83% in patient with and those without DSA, respectively. A recent study showed that DSAs in combination with other risk factors can be even more detrimental for graft function. In this study, DSAs were associated with an increased incidence of T cell mediated rejection (TCMR) and led to a three-fold increase in graft loss (37). Lemoine et al. (16) showed that anti HLA antibodies are an independent risk factor for patient death and graft loss within the 1st year in patients older than 70 years. In elderly their role was recently debated by von Moos et al. (38) since elderly have a lower risk in developing DSAs Frontiers in Immunology | www.frontiersin.org 3 March 2020 | Volume 11 | Article 359 Dreyer and de Fijter Transplanting the Elderly likelihood of delayed graft function and/or rejection. To reach these goals, HLA matching was neglected, obviously resulting in a higher HLA mismatch rates in ‘old for old’ transplant programs. In 2008 the 5 years results were published and main goals were reached, waiting time decreased and CIT went down to 11.9 h compared to > 17 h in the regular ETKAS allocation program (62). However, there was a 5 to 10% higher rejection rate within ESP (29.1%) as compared to regular allocation. As mentioned in the study of Halleck et al. (33), this could be due to a higher HLA mismatch, especially HLADR, which led to significantly impaired graft survival. Indeed, in the ESP 92.9% of the recipients had 2 HLA-DR mismatches compared to 54.9% ≥ 1 HLA-DR mismatch in the normal allocation scheme. to conventional HLA mismatch. However, the threshold in this study was 7 epitope mismatches for HLA-DR and 9 for HLADQ (57). Also, Snanoudj et al. (58) investigated the epitope mismatch load by using HLA Matchmaker in 89 renal recipients. They found that epitope load was more strongly associated with dnDSAs compared to the number of serologic HLA mismatches. Of note, in this study the optimal threshold was 27 epitope mismatches (58). So, one can easily appreciate potential pitfalls in these newer matching methods that were developed based on the epitope level. Although more accurate in predicting dnDSA development than conventional matching, defining a reliable threshold as a risk factor is difficult and needs to be solved. To identify patients at risk, or maybe equally relevant those with a lower risk and safer option to adjust immunosuppressive load, there is an urgent need for well-defined risk factors to guide clinical decision making. CHANGING THE STRATEGY FOR OLDER TRANSPLANT CANDIDATES THE ELDERLY AND AGE-MATCHING: THE EUROTRANSPLANT SENIOR PROGRAM At the moment only a minority of selected elderly transplant candidates actually receive a kidney transplant and the mortality rate among this patient group is relatively high, especially the 1st year after transplantation or in case complications occur such as an acute rejection episode. In order to increase transplant rates, more older donors are accepted and preferably for older recipients, which in turn leads to more acute rejection episodes and rejection treatments. In younger transplant recipients, the increased risk of acute rejection with the use of older donors could possibly be overcome with induction therapy or more potent maintenance therapy. In elderly the complex interplay between immunosuppression on the one hand and immune defense on the other hand is even more challenging due to pre-existing comorbidities, changes in pharmacokinetics of immunosuppressive drugs, polypharmacy and the immunosenescence mentioned earlier. Probably more balanced immunosuppressive protocols and more advanced immunological monitoring strategies are needed to balance this critical equipoise. A second, more feasible and practical strategy could be to change the allocation protocol to decrease the risk of acute rejection and/or DSA formation without the need of more clinical immunosuppression. Organ shortage and the continuously growing waiting list, demands a progressive expansion of the potential kidney donor pool. Therefore, boundaries of organ quality criteria are continuously stretched and more and more older donors with or without comorbid conditions are accepted for renal transplantation (8). With the acceptance of older donors, the proportion of what was historically called extended criteria donors (ECD) also increased significantly. Since 2015 donors in the US have been assessed by the so-called Kidney Donor Profile Index (KDPI) score, which is associated with the life expectancy of the graft. Kidneys with a KDPI > 85%, or high risk kidneys, are expected to function for more than 5.5 years and are therefore considered to be comparable to the previous so-called ECD kidneys (59). It is well known that graft survival decreases with increasing donor age and decreasing organ quality, but also that the elderly still benefited from a successful kidney transplant using high risk kidneys in terms of life expectancy as compared to their waitlisted counterparts (60). Recipients of a high-risk kidney had a significantly lower mortality risk (RR 0.75; 95% CI 0.65-0.86), results confirmed by several studies (6, 60, 61). It is widely accepted that each kidney should be allocated to the recipients in whom is it expected to survive the longest to improve the match between life expectancy of donor and recipient. Since older transplant recipients are more likely to die with a functioning graft and younger recipients have a higher chance on re-transplantation later in life, it seems logical to allocate older kidneys, with an increased chance of graft failure, to older recipients. Therefore, in 1999 the Eurotransplant Senior Program (ESP) was implemented to shorten the waiting time for older transplant candidates and improve the perspective on patient survival with ESRD. In this program kidneys from donors > 65 years are allocated to recipients > 65 years with preferred local allocation in order to shorten cold ischemia times (CIT) and the Frontiers in Immunology | www.frontiersin.org Adjusting Maintenance Immunosuppressive Protocols Calcineurin Inhibitors Calcineurin inhibitors (CNI) remain the most potent immunosuppressive drugs in preventing acute rejection and have been critical to improve short-term graft survival. Due to the nephrotoxic potential of CNIs on long-term graft failure, there has been an overall shift toward reduction or CNI-withdrawal preferably later after transplantation. Since elderly are more susceptible to infections and the other side effects of immunosuppressive drugs and older kidney grafts are more vulnerable to CNI induced vasoconstriction and/or nephrotoxicity, several studies have suggested that especially elderly could benefit from CNI withdrawal or avoidance (63). In 4 March 2020 | Volume 11 | Article 359 Dreyer and de Fijter Transplanting the Elderly study population. From the patients who were randomized, 27.8% discontinued everolimus due to adverse events. This study underscores the challenge of randomized studies in elderly transplant recipients and general need for tailored treatment in this group. addition, the pharmacokinetics of CNIs change with increasing age and Staatz et al. (64) concluded in their review that especially maintenance therapy in older patients potentially needs more frequent monitoring and adjustments. Jacobson et al. (65) reported in a clinical trial that elderly (> 65 year) yielded similar trough levels with lower CNI dose and that dose-normalized trough levels were more than 50% higher in older patients. Various studies have indicated that CNI-withdrawal in the regular population of renal transplant recipients may not be successful (66–71). The results of reduction of tacrolimus differ in literature, but the CTS study showed that graft survival is compromised below a trough level of 5 ng/ml and in those with high intra-patient variability (48). Several studies have reported an increase in dnDSA formation below a certain trough level. Gatault et al. (72) found only dnDSAs in the group with a mean tacrolimus trough level of 4.1 ng/ml. Recently Davis et al. (73) reported a 4-fold risk of dnDSAs for patients with a mean tacrolimus through level of 4-6 ng/ml as compared to ≥ 8 ng/ml in the 1st year after kidney transplantation. As mentioned before, the Winnipeg group addressed the risk of minimization of calcineurin inhibitors and the development of dnDSA in relation to epitope mismatch load. Both studies confirmed that patients with a higher epitope load were at risk for dnDSAs after minimizing immunosuppression (56, 58). In elderly, Arbogast et al. (74) used an CNI free protocol after ATG induction followed by mycophenolate mofetil (MMF) and prednisone. Cumulative 5-year patient and allograft survival was 88 and 70%, respectively. And although these results are in itself excellent for older renal transplant recipients, the acute rejection rate was more than 25% and these patients returned to a regimen with a CNI after the rejection treatment which underlines the importance of a tailormade strategy rather than a standard protocol regarding immunosuppression (74). Allocation With Prospective HLA Matching As expected, the ESP program achieved the goal to minimize cold ischemia time and also the anticipated reduction in the rate of delayed graft function. The higher incidence of acute rejection was not expected and this could suggest a greater role of immunogenicity in the context of less histocompatibility. One could overcome this increased rejection risk by increasing clinical immunosuppression. The elderly, however, already have a compromised immune system and are more vulnerable for infectious complications. In addition, marginal donors are more vulnerable for the nephrotoxic side effects of immunosuppressive drugs. Therefore, at least in theory, this may be a suitable strategy in a proportion of younger patients receiving older and more immunogenic kidneys but may not be the best options for the older transplant recipients. A different strategy is to require a minimal degree of histocompatibility between donor and recipient while maintaining the shorter CIT and therefore the benefit of less delayed graft function. Due to a high degree of linkage between HLA-DR and HLA-DQ antigens, matching for HLA DR frequently results in matching on HLA-DQ (76). As previous studies proved, graft survival is worse even with 1 HLA-DR mismatch. Therefore, prospective HLA-DR matching with zero mismatches would be a potentially elegant strategy to improve rejection free survival without the need of excessive immunosuppression. mTOR Inhibitors In order to reduce CNI exposure, also the mammalian target of rapamycin inhibitors (mTORi) have been introduced and positioned. Several randomized trials have been performed of which the most recent one is the large TRANSFORM study. In this study 2037 renal recipients were randomized to standard dose CNI + MMF or reduced CNI + mTORi. The latter proved to be non-inferior regarding a binary endpoint of BPAR or glomerular filtration rate (GFR) < 50ml/min/1.73m2 . Benefits of the regimen with mTORi were a significantly reduced incidence of viral infections, which could be direct clinical benefit in the elderly. Although elderly were not excluded from this trial, mean age was 49.3 year (75). Recently the results from the SENATOR trial were reported. In this trial renal recipients participating in the Eurotransplant Senior Program (ESP) were included and 7-weeks after transplantation randomized to standard therapy with CNI + MMF or converted to MMF + everolimus and basiliximab at weeks 7 and 12. The patients who were converted and remained on everolimus had comparable kidney function and comparable rates of BPAR. Only 37.2% of the patients were actually randomized, identifying elderly as a vulnerable Frontiers in Immunology | www.frontiersin.org CONCLUDING REMARKS Given the inherent limited life expectancy of older patients, their best option when encountering ESRD would be the option of a kidney transplant as soon as possible. In order to reach this goal age matching is a suitable strategy and most patients will receive a kidney from an older deceased donor. Even with a timely kidney transplant offer from an agematched donor, there are other issues to consider in elderly recipients. Recipients of older kidneys are more susceptible to acute rejection with HLA class-II mismatch being a potentially preventable key risk factor also for the subsequent formation of DSAs. The mere fact that the older recipient has an older immune system as compared to adolescents, does not overcome the dominant effect of donor age over recipient age. We therefore underlined the importance of prospective HLA matching in the allocation algorithm of older kidneys to older kidney transplant candidates. Since most DSAs are directed against HLA class II antigens, HLA-DR matching is likely to reduce the need for more intense clinical immunosuppression and/or additional acute rejection treatments, ensuing reduction 5 March 2020 | Volume 11 | Article 359 Dreyer and de Fijter Transplanting the Elderly of excess infectious cause morbidity and mortality while delivering the prospect of prolonged life expectancy. 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Susal C, Wettstein D, Dohler B, Morath C, Ruhenstroth A, Scherer S, et al. Association of kidney graft loss with de novo produced donor-specific and non-donor-specific HLA Antibodies detected by single antigen testing. Transplantation. (2015) 99:1976–80. doi: 10.1097/tp.0000000000000672 46. Wiebe C, Gibson IW, Blydt-Hansen TD, Pochinco D, Birk PE, Ho J, et al. Rates and determinants of progression to graft failure in kidney allograft recipients with de novo donor-specific antibody. Am J Transplant. (2015) 15:2921–30. doi: 10.1111/ajt.13347 47. Rodrigo E, Segundo DS, Fernandez-Fresnedo G, Lopez-Hoyos M, Benito A, Ruiz JC, et al. Within-patient variability in tacrolimus blood levels predicts kidney graft loss and donor-specific antibody development. Transplantation. (2016) 100:2479–85. doi: 10.1097/tp.0000000000001040 48. Susal C, Dohler B. Late intra-patient tacrolimus trough level variability as a major problem in kidney transplantation: a collaborative transplant study report. 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(2016) 16:3255–61. doi: 10.1111/ajt.13946 March 2020 | Volume 11 | Article 359 Dreyer and de Fijter Transplanting the Elderly 72. Gatault P, Kamar N, Buchler M, Colosio C, Bertrand D, Durrbach A, et al. Reduction of extended-release tacrolimus dose in low-immunological-risk kidney transplant recipients increases risk of rejection and appearance of donor-specific antibodies: a randomized study. Am J Transplant. (2017) 17:1370–9. doi: 10.1111/ajt.14109 73. Davis S, Gralla J, Klem P, Tong S, Wedermyer G, Freed B, et al. Lower tacrolimus exposure and time in therapeutic range increase the risk of de novo donor-specific antibodies in the first year of kidney transplantation. Am J Transplant. (2018) 18:907–15. doi: 10.1111/ajt.14504 74. Arbogast H, Huckelheim H, Schneeberger H, Illner WD, Tarabichi A, Fertmann J, et al. A calcineurin antagonist-free induction/maintenance strategy for immunosuppression in elderly recipients of renal allografts from elderly cadaver donors: long-term results from a prospective single centre trial. Clin Transplant. (2005) 19:309–15. doi: 10.1111/j.1399-0012.2005.00309.x 75. Berger SP, Sommerer C, Witzke O, Tedesco H, Chadban S, Mulgaonkar S, et al. Two-year outcomes in de novo renal transplant recipients receiving Frontiers in Immunology | www.frontiersin.org everolimus-facilitated calcineurin inhibitor reduction regimen from the TRANSFORM study. Am J Transplant. (2019) 19:3018–34. doi: 10.1111/ajt. 15480 76. Freedman BI, Thacker LR, Heise ER, Adams PL. HLA-DQ matching in cadaveric renal transplantation. Clin Transplant. (1997) 11(5 Pt 2):480–4. Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. 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A New Thermosensitive smc-3 Allele Reveals Involvement of Cohesin in Homologous Recombination in C. elegans
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Introduction itself and forms a central region (coiled coil) with the hinge domain and the two NBDs at either end. Smc1p and Smc3p dimerize via the hinge domain, and the non-SMC subunits bind to the NBDs of the two SMCs. This ring is closed by the non-SMC subunit Scc1p, a member of the a-kleisin family [6]. Scc1 belongs to the mitotic specific cohesin complex, whereas during meiosis, cohesin complexes include the meiosis-specific kleisin Rec8 [1]. The cohesin complex contains members of the highly conserved structural maintenance of chromosomes (SMC) protein family [1]. SMC proteins are involved in DNA condensation, cohesion, and repair. During mitosis, replicated sister chromatids are held together by cohesins in metaphase; this cohesion permits the bipolar orientation of the spindle kinetochores, allowing microtu- bules to separate the sister chromatids into the two daughter cells (for review see [2]). During meiosis, chromosomes face a new challenge: separation of the homologs during meiosis I to halve the ploidy of the cell. During metaphase I, cohesion supports the co- orientation of the kinetochores of bivalents (pairs of homologous chromosomes) [3]. This co-orientation leads to the separation of homologous chromosomes in anaphase I. Coordinated separation of homologous chromosomes and sister chromatids during meiosis I and II, respectively, is achieved by the two-step loss of cohesin from the arms and the centromeric regions [4]. Homologs of the cohesin proteins have been identified in C. elegans [7,8,9,10,11]. In C. elegans, homozygous smc-1 and smc-3 deletion mutants cease their development at larval stages L1–L2, suggesting a maternal rescue of cohesins during the first stage of embryonic development [12]. Moreover, depletion of SMC-1 and SMC-3 by RNAi results in embryonic lethality with complete penetrance [9]. Cohesins delineate the axes of meiotic prophase chromosomes. These axes become the lateral elements of the synaptonemal complex (SC) [13]. In addition to the meiotic cohesin complex (SMC-1, SMC-3, REC-8, and SCC-3), C. elegans lateral elements contain HIM-3 and HTP-1, 2, and 3, which are related to budding yeast Hop1 [14,15,16] HTP-3 is required to load cohesins onto chromosomes during meiosis [7]. Additionally, HTP-3 is involved in the formation of DSBs [17]. Cohesin is a tetrameric complex composed of two SMC subunits, Smc1p (the worm homolog would be HIM-1) and Smc3p, and two non-SMC subunits, such as Scc1p and Scc3p in yeast [5]. Abstract The cohesin complex is required for the cohesion of sister chromatids and for correct segregation during mitosis and meiosis. Crossover recombination, together with cohesion, is essential for the disjunction of homologous chromosomes during the first meiotic division. Cohesin has been implicated in facilitating recombinational repair of DNA lesions via the sister chromatid. Here, we made use of a new temperature-sensitive mutation in the Caenorhabditis elegans SMC-3 protein to study the role of cohesin in the repair of DNA double-strand breaks (DSBs) and hence in meiotic crossing over. We report that attenuation of cohesin was associated with extensive SPO-11–dependent chromosome fragmentation, which is representative of unrepaired DSBs. We also found that attenuated cohesin likely increased the number of DSBs and eliminated the need of MRE-11 and RAD-50 for DSB formation in C. elegans, which suggests a role for the MRN complex in making cohesin-loaded chromatin susceptible to meiotic DSBs. Notably, in spite of largely intact sister chromatid cohesion, backup DSB repair via the sister chromatid was mostly impaired. We also found that weakened cohesins affected mitotic repair of DSBs by homologous recombination, whereas NHEJ repair was not affected. Our data suggest that recombinational DNA repair makes higher demands on cohesins than does chromosome segregation. Citation: Baudrimont A, Penkner A, Woglar A, Mamnun YM, Hulek M, et al. (2011) A New Thermosensitive smc-3 Allele Reveals Involvement of Cohesin in Homologous Recombination in C. elegans. PLoS ONE 6(9): e24799. doi:10.1371/journal.pone.0024799 Editor: Michael Polymenis, Texas A&M University, United States of America Received June 14, 2011; Accepted August 17, 2011; Published September 21, 2011 Copyright:  2011 Baudrimont et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. supported by the Austrian Science Fund FWF grant P21338-B03. The funders had no role in study design, data collection and analysis eparation of the manuscript. Funding: This work was supported by the Austrian Science Fund FWF grant P21338-B03. The funders had no role in study design, d decision to publish, or preparation of the manuscript. Funding: This work was supported by the Austrian Science Fund FWF grant P21338-B03. decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: verena.jantsch@univie.ac.at A New Thermosensitive smc-3 Allele Reveals Involvement of Cohesin in Homologous Recombination in C. elegans Antoine Baudrimont1, Alexandra Penkner1, Alexander Woglar1, Yasmine M. Mamnun1, Margot Hulek1, Cathrin Struck2, Ralf Schnabel2, Josef Loidl1, Verena Jantsch1* 1 Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna, Vienna, Austria, 2 Department of Genetics, Technical University of Braunschweig, Braunschweig, Germany partment of Chromosome Biology, University of Vienna, Vienna, Austria, 2 Department of Genetics, Technical University of Braunschweig PLoS ONE | www.plosone.org September 2011 | Volume 6 | Issue 9 | e24799 Citation: Baudrimont A, Penkner A, Woglar A, Mamnun YM, Hulek M, et al. (2011) A New Thermosensitive smc-3 Allele Reveals Involvement of Cohesin in Homologous Recombination in C. elegans. PLoS ONE 6(9): e24799. doi:10.1371/journal.pone.0024799 Cohesion and Homologous Repair in C. elegans entailing chiasmata takes place in the context of the SC [19]. Repair of DSBs requires the MRN complex to generate 59 to 39 resected DNA overhangs [20]. This resection is necessary to allow loading of the strand invasion protein RAD-51. As in yeast, in worms, the MRN complex is also needed for the formation of DSBs [21,22]. However, under conditions of weakened REC-8 function, DSBs can be formed in the absence of RAD-50 or MRE-11 [23], which are components of the MRN complex. In meiosis, effective repair depends on the availability of a homologous chromosome as the template, because repair via the sister is inhibited by HIM-3, a constraint that is lost in late pachytene. t2553 as a new allele of C. elegans smc-3. Sequencing of the locus revealed a point mutation (a C-to-T transition) in the coding sequence of smc-3 at position 3241, resulting in a leucine (L)-to- phenylalanine (F) amino acid change at position 1081. The L1081F mutation resides in a coiled-coil region in proximity to the C-terminal ATPase domain (Figure 1A). Alignment of SMC-3 proteins from various phyla revealed that this leucine is widely conserved (Figure 1B). entailing chiasmata takes place in the context of the SC [19]. Repair of DSBs requires the MRN complex to generate 59 to 39 resected DNA overhangs [20]. This resection is necessary to allow loading of the strand invasion protein RAD-51. As in yeast, in worms, the MRN complex is also needed for the formation of DSBs [21,22]. However, under conditions of weakened REC-8 function, DSBs can be formed in the absence of RAD-50 or MRE-11 [23], which are components of the MRN complex. In meiosis, effective repair depends on the availability of a homologous chromosome as the template, because repair via the sister is inhibited by HIM-3, a constraint that is lost in late pachytene. t2553 as a new allele of C. elegans smc-3. Sequencing of the locus revealed a point mutation (a C-to-T transition) in the coding sequence of smc-3 at position 3241, resulting in a leucine (L)-to- phenylalanine (F) amino acid change at position 1081. The L1081F mutation resides in a coiled-coil region in proximity to the C-terminal ATPase domain (Figure 1A). Alignment of SMC-3 proteins from various phyla revealed that this leucine is widely conserved (Figure 1B). smc-3 mutants displayed a reduced brood size compared to wild type when grown at 16uC (Table 1). Repair of programmed DSBs impaired in smc-3 Repair of programmed DSBs impaired in smc-3 Chromatin masses that varied in numbers and size could be seen instead of the normal six DAPI-stained bodies in smc-3 diakinesis (Figure 2Ai). The numerous small chromatin structures in diakinesis nuclei of smc-3 hermaphrodites were indicative of DNA fragmentation, which is also observed in DNA repair– deficient mutants [10]. Depleting the SPO-11 endonuclease in smc- 3 mutants suppressed the formation of chromatin fragments in diakinesis (Figure 2Aii, bottom). In 49 diakinesis nuclei of spo- 11;smc-3 double mutants, 12 DAPI-positive structures could be seen on average (standard deviation [SD]: 0.2). Smaller chromatin fragments were completely absent. We therefore conclude that the fragmentation observed at diakinesis in smc-3 mutants originated from defective meiotic crossing over resulting from SPO-11– induced DSBs. Introduction SMC subunits bear nucleotide-binding domains (NBDs) at the amino and carboxy termini of linked long coiled-coil domains separated by a hinge domain. Each SMC protein folds on Unlike in yeast, synapsis (i.e., the connection of axial elements by transversal filaments) is independent of the formation of DSBs in C. elegans [18]. However, as in other organisms, repair of DSBs PLoS ONE | www.plosone.org September 2011 | Volume 6 | Issue 9 | e24799 1 September 2011 | Volume 6 | Issue 9 | e24799 Cohesion and Homologous Repair in C. elegans Cohesion and Homologous Repair in C. elegans A total of 8963% of the smc-3 embryos hatched (wild type: 9863%), and 462% of the viable offspring were males (wild type: 0%). Both the reduced brood size and the documented Him (high incidence of males) phenotype are consistent with a chromosome segregation failure and a putative meiotic defect in smc-3 mutants. Shifting L1 larvae to 25uC for approximately 55 h reduced the brood size even further (Table 1) with a high embryonic lethality (hatch rate: smc-3, 262%; wild type: 9863%). No obvious growth or morphological defects were observed in the surviving progeny. This particular smc-3 allele therefore allowed us to analyze the role of SMC-3 in meiotic chromosome behavior. C. elegans hermaphrodite gonads are organized in a spatial gradient form distal to proximal representing consecutive stages of meiotic prophase I (leptotene/zygotene (transition zone, TZ), pachytene, diplotene, diakinesis) that follow the most distally positioned proliferative mitotic zone [13]. In leptotene, chromosomes condense and engage in the homolog search. During the zygotene stage, the SC starts to polymerize between paired homologs. After successful repair of the DSBs via the homolog in pachytene the chromosomes condense upon entry into diplotene and reach maximal condensa- tion in diakinesis. In diakinesis the paired homologs (6 bivalents in C. elegans) are physically linked by one crossover. Here, we report the isolation of a new thermosensitive smc-3 allele with distinct reduced viability at the restrictive temperature (25uC). Our analysis revealed that smc-3 mutant worms formed organized gonads, but they were defective in meiotic repair, with highly fragmented chromatin at diakinesis. We found significantly reduced cohesin complexes associated with chromatin and show that the homolog search process started with wild-type kinetics but because of defective synapsis, pairing could not be stabilized. Reduced amounts of cohesins rendered the chromatin more susceptible to meiotic DSB formation. We analyzed the repair defect observed in smc-3 during meiosis by epistasis analysis. We also show that mitotic repair was impaired as soon as it relied on homologous recombination. Our results demonstrate the essential role of cohesin in mitosis and meiosis separate from its role in cohesion, the latter requires less cohesins than the repair of DSBs. Cohesion and Homologous Repair in C. elegans Table 1. Brood size and hatch rates 166C 256C brood size hatch rate brood size hatch rate wild type 258625 eggsa 9861% 187620 eggsa 9862% smc-3 188638 eggsa,b8963%a,b 81621 eggsa,b 262%a,b aStudent’s t-test, p,0.05 comparing genotypes at 16uC and 25uC. bStudent’s t-test, p,0.05 comparing smc-3 to the wild type at respective temperature. Brood size and hatch rate of wild-type and smc-3 mutant worms at 16uC and 25uC (mean6SD). Progeny of seven worms were scored. doi:10.1371/journal.pone.0024799.t001 Table 1. Brood size and hatch rates 166C 256C brood size hatch rate brood size hatch rate wild type 258625 eggsa 9861% 187620 eggsa 9862% smc-3 188638 eggsa,b8963%a,b 81621 eggsa,b 262%a,b aStudent’s t-test, p,0.05 comparing genotypes at 16uC and 25uC. bStudent’s t-test, p,0.05 comparing smc-3 to the wild type at respective temperature. Brood size and hatch rate of wild-type and smc-3 mutant worms at 16uC and 25uC (mean6SD). Progeny of seven worms were scored. doi:10.1371/journal.pone.0024799.t001 double mutant. However, we observed massive fragmentation at diakinesis (Figure 2Aiii, bottom). Table 1. Brood size and hatch rates Because both the smc-3 single mutant and the smc-3;mre-11 double mutant displayed repair defects, we sought to quantify the fragmentation observed at diakinesis. To avoid artifacts generated by projections of pictures, this quantification was done on picture stacks measuring the volume and the ‘‘sphericity’’ of the DAPI structures (see Materials and Methods). In contrast to the wild type, where 3.761.8 (mean6SD) DAPI structures represented connected bivalents (Figure 2Ai, top and 2B, n = 15 diakinesis), quantification showed that chromosome fragments (3.762.9, n = 14 diakinesis) and ‘‘chromatin masses’’ (5.862.5 SD, n = 14 diakinesis) were the most prevalent classes of DAPI structures in smc-3 mutants (Figure 2B). Using this method, we detected an overall number of 10.960.9 (n = 18 diakinesis) DAPI structures and on average 7.462.2 (n = 18 Figure 2. Fragmentation at diakinesis resulting from defective DSBs repair. (A) Representative DAPI structures found at diakinesis in: (i) top: wild type, bottom: smc-3; (ii) top: spo-11, bottom: smc-3; spo-11; (iii) top: mre-11, bottom: smc-3;mre-11; (iv) top: him-3, bottom: smc-3;him-3; and (v) top: him-17, bottom: smc-3;him-17. (B) Quantification of DNA fragmentation at last diakinesis. Classes (fragments, univalents, bivalents, and DNA masses) were defined by the volume (v) and the ‘‘sphericity’’ (s) of the DAPI structures at the last diakinesis before the spermatheca (see Materials and Methods). Cohesion and Homologous Repair in C. elegans Single star indicates significant differences (p,0.05, Student’s t-test) for fragments, univalents, bivalents, and masses between double mutants and the smc-3 single mutant. Error bars represent SD. doi:10.1371/journal.pone.0024799.g002 t2553: a new temperature-sensitive allele of the cohesin subunit smc-3 In C. elegans, MRE-11 is required for both formation and repair of DSBs [21,22]. In the double mutant smc-3;mre-11, we would therefore expect 12 univalents, as was seen in the smc-3;spo-11 t2553 was isolated as a temperature-sensitive maternal effect lethal mutant. Mapping and complementation tests confirmed Figure 1. The new allele smc-3 (t2553). (A) Domain organization of C. elegans SMC-3 highlighting the position of the L1081F amino acid change; domain organizations predicted by CDART [45]. (B) Alignment of SMC-3 sequences for the indicated organisms highlights conservation of the mutated leucine (highlighted in red in t2553). doi:10.1371/journal.pone.0024799.g001 Figure 1. The new allele smc-3 (t2553). (A) Domain organization of C. elegans SMC-3 highlighting the position of the L1081F amino acid change; domain organizations predicted by CDART [45]. (B) Alignment of SMC-3 sequences for the indicated organisms highlights conservation of the mutated leucine (highlighted in red in t2553). doi:10.1371/journal.pone.0024799.g001 Figure 1. The new allele smc-3 (t2553). (A) Domain organization of C. elegans SMC-3 highlighting the position of the L1081F amino acid change; domain organizations predicted by CDART [45]. (B) Alignment of SMC-3 sequences for the indicated organisms highlights conservation of the mutated leucine (highlighted in red in t2553). doi:10.1371/journal.pone.0024799.g001 September 2011 | Volume 6 | Issue 9 | e24799 PLoS ONE | www.plosone.org 2 Cohesion and Homologous Repair in C. elegans Cohesion and Homologous Repair in C. elegans detergent led to a strong reduction in REC-8 levels in smc-3 mutants (Figure 3B), suggesting that the point mutation in the coiled-coil domain impaired the stability of the cohesin complex on chromatin. However, this assay cannot judge on the amount of cohesin loaded in the mutant. diakinesis) univalents (Figure 2B) in smc-3;spo-11 double mutants. Quantification confirmed that fragmentation was increased in smc- 3;mre-11 compared to smc-3 worms (Figure 2B). In smc-3;mre-11 worms, the number of fragments and univalents was significantly increased compared to the smc-3 single mutant (Student’s t-test, p,0.05). The smc-3;rad-50 double mutant likewise displayed an increase in fragmentation (unpublished data). To test the validity of the detergent assay, we also probed for HTP-3. Proper loading of the cohesin complex requires efficient HTP-3 loading [7]. The detergent washes did not remove HTP-3 from either wild-type or smc-3 mutant squashed nuclei. (Figure 3C), confirming the validity of the approach. Furthermore, we subjected syp-2 squashed nuclei to the same assays (REC-8 and HTP-3 staining with and without sarkosyl). Deletion of SYP-2, a central element component of the SC, results in unsynapsed chromosomes [19]. We did not observe a decrease in REC-8 or HTP-3 signals after washing syp-2 mutants with sarkosyl (Figure S1B). This reinforces the specificity of the assay, because a lack of synapsis could not account for the decrease in REC-8 loading that we observed after washing with sarkosyl. Similarly, no defects in SMC-3 loading were detectable after depletion of SYP-2 (Figure S1A). These results indicate that the MRN complex was dispensable for the formation of DSBs in smc-3 mutants. Figure 2. Fragmentation at diakinesis resulting from defective DSBs repair. (A) Representative DAPI structures found at diakinesis in: (i) top: wild type, bottom: smc-3; (ii) top: spo-11, bottom: smc-3; spo-11; (iii) top: mre-11, bottom: smc-3;mre-11; (iv) top: him-3, bottom: smc-3;him-3; and (v) top: him-17, bottom: smc-3;him-17. (B) Quantification of DNA fragmentation at last diakinesis. Classes (fragments, univalents, bivalents, and DNA masses) were defined by the volume (v) and the ‘‘sphericity’’ (s) of the DAPI structures at the last diakinesis before the spermatheca (see Materials and Methods). Single star indicates significant differences (p,0.05, Student’s t-test) for fragments, univalents, bivalents, and masses between double mutants and the smc-3 single mutant. Error bars represent SD. doi:10.1371/journal.pone.0024799.g002 September 2011 | Volume 6 | Issue 9 | e24799 PLoS ONE | www.plosone.org 3 Cohesion and Homologous Repair in C. elegans Cohesion and Homologous Repair in C. elegans chromatids in spo-11;smc-3 diakinesis (Figure 2Aii, bottom) suggests intact cohesion with this particular allele. zone of smc-3 gonads only rarely, indicating that cohesion in most cells is effective (Figure S3). In contrast, during the meiotic time course homologous associations were unstable which can be explained by the failure to establish a proper SC (text S1 and Figures S4 and 5). However homologous pairing prior to SC formation was normal in the mutant. To test this assumption, cohesin loading was further reduced by RNAi-mediated depletion of the cohesin subunit REC-8. Indeed, diakinesis nuclei of spo-11;smc-3;rec-8(RNAi) triple mutants always showed more than 20 signals (in all 26 diakinesis nuclei scored from eight independent gonads), consistent with the expected 24 isolated sister chromatids in cohesion-deficient mutants (Figure S2). spo-11;rec-8(RNAi) control worms also displayed more than 20 DAPI-positive structures (unpublished data). The reduced amount of cohesins appeared to be sufficient for the establishment of cohesion but insufficient for DSB repair in smc-3. Additionally, when pairing of the pairing center (PC) protein HIM-8 was assayed, more than two HIM-8 signals were detected in the mitotic Fewer cohesin complexes on smc-3 chromosomes not associated with defective cohesion We compared loading of SMC-3 onto chromosome axes in C. elegans smc-3 and wild-type worms. In wild-type worms, SMC-3 delineated the chromosome axes, whereas in smc-3, only short and weakened stretches were observed (Figure 3A). The reduced amounts of SMC-3 could result either from reduced loading or reduced stability of the complex; notably, we did not see a gradual decrease in the SMC-3 signal during meiotic progression. To discriminate between these two possibilities, we examined the abundance of REC-8 in squashed nuclei with stringent sarkosyl washes. (Figure 3B). We reasoned that the addition of detergent should not further decrease the REC-8 signal if cohesin loading was already reduced in the mutant. However, the addition of Altogether, these results reinforce the idea that the L1081F mutation in smc-3 leads to unstable chromatin-associated cohesin complexes entailing a reduced amount of cohesin complexes on chromatin. The presence of 12 univalents instead of 24 sister Figure 3. Chromosomes axes are impaired in smc-3. (A) Immunostaining of SMC-3 in wild-type and smc-3 worms. (B) Squashed nuclei untreated and washed with sarkosyl in wild-type and smc-3 worms in the TZ and pachytene stained with anti-REC-8 antibody. (C) Squashed nuclei washed with sarkosyl stained with anti-HTP-3 in wild-type and smc-3 worms in TZ and pachytene. Bar: 10 mm. doi:10.1371/journal.pone.0024799.g003 Figure 3. Chromosomes axes are impaired in smc-3. (A) Immunostaining of SMC-3 in wild-type and smc-3 worms. (B) Squashed nuclei untreated and washed with sarkosyl in wild-type and smc-3 worms in the TZ and pachytene stained with anti-REC-8 antibody. (C) Squashed nuclei washed with sarkosyl stained with anti-HTP-3 in wild-type and smc-3 worms in TZ and pachytene. Bar: 10 mm. doi:10.1371/journal.pone.0024799.g003 September 2011 | Volume 6 | Issue 9 | e24799 PLoS ONE | www.plosone.org 4 Cohesion and Homologous Repair in C. elegans Cohesion and Homologous Repair in C. elegans September 2011 | Volume 6 | Issue 9 | e24799 smc-3 mutation affects mitotic HR but not NHEJ repair smc-3 mutation affects mitotic HR but not NHEJ repair C. elegans genetics is a powerful tool that can be used to separately study two different mitotic repair pathways (Figure 5A). Early embryos repair DSBs by homologous recombination (HR), whereas late-stage embryos repair via the nonhomologous end joining (NHEJ) repair pathway [26]. In addition, repair of DSBs via HR takes place in the primordial germ cells Z2 and Z3 during larval development of the worm (Figure 5A). Next, we wanted to confirm that RAD-51 foci accumulation was SPO-11 dependent. Depletion of SPO-11 in smc-3 decreased RAD-51 signals (Figure 4C, left). Indeed, in the double mutant smc-3;spo-11, a maximum of one or two RAD-51 foci could be observed during the time course (Figure 4C, right). When we scored loading of RAD-51 foci in smc-3;mre-11 double mutants (Figure 4D, left), we found that until late pachytene (before zone 6), only the class of nuclei with one or two RAD-51 foci was observed. Strikingly, in late pachytene, a significant increase in the number of RAD-51 foci for all classes was found, with a maximum of about 7–12 foci (Figure 4D, right). smc-3;rad-50(ok197) double mutants displayed the same phenotype (unpublished data). Irradiation of late-stage embryos allowed us to test the proficiency of the NHEJ repair pathway using a dose of 60 Gy. lig-4 mutants, which are defective in the NHEJ repair pathway, slowed down their development when irradiated with 60 Gy as late-stage embryos: all of the worms were still at the L4 stage 66 h after irradiation (Figure 5B). This was in contrast to wild-type worms and smc-3 mutants, in which only 19% and 24%, respectively, of arrested worms were at the L4 stage 66 h after irradiation (Figure 5B). We therefore concluded that smc-3 mutants were proficient in the somatic NHEJ repair pathway. We next tested whether this appearance of RAD-51 foci in smc- 3;mre-11 mutants in late pachytene depended on breaks introduced by SPO-11. In the triple mutant smc-3;spo-11;mre-11, the number of nuclei with 1–2 RAD-51 foci was significantly decreased compared to smc-3;mre-11 mutants (Fisher’s exact test per class and per zone, p,0.05). Remarkably, we did not observe an increase in the number of RAD-51 foci during the time course (Figure 4E, right), confirming that the appearance of excess RAD-51 foci in smc-3;mre-11 mutants was due to breaks introduced by SPO-11. Repair via the sister chromatid is impaired in smc-3 p p Next, we tested the effectiveness of DSB repair via the sister chromatid. HIM-3 is a major constituent of the lateral element of the SC and exerts an inhibitory effect on meiotic DSB repair via the sister chromatid [14,15]. Fragmentation at diakinesis was still present in the double mutant smc-3;him-3 (Figure 2Aiv, bottom), suggesting that repair via the sister chromatid was not taking place efficiently. Quantification of the DAPI signals revealed a shift to ‘‘univalents’’ from ‘‘chromatin masses’’ (Student’s t-test, p,0.05) suggesting that some repair might still be taking place (Figure 2B). Therefore, we concluded that despite effective sister chromatid cohesion in smc-3 mutants, repair of DSBs via the sister chromatid was impaired. We next asked whether the DNA damage checkpoint was properly activated. Triggering the checkpoint in the mitotic compartment leads to enlargement of nuclei [27]; therefore, we fixed and DAPI stained gonads and then counted nuclei with increased diameters within the first 50 mms from the distal tip of the gonad. In mrt-2 mutants, which are deficient in DNA damage signaling [28], there was only a slight increase in nuclei diameter 8 h after 60 Gy irradiation (0 Gy: 3.0360.3 mm [mean6 SD; n = 25 nuclei], 60 Gy: 3.560.3 mm [n = 23 nuclei]) compared to wild type (0 Gy: 3.0360.3 mm [n = 28 nuclei], 60 Gy: 5.760.9 mm [n = 30 nuclei]). The average size of mrt-2 nuclei plus the SD was used to define the threshold of checkpoint activation. The analysis revealed that even without irradiation challenge (0 Gy), a significant number of cells in the mitotic portion of smc-3 gonads had activated the DNA damage checkpoint (Figure 6A), whereas no activation of the checkpoint was observed in wild-type or mrt-2 worms. We cannot exclude the possibility that the increased number of enlarged nuclei in smc-3 mutants before irradiation might also be triggered by the activation of the mitotic spindle smc-3 mutants deficient in early steps of meiotic DSB repair To study meiotic DNA repair, we stained nuclei for the strand- invasion protein RAD-51 [24]. Gonads were divided into six zones of equal lengths, and the number of RAD-51 foci were counted per nucleus. In wild-type worms, RAD-51 foci were observed from early pachytene until mid-pachytene (Figure 4A, left) with a Figure 4. smc-3 mutants are defective in repair of meiotic DSBs. Left, immunostaining of RAD-51. Right, quantification of RAD-51 foci in type (A), smc-3 (tm2553) (B), smc-3;spo-11 (C), smc-3;mre-11 (D). and smc-3;spo-11; mre-11 (E) worms. Gonads were divided into six zones of e length for quantification. Arrowheads indicate the zone with clustered chromatin. Bar: 10 mm. doi:10.1371/journal.pone.0024799.g004 Figure 4. smc-3 mutants are defective in repair of meiotic DSBs. Left, immunostaining of RAD-51. Right, quantification of RAD-51 foci in wild- type (A), smc-3 (tm2553) (B), smc-3;spo-11 (C), smc-3;mre-11 (D). and smc-3;spo-11; mre-11 (E) worms. Gonads were divided into six zones of equal length for quantification. Arrowheads indicate the zone with clustered chromatin. Bar: 10 mm. doi:10.1371/journal.pone.0024799.g004 September 2011 | Volume 6 | Issue 9 | e24799 September 2011 | Volume 6 | Issue 9 | e24799 PLoS ONE | www.plosone.org 5 Cohesion and Homologous Repair in C. elegans maximum number of 7–12 RAD-51 foci in zone 4 (Figure 4A, right). In smc-3 mutants, the first RAD-51 signals were seen earlier (Figure 4B, left). The number of RAD-51 foci rose from entry into meiosis (zone 2) until late pachytene (zone 6) and continued to accumulate (.12 foci in 70% of nuclei in zone 6; Figure 4B, right), in fact the frequency of foci increased faster in smc-3. Few RAD-51 foci could be detected at diakinesis (unpublished data). These data suggest that early steps of HR require functional cohesins and that more DSBs may be formed in smc-3 mutants. worms with respect to DSB induction in the DSB compromised mutant him-17. Depleting HIM-17 in smc-3 resulted in diakinesis similar to that seen in smc-3;spo-11 double mutants, with mostly univalents and reduced fragmentation (Figure 2Av, bottom). This suggests that in contrast to compromised condensin complexes, weakened cohesion could not reverse a failure to induce DSBs in him-17 mutants. smc-3 mutation affects mitotic HR but not NHEJ repair Furthermore, in smc-3;spo-11;mre-11 mutants, chromosome frag- mentation at diakinesis was absent (Figure S6). To assess the proficiency of the HR occurring in Z2 and Z3 cells, gonads of adult wild-type and smc-3 worms that were irradiated (60 Gy) as late-stage embryos were released. DAPI- stained smc-3 gonads were disorganized, and some showed a lack of meiotic entry (absence of a transition zone) and lacked mature sperm, supporting the idea that mitotic HR repair was also defective (Figure 5, inset) Surprisingly, cells with nuclei of different sizes, indicative of chromosomal nondisjunction, were absent, reinforcing the idea that a reduced amount of cohesin was sufficient for proper segregation of mitotic chromosomes. The results of our analysis confirm previous reports (using different components of the protein complexes involved) that the MRN complex is required to restrain the inhibitory action of cohesins on DSB induction [23]. In addition, weakened cohesion led to an increased number of detectable RAD-51 foci, likely due to more DSB induction, suggesting that intact chromosome axes restrain the action of the DSB break machinery. DNA damage checkpoint is operating in smc-3 Intrigued by the large number of nuclei with more than 12 RAD-51 foci in the last zone of smc-3 gonads (Figure 4B, left), we first assayed apoptosis in smc-3 mutants. Acridine orange staining revealed that apoptosis was significantly increased in smc-3 worms, with 7.862.1 (mean6SD) apoptotic corpses (n = 36 gonads), compared to wild-type worms, with 3.761.3 apoptotic corpses (n = 31 gonads). PLoS ONE | www.plosone.org Discussion We isolated a conditional partial loss-of-function mutant of the cohesin component SMC-3 and showed that a reduction in cohesin molecules mainly impaired repair of DSBs in mitosis and meiosis. The mutation (L1081F) in the newly identified thermo- sensitive allele smc-3(t2553) resides in the coiled-coil region close to the NBDs. In human Hela cells, Smc1 is phosphorylated in the coiled-coil region (serines 957 and 966) after induction of DSBs in an ATM-dependent manner [30,31]. Two similar sites of phosphorylation (serines 1067 and 1083) are found in the coiled- coil region close to the NBDs of Smc3. Recently, phosphorylation of Smc3 at serine 1083 was shown to take place in response to DNA damage in Hela cells [32]. In the t2553 allele, the mutation L1081F might interfere with phosphorylation of SMC-3 upon DNA damage signaling, in addition to the overall reduction in stably DNA bound cohesin molecules that could contribute to the observed DNA repair defects. From our analysis, it appears that the mutation introduced in the t2553 allele (L1081F) led to reduced stability of the cohesin complexes on chromosome arms during meiosis, as shown by a weaker SMC-3 signal in immunofluorescence assays. In addition, the cohesin component REC-8 could be expelled from chromatin by detergent treatment of the smc-3 mutant. This suggests that stable association of cohesin with chromatin was reduced, but sister chromatid cohesion remained robust. Indeed, smc-3 mutants formed organized gonads at the restrictive temperature (25uC) and segregation defects were only rarely detectable in the mitotic zone in smc-3 gonads. In addition, in smc-3;spo-11 worms, 12 DAPI structures were observed at diakinesis, whereas 24 DAPI structures were observed after REC-8 RNAi treatment in this double mutant. This smc-3 mutant, which lacks a major subunit of the cohesin complex, demonstrates that even a considerable reduction in the number of cohesin molecules on chromatin does not notably affect cohesion in either mitosis or meiosis in C. elegans. This is in agreement with a recent report that reducing functional cohesin rings by 87% does not notably affect cohesion in yeast [33]. Figure 5. The t2553 allele impairs mitotic HR repair but not NHEJ repair. (A) Schematic drawing of an embryo with germ (bold circle) and somatic cells (circle). Green color highlights cells repairing DSBs by NHEJ; red cells repair via HR. In the adult, small red circles represent spermatozoa and open ovals represent embryos. Cohesion and Homologous Repair in C. elegans Figure 5. The t2553 allele impairs mitotic HR repair but not NHEJ repair. (A) Schematic drawing of an embryo with germ (bold circle) and somatic cells (circle). Green color highlights cells repairing DSBs by NHEJ; red cells repair via HR. In the adult, small red circles represent spermatozoa and open ovals represent embryos. (B) Percentage of arrested L4 66 h after 60 Gy irradiation of late-stage embryos with the indicated genotypes. Error bars represent standard PLoS ONE | www.plosone.org error of the mean (SEM). (C) DAPI staining of wild-type and smc-3 gonads released from worms irradiated (60 Gy) as late-stage embryos. Stars mark the distal tip of the gonad. Bar: 10 mm. doi:10.1371/journal.pone.0024799.g005 error of the mean (SEM). (C) DAPI staining of wild-type and smc-3 gonads released from worms irradiated (60 Gy) as late-stage embryos. Stars mark the distal tip of the gonad. Bar: 10 mm. doi:10.1371/journal.pone.0024799.g005 checkpoint due to a slight cohesion or chromosome alignment defect. Moreover, 8 h after irradiation, the proportion of cells activating the DNA damage checkpoint in smc-3 mutants was even larger than in wild type (Figure 6A). Therefore, the DNA damage checkpoint was properly activated in smc-3 worms. To test if the DNA damage checkpoint was also properly activated during the development of the worms, we performed the L1 assay as described in [29]. C. elegans develops through four larval stages (L1–L4). Worms deficient for the DNA damage checkpoint do rarely survive to the adult stage upon irradiation. Irradiation with 60 Gy had almost no impact on the development of smc-3 worms into adults, the same as for wild-type worms; however, only 20% of mrt-2 worms reached the adult stage (Figure 6B). This supports our conclusion that during worm development, the DNA damage checkpoint was properly activated in smc-3 worms. September 2011 | Volume 6 | Issue 9 | e24799 Can weakened cohesion lead to reversion of DSB-refractory chromatin? The dramatic fragmentation at diakinesis in smc-3 mutants could reflect a defect in the repair of DSBs, result from an open chromatin conformation that is more permissive to formation of DSBs, or both. The early accumulation of RAD-51 in smc-3 lends support to the second argument. Previously, it was shown that a mutation in the condensing component DYP-28 could ‘‘re-open’’ chromatin during DSB-refractory chromatin states in him-17 mutants [25]. Therefore, we compared our smc-3 mutant to dpy-28 PLoS ONE | www.plosone.org September 2011 | Volume 6 | Issue 9 | e24799 September 2011 | Volume 6 | Issue 9 | e24799 6 Discussion (B) Percentage of arrested L4 66 h after 60 Gy irradiation of late-stage embryos with the indicated genotypes. Error bars represent standard Nevertheless, this smc-3 mutant displays defects in meiotic and radiation-induced mitotic DSB repair. It is known that cohesion supports DSB repair, presumably by connecting the damaged site to the sister template in mitosis [34], and cohesin complexes are recruited to DSB-flanking regions extending up to several kilobases September 2011 | Volume 6 | Issue 9 | e24799 PLoS ONE | www.plosone.org 7 Cohesion and Homologous Repair in C. elegans Figure 6. DNA damage checkpoints are working in smc-3. Proportion of nuclei with ‘‘normal’’ (,3.85 mm) or ‘‘double’’ ($3.85 mm) diameters before and 8 h after 60 Gy irradiation (more than 200 nuclei assayed in five different gonads per genotype for the indicated genotypes (N2, smc-3, and mrt-2). Error bars represent SEM. (B) Percentage of surviving worms 48 h after 60 Gy irradiation. Error bars represent SEM. More than 500 L1s were scored per genotype. doi:10.1371/journal.pone.0024799.g006 Figure 6. DNA damage checkpoints are working in smc-3. Proportion of nuclei with ‘‘normal’’ (,3.85 mm) or ‘‘double’’ ($3.85 mm) diameters before and 8 h after 60 Gy irradiation (more than 200 nuclei assayed in five different gonads per genotype for the indicated genotypes (N2, smc-3, and mrt-2). Error bars represent SEM. (B) Percentage of surviving worms 48 h after 60 Gy irradiation. Error bars represent SEM. More than 500 L1s were scored per genotype. doi:10.1371/journal.pone.0024799.g006 signals right after meiotic entry, suggesting that weakened cohesion augments DSB induction. [34]. The reduced amount of stably chromatin-bound cohesin complexes in the smc-3 mutant could explain the sensitivity to DNA damage that we observed during mitosis. Indeed, a sufficient amount of cohesin might not be established at the site of the DSBs. Smc3 is required for the complete activation of damage signaling to checkpoints upon introduction of artificial DSBs in human cells [32] involving the cohesin complex in the activation of the DNA damage checkpoint. We can state with certainty that the NHEJ repair pathway in mitotic divisions still takes place in the weakened cohesion mutant smc-3. Although repair of meiotic lesions was impaired in worms with the t2553 allele, we found that the few cohesion molecules left were nonetheless able to activate DNA damage checkpoints effectively. It has been proposed that cohesins inhibit repair via the homologous chromosome [35]. Discussion In fact, holding sister chromatids together in meiosis might be unproductive when DSB-carrying DNA strands should detach from their sisters in order to undergo recombination with the homolog [36]. Therefore, in meiosis, the requirement for cohesin might be different, and might rather be required to create the platform for lateral element assembly as the backbone of the synaptonemal complex [5,10,37]. The dramatic increase in RAD-51 signals and their persistence until later stages of meiotic prophase I in smc-3 argue for a defect in DSB repair downstream of the loading of RAD-51. We found that weakened SMC-3 did not allow DSB formation in the absence of HIM-17, but did in the absence of MRE-11/RAD-50. Therefore, the role of cohesion in supporting DSB generation is distinct from that of HIM-17, which confers competence for meiotic DSB formation by methylation of histone H3 [38]. This demonstrates that the MRN complex and HIM-17 act in different pathways upstream of SPO- 11. To summarize, this work reinforces the idea that effective repair of DSBs during mitosis and meiosis is more vulnerable to loss of cohesin complexes compared to proper chromosome segregation. It also confirms that, even for holocentric chromosomes, few cohesin complexes are required for proper segregation. Further- more, the newly isolated temperature-sensitive smc-3 allele represents a new tool with which to study the effects of weakened cohesion in worms. Materials and Methods Nematode strains, strain construction and culture conditions Nematode strains, strain construction and culture conditions In the double mutant smc-3;mre-11, we observed pachytene chromosome fragmentation and increased RAD-51 foci as hallmarks of DSBs. In the absence of MRE-11 or RAD-50, DSBs are not observed [21,23]. It should be noted that the dependence on rad-50 for DSB formation is also partially abrogated in htp-1 and him-3 mutants, both of which are defective in functions connected to axial elements [23]. These mutants are most likely altered in composition or organization of chromosome axes, thereby making the requirement for the MRN complex dispens- able for DSB formation. Weakened SMC-3 suspends the requirement for MRE-11 (or MRN) for DSB formation, as does weakened REC-8. Because both SMC-3 and REC-8 are components of meiotic cohesin, it is likely that weakening the cohesin complex as a whole promotes the generation of DSBs by SPO-11. It is conceivable that the chromosome axis structure interferes with the access or activity of SPO-11 and that this obstacle is locally and/or temporally released by the activity of MRN. This could represent yet another layer in the control of meiotic recombination. Notably, we observed increased RAD-51 All C. elegans strains were cultured using standard techniques (Brenner, 1974). The following C. elegans strains were used: N2 Bristol, GE4345 smc-3(t2553) AV276 syp-2(ok307) [19], AV106 spo-11(ok79) [18], AV112 mre-11(ok179) [21], VC418 him-3(gk149) [15], VC255 him-17(ok424) [38], CB5348 mrt-2(e2663) [28]. Nematode strains were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR). Cytological preparation of gonads and immunostaining Hermaphrodite gonads were dissected and fixed as described in Cytological preparation of gonads and immunostaining Hermaphrodite gonads were dissected and fixed as described in [39]. For chromatin staining, the preparations were mounted in Vectashield anti-fade (Vector Laboratories Inc., Burlingame, CA) containing 2 mg/ml 496-diamidino-2-phenylindole (DAPI). For immunostaining, gonads were blocked in 3% BSA/1x PBS for 20 min. Primary antibodies were applied overnight at 4uC. Antibodies were diluted in 1x PBS/0.01% sodium azide as September 2011 | Volume 6 | Issue 9 | e24799 PLoS ONE | www.plosone.org 8 Cohesion and Homologous Repair in C. elegans follows: anti-SUN-1 Ser8-Pi [40] 1:700, anti-HIM-8 [41] 1:500, anti-ZIM-3 [42] 1:100, anti-RAD-51 [24] 1:300, anti-SYP-1 [43] 1:200, anti-HTP-3 [17] 1:500, anti-SMC-3 [44] 1:10. After 3 washes in 1x PBST (1x PBS, 0.1% Tween-20), secondary antibodies were applied for 2 h at RT. After washes in PBST, samples were mounted. RNA interference of rec-8 Double stranded RNA was produced by in vitro transcription and injected after [10]. Supporting Information Figure S1 Lack of synapsis cannot account for a decrease in immunostaining after washing with sarko- syl. A. Immunostaining of SMC-3 in syp-2 mutant worms. B. syp-2 squashed nuclei untreated and washed with sarkosyl stained with anti-REC-8 in TZ and pachytene. C. syp-2 squashed nuclei washed with sarkosyl stained with anit-HTP-3 in TZ and pachytene. Bar: 10 mm. (TIFF) (TIFF) Figure S4 Proper loading of the PC protein ZIM-3 in smc-3 but defective synapsis. A. Immunostaining of the pairing center protein ZIM-3 in wild type and smc-3 (DAPI blue). B. Immunostaining of SUN-1S8Pi in wild type and smc-3; (DAPI blue). C. Time course for pairing of HIM-8 in wild type and smc-3. Gonads were subdivided into 6 zones of equal lengths. D. Time course for pairing with the 5S rDNA FISH probe (chromosome V) in wild type and smc-3. Gonads were subdivided into 6 zones of equal lengths. E. Immunostaining of SYP-1 in wild type and smc-3; pachytene nuclei enlarged in the inset; bar 10 mm. (TIFF) Fluorescence in situ hybridization (FISH) The PCR-amplified 5S rDNA was used as a probe for the right arm of chromosome V. The 5S rDNA was labeled by PCR with digoxigenin-11-dUTP. FISH was performed as described in [10]. Hybridized digoxigenin-labeled probes were detected with FITC- conjugated anti-digoxigenin antibodies (1:100). Slides were mounted in Vectashield/DAPI. Figure S2 Meiotic cohesion is effective in smc-3. Representative diakinesis of indicated genotypes (wild type, spo- 11, smc-3, smc-3;spo-11, smc-3;spo-11;rec-8(RNAi). (TIFF) Figure S3 Rare mitotic defects in smc-3 mutants worms. Time course of HIM-8 pairing in wild type and smc-3 revealed the presence of 3 foci in the mitotic zone of smc-3 on rare occasions. (TIFF) Figure S6 Absence of fragmentation in the triple mutant smc-3;spo-11;mre-11. A. Representative diakinesis of the indicated genotypes (wild type, smc-3, smc-3;mre-11, smc-3;mre- 11;spo-11). Bar 5 mm. B. Quantification of DAPI structures at diakinesis in smc-3;spo-11;mre-11. (TIFF) Video S1 3-dimensional projection of deconvolved stack pictures (left) and colored surface of the DAPI structures (right) in wild type. (AVI) Mitotic repair assay Figure S5 HIM-3 loading is strongly reduced in smc-3. Immunostaining of HIM-3 (red) in wild type and smc-3; bar 10 mm. Ten young adult worms for each genotype (wild type, smc-3, mrt-2) were allowed to lay eggs at the restrictive (25uC) for 2 h. Next, hermaphrodites were removed from the plates and after 3,4 h at 25uC the eggs were c-irradiated with a dose of 60 Gy using a 137Cs source. Synchrony of the late-stage embryo at the bean stage was controlled before irradiation. Worms were kept at the restrictive temperature for 66 hours and then the number of arrested worms was scored. The L1 assay was performed as described in [29]. Microscopy and evaluation A Zeiss Axioskop epifluorescence microscope was used and images were recorded with a cooled CCD camera (Photometrics Ltd., Tucson, AZ). Evaluation of cytological phenotypes was performed in animals shifted to 25uC at the L1 stage for 66 hours. 3D stacks of images were taken (MetaVue software, Universal Imaging Co., Downingtown, PA), deconvolved (AutoDeblur software, AutoQuant Imaging Inc., Troy, NY) and projected (Helicon Focus software http://helicon.com.ua/heliconfocus/). Artificial coloring and merging were undertaken with Adobe Photoshop 7.0 software (Adobe Systems Incorporated). References Mito Y, Sugimoto A, Yamamoto M (2003) Distinct developmental function of two Caenorhabditis elegans homologs of the cohesin subunit Scc1/Rad21. Mol Biol Cell. pp 2399–2409. 31. Yazdi PT, Wang Y, Zhao S, Patel N, Lee EY, et al. (2002) SMC1 is a downstream effector in the ATM/NBS1 branch of the human S-phase checkpoint. Genes Dev 16: 571–582. pp 10. Pasierbek P, Jantsch M, Melcher M, Schleiffer A, Schweizer D, et al. (2001) A Caenorhabditis elegans cohesion protein with functions in meiotic chromosome pairing and disjunction. 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(2004) DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain. Mol Cell. pp 991–1002. 13. Colaia´covo MP (2006) The many facets of SC function during C. elegans meiosis. Chromosoma. pp 195–211. 35. Covo S, Westmoreland JW, Gordenin DA, Resnick MA (2010) Cohesin Is Limiting for the Suppression of DNA Damage-Induced Recombination between Homologous Chromosomes. PLoS Genet. e1001006 p. 14. Zetka MC, Kawasaki I, Strome S, Mu¨ller F (1999) Synapsis and chiasma formation in Caenorhabditis elegans require HIM-3, a meiotic chromosome core component that functions in chromosome segregation. Genes Dev. pp 2258–2270. 36. Kim KP, Weiner BM, Zhang L, Jordan A, Dekker J, et al. (2010) Sister cohesion and structural axis components mediate homolog bias of meiotic recombination. Cell 143: 924–937. 15. Couteau F, Nabeshima K, Villeneuve A, Zetka M (2004) A component of C. elegans meiotic chromosome axes at the interface of homolog alignment, synapsis, nuclear reorganization, and recombination. Curr Biol. pp 585–592. 37. References 24. Alpi A, Pasierbek P, Gartner A, Loidl J (2003) Genetic and cytological characterization of the recombination protein RAD-51 in Caenorhabditis elegans. Chromosoma. pp 6–16. 1. Wood AJ, Severson AF, Meyer BJ (2010) Condensin and cohesin complexity: the expanding repertoire of functions. Nat Rev Genet 11: 391–404. 2. Marston AL, Amon A (2004) Meiosis: cell-cycle controls shuffle and deal. Nat Rev Mol Cell Biol. pp 983–997. 25. Tsai CJ, Mets DG, Albrecht MR, Nix P, Chan A, et al. (2008) Meiotic crossover number and distribution are regulated by a dosage compensation protein that resembles a condensin subunit. Genes Dev. pp 194–211. 3. Monje-Casas F, Prabhu VR, Lee BH, Boselli M, Amon A (2007) Kinetochore orientation during meiosis is controlled by Aurora B and the monopolin complex. Cell. pp 477–490. resembles a condensin subunit. Genes Dev. pp 194–211. 26. Clejan I, Boerckel J, Ahmed S (2006) Developmental modulation of nonhomologous end joining in Caenorhabditis elegans. Genetics 173: 1301–1317. 4. Kitajima TS, Kawashima SA, Watanabe Y (2004) The conserved kinetochore protein shugoshin protects centromeric cohesion during meiosis. Nature. pp 510–517. 27. Gartner A, MacQueen A, Villeneuve AM (2004) Methods for analyzing checkpoint responses in Caenorhabditis elegans. Methods Mol Biol 280: 257–274. 5. Nasmyth K, Haering CH (2009) Cohesin: its roles and mechanisms. Annu Rev Genet 43: 525–558. 6. Haering CH, Lo¨we J, Hochwagen A, Nasmyth K (2002) Molecular architecture of SMC proteins and the yeast cohesin complex. Mol Cell. pp 773–788. 28. Gartner A, Milstein S, Ahmed S, Hodgkin J, Hengartner M (2000) A conserved checkpoint pathway mediates DNA damage–induced apoptosis and cell cycle arrest in C. elegans. Mol Cell 5: 435–443. 7. Severson AF, Ling L, van Zuylen V, Meyer BJ (2009) The axial element protein HTP-3 promotes cohesin loading and meiotic axis assembly in C. elegans to implement the meiotic program of chromosome segregation. Genes Dev. pp 1763–1778. 29. Bailly AP, Freeman A, Hall J, De´clais A-C, Alpi A, et al. (2010) The Caenorhabditis elegans homolog of Gen1/Yen1 resolvases links DNA damage signaling to DNA double-strand break repair. PLoS Genet 6: e1001025. 8. Chan RC, Chan A, Jeon M, Wu TF, Pasqualone D, et al. (2003) Chromosome cohesion is regulated by a clock gene paralogue TIM-1. Nature. pp 1002–1009. 30. Kim S-T, Xu B, Kastan MB (2002) Involvement of the cohesin protein, Smc1, in Atm-dependent and independent responses to DNA damage. Genes & Development. pp 560–570. 9. References Klein F, Mahr P, Galova M, Buonomo SB, Michaelis C, et al. (1999) A central role for cohesins in sister chromatid cohesion, formation of axial elements, and recombination during yeast meiosis. Cell 98: 91–103. 16. Couteau F, Zetka M (2005) HTP-1 coordinates synaptonemal complex assembly with homolog alignment during meiosis in C. elegans. Genes Dev. pp 2744–2756. 38. Reddy KC, Villeneuve AM (2004) C. elegans HIM-17 links chromatin modification and competence for initiation of meiotic recombination. Cell. pp 439–452. 17. Goodyer W, Kaitna S, Couteau F, Ward JD, Boulton SJ, et al. (2008) HTP-3 Links DSB Formation with Homolog Pairing and Crossing Over during C. elegans Meiosis. Dev Cell. pp 263–274. 39. Martinez-Perez E, Villeneuve AM (2005) HTP-1-dependent constraints coordinate homolog pairing and synapsis and promote chiasma formation during C. elegans meiosis. Genes Dev. pp 2727–2743. g pp 18. Dernburg AF, McDonald K, Moulder G, Barstead R, Dresser M, et al. (1998) Meiotic recombination in C. elegans initiates by a conserved mechanism and is dispensable for homologous chromosome synapsis. Cell. pp 387–398. 40. Penkner A, Fridkin A, Gloggnitzer J, Baudrimont A, Machacek T, et al. (2009) Meiotic Chromosome Homology Search Involves Modifications of the Nuclear Envelope Protein Matefin/SUN-1. Cell 139: 920–933. 19. Colaia´covo MP, MacQueen AJ, Martinez-Perez E, McDonald K, Adamo A, et al. (2003) Synaptonemal complex assembly in C. elegans is dispensable for loading strand-exchange proteins but critical for proper completion of recombination. Dev Cell. pp 463–474. 41. Phillips CM, Wong C, Bhalla N, Carlton PM, Weiser P, et al. (2005) HIM-8 binds to the X chromosome pairing center and mediates chromosome-specific meiotic synapsis. Cell. pp 1051–1063. 42. Tang L, Machacek T, Mamnun YM, Penkner A, Gloggnitzer J, et al. (2010) Mutations in Caenorhabditis elegans him-19 show meiotic defects that worsen with age. Mol Biol Cell. pp 885–896. 20. Gerton JL, Hawley RS (2005) Homologous chromosome interactions in meiosis: diversity amidst conservation. Nat Rev Genet. pp 477–487. 21. Chin GM, Villeneuve AM (2001) C. elegans mre-11 is required for meiotic recombination and DNA repair but is dispensable for the meiotic G(2) DNA damage checkpoint. Genes Dev. pp 522–534. 43. MacQueen AJ, Colaia´covo MP, McDonald K, Villeneuve AM (2002) Synapsis- dependent and -independent mechanisms stabilize homolog pairing during meiotic prophase in C. elegans. Genes Dev. pp 2428–2442. g p pp 22. Author Contributions Conceived and designed the experiments: AB AP YM RS JL VJ AW. Performed the experiments: AB AP YM MH CS AW. Analyzed the data: Acknowledgments AB AP VJ AW. Contributed reagents/materials/analysis tools: RS. Wrote the paper: AB VJ. AB AP VJ AW. Contributed reagents/materials/analysis tools: RS. Wrote the paper: AB VJ. We thank Christian Pflu¨gl for technical assistance. We are grateful to We thank Christian Pflu¨gl for technical assistance. We are grateful to Raymond Chan, Abby Dernburg, Adriana La Volpe, Monique Zetka, Cohesion and Homologous Repair in C. elegans Cohesion and Homologous Repair in C. elegans Video S6 3-dimensional projection of deconvolved stack pictures (left) and colored surface of the DAPI structures (right) in smc-3; him-17. (AVI) Anne Villeneuve and the Caenorhabditis Genetics Center for antibodies and strains. We thank Alexander Schleiffer, Enrique Martinez-Perez and Anton Gartner for discussion. Quantification of DNA fragmentation Stack pictures from diakinesis were deconvolved (AutoDeblur software, AutoQuant Imaging Inc., Troy, NY). Volumes were quantified with the 3D Object Counter plugin using ImageJ. Classes were defined by the volume (v) and the sphericity (s) of the DAPI structures at the last diakinesis before the sperma- theca. Sphericity, as a measure of the roundness of an object, is the ratio of the surface area of a sphere (with the same volume as the given object) to the surface area of the object. Using this method bivalents and univalents could be identified (bivalents: v = 3.061.1 mm3 (mean6SD), s = 0.6560.07 (mean6SD), n = 15 diakinesis; univalents: v = 1.260.4 mm3, s = 0.8060.06, SD, n = 16 diakinesis). DAPI structures with a larger volume than the defined volume of bivalents or with a volume in the range of bivalents but with different sphericity than bivalents were classified as ‘‘chromatin masses’’. DAPI structures with a smaller volume than a univalent or with a volume of a univalent but different sphericity were defined as fragments. 3-dimen- sional projections of deconvolved pictures and counted volumes are provided for each genotype (Video S1, S2, S3, S4, S5 and S6). Video S2 3-dimensional projection of deconvolved stack pictures (left) and colored surface of the DAPI structures (right) in smc-3. (AVI) Video S3 3-dimensional projection of deconvolved stack pictures (left) and colored surface of the DAPI structures (right) in smc-3; spo-11. (AVI) Video S4 3-dimensional projection of deconvolved stack pictures (left) and colored surface of the DAPI structures (right) in smc-3; mre-11. (AVI) Video S5 3-dimensional projection of deconvolved stack pictures (left) and colored surface of the DAPI structures (right) in smc-3; him-3. (AVI) PLoS ONE | www.ploso PLoS ONE | www.plosone.org September 2011 | Volume 6 | Issue 9 | e24799 9 References Rinaldo C, Bazzicalupo P, Ederle S, Hilliard M, La Volpe A (2002) Roles for Caenorhabditis elegans rad-51 in meiosis and in resistance to ionizing radiation during development. Genetics. pp 471–479. 44. Howe M, McDonald KL, Albertson DG, Meyer BJ (2001) HIM-10 is required for kinetochore structure and function on Caenorhabditis elegans holocentric chromosomes. The Journal of Cell Biology 153: 1227–1238. g p pp 23. Hayashi M, Chin G, Villeneuve A (2007) C. elegans Germ Cells Switch between Distinct Modes of Double-Strand Break Repair During Meiotic Prophase Progression. PLoS Genet. pp e191. 45. Geer LY, Domrachev M, Lipman DJ, Bryant SH (2002) CDART: protein homology by domain architecture. Genome Res 12: 1619–1623. September 2011 | Volume 6 | Issue 9 | e24799 PLoS ONE | www.plosone.org 10
https://openalex.org/W4390519834
https://jurnal.ugm.ac.id/ijbiotech/article/download/81544/38151
English
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Chitosan Xylotrupes gideon encapsulated lemongrass leaf ethanol extract reduce H2O2‐induced oxidative stress in human dermal fibroblast
Indonesian Journal of Biotechnology
2,023
cc-by-sa
6,064
Komariah Komariah1,*, Pretty Trisfilha2, Rahman Wahyudi2, Nada Erica3, Didi Nugroho4, Yessy Ariesanti5, Sarat Kumar 6 1Department of Oral Biology sub‐division of Histology Faculty of Dentistry, Universitas Trisakti, Jakarta 11440, Indonesia 2Department of Oral Biology sub‐division of Oral Pathology, Faculty of Dentistry, Universitas Trisakti, Jakarta 11440, Indonesia 3Student of Dentistry, Faculty of Dentistry, Trisakti University, Jakarta 11440, Indonesia 4Department of Oral Biology sub‐division of Pharmacology, Faculty of Dentistry, Universitas Trisakti, Jakarta 11440, Indonesia 5Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Universitas Trisakti, Jakarta 11440, Indonesia 6Department of Chemistry, Veer Surendra Sai University of Technology (VSSUT), Burla, Sambalpur‐768018 Orissa, India *Corresponding author: komariah@trisakti.ac.id SUBMITTED 20 January 2023 REVISED 4 July 2023 ACCEPTED 15 August 2023 SUBMITTED 20 January 2023 REVISED 4 July 2023 ACCEPTED 15 August 2023 ABSTRACT During phagocytosis, phagocyte cells discharge reactive oxygen species referred to as respiratory bursts, inducing a rise in pro‐oxidants and subjecting the cell to oxidative stress. Such stress is a biological mechanism related to an imbalance in pro‐oxidant/antioxidant homeostasis, which generates toxic reactive oxygen. Encapsulation is a coating process to improve the stability of bioactive compounds from lemongrass extract. Therefore, this study aims to determine the encapsulation activity of lemongrass leaf extract with chitosan X. gideon (LEChXg) to reduce the oxidative stress of fibroblasts. The research used the human dermal fibroblast (HDF) cell line, comprising negative and positive controls and use of LEChXg 100, 200, 300, 400, and 500 µg/mL. HDF cell migration was evaluated by employing the scratch wound healing method and the wound closure was oberseved at 0, 2, 4, 6, and 24 h intervals. The cell proliferation was observed at 24, 48, and 72 h using CCK‐8 at a 450 nm wavelength. The results showed that the observations at 0, 2, and 4 h did not demonstrate any significant difference on the cell migration (p > 0.05) among the groups. However, the wound closure at 4 and 6 h showed a significant difference (p < 0.05) with LEChXg 300 µg/mL. Despite the lack of any significant variation observed up to 24 h, fibroblast subjected to the stressor did not achieve complete closure. The groups treated with LEChXg were more stable in maintaining fibroblast proliferation up to the end of the observation than those with stressors at 24, 48, and 72 h. Fibroblast induced with a stressor was also more stable in maintaining migration and proliferation in groups receiving LEChXg 300 µg/mL. Komariah Komariah1,*, Pretty Trisfilha2, Rahman Wahyudi2, Nada Erica3, Didi Nugroho4, Yessy Ariesanti5, Sarat Kumar 6 and macrophages migrate to the ulcer area, resolve respi­ ratory bursts using high oxygen during phagocytosis, and increase reactive oxygen species (ROS), such as superox­ ide and hydrogen peroxide (Arief and Widodo 2018). Fur­ thermore, high ROS production can cause a pro­oxidant increase and oxidative stress (Bhattacharyya et al. 2014; Phaniendra et al. 2015). This condition interferes the cells communication and causes damage to influence the ulcer healing process (Pisoschi and Pop 2015), such as length­ ening the inflammation phase as well as hindering migra­ tion process and fibroblast proliferation (Buranasin et al. 2018). Copyright © 2023 THE AUTHOR(S). This article is distributed under a Creative Commons Attribution‐ShareAlike 4.0 International license. Indonesian Journal of Biotechnology VOLUME 28(4), 2023, 191‐199 | RESEARCH ARTICLE VOLUME 28(4), 2023, 191‐199 | RESEARCH ARTICLE Indones J Biotechnol 28(4), 2023, 191‐199 | DOI 10.22146/ijbiotech.81544 www.jurnal.ugm.ac.id/ijbiotech KEYWORDS Chitosan X. gideon; Lemongrass leaf; Migration; Oxidative stress; Proliferation Chitosan Xylotrupes gideon encapsulated lemongrass leaf ethanol extract reduce H2O2‐induced oxidative stress in human dermal fibroblast Komariah Komariah1,*, Pretty Trisfilha2, Rahman Wahyudi2, Nada Erica3, Didi Nugroho4, Yessy Ariesan Swain6 2.2. Lemongrass extract (LE) preparation The pharmacological activity of the active compound has bioavailability and absorption limitations in the body that can be controlled with encapsulation technology (Rahim et al. 2022), i.e. by protecting the active compound from oxidation to improve its therapeutic potential (Negi and Kesari 2022). The common polymer material used as a trapping matrix for encapsulation is chitosan (Andikop­ utri et al. 2021), which is a natural polymer compound ob­ tained from insect exoskeleton (Baharlouei and Rahman 2022), such as horn beetle (Xylotrupes gideon) (Veronica et al. 2021). Thus, it can be developed to facilitate a drug delivery system due to its biocompatible, biodegradable, low toxicity level (Agarwal et al. 2018), and simple prepa­ ration method (Mohammed et al. 2017). Chitosan physical modification also increases the absorption, diffusion, and penetration to the mucosal layer better than its normal size (Detsi et al. 2020). Lemongrass (Cymbopogon citratus) was collected from Balai Penelitian Tanaman Rempah dan Obat (BALITRO), Indonesian Medicinal and Aromatic Crops Research Insti­ tute (IMACRI), West Java, Indonesia. The determination was carried out at Pusat Riset Biologi, Badan Riset dan Or­ ganisasi Nasional (BRIN), Cibinong, West Java, Indone­ sia. The leaves were dried in an oven at a temperature of 45 °C for one week and extracted using the maceration method (Felicia et al. 2022). They were soaked in 70% ethanol at a 1:10 (w/v) ratio for 24 h at room temperature. The macerated mixture was filtered using a filter paper and evaporated with a rotary vacuum evaporator at a tempera­ ture of 40 °C at 100 rpm for 2 h (Fitria et al. 2022). 1. Introduction Mouth or oral ulcers are generally known as discontinu­ ities of oral mucosa characterized by epithelial tissue dam­ age and connective tissue in lamina propria of the mucosa in oral cavity (Zakiawati et al. 2020). About 40% of peo­ ple have been estimated to suffer from oral ulcers disease (Zakiawati et al. 2020) due to trauma during medical treat­ ment. Fibroblast is a crucial cell for mouth ulcers heal­ ing, which undertakes essential functions like synthesis and replenishment of the connective fibers and the amor­ phous substance during tissue repair (Lendahl et al. 2022). By the primary defence mechanism, the ulcer disappears through the healing process, which is divided into three phases, namely inflammation, proliferation, and remod­ elling (Toma et al. 2021). In inflammation, neutrophils Herbal medicine for the ulcer healing process has been widely used, such as lemongrass (Cymbopogon cit­ ratus DC) (Veronica et al. 2021). Lemongrass is one of the spices growing in the tropics and is widely used in Indones J Biotechnol 28(4), 2023, 191‐199 | DOI 10.22146/ijbiotech.81544 www.jurnal.ugm.ac.id/ijbiotech Indonesian Journal of Biotechnology 28(4), 2023, 191‐199 Komariah et al. 2. Materials and Methods Southeast Asia, including Indonesia (Maria et al. 2021). Lemongrass leaf is often discarded without being utilized, whereas its stem serves as a highly valued spice in culi­ nary applications. The leaf contains valuable active com­ pounds, including alkaloids, flavonoids, tannins, steroids, triterpenoids, and saponins, which possess notable antiox­ idant properties (Comino­Sanz et al. 2021). Natural in­ gredient with antioxidant content is proven to accelerate the ulcer healing process (Ozougwu 2016) by reducing fi­ broblast oxidative due to respiratory burst from phagocytic cells (Deng et al. 2021) and to accelerate migration and proliferation (Grgić et al. 2020). 2.3. The preparation of LE‐loaded on chitosan X. gideon (LEChXg) Chitosan with 83% degrees of deacetylation and a weight value of 0.5 g was dissolved in 1% acetic acid (Merck, Germany). Subsequently, 2 mL of 10% lemongrass leaf extract (LE) and 100 mL of distilled water were added (Veronica et al. 2021). Stirring was conducted using a magnetic stirrer (IKA RH basic 2, Germany) and heating at 40 °C with a speed of 2,500 rpm for 20 min and was subsequently carried out without heating for 100 min. Fol­ lowing the previous step, 40 mL of 0.1% tripolyphosphate (Sigma­Aldrich, USA) was added dropwise while stir­ ring for one hour. Subsequently, 0.1 mL of 0.1% Tween 80 (Merck, France) was introduced, and the mixture was stirred again at a speed of 2,500 rpm for 30 min (Andikop­ utri et al. 2021; Veronica et al. 2021). The particle size of lemongrass extract was determined using a particle size analyzer (PSA) (Horiba Scientific, Nano Particle Analyzer SZ­100, UK) (Budi et al. 2020). Chitosan is a polymer widely used as an active com­ pound trap of a natural ingredient. Previous studies show that Prunus avium L. extract encapsulation using nanochi­ tosan and gallic acid can decrease oxidative stress on en­ dothelium cells (Beconcini et al. 2018) and 3T3 fibrob­ last cells (de Paiva et al. 2021), respectively. Further­ more, the active compound encapsulation of lemongrass with chitosan polymer reduces ROS production of fibrob­ last by inducing hydrogen peroxide stressor (Fitria et al. 2022). The observation with 2’7’ dichlorodihydrofluo­ rescein diacetate (H2DCF­DA) staining using a fluores­ cent microscope also shows the intensity of green fluores­ cent cells, indicating reduced ROS production (Andikop­ utri et al. 2021; Veronica et al. 2021). This study assesses the activity of chitosan­ encapsulated active compounds of lemongrass leaf ethanol exctract. The chitosan was derived from X. gideon through the ionic gelation method. It mitigates fibroblast oxidative stress induced by hydrogen peroxide to promote a decrease in oxidative stress. This reduc­ tion in oxidative stress can be demonstrated through enhanced migration and proliferation of fibroblast during the healing process in mouth ulcers. Encapsulation of the lemongrass bioactive compounds is an innovative approach allowing protection against oxidation, thermal degradation and increasing bioavailability. Encapsulation is promising to improve the performance of medicines in oral health, such as mouthwashes. 2.1. Polymeric materials The source of chitosan in this study was X. gideon obtained from Cangkurawok, Damaga, and Balumbang Jaya, Bo­ gor, East Java. All parts of X. gideon body were detached, followed by drying for five days, and then continied to the processes of demineralization (3N HCl), deproteinization (3N NaOH), discoloration (4% H2O2) and deacetylation (50% NaOH) (Komariah et al. 2019). 2.7. Data Analysis Statistical quantification was conducted using SPSS ver­ sion 2.3 and the data were presented as mean ± standard deviation (SD). Meanwhile, MANOVA was used to com­ pare the groups against several dependent variables (times) in migration and proliferation assays. For a significant dif­ ference (p < 0.05), Post Hoc’s Tukey test was performed. The observation of fibroblast migration when closing the gap is related to the ulcer healing process. The inflam­ mation cells are stimulated to release various mediators (Chen et al. 2018) and growth factors such as the trans­ forming growth factor­beta 1 (TGF­β) factor of fibroblast when oxidative stress is reduced (Jimi et al. 2020). H2O2 is one of the most critical compounds in ROS signaling studies due to its physicochemical properties, relatively low reactivity, and ability to diffuse through membranes. The addition at low concentrations increases intracellular ROS levels without causing oxidative stress. It also in­ creases the migration of mesenchymal cells through extra­ cellular signal­regulated kinases (ERK) 1/2 and focal ad­ hesion kinase (FAK) pathways. Cellular abnormalities are increased when cells experience oxidative stress (Waheed 2.5. Proliferation assay Fibroblasts planted at a density of 1 × 103 cells/well in a 96­well plate were incubated at 37 ºC for 24 h. After 24, 48, and 72 h of treatment with a various concentration of LEChXg, the cells were washed by PBS 1×, and 100 μL of CCK­8 solution was added. The absorbance was measured at 450 nm using a microplate reader (Tecan Group Ltd. Mannedorf, Switzerland) and the percentage of fibroblast proliferation was calculated as shown below (Felicia et al. 2022). proliferation rate (%) = absorbance of sample absorbance of negative control ×100 (1) (1) (1) 2.4. Culture of fibroblast Human dermal fibroblast (HDF) was obtained from the Biorepository of Stem Cell Research Center, Yarsi Univer­ sity, Indonesia (Fitria et al. 2022). Fibroblast was planted in a cell culture dish and incubated at 37 °C with 5% CO2 for 24 h. The growth medium was replaced by media containing DMEM, 10% FBS, and antibiotic­antimycotic (penicillin, streptomycin, and amphotericin B). The cul­ tured cells were divided into eight treatment groups as fol­ lows: (1) without any treatment or stressor, (2) treated with hydrogen peroxide stressor (H2O2) as a negative con­ 192 Indonesian Journal of Biotechnology 28(4), 2023, 191‐199 Komariah et al. PSA with a repetition of three times. The result of particle measurement and polydispersity index (PDI) LEChXg is shown in Table 1. trol, (3) treated with H2O2 plus ascorbic acid as a posi­ tive control, (4–8) treated with H2O2 plus nanochitosan­ encapsulated lemongrass (LEChXg) at concentrations of 100, 200, 300, 400, and 500 µg/mL, respectively. The stressor was given as the addition of 100 µM H2O2 (Li­ onetti et al. 2019) followed by incubation at 37 °C with 5% CO2 for 60 min (Fitria et al. 2022). The LEChXg particle measurement indicated that the average size was 489.57 nm. Therefore, LEChXg fulfilled the requirements as a nanoparticle with a size range be­ tween 50–500 nm particle (Ismail and Harun 2019). Ac­ cording to Idacahyati et al. (2021), a nano­size particle should range from 1–1000 nm. PDI is a value that shows particle size distribution with a range of 0–1. A sample with a bigger and smaller size range has higher PDI values (Karmakar 2019). The result of particle distribution with PDI values 0.035 to 0.05 is considered to have monodis­ perse particle distribution (Clayton et al. 2016). Poly­ dispersity is a macromolecule with various good weights, sizes, and mass distribution (Kim et al. 2019). The zeta po­ tential value of LEChXg was 31.2 mV. Nanoparticles with zeta potential values smaller than 31.2 mV and greater than +30 mV also indicated good stability (Prakash et al. 2014). A dispersion system with a small zeta potential value was easier to form, such as the Van der Waals style in particle interaction (Juliantoni et al. 2020). 3.2. Migration of fibroblast The cells were planted in a 24­well plate (2.9 × 103 cells/well) (Kauanova et al. 2021) and incubated until con­ fluent. After reaching confluency, the monolayer was scratched gently using a white tip perpendicularly to the bottom of the monolayer. After the first scratch was con­ ducted, a second scratch was made by crossing the first one. Thus, a cross pattern would be formed. Next, the cells were washed in PBS once and subsequently were treated (Felicia et al. 2022). The cell migration was observed af­ ter 0, 2, 4, 6, 24, and 48 h after the that and photographed using a microscope (EVOS FLc Cell Imaging System). At the end of the experiment, the wound closure was analyzed using ImageJ. The migration test was conducted using scratch by mak­ ing an artificial gap (scratch) in confluent monolayer cells. The gap allowed cells to communicate with each other. It also showed the ability of fibroblasts to move toward the ulcer, carry out proliferation, and form an extracellu­ lar matrix. The results of fibroblast migration showed that migration in 0 and 2 h did not indicate a significant differ­ ence (p = 0.222). However, at the observations of 4 and 6 h, there was a significant difference (p < 0.05) between the group with a stressor and the LEChXg group at a con­ centration of 300 µg/mL. The group treated with LEChXg showed a good migration activity by closing the most sig­ nificant gap compared to those treated with a H2O2 stres­ sor only. At 24 h, all study groups had no significant dif­ ference (p > 0.05). However, the fibroblast group treated with stressor showed less optimal migration due to an open gap of 0.51 ± 0.88 µm2. The average fibroblast migration ability is shown in Table 2. Microscopic observation of the cell migration can be seen in Figure 1. 3.1. Characteristics of LEChXg particle Characteristic of LEChXg particle was used to estimate and determine the particle size and distribution of parti­ cle size. Meanwhile, particle size was measured using a TABLE 1 Characterization of LEChXg nanoparticles. TABLE 1 Characterization of LEChXg nanoparticles. Sample Particle size (nm) PDI Zeta Potential (mV) LEChXg 489.57 ± 3.44 0.69 ± 0.06 31.2 ± 0.87 PDI: poly dispersity index. 193 Indonesian Journal of Biotechnology 28(4), 2023, 191‐199 Komariah et al. 0 h (a) 2 h 4 h 6 h 24 h (b) (c) (d) (e) (f) (g) (h) FIGURE 1 Fibroblast migration at 0, 2, 4, 6, and 24‐h observation after the scratch wound. The yellow arrow shows a shaped artificial gap The red arrow shows the artificial gap closing caused by the fibroblast migration. A: negative control, B: H2O2 only. C‐H received H2O2 with treatment as follows: C: ascorbic acid as positive control, D: LEChXg 100 µg/mL, E: LEChXg 200 µg/mL, F. LEChXg 300 µg/mL, G. LEChXg 400 µg/mL, and H LEChXg 500 µg/mL. The observation was at 1,000× magnification. Scale bar = 1000µm. 194 0 h (a) 2 h 4 h 6 h 24 h (b) (c) (d) (e) (f) (g) (h) FIGURE 1 Fibroblast migration at 0, 2, 4, 6, and 24‐h observation after the scratch wound. The yellow arrow shows a shaped artificial gap The red arrow shows the artificial gap closing caused by the fibroblast migration. A: negative control, B: H2O2 only. C‐H received H2O2 with treatment as follows: C: ascorbic acid as positive control, D: LEChXg 100 µg/mL, E: LEChXg 200 µg/mL, F. LEChXg 300 µg/mL, G. LEChXg 400 µg/mL, and H LEChXg 500 µg/mL. The observation was at 1,000× magnification. Scale bar = 1000µm. 0 h (a) (b) (b) (c) (c) (d) (d) (e) (e) (f) (f) ( ) (g) (h) (h) FIGURE 1 Fibroblast migration at 0, 2, 4, 6, and 24‐h observation after the scratch wound. The yellow arrow shows a shaped artificial gap. The red arrow shows the artificial gap closing caused by the fibroblast migration. A: negative control, B: H2O2 only. C‐H received H2O2 with treatment as follows: C: ascorbic acid as positive control, D: LEChXg 100 µg/mL, E: LEChXg 200 µg/mL, F. LEChXg 300 µg/mL, G. LEChXg 400 µg/mL, and H LEChXg 500 µg/mL. The observation was at 1,000× magnification. Scale bar = 1000µm. 194 Indonesian Journal of Biotechnology 28(4), 2023, 191‐199 Komariah et al. 3.1. Characteristics of LEChXg particle TABLE 2 Fibroblast migration. Group Measurement Migration (µm2) number (n) 0 h 2 h 4 h 6 h 24 h Untreated 3 2.87 ± 0.14 2.71 ± 0.28 2.53 ± 0.18ab 2.50 ± 0.18ab 0.00 ± 0.00 H2O2 3 3.82 ± 0.88 3.75 ± 0.91 3.41 ± 1.04a 3.21 ± 1.04a 0.51 ± 0.88 H2O2 + Ascorbic Acid 3 2.99 ± 0.20 2.82 ± 0.18 2.74 ± 0.19ab 2.61 ± 0.17ab 0.00 ± 0.00 H2O2 + LEChXg 100 µg/mL 3 2.70 ± 0.27 2.55 ± 0.28 2.24 ± 0.49ab 1.88 ± 0.33ab 0.00 ± 0.00 H2O2 + LEChXg 200 µg/mL 3 3.31 ± 0.05 2.89 ± 0.23 2.58 ± 0.18ab 2.49 ± 0.18ab 0.00 ± 0.00 H2O2 + LEChXg 300 µg/mL 3 2.92 ± 0.08 2.61 ± 0.18 1.44 ± 0.20b 1.38 ± 0.16a 0.00 ± 0.00 H2O2 + LEChXg 400 µg/mL 3 3.99 ± 1.73 3.43 ± 1.50 3.16 ± 1.38ab 2.55 ± 1.11ab 0.00 ± 0.00 H2O2 + LEChXg 500 µg/mL 3 2.68 ± 0.04 2.32 ± 0.16 2.03 ± 0.21ab 1.94 ± 0.21ab 0.00 ± 0.00 a‐b in different columns migration shows a significant difference (p < 0.05), The superscript ’a’ indicates a higher migration compared to group ’b,’ while ’ab’ indicates migration that is not different from groups ’a’ and ’b’. TABLE 2 Fibroblast migration. et al. 2022). Buranasin et al. (2018) stated that gingival fibroblast exposed to high glucose concentrations causes oxidative stress by increasing ROS production and inhibit­ ing the migration process associated with inhibiting basic fibroblast growth factor (bFGF) signaling. ing any adverse impact on the proliferation of stressor­ unexposed cells (Tsuneda 2020) The group treated with ascorbic acid showed good proliferation after exposing the cells to stressors H2O2. Ascorbic acid is an antioxidant that can neutralize oxidative stress by donating an electron to prevent other oxidized compounds and scavenging su­ peroxide anion, hydroxyl radical, and lipid hydroperoxide (Pehlivan 2017). 3.3. Fibroblast proliferation 24 h (a) 48 h 72 h (b) (c) (d) (e) (f) (g) (h) FIGURE 3 Fibroblast proliferation at 24, 48, and 72‐h observation as indicated. The yellow arrow shows the fibroblast, which is liv‐ ing with a clearly visible cell nucleus, while the red arrow shows a dead fibroblast by shrinking in the cells. A: negative control, B: H2O2 only. C‐H received H2O2 with treatment as follows: C: ascorbic acid as positive control, D: LEChXg 100 µg/mL, E: LEChXg 200 µg/mL, F. LEChXg 300 µg/mL, G. LEChXg 400 µg/mL, and H LEChXg 500 µg/mL. The observation was at 1,000× magnification. 72 h 24 h (a) 48 h tions could detoxify or repair the damages resulting from increased free radicals to enable a relatively stable prolif­ eration. 24 h (a) 48 h 72 h (b) (c) (d) (e) (f) (g) (h) FIGURE 3 Fibroblast proliferation at 24, 48, and 72‐h observation as indicated. The yellow arrow shows the fibroblast, which is liv‐ ing with a clearly visible cell nucleus, while the red arrow shows a dead fibroblast by shrinking in the cells. A: negative control, B: H2O2 only. C‐H received H2O2 with treatment as follows: C: ascorbic acid as positive control, D: LEChXg 100 µg/mL, E: LEChXg 200 µg/mL, F. LEChXg 300 µg/mL, G. LEChXg 400 µg/mL, and H LEChXg 500 µg/mL. The observation was at 1,000× magnification. The observation at 72 h showed that the group treated with stressor was significantly different (p < 0.05) from LEChXg concentrations 100, 200, 300, and 400 µg/mL. The difference showed increased proliferation higher than the group treated with a stressor. In contrast, the non­ stressor, ascorbic acid, and LEChXg 500 µg/mL groups showed no significant difference (p = 1.000). Even though there was no difference, these groups exhibited higher pro­ liferation cells than those treated with stressors. The pro­ liferation of fibroblast in 24, 48, and 72 h observation is shown in Figure 3. (a) (b) (b) (c) The results of the proliferation of the non­stressor, stressor, and ascorbic acid groups experienced decreased proliferation. However, a proliferation of the group treated with LEChXg was relatively stable. LEChXg maintained or stabilized proliferation until 72 h observation of fibrob­ last, which experienced oxidative stress. Pan et al. (2022) showed that active compounds of lemongrass increase cell proliferation power by reducing oxidative stress resulting from high ROS. Similarly, Roriz et al. 3.3. Fibroblast proliferation The results of fibroblast proliferation in 24 h showed that the group treated with stressor was significantly differ­ ent (p < 0.05) from those without stressor, as well group treated with ascorbic acid as a non­enzymatic antioxidant and LEChXg. The group treated with stressors indicated low cell proliferation compared to the others. Hydrogen peroxide is a molecule with low reactivity but can easily penetrate the cell membrane, generating the most reactive type of oxygen, hydroxyl radical, and converting Fe2+ atau Cu+ to OH (Nita and Grzybowski 2016). Fibroblast proliferation in 48 h of observation showed that the group treated with H2O2 is significantly differ­ ent (p < 0.05) from those without stressor, as well as the group treated with ascorbic acid, and LEChXg concentra­ tions at 200, 300, and 400 µg/mL. Meanwhile, the group with stressors did not report a significant difference (p > 0.05) from LEChXg 100 and 500 µg/mL. The group treated with H2O2 at 48 h showed a decrease in proliferation compared to the 24­h observation. It indi­ cates that the cells experienced oxidative stress could not detoxify or repair the damage resulting from free radicals (Phaniendra et al. 2015). Therefore, it caused cell damage and affected proliferation. The ascorbic acid group and those treated with LEChXg at all the the tested concentra­ Fibroblast proliferation without stressors had the high­ est proliferative compared to the other groups. The av­ erage proliferation is shown in Figure 2. Fibroblast can counteract an elevation in free radicals by augmenting the synthesis of endogenous antioxidants, thereby prevent­ FIGURE 2 Fibroblast proliferation. a‐c in different hours shows a significant difference (p < 0.05) The superscript ’a’ indicates higher prolif‐ eration compared to groups ’b’ and ’c,’ while ’b’ indicates higher proliferation than group ’c.’ Superscript ’ab’ implies no significant difference between groups ’a’ and ’b,’ and superscript ’bc’ no significant difference between groups ’b’ and ’c’. FIGURE 2 Fibroblast proliferation. a‐c in different hours shows a significant difference (p < 0.05) The superscript ’a’ indicates higher prolif‐ eration compared to groups ’b’ and ’c,’ while ’b’ indicates higher proliferation than group ’c.’ Superscript ’ab’ implies no significant difference between groups ’a’ and ’b,’ and superscript ’bc’ no significant difference between groups ’b’ and ’c’. 195 Indonesian Journal of Biotechnology 28(4), 2023, 191‐199 Komariah et al. 3.3. Fibroblast proliferation (2014) indicated that lemongrass showed an antioxidant effect by improv­ ing the superoxide dismutase enzyme (SOD) activity and reducing the production of ROS in macrophages. Chitosan plays a role in scavenging free radicals and inhibiting ox­ idative damage (Pellis et al. 2022). The leading functional group, such as hydroxyl and an amino groups can reduce free radicals after a reaction at C­2, C­3, and C­6 positions of the pyranose ring to produce a stable macromolecule (Muthu et al. 2021). At the end of our observation, there was an aggregate formed in the LEChXg group due to polydisperse particle distribution with various molecular weights, sizes, and mass distributions, as well as zeta po­ tential value which was relatively greater than +30 mV (Dipahayu and Kusumo 2021). (c) (d) (c) (d) ( ) (e) (e) (f) (f) Our results were consistent with Beconcini et al. (2018), where the encapsulation of Prunus avium extract with chitosan and its derivatives reduces oxidative stress in human umbilical vein endothelial cells (HUVEC). An in vivo study on rat liver cells showed that encapsulated Pinus merkusii extract with chitosan reduces malondialde­ hyde (MDA) levels. An increase in MDA levels indicates hepatocyte cell membrane damage after exposure to ROS. Meanwhile, the decrease showed that the encapsulation of P. merkusii extract inhibits ROS production (Di Santo et al. 2021). (g) (h) (g) (h) FIGURE 3 Fibroblast proliferation at 24, 48, and 72‐h observation as indicated. The yellow arrow shows the fibroblast, which is liv‐ ing with a clearly visible cell nucleus, while the red arrow shows a dead fibroblast by shrinking in the cells. A: negative control, B: H2O2 only. C‐H received H2O2 with treatment as follows: C: ascorbic acid as positive control, D: LEChXg 100 µg/mL, E: LEChXg 200 µg/mL, F. LEChXg 300 µg/mL, G. LEChXg 400 µg/mL, and H LEChXg 500 µg/mL. The observation was at 1,000× magnification. Damage in the epithelium and lamina propria as con­ nective tissue with a predominance of fibroblast in mouth ulcers accelerated the healing process by encapsulating lemongrass leaf extract ethanol with chitosan X. gideon. The acceleration of the process was determined through increased migration and proliferation of fibroblasts after experiencing oxidative stress during the inflammatory pro­ cess. 196 Indonesian Journal of Biotechnology 28(4), 2023, 191‐199 Komariah et al. Bhattacharyya A, Chattopadhyay R, Mitra S, Crowe SE. 2014. 3.3. Fibroblast proliferation Oxidative stress: An essential fac­ tor in the pathogenesis of gastrointestinal mu­ cosal diseases. Physiol. Rev. 94(2):329–354. doi:10.1152/physrev.00040.2012. Authors’ contributions Clayton KN, Salameh JW, Wereley ST, Kinzer­Ursem TL. 2016. Physical characterization of nanoparti­ cle size and surface modification using particle scat­ tering diffusometry. Biomicrofluidics 10(5):054107. doi:10.1063/1.4962992. KK designed the study, analysed the data, carried out the laboratory work and wrote the manuscript; PT wrote the manuscript; RW wrote the manuscript and analysed the data; NE carried out the laboratory work; DN wrote the manuscript. All authors read and approved the final ver­ sion of the manuscript. Comino­Sanz IM, López­Franco MD, Castro B, Pancorbo­Hidalgo PL. 2021. The role of an­ tioxidants on wound healing: A review of the current evidence. J. Clin. Med. 10(16):3558. doi:10.3390/jcm10163558. 4. Conclusions In conclusion, encapsulation of lemongrass leaf extract ethanol with chitosan X. gideon reduced fibroblast oxida­ tive stress and was shown with good migration and prolif­ eration at a range of 100–500 µg/mL, with the best con­ centrations at 300 µg/mL. Budi S, Asih Suliasih B, Rahmawati I, Erdawati. 2020. Size­controlled chitosan nanoparticles prepared us­ ing ionotropic gelation. ScienceAsia 46(4):457–461. doi:10.2306/scienceasia1513­1874.2020.059. Acknowledgments Buranasin P, Mizutani K, Iwasaki K, Mahasarakham CPN, Kido D, Takeda K, Izumi Y. 2018. High glucose­ induced oxidative stress impairs proliferation and mi­ gration of human gingival fibroblasts. PLoS One 13(8):e0201855. doi:10.1371/journal.pone.0201855. The authors are grateful to the Universitas Trisakti study institute for supporting the fund. 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Quem precisa de Direitos? O fenômeno violência em contraposição aos direitos e à moralidade cristã
Revista Pistis & Praxis
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Gleyds Silva Domingues, Ana Carolina Silva Domingues* [a] Faculdades Batista do Paraná, (FABAPAR), Curitiba, PR, Brasil [b] Universidade Federal do Paraná, (UFPR), Curitiba, PR, Brasil http://dx.doi.org/10.7213/2175-1838.10.001.DS03 http://dx.doi.org/10.7213/2175-1838.10.001.DS03 ISSN 2175-1838 Licenciado sob uma Licença Creative Commons Resumo A proposta deste artigo é analisar o fenômeno violência em contraposição aos direitos fundamentais e à moralidade cristã. Para tal finalidade busca-se compreender a forma como este fenômeno se evidencia na realidade social, na tentativa de sinalizar sobre o grau de impacto que exerce nas relações humanas, na medida em que os direitos e a moralidade são violados. Em relação aos direitos, observa seu impacto no ato de trans- gressão do que é mais valioso ao ser humano, a dignidade e a vida. Na moralidade cristã, o que se busca é ressaltar que a prática da violência causa estranhamento por * GSD: Pós Doutora em Educação e Religião, e-mail: gleyds@ftbp.com.br ACSD: Mestranda em Direito, e-mail: dominguesanac@gmail.com * GSD: Pós Doutora em Educação e Religião, e-mail: gleyds@ftbp.com.br DOMINGUES, G. S.; DOMINGUES, A. C. S. 60 se distanciar de normas sociais que regem o comportamento e que são aceitas e legiti- madas no âmbito da cultura. Compreende-se que a violência é um fato social complexo e polissêmico e, por isso, exige certo grau de interpretação quanto ao seu alcance e presença. O artigo elege como problemática a seguinte questão: em que medida o fenômeno violência ao infringir os direitos fundamentais e a moralidade cristã continu- am sendo acomodados e maximizados na realidade social, sem que ocorra uma ree- ducação do ser humano biopsicossocial e espiritual? Neste sentido, o entendimento a ser construído sustenta-se nos estudos de teóricos sobre o fenômeno da violência, dos direitos e da moralidade. O método de pesquisa adotado é o da análise do discurso por contemplar os processos de significação que são impressos nos discursos defendidos. Não se quer apresentar um estudo finalístico sobre o fenômeno, mas contribuir com as investigações nesta área, reconhecendo que pela natureza interdisciplinar impressa neste artigo, o esforço e o desafio são ainda maiores. se distanciar de normas sociais que regem o comportamento e que são aceitas e legiti- madas no âmbito da cultura. Compreende-se que a violência é um fato social complexo e polissêmico e, por isso, exige certo grau de interpretação quanto ao seu alcance e presença. O artigo elege como problemática a seguinte questão: em que medida o fenômeno violência ao infringir os direitos fundamentais e a moralidade cristã continu- am sendo acomodados e maximizados na realidade social, sem que ocorra uma ree- ducação do ser humano biopsicossocial e espiritual? Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Resumo Neste sentido, o entendimento a ser construído sustenta-se nos estudos de teóricos sobre o fenômeno da violência, dos direitos e da moralidade. O método de pesquisa adotado é o da análise do discurso por contemplar os processos de significação que são impressos nos discursos defendidos. Não se quer apresentar um estudo finalístico sobre o fenômeno, mas contribuir com as investigações nesta área, reconhecendo que pela natureza interdisciplinar impressa neste artigo, o esforço e o desafio são ainda maiores. Palavras-chave: Violência(s). Direitos Fundamentais. Moralidade Cristã. Abstract The purpose of this paper is to analyze violence in opposition to fundamental rights and Christian morality. To such end, it intends to comprehend the way this phenome- non takes place in social reality, in an attempt to signal the degree of impact it exerts on human relation, as rights and morality are violated. In relation to rights, I observe their impact on the act of transgression of what is most valuable to the human being: dignity and life. Through the lens of Christian morality, what is sought is to emphasize that the practice of violence causes estrangement because it distances itself from the social norms that condition behavior, and that are accepted and legitimized culturally. Violence is portrayed as a complex and polysemous social fact, and as such demands a certain degree of interpretation as for its reach and presence. This paper is deri- ved from the following question: how violence – as it infringes fundamental rights and Christian morality – continues to be accommodated and maximized in social reality, without the occurrence of a reeducation of this biological (psychological/spiritual) hu- man beign? In this sense, the understanding to be built is sustained on theorists’ stu- dies on violence, rights, and morality. The research method is the discourse analysis as it contemplates the signification processes that are imprinted on defended discourses. Quem precisa de Direitos? 61 I do not intend to present a finalistic study of the phenomenon, but to contribute with the literature, recognizing that because of the interdisciplinary nature of this work, effort and the challenge are even greater. Keywords: Violence(s). Fundamental Rights. Christian Morality. Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Introdução Estudar o fenômeno da violência é percorrer a história da humanidade, no sentido de compreender como, no decurso de sua evolução, a sociedade enfrentou e vem enfrentando este problema social. Afinal, não se pode restringir este fenômeno somente ao ato material da agressão sofrida. Este envolve muito mais que uma ameaça ao direito de ser humano, visto que está entranhado por distanciamentos sobre o sentido de alteridade, constituindo-se, antes, na prerrogativa de um poder exercido sobre o outro. Seja este poder instrumentalizado ou simbólico, o certo é que o mesmo se concretiza nas relações sociais estabelecidas. É preciso, ainda, perceber que na presença da prática da violência(s) são instituídos mecanismos de segurança/inibidores, que tentam ora assegurar ou suspender direitos, enquanto uma faculdade dos sujeitos de agir sobre a realidade. A questão que precisa ser ressaltada é que o ato de constituição dos direitos deve objetivar a busca da paz e da coexistência social. Afinal, não se pode vislumbrar os direitos como uma prerrogativa apenas correcional de um instituto legal, mas de uma necessidade advinda da própria sociedade para fazer valer acordos, contratos, regras, procedimentos, direitos e deveres, que visem produzir ou provocar o equilíbrio moral e justo nas práticas de convivência e existência sociais. Interessante que o fazer direito também pode ser considerado como um fato social, o qual demanda a necessidade de estabelecer padrões de justiça a serem contemplados e até mesmo respeitados a partir da imposição de normas implicadoras da luta e da conquista pelo direito, por meio da prevenção, composição e resolução de conflitos, cuja decisão pode vir a ser materializada por intermédio de uma sanção, na medida em Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 DOMINGUES, G. S.; DOMINGUES, A. C. S. 62 que restringe o desejo do fazer por uma medida a ser aplicada quando não há observância legal da norma imposta. que restringe o desejo do fazer por uma medida a ser aplicada quando não há observância legal da norma imposta. Quando se fala do fenômeno violência(s), vislumbra-se, logo de antemão, a não subserviência de uma norma padrão, a qual resulta na ilicitude do ato e por conta disso pode trazer o desequilíbrio, no tocante às regras que conformam a convivência entre homens e mulheres. Tanto é assim, que sua prática reserva em si a ausência de limites e regras. 1 Palombella, em sua obra “La autoridad de los derechos: los derechos entre instituciones y normas” (2006, p. 71-72) revela que existem tensões no tocante às teorias que tratam da relação entre moral, ética e direito. Ele reporta que há teóricos que sustentam que a moral dá legitimidade ao direito, como o faz Dworkin, bem como aqueles que entendem que os valores morais até podem ser positivados, mas não conferem legitimidade ao direito, já que o reconhecimento das normas, ao menos pelos funcionários, conferiria sua legitimidade e obrigatoriedade, como se vê em Hart. Esta tensão se reproduz ao se tratar dos direitos fundamentais e da autoridade de tais direitos, de forma que o autor os coloca como inseridos em uma “zona franca” entre ambos os campos (moral e jurídico) [Tradução nossa]. Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 ambos os campos (moral e jurídico) [Tradução nossa]. 2 Alexy desenvolve um sistema que permite analisar as normas de acordo com sua qualidade moral. Nesse sistema, ele faz a diferenciação entre as normas injustas e as consideradas sanáveis (ALEXY, 2009). Introdução Há, sim, uma negação do que se legitima como postulados do exercício da moral e justiça. A análise do fenômeno da violência revela o alto grau de complexidade em que está envolvido, visto tratar-se de um fato concreto que desestabiliza a harmonia tão defendida pela sociedade, uma vez que atinge diferentes dimensões da vida. Não é por acaso que há uma concentração interdisciplinar de pesquisadores e estudiosos advindos das áreas da filosofia, da saúde, do direito, da educação, da teologia, da antropologia, dentre outras, no sentido de debruçar sobre este objeto. Pensa-se na cooperação e no diálogo a ser construído, com vistas a encontrar possibilidades de ação socioeducativas que de modo efetivo e que vise minimizar os danos provocados. Elege-se como finalidade deste artigo analisar o fenômeno da violência enquanto uma prática que se distancia dos direitos humanos e da moralidade cristã, o que evoca a necessidade de olhar para este fenômeno com cuidado, visto que sua ação informa sobre o não reconhecimento de um outro, conceito de desvalor. Além do distanciamento evidenciado, é preciso ainda, reconhecer uma área de tensão conceitual entre direito e moral, sendo esta área movediça, visto a discordância gerada entre os teóricos do Direito1. Isso porque, para alguns deles, como Alexy2, não 2 Alexy desenvolve um sistema que permite analisar as normas de acordo com sua qualidade moral. Nesse sistema, ele faz a diferenciação entre as normas injustas e as consideradas sanáveis (ALEXY, 2009). Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Quem precisa de Direitos? 63 se pode pensar o direito sem a moralidade, enquanto para outros, como Kelsen3, essa relação não se estabelece em forma de codependência. A intenção a ser expressa sinaliza para a compreensão do fenômeno violência, a partir de uma moral cristã e humanizadora do sentido de ser pessoa. Visão que se encontra ancorada nas perspectivas da teologia cristã e dos Direitos Humanos. Afinal, o sentido atribuído ao ser humano pode ser revelador para a construção de um conceito sobre dignidade, igualdade, liberdade, responsabilidade, alteridade a ser corporificado nos relacionamentos. Diante disto, o ensaio elege como problemática a seguinte questão: em que medida o fenômeno violência ao infringir os direitos fundamentais e a moralidade cristã continuam sendo acomodados e maximizados na realidade social, sem que ocorra uma reeducação deste ser humano biopsicossocial e espiritual? 3 Kelsen objetivou tornar o Direito uma ciência. Para tanto, precisou separar as normas jurídicas da moralidade, psicologia, ciências sociais e outros ramos. A instrumentalização de tal ideia perpassou a criação de um sistema jurídico composto apenas por normas jurídicas, em que tanto seu fundamento de validade, como de existência são pautadas na norma fundamental, a qual dá margem para a hierarquia do sistema (KELSEN, 1998, p. VII-IX). 4 Orlandi sobre a questão da polissemia, ressalta que ela é a fonte da linguagem, uma vez que por sua natureza múltipla possibilita a existência do espaço do dizer, ou seja, dos discursos. E se assim o é, pode-se verificar a multiplicidade de significados gerados a partir de um vocábulo empregado. Tanto que o vocábulo violência não se limita apenas ao campo material, mas engloba o campo simbólico e afetivo. Reitera-se que a polissemia de significados é real, uma vez que o ato gerador do sentido atribuído à palavra, nem sempre pode ser restrito a um sentido, antes sua significação ocorre no contexto real e é nele que os sentidos são reconhecidos, apropriados, legitimados e materializados na realidade social (ORLANDI, 2003, p. 18). Introdução A proposta, então, lança mão da metodologia da análise do discurso, por entender que a mesma se debruça sobre ideias, sentidos, significados, discursos e modos de pensar a realidade social, o que se verifica nas relações que os sujeitos tecem sobre o mundo onde se encontram mergulhados como protagonistas de uma história ou histórias significadas. A análise do discurso situa seu olhar na prática da linguagem, pois nela homens e mulheres apresentam suas ideias e, ainda, revelam-se, mostram-se e significam por meio dos discursos travados. Ela firma-se como uma prática social munida de sentidos que, segundo Fairclough (2012), se inscreve na presença de três momentos da linguagem: identitário, relacional e ideacional. Esses três momentos se explicitam na forma como o discurso se apresenta, oferecendo subsídios para a realização e para construção discursiva. Assim, espera-se com este artigo despertar o desejo de novas investigações em relação ao objeto violência(s), sendo essa uma tentativa de provocação e alerta para um fato social que se consolida na realidade da “cidade” e que por isso mesmo se torna alvo direto de reflexões. Assim, que comece a incursão sobre este fato social. 3 Kelsen objetivou tornar o Direito uma ciência. Para tanto, precisou separar as normas jurídicas da moralidade, psicologia, ciências sociais e outros ramos. A instrumentalização de tal ideia perpassou a criação de um sistema jurídico composto apenas por normas jurídicas, em que tanto seu fundamento de validade, como de existência são pautadas na norma fundamental, a qual dá margem para a hierarquia do sistema (KELSEN, 1998, p. VII-IX). Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 DOMINGUES, G. S.; DOMINGUES, A. C. S. 64 Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Violência, Violências: desvio ou ausência de moral O termo violência tem natureza polissêmica4, por isso se torna complexo apresentar uma definição de forma padrão e definitiva, porém faz-se necessário apresentar o sentido que se está atribuindo a este termo, uma vez que a compreensão do sentido lança possíveis caminhos de análise sobre o fenômeno a ser investigado. Nessa direção, lança-se mão da reflexão de Michel Misse (2006, p. 1), sobre o fenômeno violência. Nela, o autor já aponta o desafio de compreender o seu significado, ao dizer que: A tal da violência que parece agir como um espectro ou fantasma, escon- de-se ou dissemina-se, é tratada como uma epidemia, um vírus, um micró- bio, ou como um Sujeito onipresente, onisciente, onipotente. Que diabo é esse? O que unifica nesse nome conflitos, crimes e comportamentos tão diferentes? O que nos faz pensar que tudo isso tem um nome só? A palavra violência do ponto de vista de sua origem deriva-se do latim violentia, associado a vis, cujo significado remete ao caráter de alguém violento e que usa a força física ou seu vigor contra um outro. Ainda acerca da palavra é possível associar os significados de quantidade, abundância, potência, energia e força em ação. O que enfatiza ainda mais a ideia de uma ação de força contra algo ou alguém. Quando se deseja tratar da violência, enquanto um fato social, torna-se indispensável apresentar o seu conceito, visto que por seu intermédio são estabelecidas as fronteiras sobre a mesma. Diante disso e com a ajuda de Hannah Arendt, é possível dizer que a violência pode ser considerada sob a perspectiva da instrumentalidade, a qual lança mão de meios na concretização de seus atos e efeitos. O que implica em dizer que “a própria substância da violência é regida pela categoria meio/objetivo Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Quem precisa de Direitos? 65 cuja mais importante característica, se aplicada às atividades humanas, foi sempre a de que os fins correm perigo de serem dominados pelos meios” (ARENDT, 1970, p. 4). Assim, “a violência é por natureza instrumental; como todos os meios ela sempre depende da orientação e da justificação pelo fim que almeja” (ARENDT, 1970, p. 40-41). Isso implica em pensar no fenômeno da violência como um fato impregnado de intencionalidade, o que retira, exclusivamente, o seu caráter involuntário que muitas vezes é invocado na prática de violência cometida. Violência, Violências: desvio ou ausência de moral Afinal, a violência é proveniente da violação de um direito. Essa violação produz consequências na forma como se evidencia na vida quer do infrator como do lesado. De tal modo, pode-se dizer que “as violações dos direitos provêm de que todo detentor de poder está tentando dele abusar” (MORANGE, 2004, p. 31). Há, portanto, sinalizado que o ato de violência pode se originar na esteira do poder e, ainda, que “a violência abriga em seu seio um elemento adicional de arbitrariedade” (ARENDT, 1970, p. 5). Surge neste contexto da prática da violência um novo elemento a ela vinculado, o poder. A partir deste novo elemento, pode-se entender que o ato de violência também pode ser principiado no contexto e na presença de um poder, quer seja real ou simbólico. O primeiro indica um instituto de autoridade conferido legitimamente, como o é no caso do Estado e o segundo sinaliza para um estado de força exercido por intermédio de uma prática da linguagem corporal, imagética ou emocional. A partir dessa ótica, a violência pode ser pensada como uma deturpação do uso do bom senso. Segundo Arendt (1970, p. 7), esse poder seria “o nosso órgão mental que se destina a perceber, compreender e lidar com a realidade e com os fatos”, incluindo a capacidade de agir de maneira consciente, racional e ética. Na esteira do pensamento de Arendt, é possível concluir que o bom senso pode ser equiparado a um sensor que informa sobre as ações e ou reações de seus agentes. Não se tem a pretensão aqui de discutir sobre o fenômeno da violência emanado do Estado, mas aquele que é advindo das relações sociais, uma vez que a proposta a ser configurada persegue a ideia de deslocamento, desvirtuamento de sentido sobre o outro. É esse distanciamento que se torna o objeto a ser investigado por estar destituído de um exercício cidadão, o qual deveria ancorar os valores de respeito, autonomia e bem Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 DOMINGUES, G. S.; DOMINGUES, A. C. S. 66 comum. Exercício esse que promove o sentido de ser, existir, estar e agir em comunidade, ou seja, o exercício da prática usual do bom senso. comum. Exercício esse que promove o sentido de ser, existir, estar e agir em comunidade, ou seja, o exercício da prática usual do bom senso. Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Violência, Violências: desvio ou ausência de moral A violência seria a relação social de excesso de poder que impede o reconhecimento do outro – pessoa, classe, gênero ou raça, provocando algum tipo de dano, configurando o oposto das possibilidades da sociedade democrática contemporânea (SANTOS, 2009, p. 46). [...] a violência configura-se como um dispositivo de controle, aberto e con- tínuo. A violência seria a relação social, caracterizada pelo uso real ou virtual da força ou da coerção. A violência seria a relação social de excesso de poder que impede o reconhecimento do outro – pessoa, classe, gênero ou raça, provocando algum tipo de dano, configurando o oposto das possibilidades da sociedade democrática contemporânea (SANTOS, 2009, p. 46). Conceitua-se, assim, violência como “ações humanas de indivíduos e grupos, classes, nações que ocasionam a morte de outros seres humanos ou que afetam a sua integridade física, moral, mental ou espiritual” (MINAYO; SOUZA, 1998, p. 514). Este conceito traduz não apenas o sentido de ser da violência, mas as consequências que são desencadeadas por sua prática e que envolvem aspectos materiais e emocionais, o que implica em pensar em duas esferas de concretização da violência: física e simbólica. Na esfera física concentra-se o uso da força física sobre um outro ser. Já na esfera simbólica são utilizados meios de coação emocional e psicológica, por isso sua ação é lenta e de difícil identificação. Além da forma física e simbólica de concretização da violência é preciso pensar no sentimento de medo desencadeado pela ausência de segurança, pelo caos estabelecido e pela impunidade diante de normas infringidas. Esse sentimento é avaliado assim: O sentimento da insegurança, que se encontra no coração das discussões sobre o aumento da violência, raramente repousa sobre a experiência direta da violência. Ele corresponde à crença, fundada ou não, de que tudo pode acontecer, de que devemos esperar tudo, ou ainda de que não podemos ter certeza de nada nos comportamentos cotidianos. Aqui, novamente, impre- visibilidade, caos e violência estão juntos (MICHAUD, 1989, p. 13). O ato de concretização da violência manifesta-se, então, por uma prática humana efetivada, que diz respeito ao não reconhecimento da presença do não eu, e não somente isso, mas uma ação que fragiliza, imobiliza e afeta direta ou indiretamente a integridade da pessoa, ou seja, a sua dignidade. Violência, Violências: desvio ou ausência de moral É na esteira da violência, enquanto fenômeno social, que se pode perceber diferentes iniciativas da sociedade, não apenas para compreender sua ação, mas a forma como ela se reveste de um poder sobre um outro ser humano. Tanto é assim, que a Organização Mundial da Saúde (OMS), classifica o fenômeno da violência em três tipologias: violência coletiva, violência auto infligida e violência interpessoal. A prática efetivada pela violência coletiva incide num cenário macrossocial, político e econômico, que é desferido pela dominação de grupos e do Estado. Deste modo, incluem-se “os crimes cometidos por grupos organizados, os atos terroristas, os crimes de multidões, as guerras e os processos de aniquilamento de determinados povos e nações” (OMS, 2002, p. 6). Já a violência auto infligida diz respeito aos comportamentos considerados suicidas e de auto abuso, ou seja, são comportamentos infligidos contra a própria pessoa, o que pressupõe a existência de práticas de mutilação, negação e desvalorização quer atingindo o próprio corpo, quer atingindo sua identidade ou imagem pessoal, ou seja, são práticas atentatórias contra a própria dignidade da pessoa humana. Pode-se dizer que atentar contra a dignidade humana é o mesmo que violar os princípios da liberdade, justiça, solidariedade e moralidade. A violência interpessoal é aquela que atinge o outro, o não eu, sendo infligida quer seja pelo parceiro ou não, isso envolve a ação praticada pelo “parceiro íntimo, o abuso infantil e abuso contra idosos” (OMS, 2014, Resumo executivo, p. VII). Esse tipo de violência é uma das marcas de prática desumana, que atenta contra os direitos de um outro, incluindo o direito à vida, à honra, à identidade e à dignidade humana. Observa-se que estes tipos de violência são direcionados a um ente específico, quer seja à coletividade, à individualidade ou à alteridade. Isso demonstra que o nível de concretização da violência não é único, mas diverso, sendo muito difícil determinar uma única forma de ação infligida, o que requer a compreensão de caso a caso. Pode-se dizer que: Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Quem precisa de Direitos? 67 [...] a violência configura-se como um dispositivo de controle, aberto e con- tínuo. A violência seria a relação social, caracterizada pelo uso real ou virtual da força ou da coerção. Violência, Violências: desvio ou ausência de moral Afinal, “o contrário da violência não é a não violência, é a cidadania e a valorização da vida humana por geral e de cada indivíduo no contexto de seu grupo” (COELHO; SILVA; LINDNER, 2014, p. 528). Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 DOMINGUES, G. S.; DOMINGUES, A. C. S. 68 Se o contrário da violência é a cidadania e a valorização da vida humana, então algumas questões devem ser apresentadas como: será que o fenômeno violência ao violar os direitos da pessoa humana não está ao mesmo tempo agredindo à sua moralidade? Em que medida o direito no enfrentamento do fenômeno da violência se constitui na perspectiva da moral? Seria possível pensar na aplicação do Direito para atos de violência distanciados da moralidade? Essas questões demandam um esforço reflexivo, porque não envolvem apenas um aspecto da problemática, antes se torna determinante para compreender o fenômeno, no sentido de sinalizar sobre possíveis formas de ação e tratamento que possam redundar numa prática socializante e reeducadora das condutas humanas. Aspectos que serão melhor elucidados no tema a seguir. Direito e a Perspectiva da Moralidade Cristã Ao tentar evidenciar a relação de cumplicidade entre o Direito e a sociedade, utiliza-se da frase de Dante Alighieri, em sua obra clássica “Monarquia”, por evidenciar essa estreita dependência. Assim, ele expressa no segundo livro desta obra, capítulo V, que “O Direito é uma proporção real e pessoal, de homem para homem, que conservada, conserva a sociedade: corrompida, corrompe-a” (ALIGHIERI, 1992, p. 37). Esse olhar do dramaturgo revela a presença de uma correspondência entre normas, relações e condutas a serem mantidas e acordadas pelos seres humanos em prol de sua coexistência na sociedade. Isso indica que a partir desta ótica, o Direito não se distancia da moral, uma vez que assume como prerrogativa o bem-estar da sociedade na luta pela justiça e pela paz social. Quando se fala em direito é preciso ter em mente as diferentes acepções atribuídas a este termo. E uma delas está diretamente associada a presença de normas ou regras de conduta. Isso ocorre porque, A nossa vida se desenvolve em um mundo de normas. Acreditamos que somos livres, mas na realidade, estamos envoltos em uma rede muito es- pessa de regras de conduta que, desde o nascimento até a morte, dirigem nesta ou naquela direção as nossas ações (BOBBIO, 2016, p. 5). Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 69 Quem precisa de Direitos? É claro que não se pode desconsiderar que muitas destas ações são frutos da escolha do ser humano, ou seja, em observar ou não as normas. Assim frente a escolhas pode-se vislumbrar ou não o desencadeamento de problemas, tais como o fenômeno violência, o que induz a pensar sobre o fator ou fatores que favorecem ou não a observância de uma norma de conduta. Pensa-se na norma de conduta como uma prática consensual, em que é regida pelo viver bem em comunidade, embora há de se ressaltar que a norma de conduta traz em si mesma uma carga regulatória e previsível em forma de regras coercitivas e sanção. Assim sendo, pode-se inferir que esse viver bem é cerceado por ações valorativas de natureza moral. Para Reale (2014, p. 17), “o Direito corresponde à exigência essencial e indeclinável de uma convivência ordenada, pois nenhuma sociedade poderia subsistir sem um mínimo de ordem, de direção e solidariedade”. 5 Em relação à origem dos Direitos Humanos, Bobbio em sua obra “A era dos direitos” (1992, p. 57) ressalta que “teve início no Ocidente a partir da concepção cristã de vida, segundo a qual todos os homens são irmãos, enquanto filhos de Deus”. 6 Embora existem linhas teóricas que não aceitam tal argumento, defendendo que a origem dos direitos humanos parte de uma prática histórica evolutiva. Direito e a Perspectiva da Moralidade Cristã O que indica que um dos fatores para que haja consenso na realidade social é aquele proveniente de uma perspectiva ética. Não é de se estranhar que a base dos Direitos Humanos5 tem em sua essência a perspectiva da ética cristã6. Outro ponto a ser destacado é de que a visão cristã influenciou, sobremaneira, o Ocidente na adoção do conceito de ser humano. Isso porque, [...] a convicção de que o homem foi criado à imagem de Deus e que ele foi salvo por Jesus Cristo enraizou solidamente na história da salvação a con- vicção da dignidade humana, o respeito do direito da pessoa humana ao livre desabrochar da solidariedade com outros homens (MORANGE, 2004, p. 55). Este conceito de ser humano induz a pensar sobre a sua natureza formativa que está amalgamada com o próprio Criador. Sendo assim, por que seu comportamento não reflete a bondade e por que há desvirtuamento do seu caráter? Um possível argumento é o seu livre arbítrio, uma vez que a sua essência é de todo moral. Ainda sobre a questão do livre arbítrio, o Papa Leão XIII na Carta Encíclica Immortale Dei, posiciona-se da seguinte maneira: Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 70 DOMINGUES, G. S.; DOMINGUES, A. C. S. [...] se a inteligência adere às ideias falsas, e se a vontade escolhe o mal e se une a ele, nem uma nem outra alcançam a perfeição, ambas perdem sua dignidade inicial e se corrompem. Por isso não é permitido vir à luz e mos- trar aos olhos dos homens o que é contrário à virtude e à verdade, e muito menos colocar isto sob a tutela da proteção das leis (Immortale Dei 38). [...] se a inteligência adere às ideias falsas, e se a vontade escolhe o mal e se une a ele, nem uma nem outra alcançam a perfeição, ambas perdem sua dignidade inicial e se corrompem. Por isso não é permitido vir à luz e mos- trar aos olhos dos homens o que é contrário à virtude e à verdade, e muito menos colocar isto sob a tutela da proteção das leis (Immortale Dei 38). Direito e a Perspectiva da Moralidade Cristã Sob este prisma, o ser humano, em prol de sua dignidade, deveria ser influenciado pela virtude e verdade, o que oportunizaria sua caminhada à perfeição, o que não pode ser tutelado pela lei, visto que a mesma também tem suas limitações. Assim, o campo da dignidade humana deve ser a busca constante do ser, viver e agir de cada ser humano, que à luz da verdade presente nas Escrituras compreende seu papel na história e na sociedade. Esse ser, viver e agir deve ser norteado pela moralidade cristã, a qual se fundamenta na perspectiva da revelação, classificada em dois momentos por Geisler (2010): geral e específico. O geral é destinado para todas as pessoas, pois contém os mandamentos de Deus e o específico explicita a vontade e o propósito de Deus em Cristo para aqueles que aceitam sua verdade. É, portanto, na essência da natureza reveladora de Deus que é possível encontrar o caráter moral de seus mandamentos e, isso indica que tanto a moral quanto a ética passam a ser entendidas no interior das condições históricas em que foi escrita e interpretada a revelação. A revelação e a história impulsionam a uma compreensão mútua e reflexão mútua do caráter santo, justo e bom de Deus, que se estende ao ser humano, criado à sua imagem e semelhança. E, ainda: A partir da perspectiva da revelação tem-se o conhecimento sobre a natu- reza e o caráter daquele que se revela, ou seja, Deus. Esse, ato, portanto, oportuniza a tomada de consciência sobre sua essência e existência; e é nesse momento que se estabelece o conceito de alteridade, uma vez que não se tem um olhar limitado em si mesmo, o que sinaliza para a necessi- dade de uma prática moral de natureza relacional, que promova o sentido da convivência e respeito ao outro (DOMINGUES, 2017, p. 115). Quando se deixa de lado a moralidade cristã, desconsidera-se os fundamentos da verdade e da virtude, instala-se a corrupção e, isso, nada mais é do que o afastamento dos princípios emanados pelo Criador. É na Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Quem precisa de Direitos? 71 ausência dos princípios e da moralidade que surge a prática da violência7. De acordo com Candiotto (2011, p. 7 Para Ricci (2012, p. 17) “não podemos cultivar uma liberdade viciada, como licença para fazer tudo, inclusive o mal, podendo cair no pecado. Proclama a vocação humana para a comunhão com Deus, cujo reconhecimento fundamenta e aperfeiçoa a própria dignidade humana”. Ricci, assevera, ainda, que Jesus Cristo, o Filho de Deus, é o exemplo perfeito de dignidade, visto que revela plenamente Deus e realiza plenamente o humano. 8 Marcilio em Fundamentos Éticos dos Direitos Humanos (2012, p. 71) ressalta que “é justamente na dignidade humana que os fundamentos dos direitos humanos devem ser buscados. Tais direitos são universais, invioláveis e inalienáveis”. 9 “A ideia da humanidade nos obriga a adotar aquela perspectiva do nós, a partir da qual nos consideramos uns aos outros como membros de uma comunidade inclusiva, que não exclui ninguém” (HABERMAS, 2010, p. 78). 7 Para Ricci (2012, p. 17) “não podemos cultivar uma liberdade viciada, como licença para fazer tudo, inclusive o mal, podendo cair no pecado. Proclama a vocação humana para a comunhão com Deus, cujo reconhecimento fundamenta e aperfeiçoa a própria dignidade humana”. Ricci, assevera, ainda, que Jesus Cristo, o Filho de Deus, é o exemplo perfeito de dignidade, visto que revela plenamente Deus e realiza plenamente o humano. Direito e a Perspectiva da Moralidade Cristã 243), há que se ressaltar que mesmo diante da ausência da ética o “outro está presente em mim, eu não posso deixar de estar responsabilizado, pois até a indiferença já é uma resposta. As circunstâncias do outro me afetam, me interpelam e, principalmente, me responsabilizam”. É por esse motivo que a atitude a ser assumida é de ordem educativa, o que é enfatizado pela declaração do Concilio Vaticano II, Dignitatis Humanae sobre a liberdade religiosa, que: [...] exorta a todos, mas sobretudo aos que têm a seu cargo educar outros, a que se esforcem por formar homens que, fiéis à ordem moral, obedeçam à autoridade legítima e amem a autêntica liberdade; isto é, homens que julguem as coisas por si mesmos e à luz da verdade, procedam com sentido de responsabilidade, e aspirem a tudo o que é verdadeiro e justo, sempre prontos para colaborar com os demais (Dignitatis Humanae 8). Um ponto a ser observado é que mesmo no interior da prática educativa não é negado ao sujeito a sua capacidade de agir com liberdade, porém, essa liberdade deve estar fundamentada na verdade e no exercício da moral. Ainda sob o aspecto da ação educadora, é preciso compreender que o que está em jogo é o princípio da dignidade8, na medida em que é ela “inerente a todos os membros da humanidade, funda seus direitos iguais e inalienáveis e garante a liberdade, a justiça e a paz no mundo. Essa dignidade advém da natureza mesma do ser humano e do fato de ser uma pessoa” (RICCI, 2012, p. 15). A dignidade torna-se a marca da humanidade9 e, por isso, deve ser buscada, pleiteada e conquistada. Quando se trabalha no terreno da dignidade pode-se dizer que o desejo é de manter e fazer uma sociedade 9 “A ideia da humanidade nos obriga a adotar aquela perspectiva do nós, a partir da qual nos consideramos uns aos outros como membros de uma comunidade inclusiva, que não exclui ninguém” (HABERMAS, 2010, p. 78). Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 DOMINGUES, G. S.; DOMINGUES, A. C. S. 72 que se fundamenta nos princípios elementares do respeito, da liberdade, da solidariedade, da comunhão, da justiça e da paz. Por ser desejo, isso implica em dizer que sua concretização no plano real ainda é muito ideal, principalmente pelo apelo à noção de igualdade entre os homens. Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Direito e a Perspectiva da Moralidade Cristã Habermas (2010, p. 78) assevera que “a universalidade das normas morais, que assegura a todos um tratamento igual, não pode permanecer abstrata; ela precisa permanecer sensível para levar em consideração as situações e os projetos individuais de vida de todos os indivíduos”. Ainda sobre a dignidade, deve ser ressaltado que a prática da ética não pode ser autocentrada na pessoa, mas no espírito de coletividade, o que representa uma postura que contraria aos pressupostos da pós- modernidade, presentes no hedonismo e no individualismo exacerbado, o que contribui para acentuar a competitividade e o exercício do poder de um sobre o outro, trazendo desequilíbrio ao que se entende por bem comum. Define-se bem comum como “o favorecimento do conjunto das condições sociais que permitem aos grupos sociais e às pessoas procurar atingir de forma mais completa possível a própria perfeição” (MARCILIO, 2012, p. 71). Para tal finalidade é preciso que se assegure os direitos fundamentais associados à alimentação, habitação, educação, saúde, cultura, informação, ao trabalho e ao transporte, além da liberdade e da igualdade de condições entre homens e mulheres. Isso implica em dizer que o bem comum é um valor intrínseco ao viver em sociedade. Deste modo, cada cidadão deve cooperar para sua efetivação na realidade, visando que sua consolidação seja impressa por meio da ética e dos valores sociais. Para isso “é preciso denunciar circunstâncias que estão em contraste com a dignidade humana” (MARCILIO, 2012, p. 73). Dentre essas circunstâncias está a prática da violação dos direitos humanos, a qual é denegatória da moral e, assumida aqui como denegatória da moral cristã. O bem comum, também, pode ser considerado como alvo da ação educativa que se inicia no contexto da família, sendo extensivo aos diferentes grupos sociais. Percebe-se, então, que a prática dos direitos humanos e da moralidade cristã se complementam na consecução deste objetivo, o que pode servir como ponto de partida para rever posicionamentos e comportamentos construídos socialmente. O certo é Quem precisa de Direitos? 73 pensar que “a educação em direitos humanos não permite a passividade, mas propõe a indignação ante situações de injustiça, de arbitrariedade, de corrupção, de violências” (MARCILIO, 2012, p. 73-74). Não se pode ficar inerte a tal brutalidade e desumanização do ser humano, mas agir como portador de voz profética que anuncia e denuncia a barbárie. Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Considerações finais Afinal, a máxima em que se funda sua razão de ser é no amar a Deus e ao próximo como a si mesmo, o que afasta das atitudes humanas ações que depreciam ou excluem o outro. Antes, a moralidade cristã ainda se posiciona com uma fé altruística. A presença de uma fé altruística pode ser contemplada nos Evangelhos, a partir da vida e do exemplo do próprio Cristo, que em seus ensinos demonstra o valor dos relacionamentos pautados no amor, no respeito e na consciência do outro. São inúmeras as passagens bíblicas que revelam tal posicionamento. Dentre elas e a título de ilustração podem-se citar as bem- aventuranças em Mt 5,3-11; o amor aos inimigos em Mt 5,43-48; o ato de não julgar ao próximo em Mt 7,1-6; Lc 6,37-38; 41-42; o maior mandamento em Mc 12,28-34; o ajudar o próximo — parábola do bom samaritano — em Lc 10,28-37; o sentido de resplandecer e nutrir a luz em Lc 11,33-36; as consequências dos atos na prática de partilha em Lc 12,13-21; a comparação entre humildade e hospitalidade em Lc 14,7-14; a figura do bom pastor em Jo 10,11-16; a prática do lava pés em Jo 13,1-20, entre outras. Ainda com relação à problemática levantada: em que medida o fenômeno violência ao infringir os direitos fundamentais e a moralidade cristã continuam sendo acomodados e maximizados na realidade social, sem que ocorra uma reeducação deste ser humano biopsicossocial e espiritual, pode-se inferir que sua ação é tão nociva quanto a incidência da prática da barbárie. Isso quer dizer que enquanto a sociedade sofrer com a violência, com a individualização narcisista, o processo de reeducação não se mostra como uma prioridade, o que incentiva ainda mais o grau de banalização da vida. Quanto mais a sociedade possibilitar ações educativas, mais perto se chegará do sentido do bem comum. A atitude de olhar o outro não como oponente ou opositor, mas com o sentido de alteridade pode modificar a forma de convivência entre iguais e diferentes, sendo um passo para alcançar o tão idealizado bem comum. O sentido do bem comum já sinaliza para uma ação significada em comunidade, ou seja, na esteira da coletividade. O bem comum se materializa na prática efetiva da koinonia, que significa dividir o pão. O que se pode dizer então? Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 Considerações finais Discutir sobre o fenômeno da violência não é uma ação simples, mas nem por isso pode ser negligenciada, antes a atitude precisa ser de denúncia e anúncio a partir de uma postura educadora, que demanda reconhecer a complexidade e a pluralidade de perspectivas que se fazem presentes na realidade social para debater e refletir sobre este fenômeno. É preciso sentir- se responsável e parte integrante do problema e da solução. Afinal, “enquanto nos compreendermos como pessoas morais, partiremos intuitivamente do fato que agimos e julgamos, in propria persona, de maneira insubstituível — de que nenhuma outra voz além da nossa própria nos fala” (HABERMAS, 2010, p. 80). Isso sinaliza que cada pessoa é responsável direta por suas ações, julgamentos e escolhas, porque a moral faz parte de sua essência e persona. Uma das possibilidades de encarar o fenômeno da violência é aquela que parte da visão do direito e da moralidade cristã, na medida em que se apresenta com um olhar atento e responsivo à questão da dignidade humana, visto que a busca por uma sociedade justa deve ser encarada como parte de um desejo coletivo de concretização e acesso aos direitos fundamentais. Direitos esses que humanizam e possibilitam a convivência entre iguais e diferentes. Por outro lado, reconhece-se que o fenômeno violência(s) contraria o sentido atribuído à dignidade humana, pois se existe a violação pelo ser humano de um direito, não se pode falar de respeito, solidariedade, igualdade, justiça ou sentimento de alteridade. A violação do direito avilta também a prática da moralidade cristã, por ser ela aquela que espelha a essência de um valor absoluto e universal, revelado pelo próprio Criador à criatura. Longe de apresentar uma perspectiva puramente moralista, a intenção defendida caminha na esperança de que, a partir de uma perspectiva Rev. Pistis Prax., Teol. Pastor., Curitiba, v. 10, n. 1, 59-77, jan./abr. 2018 DOMINGUES, G. S.; DOMINGUES, A. C. S. 74 educadora, os direitos humanos sejam resgatados assim como a moralidade cristã, tão injustamente criticada e desprezada. Afinal, a máxima em que se funda sua razão de ser é no amar a Deus e ao próximo como a si mesmo, o que afasta das atitudes humanas ações que depreciam ou excluem o outro. Antes, a moralidade cristã ainda se posiciona com uma fé altruística. educadora, os direitos humanos sejam resgatados assim como a moralidade cristã, tão injustamente criticada e desprezada. Considerações finais No exercício da voz profética é preciso declarar que o bem comum seja o alvo das práticas e ações sociais, pois se há Quem precisa de Direitos? 75 o bem comum, com certeza haverá respeito e dignidade estendida a todos os seres humanos. O Apóstolo Paulo na Carta aos Filipenses 4,8 alerta: “Quanto ao mais, irmãos, tudo o que é verdadeiro, tudo o que é honesto, tudo o que é justo, tudo o que é puro, tudo o que é amável, tudo o que é de boa fama, se há alguma virtude, e se há algum louvor, nisso pensai”. O apóstolo, ainda, arremata sua reflexão de uma forma imperativa, ao dizer que aquilo recebido e aprendido por eles fosse colocado em prática, quer em palavras, quer em ações. p q p q Sobre a ênfase atribuída pelo apóstolo Paulo à palavra e a ação é preciso destacar que a prática revela a tomada de decisão efetivada diante das circunstâncias da vida. A prática, ainda, demonstra o que de fato é prioridade nos relacionamentos. Assim, pode-se dizer que a prática constitui a palavra em movimento, ela é ação que dinamiza o sentir e o fazer presente nas relações humanas. Assim, quiçá seja essa a sua finalidade: buscar, significar e cultivar o bem comum em prol da convivência, da solidariedade e da paz entre os seres humanos. 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Recebido: 27/07/2017 Received: 07/27/2017 Aprovado: 17/11/2017 Approved: 11/17/2017 Aprovado: 17/11/2017 Approved: 11/17/2017